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Yee SW, Macdonald CB, Mitrovic D, Zhou X, Koleske ML, Yang J, Buitrago Silva D, Rockefeller Grimes P, Trinidad DD, More SS, Kachuri L, Witte JS, Delemotte L, Giacomini KM, Coyote-Maestas W. The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics. Mol Cell 2024; 84:1932-1947.e10. [PMID: 38703769 DOI: 10.1016/j.molcel.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/04/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
Mutations in transporters can impact an individual's response to drugs and cause many diseases. Few variants in transporters have been evaluated for their functional impact. Here, we combine saturation mutagenesis and multi-phenotypic screening to dissect the impact of 11,213 missense single-amino-acid deletions, and synonymous variants across the 554 residues of OCT1, a key liver xenobiotic transporter. By quantifying in parallel expression and substrate uptake, we find that most variants exert their primary effect on protein abundance, a phenotype not commonly measured alongside function. Using our mutagenesis results combined with structure prediction and molecular dynamic simulations, we develop accurate structure-function models of the entire transport cycle, providing biophysical characterization of all known and possible human OCT1 polymorphisms. This work provides a complete functional map of OCT1 variants along with a framework for integrating functional genomics, biophysical modeling, and human genetics to predict variant effects on disease and drug efficacy.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christian B Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donovan D Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Swati S More
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA.
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2
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Guerra G, Nakase T, Kachuri L, McCoy L, Hansen HM, Rice T, Wiemels JL, Wiencke JK, Molinaro AM, Wrensch M, Francis SS. Association of immunoglobulin E levels with glioma risk and survival. medRxiv 2024:2024.05.09.24307132. [PMID: 38766059 PMCID: PMC11100947 DOI: 10.1101/2024.05.09.24307132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Previous epidemiological studies have reported an association of serum immunoglobulin E (IgE) levels with reduced glioma risk, but the association between IgE and glioma prognosis is not well characterized. This study aimed to examine how sex, tumor subtype, and IgE class modulate the association of serum IgE levels with glioma risk and survival. Methods We conducted a case-control study using participants from the University of California, San Francisco Adult Glioma Study (1997-2010). Serum IgE levels for total, respiratory and food allergy were measured in adults diagnosed with glioma (n=1,696) and cancer-free controls (n=1,135) matched based on age, sex, and race/ethnicity. Logistic regression was adjusted for patient demographics to assess the association between IgE levels and glioma risk. Multivariable Cox regression adjusted for patient-specific and tumor-specific factors compared survival between the elevated and normal IgE groups. Results Elevated total IgE was associated with reduced risk of IDH wildtype (OR=0.65, 95% CI: 0.54-0.78) and IDH mutant glioma (OR=0.65, 95% CI: 0.50-0.85). In multivariable Cox regression, elevated respiratory IgE was associated with improved survival for IDH wildtype glioma (HR=0.78, 95% CI: 0.67-0.91). The reduction in mortality risk was more pronounced in females (HR=0.71, 95% CI: 0.53-0.96) than in males (HR=0.80, 95% CI: 0.66-0.97), with improvements in median survival of 6.2 months (P<.001) and 1.6 months (P=0.003), respectively. Conclusion Elevated serum IgE was associated with improved prognosis for IDH wildtype glioma, with a more pronounced protective effect in females. These results suggest a possible sexual dimorphism and antitumor activity of IgE-mediated immune responses.
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Lu Z, Wang X, Carr M, Kim A, Gazal S, Mohammadi P, Wu L, Gusev A, Pirruccello J, Kachuri L, Mancuso N. Improved multi-ancestry fine-mapping identifies cis -regulatory variants underlying molecular traits and disease risk. medRxiv 2024:2024.04.15.24305836. [PMID: 38699369 PMCID: PMC11065034 DOI: 10.1101/2024.04.15.24305836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Multi-ancestry statistical fine-mapping of cis -molecular quantitative trait loci ( cis -molQTL) aims to improve the precision of distinguishing causal cis -molQTLs from tagging variants. However, existing approaches fail to reflect shared genetic architectures. To solve this limitation, we present the Sum of Shared Single Effects (SuShiE) model, which leverages LD heterogeneity to improve fine-mapping precision, infer cross-ancestry effect size correlations, and estimate ancestry-specific expression prediction weights. We apply SuShiE to mRNA expression measured in PBMCs (n=956) and LCLs (n=814) together with plasma protein levels (n=854) from individuals of diverse ancestries in the TOPMed MESA and GENOA studies. We find SuShiE fine-maps cis -molQTLs for 16 % more genes compared with baselines while prioritizing fewer variants with greater functional enrichment. SuShiE infers highly consistent cis -molQTL architectures across ancestries on average; however, we also find evidence of heterogeneity at genes with predicted loss-of-function intolerance, suggesting that environmental interactions may partially explain differences in cis -molQTL effect sizes across ancestries. Lastly, we leverage estimated cis -molQTL effect-sizes to perform individual-level TWAS and PWAS on six white blood cell-related traits in AOU Biobank individuals (n=86k), and identify 44 more genes compared with baselines, further highlighting its benefits in identifying genes relevant for complex disease risk. Overall, SuShiE provides new insights into the cis -genetic architecture of molecular traits.
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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. Cell Genom 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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5
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Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E. Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis. Nat Commun 2024; 15:2568. [PMID: 38531883 PMCID: PMC10966072 DOI: 10.1038/s41467-023-44512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/15/2023] [Indexed: 03/28/2024] Open
Abstract
Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.
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Affiliation(s)
- Pooja Middha
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lydia Yao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zoe Quandt
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Cardenas
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina J Falcon
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew A Gubens
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University of Medicine, Stanford, CA, USA
| | - Khaleeq Khan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Min Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Megan H Murray
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kristin Werking
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luna Jia Zhan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Temerty School of Medicine, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Center for Genes, Environment and Health, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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Nakase T, Guerra G, Ostrom QT, Ge T, Melin B, Wrensch M, Wiencke JK, Jenkins RB, Eckel-Passow JE, Bondy ML, Francis SS, Kachuri L. Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes. medRxiv 2024:2024.01.10.24301112. [PMID: 38260701 PMCID: PMC10802631 DOI: 10.1101/2024.01.10.24301112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Polygenic risk scores (PRS) aggregate the contribution of many risk variants to provide a personalized genetic susceptibility profile. Since sample sizes of glioma genome-wide association studies (GWAS) remain modest, there is a need to find efficient ways of capturing genetic risk factors using available germline data. Methods We developed a novel PRS (PRS-CS) that uses continuous shrinkage priors to model the joint effects of over 1 million polymorphisms on disease risk and compared it to an approach (PRS-CT) that selects a limited set of independent variants that reach genome-wide significance (P<5×10-8). PRS models were trained using GWAS results stratified by histological (10,346 cases, 14,687 controls) and molecular subtype (2,632 cases, 2,445 controls), and validated in two independent cohorts. Results PRS-CS was consistently more predictive than PRS-CT across glioma subtypes with an average increase in explained variance (R2) of 21%. Improvements were particularly pronounced for glioblastoma tumors, with PRS-CS yielding larger effect sizes (odds ratio (OR)=1.93, P=2.0×10-54 vs. OR=1.83, P=9.4×10-50) and higher explained variance (R2=2.82% vs. R2=2.56%). Individuals in the 95th percentile of the PRS-CS distribution had a 3-fold higher lifetime absolute risk of IDH mutant (0.63%) and IDH wildtype (0.76%) glioma relative to individuals with average PRS. PRS-CS also showed high classification accuracy for IDH mutation status among cases (AUC=0.895). Conclusions Our novel genome-wide PRS may improve the identification of high-risk individuals and help distinguish between prognostic glioma subtypes, increasing the potential clinical utility of germline genetics in glioma patient management.
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Affiliation(s)
- Taishi Nakase
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Geno Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Melissa L. Bondy
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen S. Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Linda Kachuri
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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7
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Kachuri L, Chatterjee N, Hirbo J, Schaid DJ, Martin I, Kullo IJ, Kenny EE, Pasaniuc B, Witte JS, Ge T. Principles and methods for transferring polygenic risk scores across global populations. Nat Rev Genet 2024; 25:8-25. [PMID: 37620596 PMCID: PMC10961971 DOI: 10.1038/s41576-023-00637-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
Polygenic risk scores (PRSs) summarize the genetic predisposition of a complex human trait or disease and may become a valuable tool for advancing precision medicine. However, PRSs that are developed in populations of predominantly European genetic ancestries can increase health disparities due to poor predictive performance in individuals of diverse and complex genetic ancestries. We describe genetic and modifiable risk factors that limit the transferability of PRSs across populations and review the strengths and weaknesses of existing PRS construction methods for diverse ancestries. Developing PRSs that benefit global populations in research and clinical settings provides an opportunity for innovation and is essential for health equity.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jibril Hirbo
- Department of Medicine Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Iman Martin
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bogdan Pasaniuc
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ, Benlloch S, Dadaev T, Brook MN, Plym A, Sahimi A, Hoffman TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Laisk T, Figuerêdo J, Muir K, Ito S, Liu X, Uchio Y, Kubo M, Kamatani Y, Lophatananon A, Wan P, Andrews C, Lori A, Choudhury PP, Schleutker J, Tammela TL, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokolorczyk D, Lubinski J, Rentsch CT, Cho K, Mcmahon BH, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder A, Stroomberg HV, Batra J, Chambers S, Horvath L, Clements JA, Tilly W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordstrom T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein S, Cook MB, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Koutros S, Beane Freeman LE, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CM, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Butler EN, Mohler JL, Taylor JA, Kogevinas M, Dierssen-Sotos T, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Pilie P, Yu Y, Bohlender RJ, Gu J, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Brenner H, Chen X, Holleczek B, Schöttker B, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJ, Carpten J, Pandha H, Michael A, Ruyck KD, Meerleer GD, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas CM, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Abraham A, Singhal S, Parliament M, Claessens F, Joniau S, den Broeck TV, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen J, Petrovics G, Casey G, Wang Y, Tettey Y, Lachance J, Tang W, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Yamoah K, Govindasami K, Chokkalingam AP, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Shittu O, Amodu O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Diop H, Gundell SM, Roobol MJ, Jenster G, van Schaik RH, Hu JJ, Sanderson M, Kachuri L, Varma R, McKean-Cowdin R, Torres M, Preuss MH, Loos RJ, Zawistowski M, Zöllner S, Lu Z, Van Den Eeden SK, Easton DF, Ambs S, Edwards TL, Mägi R, Rebbeck TR, Fritsche L, Chanock SJ, Berndt SI, Wiklund F, Nakagawa H, Witte JS, Gaziano JM, Justice AC, Mancuso N, Terao C, Eeles RA, Kote-Jarai Z, Madduri RK, Conti DV, Haiman CA. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants. Nat Genet 2023; 55:2065-2074. [PMID: 37945903 PMCID: PMC10841479 DOI: 10.1038/s41588-023-01534-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/15/2023] [Indexed: 11/12/2023]
Abstract
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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Affiliation(s)
- Anqi Wang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rohini Janivara
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yili Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alisha J. Chou
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara Benlloch
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,University of Cambridge, Cambridge, UK
| | | | | | - Anna Plym
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Urology Division, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ali Sahimi
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Thomas J. Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Atushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing,Graduate school of Frontier Sciences,The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jéssica Figuerêdo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Shuji Ito
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - The Biobank Japan Project
- Corresponding Author: Christopher A. Haiman, Harlyne J. Norris Cancer Research Tower, USC Norris Comprehensive Cancer Center, 1450 Biggy Street, Rm 1504, Los Angeles, CA 90033 or
| | - Yuji Uchio
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences,Dana Farber Cancer Institute, Boston, MA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | | | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | | | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J. MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Christopher T. Rentsch
- Yale School of Medicine, New Haven, CT, USA
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kelly Cho
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
- University of Cambridge, Department of Oncology, Addenbrooke’s Hospital, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard M. Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Borge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Sune F. Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hein V. Stroomberg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Lisa Horvath
- Chris O’Brien Lifehouse (COBLH), Camperdown, Sydney, NSW, Australia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Wayne Tilly
- Dame Roma Mitchell Cancer Research Laboratories, University of Adelaide, Adelaide, Australia
| | - Gail P. Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Szulkin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- SDS Life Sciences, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Nordstrom
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nora Pashayan
- University College London, Department of Applied Health Research, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Sanger Institute, Hinxton, Saffron Walden, Hinxton, UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH,, Bethesda, MD, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David J. Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kathryn L. Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M. Thompson
- CHRISTUS Santa Rosa Hospital – Medical Center, San Antonio, TX, USA
| | - Robert J. Hamilton
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
- Dept. of Surgery (Urology), University of Toronto, Toronto, Canada
| | - Neil E. Fleshner
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gerald L. Andriole
- Brady Urological Institute in National Capital Region, Johns Hopkins University, Baltimore, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - James E. Mensah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, Jiangzhu Province, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zan Sun
- The People’s Hospital of Liaoning Proviouce, The People’s Hospital of China Medical University, Shenyang, China, Shenyang, China
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Catharine M.L. West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Gill Barnett
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | - Olivier Cussenot
- GRC 5 Predictive Onco-Urology, Sorbonne Université, Paris, France
- CeRePP, Paris, France
| | | | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France
| | - Esther M. John
- Department of Medicine, Stanford Cancer Institute,Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Sue A. Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Laura Fachal
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, Spain
| | - Barry S. Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L. Kerns
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Harry Ostrer
- Professor of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | | | | | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebonee N. Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L. Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Trinidad Dierssen-Sotos
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Craig C. Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Chad D. Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Patrick Pilie
- Department of Genitourinary Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S. Strom
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Robin J. Leach
- Department of Cell Systems and Anatomy and Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric A. Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ann W. Hsing
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Christopher J. Logothetis
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Jeri Kim
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J.M. Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent, Belgium
| | - Gert De Meerleer
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Piet Ost
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Lisa F. Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Daniel W. Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Jay H. Fowke
- Department of Preventive Medicine, Division of Epidemiology,The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Detroit, MI, USA
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Aswin Abraham
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), Vigo (Pontevedra), Spain
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Samantha Larkin
- Scientific Education Support, Thames Ditton, Surrey, Formerly Cancer Sciences, University of Southampton, Southampton, UK
| | - Paul A. Townsend
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | | | - William S. Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C. Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics,University of Virginia, Charlottesville, VA, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- Department of Pathology, University of Ghana, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Andrew A. Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | - Jacob M. Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N. Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E. Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayiwola Shittu
- Department of Surgery, College of Medicine, University of Ibadan and Univerity College Hospital, Ibadan, Nigeria
| | - Olukemi Amodu
- Institute of Child Health, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O. Adebiyi
- Clinical Epidemiology Unit, Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oseremen I. Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O. Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A. Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P. Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Susan M. Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ron H.N. van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jennifer J. Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Zeyun Lu
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | | | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,, Cambridge, UK
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Lars Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
- Departments of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Michael Gaziano
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nick Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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9
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Shi M, Shelley JP, Schaffer KR, Tosoian JJ, Bagheri M, Witte JS, Kachuri L, Mosley JD. Clinical consequences of a genetic predisposition toward higher benign prostate-specific antigen levels. EBioMedicine 2023; 97:104838. [PMID: 37865044 PMCID: PMC10597757 DOI: 10.1016/j.ebiom.2023.104838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Prostate-specific antigen (PSA) levels are influenced by genetic variation unrelated to prostate cancer risk. Whether a genetic predisposition to a higher PSA level predisposes to a diagnostic work-up for prostate cancer is not known. METHODS Participants were 3110 men of African and European ancestries ages 45-70, without prostate cancer and with a baseline PSA < 4 ng/mL, undergoing routine clinical PSA screening. The exposure was a polygenic score (PGS) comprising 111 single nucleotide polymorphisms associated with PSA level, but not prostate cancer. We tested whether the PGS was associated with a: 1) PSA value > 4 ng/mL, 2) International Classification of Diseases (ICD) code for an elevated PSA, 3) encounter with a urologist, or 4) prostate biopsy. Multivariable Cox proportional hazards models were adjusted for age and genetic principal components. Analyses were stratified by age (45-59 years, and 60-70 years old). Association estimates are per standard deviation change in the PGS. FINDINGS The median age was 56.6 years, and 2118 (68%) participants were 45-59 years. The median (IQR) baseline PSA level was 1.0 (0.6-1.7) ng/mL. Among men ages 45-59, the PGS was associated with a PSA > 4 (hazard ratio [HR] = 1.35 [95% CI, 1.17-1.57], p = 4.5 × 10-5), an ICD code for elevated PSA (HR = 1.30 [1.12-1.52], p = 8.0 × 10-4), a urological evaluation (HR = 1.34 [1.14-1.57], p = 4.8 × 10-4), and undergoing a prostate biopsy (HR = 1.35 [1.11-1.64], p = 0.002). Among men ages 60-70, association effect sizes were smaller and not significant. INTERPRETATION A predisposition toward higher PSA levels was associated with clinical evaluations of an elevated PSA among men ages 45-59 years. FUNDING National Institutes of Health (NIH).
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Affiliation(s)
- Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John P Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kerry R Schaffer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey J Tosoian
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Minoo Bagheri
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science and Genetics (by Courtesy), Stanford University, Stanford, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Jonathan D Mosley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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10
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Hoffmann TJ, Graff RE, Madduri RK, Rodriguez AA, Cario CL, Feng K, Jiang Y, Wang A, Klein RJ, Pierce BL, Eggener S, Tong L, Blot W, Long J, Rebbeck T, Lachance J, Andrews C, Adebiyi AO, Adusei B, Aisuodionoe-Shadrach OI, Fernandez PW, Jalloh M, Janivara R, Chen WC, Mensah JE, Agalliu I, Berndt SI, Shelley JP, Schaffer K, Machiela MJ, Freedman ND, Huang WY, Li SA, Goodman PJ, Till C, Thompson I, Lilja H, Van Den Eeden SK, Chanock SJ, Mosley JD, Conti DV, Haiman CA, Justice AC, Kachuri L, Witte JS. Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction. medRxiv 2023:2023.10.27.23297676. [PMID: 37961155 PMCID: PMC10635224 DOI: 10.1101/2023.10.27.23297676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
We conducted a multi-ancestry genome-wide association study of prostate-specific antigen (PSA) levels in 296,754 men (211,342 European ancestry; 58,236 African ancestry; 23,546 Hispanic/Latino; 3,630 Asian ancestry; 96.5% of participants were from the Million Veteran Program). We identified 318 independent genome-wide significant (p≤5e-8) variants, 184 of which were novel. Most demonstrated evidence of replication in an independent cohort (n=95,768). Meta-analyzing discovery and replication (n=392,522) identified 447 variants, of which a further 111 were novel. Out-of-sample variance in PSA explained by our new polygenic risk score reached 16.9% (95% CI=16.1%-17.8%) in European ancestry, 9.5% (95% CI=7.0%-12.2%) in African ancestry, 18.6% (95% CI=15.8%-21.4%) in Hispanic/Latino, and 15.3% (95% CI=12.7%-18.1%) in Asian ancestry, and lower for higher age. Our study highlights how including proportionally more participants from underrepresented populations improves genetic prediction of PSA levels, with potential to personalize prostate cancer screening.
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11
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Kachuri L, Guerra GA, Wendt GA, Hansen HM, Molinaro AM, Bracci P, McCoy L, Rice T, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival. medRxiv 2023:2023.10.15.23296448. [PMID: 37905116 PMCID: PMC10614986 DOI: 10.1101/2023.10.15.23296448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Glioma is a highly fatal brain tumor comprised of molecular subtypes with distinct clinical trajectories. Observational studies have suggested that variability in immune response may play a role in glioma etiology. However, their findings have been inconsistent and susceptible to reverse causation due to treatment effects and the immunosuppressive nature of glioma. We applied genetic variants associated (p<5×10-8) with blood cell traits to a meta-analysis of 3418 glioma cases and 8156 controls. Genetically predicted increase in the platelet to lymphocyte ratio (PLR) was associated with an increased risk of glioma (odds ratio (OR)=1.25, p=0.005), especially in IDH-mutant (IDHmut OR=1.38, p=0.007) and IDHmut 1p/19q non-codeleted (IDHmut-noncodel OR=1.53, p=0.004) tumors. However, reduced glioma risk was observed for higher counts of lymphocytes (IDHmut-noncodel OR=0.70, p=0.004) and neutrophils (IDHmut OR=0.69, p=0.019; IDHmut-noncodel OR=0.60, p=0.009), which may reflect genetic predisposition to enhanced immune-surveillance. In contrast to susceptibility, there was no association with survival in IDHmut-noncodel; however, in IDHmut 1p/19q co-deleted tumors, we observed higher mortality with increasing genetically predicted counts of lymphocytes (hazard ratio (HR)=1.65, 95% CI: 1.24-2.20), neutrophils (HR=1.49, 1.13-1.97), and eosinophils (HR=1.59, 1.18-2.14). Polygenic scores for blood cell traits were also associated with tumor immune microenvironment features, with heterogeneity by IDH status observed for 17 signatures related to interferon signaling, PD-1 expression, and T-cell/Cytotoxic responses. In summary, we identified novel, immune-mediated susceptibility mechanisms for glioma with potential disease management implications.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Geno A. Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Helen M. Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Annette M. Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - Paige Bracci
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, US
| | | | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Stephen S. Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, US
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12
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Francis SS, Guerra G, Hansen HM, Wendt G, Kachuri L, Wiencke JK, Wrensch M. Inherited polymorphisms in the Human Leukocyte Antigen Region modify the association between varicella-zoster virus antibody reactivity and glioma prognosis. Neuro Oncol 2023; 25:1910-1912. [PMID: 37595256 PMCID: PMC10547499 DOI: 10.1093/neuonc/noad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023] Open
Affiliation(s)
- Stephen S Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Geno Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - George Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
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13
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Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E. Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis. medRxiv 2023:2023.05.15.23289680. [PMID: 37292751 PMCID: PMC10246037 DOI: 10.1101/2023.05.15.23289680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immune checkpoint inhibitors (ICIs) are a remarkable advancement in cancer therapeutics; however, a substantial proportion of patients develop severe immune-related adverse events (irAEs). Understanding and predicting irAEs is a key to advancing precision immuno-oncology. Immune checkpoint inhibitor-mediated colitis (IMC) is a significant complication from ICI and can have life-threatening consequences. Based on clinical presentation, IMC mimics inflammatory bowel disease, however the link is poorly understood. We hypothesized that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) may predispose to IMC. We developed and validated polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and assessed the role of each of these PRSs on IMC in a cohort of 1,316 patients with non-small cell lung cancer who received ICIs. Prevalence of all-grade IMC in our cohort was 4% (55 cases), and for severe IMC, 2.5% (32 cases). The PRSUC predicted the development of all-grade IMC (HR=1.34 per standard deviation [SD], 95% CI=1.02-1.76, P=0.04) and severe IMC (HR=1.62 per SD, 95% CI=1.12-2.35, P=0.01). PRSCD was not associated with IMC or severe IMC. The association between PRSUC and IMC (all-grade and severe) was consistent in an independent pan-cancer cohort of patients treated with ICIs. Furthermore, PRSUC predicted severe IMC among patients treated with combination ICIs (OR = 2.20 per SD, 95% CI = 1.07-4.53, P=0.03). This is the first study to demonstrate the potential clinical utility of a PRS for ulcerative colitis in identifying patients receiving ICI at high risk of developing IMC, where risk reduction and close monitoring strategies could help improve overall patient outcomes.
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Affiliation(s)
- Pooja Middha
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lydia Yao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zoe Quandt
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Cardenas
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina J Falcon
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew A Gubens
- Medical Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University of Medicine, Stanford, CA, USA
| | - Khaleeq Khan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Min Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Megan H Murray
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kristin Werking
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luna Jia Zhan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Temerty School of Medicine, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, Center for Genes, Environment and Health and Institute for Human Genetics, University of California San Francisco, San Francisco, California
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14
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Yee SW, Macdonald C, Mitrovic D, Zhou X, Koleske ML, Yang J, Silva DB, Grimes PR, Trinidad D, More SS, Kachuri L, Witte JS, Delemotte L, Giacomini KM, Coyote-Maestas W. The full spectrum of OCT1 (SLC22A1) mutations bridges transporter biophysics to drug pharmacogenomics. bioRxiv 2023:2023.06.06.543963. [PMID: 37333090 PMCID: PMC10274788 DOI: 10.1101/2023.06.06.543963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Membrane transporters play a fundamental role in the tissue distribution of endogenous compounds and xenobiotics and are major determinants of efficacy and side effects profiles. Polymorphisms within these drug transporters result in inter-individual variation in drug response, with some patients not responding to the recommended dosage of drug whereas others experience catastrophic side effects. For example, variants within the major hepatic Human organic cation transporter OCT1 (SLC22A1) can change endogenous organic cations and many prescription drug levels. To understand how variants mechanistically impact drug uptake, we systematically study how all known and possible single missense and single amino acid deletion variants impact expression and substrate uptake of OCT1. We find that human variants primarily disrupt function via folding rather than substrate uptake. Our study revealed that the major determinants of folding reside in the first 300 amino acids, including the first 6 transmembrane domains and the extracellular domain (ECD) with a stabilizing and highly conserved stabilizing helical motif making key interactions between the ECD and transmembrane domains. Using the functional data combined with computational approaches, we determine and validate a structure-function model of OCT1s conformational ensemble without experimental structures. Using this model and molecular dynamic simulations of key mutants, we determine biophysical mechanisms for how specific human variants alter transport phenotypes. We identify differences in frequencies of reduced function alleles across populations with East Asians vs European populations having the lowest and highest frequency of reduced function variants, respectively. Mining human population databases reveals that reduced function alleles of OCT1 identified in this study associate significantly with high LDL cholesterol levels. Our general approach broadly applied could transform the landscape of precision medicine by producing a mechanistic basis for understanding the effects of human mutations on disease and drug response.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Christian Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Sweden
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Donovan Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, United States
| | - Swati S More
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Current address: Center for Drug Design (CDD), College of Pharmacy, University of Minnesota, Minnesota, United States
| | - Linda Kachuri
- Epidemiology and Population Health, Stanford University, California, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - John S Witte
- Epidemiology and Population Health, Stanford University, California, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Sweden
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Quantitative Biosciences Institute, University of California, San Francisco, United States
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15
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Kachuri L, Hoffmann TJ, Jiang Y, Berndt SI, Shelley JP, Schaffer KR, Machiela MJ, Freedman ND, Huang WY, Li SA, Easterlin R, Goodman PJ, Till C, Thompson I, Lilja H, Van Den Eeden SK, Chanock SJ, Haiman CA, Conti DV, Klein RJ, Mosley JD, Graff RE, Witte JS. Genetically adjusted PSA levels for prostate cancer screening. Nat Med 2023; 29:1412-1423. [PMID: 37264206 PMCID: PMC10287565 DOI: 10.1038/s41591-023-02277-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 02/27/2023] [Indexed: 06/03/2023]
Abstract
Prostate-specific antigen (PSA) screening for prostate cancer remains controversial because it increases overdiagnosis and overtreatment of clinically insignificant tumors. Accounting for genetic determinants of constitutive, non-cancer-related PSA variation has potential to improve screening utility. In this study, we discovered 128 genome-wide significant associations (P < 5 × 10-8) in a multi-ancestry meta-analysis of 95,768 men and developed a PSA polygenic score (PGSPSA) that explains 9.61% of constitutive PSA variation. We found that, in men of European ancestry, using PGS-adjusted PSA would avoid up to 31% of negative prostate biopsies but also result in 12% fewer biopsies in patients with prostate cancer, mostly with Gleason score <7 tumors. Genetically adjusted PSA was more predictive of aggressive prostate cancer (odds ratio (OR) = 3.44, P = 6.2 × 10-14, area under the curve (AUC) = 0.755) than unadjusted PSA (OR = 3.31, P = 1.1 × 10-12, AUC = 0.738) in 106 cases and 23,667 controls. Compared to a prostate cancer PGS alone (AUC = 0.712), including genetically adjusted PSA improved detection of aggressive disease (AUC = 0.786, P = 7.2 × 10-4). Our findings highlight the potential utility of incorporating PGS for personalized biomarkers in prostate cancer screening.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yu Jiang
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John P Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ryder Easterlin
- Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Cathee Till
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian Thompson
- CHRISTUS Santa Rosa Medical Center Hospital, San Antonio, TX, USA
| | - Hans Lilja
- Departments of Laboratory Medicine, Surgery and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan D Mosley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca E Graff
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - John S Witte
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Departments of Biomedical Data Science and Genetics, Stanford University, Stanford, CA, USA.
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16
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Kachuri L, Mak ACY, Hu D, Eng C, Huntsman S, Elhawary JR, Gupta N, Gabriel S, Xiao S, Keys KL, Oni-Orisan A, Rodríguez-Santana JR, LeNoir MA, Borrell LN, Zaitlen NA, Williams LK, Gignoux CR, Burchard EG, Ziv E. Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture. Nat Genet 2023; 55:952-963. [PMID: 37231098 PMCID: PMC10260401 DOI: 10.1038/s41588-023-01377-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/21/2023] [Indexed: 05/27/2023]
Abstract
We explored ancestry-related differences in the genetic architecture of whole-blood gene expression using whole-genome and RNA sequencing data from 2,733 African Americans, Puerto Ricans and Mexican Americans. We found that heritability of gene expression significantly increased with greater proportions of African genetic ancestry and decreased with higher proportions of Indigenous American ancestry, reflecting the relationship between heterozygosity and genetic variance. Among heritable protein-coding genes, the prevalence of ancestry-specific expression quantitative trait loci (anc-eQTLs) was 30% in African ancestry and 8% for Indigenous American ancestry segments. Most anc-eQTLs (89%) were driven by population differences in allele frequency. Transcriptome-wide association analyses of multi-ancestry summary statistics for 28 traits identified 79% more gene-trait associations using transcriptome prediction models trained in our admixed population than models trained using data from the Genotype-Tissue Expression project. Our study highlights the importance of measuring gene expression across large and ancestrally diverse populations for enabling new discoveries and reducing disparities.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer R Elhawary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
| | - Kevin L Keys
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA
| | - Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Luisa N Borrell
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Esteban González Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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17
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Shieh Y, Roger J, Yau C, Wolf DM, Hirst GL, Swigart LB, Huntsman S, Hu D, Nierenberg JL, Middha P, Heise RS, Shi Y, Kachuri L, Zhu Q, Yao S, Ambrosone CB, Kwan ML, Caan BJ, Witte JS, Kushi LH, 't Veer LV, Esserman LJ, Ziv E. Development and testing of a polygenic risk score for breast cancer aggressiveness. NPJ Precis Oncol 2023; 7:42. [PMID: 37188791 PMCID: PMC10185660 DOI: 10.1038/s41698-023-00382-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
Aggressive breast cancers portend a poor prognosis, but current polygenic risk scores (PRSs) for breast cancer do not reliably predict aggressive cancers. Aggressiveness can be effectively recapitulated using tumor gene expression profiling. Thus, we sought to develop a PRS for the risk of recurrence score weighted on proliferation (ROR-P), an established prognostic signature. Using 2363 breast cancers with tumor gene expression data and single nucleotide polymorphism (SNP) genotypes, we examined the associations between ROR-P and known breast cancer susceptibility SNPs using linear regression models. We constructed PRSs based on varying p-value thresholds and selected the optimal PRS based on model r2 in 5-fold cross-validation. We then used Cox proportional hazards regression to test the ROR-P PRS's association with breast cancer-specific survival in two independent cohorts totaling 10,196 breast cancers and 785 events. In meta-analysis of these cohorts, higher ROR-P PRS was associated with worse survival, HR per SD = 1.13 (95% CI 1.06-1.21, p = 4.0 × 10-4). The ROR-P PRS had a similar magnitude of effect on survival as a comparator PRS for estrogen receptor (ER)-negative versus positive cancer risk (PRSER-/ER+). Furthermore, its effect was minimally attenuated when adjusted for PRSER-/ER+, suggesting that the ROR-P PRS provides additional prognostic information beyond ER status. In summary, we used integrated analysis of germline SNP and tumor gene expression data to construct a PRS associated with aggressive tumor biology and worse survival. These findings could potentially enhance risk stratification for breast cancer screening and prevention.
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Affiliation(s)
- Yiwey Shieh
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA.
| | - Jacquelyn Roger
- PhD Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L Nierenberg
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Pooja Middha
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel S Heise
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Yushu Shi
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Marilyn L Kwan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Laura van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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18
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Chen DM, Dong R, Kachuri L, Hoffmann T, Jiang Y, Berndt SI, Shelley JP, Schaffer KR, Machiela MJ, Freedman ND, Huang WY, Li SA, Lilja H, Van Den Eeden SK, Chanock S, Haiman CA, Conti DV, Klein RJ, Mosley JD, Witte JS, Graff RE. Transcriptome-Wide Association Analysis Identifies Novel Candidate Susceptibility Genes for Prostate-Specific Antigen Levels in Men Without Prostate Cancer. medRxiv 2023:2023.05.04.23289526. [PMID: 37205487 PMCID: PMC10187439 DOI: 10.1101/2023.05.04.23289526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility to screen for prostate cancer (PCa). We thus conducted a transcriptome-wide association study (TWAS) of PSA levels using genome-wide summary statistics from 95,768 PCa-free men, the MetaXcan framework, and gene prediction models trained in Genotype-Tissue Expression (GTEx) project data. Tissue-specific analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10e-6) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61e-6) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses that combined associations across 45 tissues identified 155 genes that were statistically significantly (p < 0.05/22,249 = 2.25e-6) associated with PSA levels. Based on conditional analyses that assessed whether TWAS associations were attributable to a lead GWAS variant, we found 20 novel genes (11 single-tissue, 9 cross-tissue) that were associated with PSA levels in the TWAS. Of these novel genes, five showed evidence of colocalization (colocalization probability > 0.5): EXOSC9, CCNA2, HIST1H2BN, RP11-182L21.6, and RP11-327J17.2. Six of the 20 novel genes are not known to impact PCa risk. These findings yield new hypotheses for genetic factors underlying PSA levels that should be further explored toward improving our understanding of PSA biology.
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Affiliation(s)
- Dorothy M. Chen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ruocheng Dong
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, 94305, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Thomas Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Yu Jiang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - John P. Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Kerry R. Schaffer
- Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - Shengchao A. Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - Hans Lilja
- Departments of Pathology and Laboratory Medicine, Surgery, Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Translational Medicine, Lund University, Malmö, 21428, Sweden
| | | | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Robert J. Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jonathan D. Mosley
- Departments of Internal Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, 94305, USA
- Departments of Biomedical Data Science and Genetics (by courtesy), Stanford University, Stanford, CA, 94305, USA
| | - Rebecca E. Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
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19
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Cortez Cardoso Penha R, Smith-Byrne K, Atkins JR, Haycock PC, Kar S, Codd V, Samani NJ, Nelson C, Milojevic M, Gabriel AAG, Amos C, Brennan P, Hung RJ, Kachuri L, Mckay JD. Common genetic variations in telomere length genes and lung cancer: a Mendelian randomisation study and its novel application in lung tumour transcriptome. eLife 2023; 12:e83118. [PMID: 37079368 PMCID: PMC10118386 DOI: 10.7554/elife.83118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Background Genome-wide association studies (GWASs) have identified genetic susceptibility variants for both leukocyte telomere length (LTL) and lung cancer susceptibility. Our study aims to explore the shared genetic basis between these traits and investigate their impact on somatic environment of lung tumours. Methods We performed genetic correlation, Mendelian randomisation (MR), and colocalisation analyses using the largest available GWASs summary statistics of LTL (N=464,716) and lung cancer (N=29,239 cases and 56,450 controls). Principal components analysis based on RNA-sequencing data was used to summarise gene expression profile in lung adenocarcinoma cases from TCGA (N=343). Results Although there was no genome-wide genetic correlation between LTL and lung cancer risk, longer LTL conferred an increased risk of lung cancer regardless of smoking status in the MR analyses, particularly for lung adenocarcinoma. Of the 144 LTL genetic instruments, 12 colocalised with lung adenocarcinoma risk and revealed novel susceptibility loci, including MPHOSPH6, PRPF6, and POLI. The polygenic risk score for LTL was associated with a specific gene expression profile (PC2) in lung adenocarcinoma tumours. The aspect of PC2 associated with longer LTL was also associated with being female, never smokers, and earlier tumour stages. PC2 was strongly associated with cell proliferation score and genomic features related to genome stability, including copy number changes and telomerase activity. Conclusions This study identified an association between longer genetically predicted LTL and lung cancer and sheds light on the potential molecular mechanisms related to LTL in lung adenocarcinomas. Funding Institut National du Cancer (GeniLuc2017-1-TABAC-03-CIRC-1-TABAC17-022), INTEGRAL/NIH (5U19CA203654-03), CRUK (C18281/A29019), and Agence Nationale pour la Recherche (ANR-10-INBS-09).
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Affiliation(s)
- Ricardo Cortez Cardoso Penha
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, University of OxfordOxfordUnited Kingdom
| | - Joshua R Atkins
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit, Bristol Population Health Science Institute, Bristol Medical School (PHS)BristolUnited Kingdom
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, Bristol Population Health Science Institute, Bristol Medical School (PHS)BristolUnited Kingdom
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Christopher Nelson
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Maja Milojevic
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Aurélie AG Gabriel
- Ludwig Lausanne Branch, Faculty of Biology and MedicineLausanneSwitzerland
| | - Christopher Amos
- Institute for Clinical and Translational Research, Baylor College of MedicineHoustonUnited States
| | - Paul Brennan
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai HealthTorontoCanada
| | - Linda Kachuri
- Departament of Epidemiology and Population Health, Stanford UniversityStanfordUnited States
| | - James D Mckay
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
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20
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Schaffer KR, Shi M, Shelley JP, Tosoian JJ, Kachuri L, Witte JS, Mosley JD. A Polygenic Risk Score for Prostate Cancer Risk Prediction. JAMA Intern Med 2023; 183:386-388. [PMID: 36877498 PMCID: PMC9989952 DOI: 10.1001/jamainternmed.2022.6795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/12/2022] [Indexed: 03/07/2023]
Abstract
This retrospective cohort study compares 2 risk calculator systems that compute the probabilities of finding high-grade or any cancer on biopsy results in men undergoing a first prostate biopsy.
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Affiliation(s)
- Kerry R. Schaffer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John P. Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey J. Tosoian
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, California
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, California
- Department of Biomedical Data Science and Genetics (by courtesy), Stanford University, Stanford, California
| | - Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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21
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Shieh Y, Roger J, Yau C, Wolf D, Hirst G, Swigart L, Huntsman S, Hu D, Nierenberg J, Middha P, Heise R, Kachuri L, Zhu Q, Yao S, Ambrosone C, Kwan M, Caan B, Witte J, Kushi L, Veer LV’T, Esserman L, Ziv E. Abstract PR008: Development and testing of a polygenic risk score for breast cancer. Aggressiveness. Cancer Prev Res (Phila) 2023. [DOI: 10.1158/1940-6215.precprev22-pr008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Background: Aggressive breast cancers have increased proliferation or metastatic potential and portend a poor prognosis. The ability to identify women at elevated risk of aggressive cancers could have major implications for screening and prevention, yet there are no available tools for predicting aggressive cancer risk. We sought to construct a polygenic risk score (PRS) for aggressive breast cancers by leveraging the associations of single nucleotide polymorphisms (SNPs) with tumor gene expression. We used as our measure of aggressiveness the risk of recurrence score weighted on proliferation (ROR-P), a validated tumor prognostic signature. We hypothesized that known breast cancer susceptibility SNPs would have differential associations with ROR-P, which could then be used to construct a PRS for ROR-P. Methods: We developed our PRS in a case-only analysis of 3 studies containing SNP genotypes and tumor gene expression: The Cancer Genome Atlas, METABRIC, and the I-SPY 2 TRIAL (total n=2,363). We used linear regression models to evaluate individual SNP associations with ROR-P, adjusted for genetic ancestry and study. We then constructed PRS using varying p-value thresholds and used cross-validation to identify the PRS with highest model r2. To assess whether the ROR-P PRS was associated with poor prognosis, we performed survival analysis in two longitudinal cohorts of breast cancer patients: the UK Biobank (women with incident invasive cancers only) and the Pathways Study. These studies included 10,196 total cases with 785 deaths. We built Cox proportional hazards models to evaluate the association between the ROR-P PRS (adjusted for genetic ancestry) and breast cancer-specific survival (BCSS) in both studies. We then performed meta-analysis of the Cox model results. We also constructed joint models containing the ROR-P PRS and a PRS representing the case-case risk of ER-negative vs. ER-positive cancer, PRSER-/ER+. Results: We tested the associations between 226 breast cancer susceptibility SNPs and ROR-P. The best-performing PRS contained 76 SNPs and had a cross-validated r2 of 0.051. In the UK Biobank and Pathways Study, higher ROR-P PRS was associated with worse BCSS, with nearly identical effects observed in each study, HR per standard deviation of 1.13 (95% CI 1.05-1.21, p=9.0x10-4) in meta-analysis. The ROR-P PRS’s effect was minimally attenuated when adjusted for PRSER-/ER+, suggesting that the ROR-P PRS was providing additional prognostic information beyond ER status. Conclusions: We used breast cancer susceptibility SNPs to construct a PRS for ROR-P, a prognostic signature recapitulating aggressiveness, and found the ROR-P PRS to be associated with worse BCSS. Our findings represent an improvement on current PRS for overall breast cancer risk, which preferentially predict cancers with favorable prognosis. Given that aggressive cancers are more likely to present as advanced cancers even among women undergoing routine screening, our findings could potentially identify women who may benefit from more intensive screening.
Citation Format: Yiwey Shieh, Jacquelyn Roger, Christina Yau, Denise Wolf, Gillian Hirst, Lamorna Swigart, Scott Huntsman, Donglei Hu, Jovia Nierenberg, Pooja Middha, Rachel Heise, Linda Kachuri, Qianqian Zhu, Song Yao, Christine Ambrosone, Marilyn Kwan, Bette Caan, John Witte, Lawrence Kushi, Laura van ’T. Veer, Laura Esserman, Elad Ziv. Development and testing of a polygenic risk score for breast cancer. Aggressiveness. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr PR008.
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Affiliation(s)
| | - Jacquelyn Roger
- 2University of California, San Francisco, San Francisco, CA,
| | - Christina Yau
- 2University of California, San Francisco, San Francisco, CA,
| | - Denise Wolf
- 2University of California, San Francisco, San Francisco, CA,
| | - Gillian Hirst
- 2University of California, San Francisco, San Francisco, CA,
| | - Lamorna Swigart
- 2University of California, San Francisco, San Francisco, CA,
| | - Scott Huntsman
- 2University of California, San Francisco, San Francisco, CA,
| | - Donglei Hu
- 2University of California, San Francisco, San Francisco, CA,
| | | | - Pooja Middha
- 2University of California, San Francisco, San Francisco, CA,
| | | | | | - Qianqian Zhu
- 4Roswell Park Comprehensive Cancer Center, Buffalo, NY,
| | - Song Yao
- 4Roswell Park Comprehensive Cancer Center, Buffalo, NY,
| | | | - Marilyn Kwan
- 5Kaiser Permanente Northern California, Oakland, CA
| | - Bette Caan
- 5Kaiser Permanente Northern California, Oakland, CA
| | | | | | | | - Laura Esserman
- 2University of California, San Francisco, San Francisco, CA,
| | - Elad Ziv
- 2University of California, San Francisco, San Francisco, CA,
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Sheng X, Xia L, Cahoon JL, Conti DV, Haiman CA, Kachuri L, Chiang CW. Inverted genomic regions between reference genome builds in humans impact imputation accuracy and decrease the power of association testing. Human Genetics and Genomics Advances 2022; 4:100159. [PMID: 36465187 PMCID: PMC9709082 DOI: 10.1016/j.xhgg.2022.100159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last two decades, the human reference genome has undergone multiple updates as we complete a linear representation of our genome. Two versions of human references are currently used in the biomedical literature, GRCh37/hg19 and GRCh38. Conversions between these versions are critical for quality control, imputation, and association analysis. In the present study, we show that single-nucleotide variants (SNVs) in regions inverted between different builds of the reference genome are often mishandled bioinformatically. Depending on the array type, SNVs are found in approximately 2-5 Mb of the genome that are inverted between reference builds. Coordinate conversions of these variants are mishandled by both the TOPMed imputation server as well as routine in-house quality control pipelines, leading to underrecognized downstream analytical consequences. Specifically, we observe that undetected allelic conversion errors for palindromic (i.e., A/T or C/G) variants in these inverted regions would destabilize the local haplotype structure, leading to loss of imputation accuracy and power in association analyses. Though only a small proportion of the genome is affected, these regions include important disease susceptibility variants that would be affected. For example, the p value of a known locus associated with prostate cancer on chromosome 10 (chr10) would drop from 2.86 × 10-7 to 0.0011 in a case-control analysis of 20,286 Africans and African Americans (10,643 cases and 9,643 controls). We devise a straight-forward heuristic based on the popular tool, liftOver, that can easily detect and correct these variants in the inverted regions between genome builds to locally improve imputation accuracy.
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23
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Cavazos TB, Kachuri L, Graff RE, Nierenberg JL, Thai KK, Alexeeff S, Van Den Eeden S, Corley DA, Kushi LH, Hoffmann TJ, Ziv E, Habel LA, Jorgenson E, Sakoda LC, Witte JS. Assessment of genetic susceptibility to multiple primary cancers through whole-exome sequencing in two large multi-ancestry studies. BMC Med 2022; 20:332. [PMID: 36199081 PMCID: PMC9535845 DOI: 10.1186/s12916-022-02535-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Up to one of every six individuals diagnosed with one cancer will be diagnosed with a second primary cancer in their lifetime. Genetic factors contributing to the development of multiple primary cancers, beyond known cancer syndromes, have been underexplored. METHODS To characterize genetic susceptibility to multiple cancers, we conducted a pan-cancer, whole-exome sequencing study of individuals drawn from two large multi-ancestry populations (6429 cases, 165,853 controls). We created two groupings of individuals diagnosed with multiple primary cancers: (1) an overall combined set with at least two cancers across any of 36 organ sites and (2) cancer-specific sets defined by an index cancer at one of 16 organ sites with at least 50 cases from each study population. We then investigated whether variants identified from exome sequencing were associated with these sets of multiple cancer cases in comparison to individuals with one and, separately, no cancers. RESULTS We identified 22 variant-phenotype associations, 10 of which have not been previously discovered and were significantly overrepresented among individuals with multiple cancers, compared to those with a single cancer. CONCLUSIONS Overall, we describe variants and genes that may play a fundamental role in the development of multiple primary cancers and improve our understanding of shared mechanisms underlying carcinogenesis.
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Affiliation(s)
- Taylor B Cavazos
- Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Population Health, Stanford University, Alway Building, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Jovia L Nierenberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA.,Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Stacey Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Stephen Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | | | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Elad Ziv
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA
| | - Eric Jorgenson
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA.,Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA. .,Department of Epidemiology and Population Health, Stanford University, Alway Building, 300 Pasteur Drive, Stanford, CA, 94305, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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24
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Gabriel AAG, Atkins JR, Penha RCC, Smith-Byrne K, Gaborieau V, Voegele C, Abedi-Ardekani B, Milojevic M, Olaso R, Meyer V, Boland A, Deleuze JF, Zaridze D, Mukeriya A, Swiatkowska B, Janout V, Schejbalová M, Mates D, Stojšić J, Ognjanovic M, Witte JS, Rashkin SR, Kachuri L, Hung RJ, Kar S, Brennan P, Sertier AS, Ferrari A, Viari A, Johansson M, Amos CI, Foll M, McKay JD. Genetic Analysis of Lung Cancer and the Germline Impact on Somatic Mutation Burden. J Natl Cancer Inst 2022; 114:1159-1166. [PMID: 35511172 PMCID: PMC9360465 DOI: 10.1093/jnci/djac087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Germline genetic variation contributes to lung cancer (LC) susceptibility. Previous genome-wide association studies (GWAS) have implicated susceptibility loci involved in smoking behaviors and DNA repair genes, but further work is required to identify susceptibility variants. METHODS To identify LC susceptibility loci, a family history-based genome-wide association by proxy (GWAx) of LC (48 843 European proxy LC patients, 195 387 controls) was combined with a previous LC GWAS (29 266 patients, 56 450 controls) by meta-analysis. Colocalization was used to explore candidate genes and overlap with existing traits at discovered susceptibility loci. Polygenic risk scores (PRS) were tested within an independent validation cohort (1 666 LC patients vs 6 664 controls) using variants selected from the LC susceptibility loci and a novel selection approach using published GWAS summary statistics. Finally, the effects of the LC PRS on somatic mutational burden were explored in patients whose tumor resections have been profiled by exome (n = 685) and genome sequencing (n = 61). Statistical tests were 2-sided. RESULTS The GWAx-GWAS meta-analysis identified 8 novel LC loci. Colocalization implicated DNA repair genes (CHEK1), metabolic genes (CYP1A1), and smoking propensity genes (CHRNA4 and CHRNB2). PRS analysis demonstrated that these variants, as well as subgenome-wide significant variants related to expression quantitative trait loci and/or smoking propensity, assisted in LC genetic risk prediction (odds ratio = 1.37, 95% confidence interval = 1.29 to 1.45; P < .001). Patients with higher genetic PRS loads of smoking-related variants tended to have higher mutation burdens in their lung tumors. CONCLUSIONS This study has expanded the number of LC susceptibility loci and provided insights into the molecular mechanisms by which these susceptibility variants contribute to LC development.
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Affiliation(s)
- Aurélie A G Gabriel
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Joshua R Atkins
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Ricardo C C Penha
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, England
| | - Valerie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Catherine Voegele
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Maja Milojevic
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Robert Olaso
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean François Deleuze
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Beata Swiatkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Vladimir Janout
- Faculty of Medicine, Palacky University, Olomouc, Czech Republic
| | | | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojšić
- Department of Thoracic Pathology, Service of Pathology, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Miodrag Ognjanovic
- International Organisation for Cancer Prevention and Research, Belgrade, Serbia
| | | | - John S Witte
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Anne-Sophie Sertier
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
| | - Anthony Ferrari
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
| | - Alain Viari
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
- Inria Centre de Recherche Grenoble Rhone-Alpes, Grenoble, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, USA
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - James D McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
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25
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Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nat Genet 2022; 54:1167-1177. [PMID: 35915169 PMCID: PMC9373844 DOI: 10.1038/s41588-022-01115-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/27/2022] [Indexed: 02/03/2023]
Abstract
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | - Wen Zhou
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ann Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | - Christine Lusk
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | | | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihao Li
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Susan Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - James C Willey
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX, USA
| | | | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan Lam
- Department of Integrative Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Stig Bojeson
- Department of Clinical Biochemistry, Herlev Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Thomas Muley
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - David C Christiani
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, KY, USA
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay Shete
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alpa Patel
- American Cancer Society, Atlanta, GA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Margaret Spitz
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xihong Lin
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Kachuri L, Graff RE, Berndt SI, Machiela M, Freedman ND, Chanock SJ, Shelley JP, Schaffer K, Mosley JD, Goodman PJ, Till C, Thompson I, Klein RJ, Van Den Eeden SK, Hoffmann TJ, Witte JS. Abstract 1441: Genetic determinants of PSA levels improve prostate cancer screening. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate-specific antigen (PSA) screening for prostate cancer (PCa) remains controversial due to poor sensitivity and specificity that lead to overdiagnosis and overtreatment. The aim of our study is to characterize genetic determinants of PSA levels in cancer-free men in order to personalize PCa screening. We hypothesize that test accuracy may be improved by accounting for PSA variation that is due to genetic factors and does not reflect PCa.
We conducted the largest ever genome-wide association study (GWAS) of PSA in men without PCa (N=95,768; 85,924 predominantly European ancestry) using data from the UK Biobank, BioVU, PLCO, and Kaiser Permanente cohorts. Our GWAS discovered 129 PSA-associated variants (P<5×10-8), 82 of which were novel. A polygenic score (PGSPSA) comprised of these 129 variants was successfully validated in two cancer prevention trials: PCPT (n=5737) and SELECT (n=22,247). PGSPSA explained 7.3% (p=7.0×10-98) of variation in baseline PSA in PCPT and 8.7% (p=7.0×10-476) in SELECT. Importantly, PGSPSA was not associated with PCa status in PCPT (OR=0.98, p=0.71) or SELECT (OR=1.04, p=0.98), which confirms that it reflects benign PSA variation.
Potential clinical utility of PSA genetic adjustment was explored by examining reclassification at thresholds used for biopsy referrals in a real-world setting at Kaiser Permanente. We estimated that correction using PGSPSA would have avoided 21.2% of negative biopsies in non-cases. Reclassification below the biopsy referral threshold was also more common in cases, particularly with low-grade disease with Gleason score <7 (7.3% below vs. 2.6% above). Overall, genetic correction of PSA appeared to improve the accuracy of referral decisions, with a Net Reclassification Index of 0.148.
Next, we evaluated genetically adjusted PSA in the context of detection of aggressive PCa, defined as Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, and/or distant or nodal metastases. Genetically adjusted baseline PSA was more robustly associated with aggressive PCa than observed PSA and yielded a higher area under the curve (AUC) in PCPT (OR=3.03, p=3.5×10-7; AUC: 0.72 vs. 0.68) and SELECT (OR=3.37, p=3.5×10-11; AUC: 0.78 vs. 0.74) when added to a baseline model with age and trial arm. Furthermore, genetically adjusted PSA provides complementary information to PCa risk variants. In PCPT, a logistic regression model that included genetically corrected PSA and the 269-variant PGSPCa achieved a significantly higher AUC than PGSPCa-269 alone for aggressive PCa (AUC: 0.73 vs. 0.65, p=3.3×10-4) and overall PCa (AUC=0.69 vs. 0.66, p=3.3×10-6).
Our work provides evidence that accounting for genetic determinants of PSA has the potential to reduce unnecessary testing and overdiagnosis of low-risk PCa, as well as increase detection of aggressive disease. Larger and more diverse study populations are required to fully characterize the genetic basis of PSA variation and optimize its clinical utility.
Citation Format: Linda Kachuri, Rebecca E. Graff, Sonja I. Berndt, Mitchell Machiela, Neal D. Freedman, Stephen J. Chanock, John P. Shelley, Kerry Schaffer, Jonathan D. Mosley, Phyllis J. Goodman, Cathee Till, Ian Thompson, Robert J. Klein, Stephen K. Van Den Eeden, Thomas J. Hoffmann, John S. Witte. Genetic determinants of PSA levels improve prostate cancer screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1441.
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Affiliation(s)
- Linda Kachuri
- 1Univeristy of California San Francisco, San Francisco, CA
| | | | | | | | | | | | | | | | | | | | - Cathee Till
- 4Fred Hutchinson Cancer Research Center, Seattle, WA
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Nierenberg JL, Kachuri L, Cavazos TB, Graff RE, Hoffmann TJ, Zhang J, Alexeeff S, Habel L, Corley D, Van Den Eeden S, Ziv E, Sakoda LC, Witte JS. Abstract 1446: Genetic risk factors for the development of multiple primary cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Individuals with one cancer are at greater risk of new primary cancers than the general population. While several hereditary cancer syndromes are known, genetic risk factors for multiple primary cancers in an individual are not well understood. Identification of susceptibility variants to multiple primary tumors could enhance screening for subsequent cancers among those at highest risk.
Methods: We conducted a pan-cancer genome-wide association study (GWAS) of multiple primary cancers among participants from 2 prospective cohorts: Kaiser Permanente and the UK Biobank. The primary GWAS within cohorts used logistic regression to estimate associations for diagnosis with ≥2 invasive or in situ primary cancers other than non-melanoma skin (N=11,773, 8,928 invasive only) compared to cancer-free controls (N=420,101). Case-case analyses were conducted to distinguish associations with multiple cancers from single-cancer (N=90,576) susceptibility signals. Regression models were adjusted for age, sex, first 10 genetic ancestry principal components, and array. Cohort-specific GWAS results were meta-analyzed. We highlight genome-wide significant (p<5×10-8) results with consistent effect direction across the 2 studies.
Results: We identified 8 variants associated with multiple primary cancers.
Discussion: To our knowledge, rs192703567 has no previous cancer associations. Three identified variants are in known cancer predisposition genes (rs2293607 in TERC, rs6983267 in CASC8, rs35850753 in TP53). Three variants (rs34379047, rs612611, and rs9419958) are previously associated with multiple cancers, 2 (rs2293607 and rs6983267) with cancer pleiotropy, and 2 (rs283732 and rs35850753) with individual cancers. Most variants from the cancer-free control analyses had consistent effects in the single-cancer case-case analyses, suggesting pleiotropic mechanisms. Our preliminary findings offer insight into genetic risk factors associated with developing multiple primary cancers.
Multiple vs. none Multiple invasive vs. none Multiple vs. single Multiple invasive vs. single Chr Position rsID A1 A2 Gene OR P OR P OR P OR P 3 169482335 rs2293607 T C TERC 1.11 1.0×10-9 1.10 2.2×10-7 1.06 2.0×10-3 1.05 0.01 8 128281644 rs283732 C T Intergenic 1.09 2.3×10-7 1.11 9.2×10-9 1.06 3.8×10-4 1.09 3.9×10-5 8 128413305 rs6983267 G T CASC8 POU5F1B CCAT2 PCAT1 1.08 4.1×10-7 1.09 2.9×10-8 1.00 0.83 1.02 0.34 10 105644473 rs34379047 T A OBFC1 1.16 8.5×10-12 1.19 6.0×10-11 1.19 2.3×10-4 1.10 4.0×10-4 10 105675946 rs9419958 T C STN1 1.14 1.8×10-11 1.16 4.5×10-11 1.08 3.1×10-4 1.09 2.8×10-4 11 69307463 rs612611 G A Intergenic 1.11 3.7×10-8 1.10 5.3×10-6 1.06 9.6×10-4 1.05 0.02 17 7578671 rs35850753 T C TP53 1.27 4.9×10-7 1.34 1.6×10-8 1.16 2.8×10-3 1.24 8.8×10-5 22 40738280 rs192703567 C T Intergenic 1.37 5.2×10-8 1.37 1.8×10-6 1.43 4.9×10-9 1.43 2.8×10-7 Chr=Chromosome; A1=Effect allele; A2=Other allele; OR=Odds ratio.
Citation Format: Jovia L. Nierenberg, Linda Kachuri, Taylor B. Cavazos, Rebecca E. Graff, Thomas J. Hoffmann, Jie Zhang, Stacey Alexeeff, Laurel Habel, Douglas Corley, Stephen Van Den Eeden, Elad Ziv, Lori C. Sakoda, John S. Witte. Genetic risk factors for the development of multiple primary cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1446.
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Affiliation(s)
| | - Linda Kachuri
- 1University of California San Francisco, San Francisco, CA
| | | | | | | | - Jie Zhang
- 2Kaiser Permanente Northern California, Oakland, CA
| | | | - Laurel Habel
- 2Kaiser Permanente Northern California, Oakland, CA
| | | | | | - Elad Ziv
- 1University of California San Francisco, San Francisco, CA
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Kapoor PM, Mak AC, Kachuri L, Hu D, Huntsman S, Kushi LH, Haiman C, John EM, Torres-Mejia G, Burchard EG, Neuhausen SL, Fejerman L, Ziv E. Abstract 3631: Transcriptome-wide association study identifies novel genes associated with breast cancer susceptibility in Latinas. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Genetic susceptibility to breast cancer has been studied extensively in European ancestry populations, but few studies have addressed genetic susceptibility in non-European women. Latinas are a genetically diverse group with contributions from European, African, and Indigenous American ancestries. Genome-wide association studies (GWAS) have identified unique variants in this population, particularly at the 6q25 locus. We conducted a transcriptome-wide association study (TWAS) to identify novel genes associated with risk of breast cancer in Latinas.
Methods: We used individual level GWAS data from 2,396 Latina cases and 6,505 Latina controls from the studies in Northern California (San Francisco Bay Area Breast Cancer Study, Northern California Breast Cancer Family Registry and Kaiser Permanente Genetic Epidemiology Research on Aging Cohort), Southern California (Multi-ethnic Cohort) and Mexico (CAMA study). We analyzed the association between genetically predicted whole blood (WB) gene expression and breast cancer risk using newly developed TWAS models based on 784 Mexican American individuals. We also conducted parallel analyses using breast mammary tissue (BT) TWAS models from GTEx v8. All analyses were adjusted for age, ancestry, and study. Associations with false discovery rate (FDR) probability <0.05 were considered statistically significant.
Results: At FDR<0.05, we identified 20 genes from BT and 39 genes from WB. Seven of the genes were significantly associated in both the WB models and GTEx BT models. Increased expression of MIB2 (pFDR = 4.74x10-17 (WB) and 1.22x10-4 (BT)), NBPF26 (pFDR = 1.30x10-7 (WB) and 7.43x10-8 (BT)), SLC35E2B (pFDR = 1.12x10-4 (WB) and 5.47x10-5 (BT)), and FAM30A (pFDR = 1.18x10-10 (WB) and 9.27x10-3 (BT)) was associated with increased risk of breast cancer risk, whereas increased expression of SLC35E2A (pFDR = 8.17x10-6 (WB) and 1.55x10-3 (BT)) and HCP5B (pFDR = 1.84x10-3 (WB) and 2.19x10-3 (BT)) was associated with decreased breast cancer risk. Increased expression of PDGFA was associated with increased risk (pFDR = 1.30x10-7) in GTEx BT reference models but decreased risk (pFDR = 2.34x10-10) in the ancestry-specific WB model.
Conclusion: Our study is the first TWAS investigating the relationship between genetically predicted gene expression and breast cancer risk in Latinas. By leveraging gene expression prediction models that capture eQTLs that are more common in populations with Indigenous American ancestry, we have identified some novel genes associated with breast cancer risk in Latinas. Of these, MIB2 is a strong candidate for a mechanistic role in breast carcinogenesis in Latinas. MIB2 is involved in Notch signaling which plays an important role in breast carcinogenesis via its mismatched receptor-ligand interaction. Our study highlights the role of ancestry-based prediction models in TWAS analyses.
Citation Format: Pooja Middha Kapoor, Angel C. Mak, Linda Kachuri, Donglei Hu, Scott Huntsman, Lawrence H. Kushi, Christopher Haiman, Esther M. John, Gabriela Torres-Mejia, Esteban G. Burchard, Susan L. Neuhausen, Laura Fejerman, Elad Ziv. Transcriptome-wide association study identifies novel genes associated with breast cancer susceptibility in Latinas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3631.
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Affiliation(s)
| | - Angel C. Mak
- 1University of California San Francisco, San Francisco, CA
| | - Linda Kachuri
- 1University of California San Francisco, San Francisco, CA
| | - Donglei Hu
- 1University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- 1University of California San Francisco, San Francisco, CA
| | | | | | | | | | | | | | | | - Elad Ziv
- 1University of California San Francisco, San Francisco, CA
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Guerra G, Kachuri L, Wendt G, Hansen HM, Mack SJ, Molinaro AM, Rice T, Bracci P, Wiencke JK, Kasahara N, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival. Am J Hum Genet 2022; 109:1105-1116. [PMID: 35550063 PMCID: PMC9247888 DOI: 10.1016/j.ajhg.2022.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Glioma is a highly fatal cancer with prognostically significant molecular subtypes and few known risk factors. Multiple studies have implicated infections in glioma susceptibility, but evidence remains inconsistent. Genetic variants in the human leukocyte antigen (HLA) region modulate host response to infection and have been linked to glioma risk. In this study, we leveraged genetic predictors of antibody response to 12 viral antigens to investigate the relationship with glioma risk and survival. Genetic reactivity scores (GRSs) for each antigen were derived from genome-wide-significant (p < 5 × 10-8) variants associated with immunoglobulin G antibody response in the UK Biobank cohort. We conducted parallel analyses of glioma risk and survival for each GRS and HLA alleles imputed at two-field resolution by using data from 3,418 glioma-affected individuals subtyped by somatic mutations and 8,156 controls. Genetic reactivity scores to Epstein-Barr virus (EBV) ZEBRA and EBNA antigens and Merkel cell polyomavirus (MCV) VP1 antigen were associated with glioma risk and survival (Bonferroni-corrected p < 0.01). GRSZEBRA and GRSMCV were associated in opposite directions with risk of IDH wild-type gliomas (ORZEBRA = 0.91, p = 0.0099/ORMCV = 1.11, p = 0.0054). GRSEBNA was associated with both increased risk for IDH mutated gliomas (OR = 1.09, p = 0.040) and improved survival (HR = 0.86, p = 0.010). HLA-DQA1∗03:01 was significantly associated with decreased risk of glioma overall (OR = 0.85, p = 3.96 × 10-4) after multiple testing adjustment. This systematic investigation of the role of genetic determinants of viral antigen reactivity in glioma risk and survival provides insight into complex immunogenomic mechanisms of glioma pathogenesis. These results may inform applications of antiviral-based therapies in glioma treatment.
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Affiliation(s)
- Geno Guerra
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - George Wendt
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Nori Kasahara
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA
| | | | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA.
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30
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Kachuri L, Walsh KM. Long telomeres in need of a SNP: Germline contributions of telomere maintenance to glioma. Neuro Oncol 2022; 24:182-183. [PMID: 34758087 PMCID: PMC8804881 DOI: 10.1093/neuonc/noab260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Kyle M Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
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Gormley M, Dudding T, Kachuri L, Burrows K, Chong AHW, Martin RM, Thomas SJ, Tyrrell J, Ness AR, Brennan P, Munafò MR, Pring M, Boccia S, Olshan AF, Diergaarde B, Hung RJ, Liu G, Tajara EH, Severino P, Toporcov TN, Lacko M, Waterboer T, Brenner N, Smith GD, Vincent EE, Richmond RC. Investigating the effect of sexual behaviour on oropharyngeal cancer risk: a methodological assessment of Mendelian randomization. BMC Med 2022; 20:40. [PMID: 35094705 PMCID: PMC8802428 DOI: 10.1186/s12916-022-02233-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human papilloma virus infection is known to influence oropharyngeal cancer (OPC) risk, likely via sexual transmission. However, sexual behaviour has been correlated with other risk factors including smoking and alcohol, meaning independent effects are difficult to establish. We aimed to evaluate the causal effect of sexual behaviour on the risk of OPC using Mendelian randomization (MR). METHODS Genetic variants robustly associated with age at first sex (AFS) and the number of sexual partners (NSP) were used to perform both univariable and multivariable MR analyses with summary data on 2641 OPC cases and 6585 controls, obtained from the largest available genome-wide association studies (GWAS). Given the potential for genetic pleiotropy, we performed a number of sensitivity analyses: (i) MR methods to account for horizontal pleiotropy, (ii) MR of sexual behaviours on positive (cervical cancer and seropositivity for Chlamydia trachomatis) and negative control outcomes (lung and oral cancer), (iii) Causal Analysis Using Summary Effect estimates (CAUSE), to account for correlated and uncorrelated horizontal pleiotropic effects, (iv) multivariable MR analysis to account for the effects of smoking, alcohol, risk tolerance and educational attainment. RESULTS In univariable MR, we found evidence supportive of an effect of both later AFS (IVW OR = 0.4, 95%CI (0.3, 0.7), per standard deviation (SD), p = < 0.001) and increasing NSP (IVW OR = 2.2, 95%CI (1.3, 3.8) per SD, p = < 0.001) on OPC risk. These effects were largely robust to sensitivity analyses accounting for horizontal pleiotropy. However, negative control analysis suggested potential violation of the core MR assumptions and subsequent CAUSE analysis implicated pleiotropy of the genetic instruments used to proxy sexual behaviours. Finally, there was some attenuation of the univariable MR results in the multivariable models (AFS IVW OR = 0.7, 95%CI (0.4, 1.2), p = 0.21; NSP IVW OR = 0.9, 95%CI (0.5 1.7), p = 0.76). CONCLUSIONS Despite using genetic variants strongly related sexual behaviour traits in large-scale GWAS, we found evidence for correlated pleiotropy. This emphasizes a need for multivariable approaches and the triangulation of evidence when performing MR of complex behavioural traits.
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Affiliation(s)
- Mark Gormley
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK.
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Tom Dudding
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, USA
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Amanda H W Chong
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Steven J Thomas
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, RILD Building, RD&E Hospital, Exeter, UK
| | - Andrew R Ness
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Paul Brennan
- Genetic Epidemiology Group, World Health Organization, International Agency for Research on Cancer, Lyon, France
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- School of Psychological Science, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Miranda Pring
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, and UPMC Hillman Cancer Center, Pittsburgh, USA
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Geoffrey Liu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, Toronto, Canada
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, São Paulo, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Tatiana N Toporcov
- Department of Epidemiology, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Martin Lacko
- Department of Otorhinolaryngology and Head and Neck Surgery, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Tim Waterboer
- Infections and Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Nicole Brenner
- Infections and Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emma E Vincent
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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32
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Jiang Y, Meyers TJ, Emeka AA, Cooley LF, Cooper PR, Lancki N, Helenowski I, Kachuri L, Lin DW, Stanford JL, Newcomb LF, Kolb S, Finelli A, Fleshner NE, Komisarenko M, Eastham JA, Ehdaie B, Benfante N, Logothetis CJ, Gregg JR, Perez CA, Garza S, Kim J, Marks LS, Delfin M, Barsa D, Vesprini D, Klotz LH, Loblaw A, Mamedov A, Goldenberg SL, Higano CS, Spillane M, Wu E, Carter HB, Pavlovich CP, Mamawala M, Landis T, Carroll PR, Chan JM, Cooperberg MR, Cowan JE, Morgan TM, Siddiqui J, Martin R, Klein EA, Brittain K, Gotwald P, Barocas DA, Dallmer JR, Gordetsky JB, Steele P, Kundu SD, Stockdale J, Roobol MJ, Venderbos LD, Sanda MG, Arnold R, Patil D, Evans CP, Dall’Era MA, Vij A, Costello AJ, Chow K, Corcoran NM, Rais-Bahrami S, Phares C, Scherr DS, Flynn T, Karnes RJ, Koch M, Dhondt CR, Nelson JB, McBride D, Cookson MS, Stratton KL, Farriester S, Hemken E, Stadler WM, Pera T, Banionyte D, Bianco FJ, Lopez IH, Loeb S, Taneja SS, Byrne N, Amling CL, Martinez A, Boileau L, Gaylis FD, Petkewicz J, Kirwen N, Helfand BT, Xu J, Scholtens DM, Catalona WJ, Witte JS. Genetic Factors Associated with Prostate Cancer Conversion from Active Surveillance to Treatment. HGG Adv 2022; 3:100070. [PMID: 34993496 PMCID: PMC8725988 DOI: 10.1016/j.xhgg.2021.100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022] Open
Abstract
Men diagnosed with low-risk prostate cancer (PC) are increasingly electing active surveillance (AS) as their initial management strategy. While this may reduce the side effects of treatment for prostate cancer, many men on AS eventually convert to active treatment. PC is one of the most heritable cancers, and genetic factors that predispose to aggressive tumors may help distinguish men who are more likely to discontinue AS. To investigate this, we undertook a multi-institutional genome-wide association study (GWAS) of 5,222 PC patients and 1,139 other patients from replication cohorts, all of whom initially elected AS and were followed over time for the potential outcome of conversion from AS to active treatment. In the GWAS we detected 18 variants associated with conversion, 15 of which were not previously associated with PC risk. With a transcriptome-wide association study (TWAS), we found two genes associated with conversion (MAST3, p = 6.9×10-7 and GAB2, p = 2.0×10-6). Moreover, increasing values of a previously validated 269-variant genetic risk score (GRS) for PC was positively associated with conversion (e.g., comparing the highest to the two middle deciles gave a hazard ratio [HR] = 1.13; 95% Confidence Interval [CI]= 0.94-1.36); whereas, decreasing values of a 36-variant GRS for prostate-specific antigen (PSA) levels were positively associated with conversion (e.g., comparing the lowest to the two middle deciles gave a HR = 1.25; 95% CI, 1.04-1.50). These results suggest that germline genetics may help inform and individualize the decision of AS-or the intensity of monitoring on AS-versus treatment for the initial management of patients with low-risk PC.
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Affiliation(s)
- Yu Jiang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Travis J. Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adaeze A. Emeka
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lauren Folgosa Cooley
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Phillip R. Cooper
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicola Lancki
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Irene Helenowski
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Lin
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Janet L. Stanford
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Lisa F. Newcomb
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Suzanne Kolb
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil E. Fleshner
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maria Komisarenko
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James A. Eastham
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Behfar Ehdaie
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Benfante
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J. Logothetis
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin R. Gregg
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cherie A. Perez
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergio Garza
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeri Kim
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard S. Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Merdie Delfin
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danielle Barsa
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danny Vesprini
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Laurence H. Klotz
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew Loblaw
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Alexandre Mamedov
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - S. Larry Goldenberg
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Celestia S. Higano
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Maria Spillane
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Eugenia Wu
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - H. Ballentine Carter
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian P. Pavlovich
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mufaddal Mamawala
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tricia Landis
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter R. Carroll
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew R. Cooperberg
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Janet E. Cowan
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Todd M. Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rabia Martin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Karen Brittain
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Paige Gotwald
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel A. Barocas
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremiah R. Dallmer
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer B. Gordetsky
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pam Steele
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilajit D. Kundu
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jazmine Stockdale
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lionne D.F. Venderbos
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin G. Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rebecca Arnold
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Dattatraya Patil
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher P. Evans
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Marc A. Dall’Era
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anjali Vij
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anthony J. Costello
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Ken Chow
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Niall M. Corcoran
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Soroush Rais-Bahrami
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Courtney Phares
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Douglas S. Scherr
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Thomas Flynn
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | | | - Michael Koch
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Courtney Rose Dhondt
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joel B. Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dawn McBride
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael S. Cookson
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kelly L. Stratton
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Stephen Farriester
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Erin Hemken
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Tuula Pera
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | | | | | | | - Stacy Loeb
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Samir S. Taneja
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Nataliya Byrne
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | | | - Ann Martinez
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Luc Boileau
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Franklin D. Gaylis
- Genesis Healthcare Partners, Department of Urology, University of California, San Diego, CA, USA
| | | | - Nicholas Kirwen
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Brian T. Helfand
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Jianfeng Xu
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Denise M. Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William J. Catalona
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Departments of Epidemiology and Population Health, Biomedical Data Science, and Genetics, Stanford University, Stanford, CA, USA
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Kachuri L, Jeon S, DeWan AT, Metayer C, Ma X, Witte JS, Chiang CWK, Wiemels JL, de Smith AJ. Genetic determinants of blood-cell traits influence susceptibility to childhood acute lymphoblastic leukemia. Am J Hum Genet 2021; 108:1823-1835. [PMID: 34469753 PMCID: PMC8546033 DOI: 10.1016/j.ajhg.2021.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite overlap between genetic risk loci for ALL and hematologic traits, the etiological relevance of dysregulated blood-cell homeostasis remains unclear. We investigated this question in a genome-wide association study (GWAS) of childhood ALL (2,666 affected individuals, 60,272 control individuals) and a multi-trait GWAS of nine blood-cell indices in the UK Biobank. We identified 3,000 blood-cell-trait-associated (p < 5.0 × 10-8) variants, explaining 4.0% to 23.9% of trait variation and including 115 loci associated with blood-cell ratios (LMR, lymphocyte-to-monocyte ratio; NLR, neutrophil-to-lymphocyte ratio; PLR, platelet-to-lymphocyte ratio). ALL susceptibility was genetically correlated with lymphocyte counts (rg = 0.088, p = 4.0 × 10-4) and PLR (rg = -0.072, p = 0.0017). In Mendelian randomization analyses, genetically predicted increase in lymphocyte counts was associated with increased ALL risk (odds ratio [OR] = 1.16, p = 0.031) and strengthened after accounting for other cell types (OR = 1.43, p = 8.8 × 10-4). We observed positive associations with increasing LMR (OR = 1.22, p = 0.0017) and inverse effects for NLR (OR = 0.67, p = 3.1 × 10-4) and PLR (OR = 0.80, p = 0.002). Our study shows that a genetically induced shift toward higher lymphocyte counts, overall and in relation to monocytes, neutrophils, and platelets, confers an increased susceptibility to childhood ALL.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA; Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
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34
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Emami NC, Cavazos TB, Rashkin SR, Cario CL, Graff RE, Tai CG, Mefford JA, Kachuri L, Wan E, Wong S, Aaronson D, Presti J, Habel LA, Shan J, Ranatunga DK, Chao CR, Ghai NR, Jorgenson E, Sakoda LC, Kvale MN, Kwok PY, Schaefer C, Risch N, Hoffmann TJ, Van Den Eeden SK, Witte JS. A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility. Cancer Res 2021; 81:1695-1703. [PMID: 33293427 PMCID: PMC8137514 DOI: 10.1158/0008-5472.can-20-2635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
To identify rare variants associated with prostate cancer susceptibility and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we conducted an integrated study of prostate cancer genetic etiology in two cohorts using custom genotyping microarrays, large imputation reference panels, and functional annotation approaches. Specifically, 11,984 men (6,196 prostate cancer cases and 5,788 controls) of European ancestry from Northern California Kaiser Permanente were genotyped and meta-analyzed with 196,269 men of European ancestry (7,917 prostate cancer cases and 188,352 controls) from the UK Biobank. Three novel loci, including two rare variants (European ancestry minor allele frequency < 0.01, at 3p21.31 and 8p12), were significant genome wide in a meta-analysis. Gene-based rare variant tests implicated a known prostate cancer gene (HOXB13), as well as a novel candidate gene (ILDR1), which encodes a receptor highly expressed in prostate tissue and is related to the B7/CD28 family of T-cell immune checkpoint markers. Haplotypic patterns of long-range linkage disequilibrium were observed for rare genetic variants at HOXB13 and other loci, reflecting their evolutionary history. In addition, a polygenic risk score (PRS) of 188 prostate cancer variants was strongly associated with risk (90th vs. 40th-60th percentile OR = 2.62, P = 2.55 × 10-191). Many of the 188 variants exhibited functional signatures of gene expression regulation or transcription factor binding, including a 6-fold difference in log-probability of androgen receptor binding at the variant rs2680708 (17q22). Rare variant and PRS associations, with concomitant functional interpretation of risk mechanisms, can help clarify the full genetic architecture of prostate cancer and other complex traits. SIGNIFICANCE: This study maps the biological relationships between diverse risk factors for prostate cancer, integrating different functional datasets to interpret and model genome-wide data from over 200,000 men with and without prostate cancer.See related commentary by Lachance, p. 1637.
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Affiliation(s)
- Nima C Emami
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Clinton L Cario
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Simon Wong
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - David Aaronson
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Joseph Presti
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Jun Shan
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Nirupa R Ghai
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Pui-Yan Kwok
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Neil Risch
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - John S Witte
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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Graff RE, Cavazos TB, Thai KK, Kachuri L, Rashkin SR, Hoffman JD, Alexeeff SE, Blatchins M, Meyers TJ, Leong L, Tai CG, Emami NC, Corley DA, Kushi LH, Ziv E, Van Den Eeden SK, Jorgenson E, Hoffmann TJ, Habel LA, Witte JS, Sakoda LC. Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts. Nat Commun 2021; 12:970. [PMID: 33579919 PMCID: PMC7880989 DOI: 10.1038/s41467-021-21288-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
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Affiliation(s)
- Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA. .,Department of Health System Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA.
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Kachuri L, Graff RE, Smith-Byrne K, Meyers TJ, Rashkin SR, Ziv E, Witte JS, Johansson M. Pan-cancer analysis demonstrates that integrating polygenic risk scores with modifiable risk factors improves risk prediction. Nat Commun 2020; 11:6084. [PMID: 33247094 PMCID: PMC7695829 DOI: 10.1038/s41467-020-19600-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022] Open
Abstract
Cancer risk is determined by a complex interplay of environmental and heritable factors. Polygenic risk scores (PRS) provide a personalized genetic susceptibility profile that may be leveraged for disease prediction. Using data from the UK Biobank (413,753 individuals; 22,755 incident cancer cases), we quantify the added predictive value of integrating cancer-specific PRS with family history and modifiable risk factors for 16 cancers. We show that incorporating PRS measurably improves prediction accuracy for most cancers, but the magnitude of this improvement varies substantially. We also demonstrate that stratifying on levels of PRS identifies significantly divergent 5-year risk trajectories after accounting for family history and modifiable risk factors. At the population level, the top 20% of the PRS distribution accounts for 4.0% to 30.3% of incident cancer cases, exceeding the impact of many lifestyle-related factors. In summary, this study illustrates the potential for improving cancer risk assessment by integrating genetic risk scores.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Karl Smith-Byrne
- Genetic Epidemiology Group, Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
| | - Mattias Johansson
- Genetic Epidemiology Group, Section of Genetics, International Agency for Research on Cancer, Lyon, France.
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Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. Genome Med 2020; 12:93. [PMID: 33109261 PMCID: PMC7590248 DOI: 10.1186/s13073-020-00790-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/07/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr virus (EBV), Varicella zoster virus (VZV), human herpesvirus 7, (HHV7), and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P < 5.0 × 10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, and CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P = 5.0 × 10-15 (MCV), NTN5: P = 1.1 × 10-9 (BKV), and P2RY13: P = 1.1 × 10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases, from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA, USA
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, CA, USA
- Department of Mathematics, The University of Texas, Austin, TX, USA
| | - George A Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Université Laval, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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Kachuri L, Helby J, Bojesen SE, Christiani DC, Su L, Wu X, Tardón A, Fernández-Tardón G, Field JK, Davies MP, Chen C, Goodman GE, Shepherd FA, Leighl NB, Tsao MS, Brhane Y, Brown MC, Boyd K, Shepshelovich D, Sun L, Amos CI, Liu G, Hung RJ. Investigation of Leukocyte Telomere Length and Genetic Variants in Chromosome 5p15.33 as Prognostic Markers in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2020; 28:1228-1237. [PMID: 31263055 DOI: 10.1158/1055-9965.epi-18-1215] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/15/2019] [Accepted: 03/29/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer mortality with relatively few prognostic biomarkers. We investigated associations with overall survival for telomere length (TL) and genetic variation in chromosome 5p15.33, an established telomere maintenance locus. METHODS Leukocyte TL was measured after diagnosis in 807 patients with non-small cell lung cancer (NSCLC) from the Princess Margaret Cancer Center in Toronto and assessed prospectively in 767 NSCLC cases from the Copenhagen City Heart Study and the Copenhagen General Population Study. Associations with all-cause mortality were tested for 723 variants in 5p15.33, genotyped in 4,672 NSCLC cases. RESULTS Short telomeres (≤10th percentile) were associated with poor prognosis for adenocarcinoma in both populations: TL measured 6 months after diagnosis [HR = 1.65; 95% confidence intervals (CI), 1.04-2.64] and for those diagnosed within 5 years after blood sampling (HR = 2.42; 95% CI, 1.37-4.28). Short TL was associated with mortality in never smokers with NSCLC (HR = 10.29; 95% CI, 1.86-56.86) and adenocarcinoma (HR = 11.31; 95% CI, 1.96-65.24). Analyses in 5p15.33 identified statistically significant prognostic associations for rs56266421-G in LPCAT1 (HR = 1.86; 95% CI, 1.38-2.52; P = 4.5 × 10-5) in stage I-IIIA NSCLC, and for the SLC6A3 gene with OS in females with NSCLC (P = 1.6 × 10-3). CONCLUSIONS Our findings support the potential clinical utility of TL, particularly for adenocarcinoma patients, while associations in chromosome 5p15.33 warrant further exploration. IMPACT This is the largest lung cancer study of leukocyte TL and OS, and the first to examine the impact of the timing of TL measurement. Our findings suggest that extremely short telomeres are indicative of poor prognosis in NSCLC.
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Affiliation(s)
- Linda Kachuri
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute of Sinai Health System, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California
| | - Jens Helby
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David C Christiani
- Departments of Epidemiology and Environmental Health, Harvard TH Chan School of Public Health, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Li Su
- Departments of Epidemiology and Environmental Health, Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adonina Tardón
- University of Oviedo and CIBERESP, Faculty of Medicine, Campus del Cristo, Oviedo, Spain
| | | | - John K Field
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P Davies
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gary E Goodman
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Frances A Shepherd
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natasha B Leighl
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming S Tsao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute of Sinai Health System, Toronto, Ontario, Canada
| | - M Catherine Brown
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Kevin Boyd
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Daniel Shepshelovich
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Geoffrey Liu
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute of Sinai Health System, Toronto, Ontario, Canada. .,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. medRxiv 2020:2020.05.01.20088054. [PMID: 32511533 PMCID: PMC7273301 DOI: 10.1101/2020.05.01.20088054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr Virus (EBV), Varicella Zoster Virus (VZV), Human Herpes virus 7, (HHV7) and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P<5.×10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, as well as CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0×10-15 (MCV), NTN5: P=1.1×10-9 (BKV), and P2RY13: P=1.1×10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases; from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
| | - Stephen S. Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | - Maike Morrison
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, USA
- Department of Mathematics, The University of Texas at Austin, Austin, USA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Université Laval, Quebec City, Canada
| | - Taylor B. Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, USA
| | - Sara R. Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Department of Medicine, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California San Francisco, San Francisco, USA
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40
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Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, Cavazos TB, Corley DA, Emami NC, Hoffman JD, Jorgenson E, Kushi LH, Meyers TJ, Van Den Eeden SK, Ziv E, Habel LA, Hoffmann TJ, Sakoda LC, Witte JS. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nat Commun 2020; 11:4423. [PMID: 32887889 PMCID: PMC7473862 DOI: 10.1038/s41467-020-18246-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Deciphering the shared genetic basis of distinct cancers has the potential to elucidate carcinogenic mechanisms and inform broadly applicable risk assessment efforts. Here, we undertake genome-wide association studies (GWAS) and comprehensive evaluations of heritability and pleiotropy across 18 cancer types in two large, population-based cohorts: the UK Biobank (408,786 European ancestry individuals; 48,961 cancer cases) and the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging cohorts (66,526 European ancestry individuals; 16,001 cancer cases). The GWAS detect 21 genome-wide significant associations independent of previously reported results. Investigations of pleiotropy identify 12 cancer pairs exhibiting either positive or negative genetic correlations; 25 pleiotropic loci; and 100 independent pleiotropic variants, many of which are regulatory elements and/or influence cross-tissue gene expression. Our findings demonstrate widespread pleiotropy and offer further insight into the complex genetic architecture of cross-cancer susceptibility.
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Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta A Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Taylor B Cavazos
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California, San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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Kachuri L, Beane Freeman LE, Spinelli JJ, Blair A, Pahwa M, Koutros S, Hoar Zahm S, Cantor KP, Weisenburger DD, Pahwa P, Dosman JA, McLaughlin JR, Demers PA, Harris SA. Insecticide use and risk of non-Hodgkin lymphoma subtypes: A subset meta-analysis of the North American Pooled Project. Int J Cancer 2020; 147:3370-3383. [PMID: 32574374 PMCID: PMC7689728 DOI: 10.1002/ijc.33164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
Abstract
Insecticide use has been linked to increased risk of non-Hodgkin lymphoma (NHL), however, findings of epidemiologic studies have been inconsistent, particularly for NHL subtypes. We analyzed 1690 NHL cases and 5131 controls in the North American Pooled Project (NAPP) to investigate self-reported insecticide use and risk of NHL overall and by subtypes: follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL) and small lymphocytic lymphoma (SLL). Odds ratios (OR) and 95% confidence intervals for each insecticide were estimated using logistic regression. Subtype-specific associations were evaluated using ASSET (Association analysis for SubSETs). Increased risks of multiple NHL subtypes were observed for lindane (OR = 1.60, 1.20-2.10: FL, DLCBL, SLL), chlordane (OR = 1.59, 1.17-2.16: FL, SLL) and DDT (OR = 1.36, 1.06-1.73: DLBCL, SLL). Positive trends were observed, within the subsets with identified associations, for increasing categories of exposure duration for lindane (Ptrend = 1.7 × 10-4 ), chlordane (Ptrend = 1.0 × 10-3 ) and DDT (Ptrend = 4.2 × 10-3 ), however, the exposure-response relationship was nonlinear. Ever use of pyrethrum was associated with an increased risk of FL (OR = 3.65, 1.45-9.15), and the relationship with duration of use appeared monotonic (OR for >10 years: OR = 5.38, 1.75-16.53; Ptrend = 3.6 × 10-3 ). Our analysis identified several novel associations between insecticide use and specific NHL subtypes, suggesting possible etiologic heterogeneity in the context of pesticide exposure.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aaron Blair
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Manisha Pahwa
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Shelia Hoar Zahm
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth P Cantor
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | | | - Punam Pahwa
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - James A Dosman
- Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John R McLaughlin
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Paul A Demers
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada.,Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Population Health and Prevention, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Shelley A Harris
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Population Health and Prevention, Cancer Care Ontario, Toronto, Ontario, Canada
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42
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Latifovic L, Villeneuve PJ, Parent MÉ, Kachuri L, Harris SA. Silica and asbestos exposure at work and the risk of bladder cancer in Canadian men: a population-based case-control study. BMC Cancer 2020; 20:171. [PMID: 32126982 PMCID: PMC7055116 DOI: 10.1186/s12885-020-6644-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 02/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Silica and asbestos are recognized lung carcinogens. However, their role in carcinogenesis at other organs is less clear. Clearance of inhaled silica particles and asbestos fibers from the lungs may lead to translocation to sites such as the bladder where they may initiate carcinogenesis. We used data from a Canadian population-based case-control study to evaluate the associations between these workplace exposures and bladder cancer. Methods Data from a population-based case-control study were used to characterize associations between workplace exposure to silica and asbestos and bladder cancer among men. Bladder cancer cases (N = 658) and age-frequency matched controls (N = 1360) were recruited within the National Enhanced Cancer Surveillance System from eight Canadian provinces (1994–97). Exposure concentration, frequency and reliability for silica and asbestos were assigned to each job, based on lifetime occupational histories, using a combination of job-exposure profiles and expert review. Exposure was modeled as ever/never, highest attained concentration, duration (years), highest attained frequency (% worktime) and cumulative exposure. Odds ratios (OR) and their 95% confidence intervals (CI) were estimated using adjusted logistic regression. Results A modest (approximately 20%) increase in bladder cancer risk was found for ever having been exposed to silica, highest attained concentration and frequency of exposure but this increase was not statistically significant. Relative to unexposed, the odds of bladder cancer were 1.41 (95%CI: 1.01–1.98) times higher among men exposed to silica at work for ≥27 years. For asbestos, relative to unexposed, an increased risk of bladder cancer was observed for those first exposed ≥20 years ago (OR:2.04, 95%CI:1.25–3.34), those with a frequency of exposure of 5–30% of worktime (OR:1.45, 95%CI:1.06–1.98), and for those with < 10 years of exposure at low concentrations (OR:1.75, 95%CI:1.10–2.77) and the lower tertile of cumulative exposure (OR:1.69, 95%CI:1.07–2.65). However, no clear exposure-response relationships emerged. Conclusions Our results indicate a slight increase in risk of bladder cancer with exposure to silica and asbestos, suggesting that the effects of these agents are broader than currently recognized. The findings from this study inform evidence-based action to enhance cancer prevention efforts, particularly for workers in industries with regular exposure.
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Affiliation(s)
- Lidija Latifovic
- Occupational Cancer Research Centre, Cancer Care Ontario, Ontario Health, 525 University Ave, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, 155 College St, 6th floor, Toronto, ON, M5T 3M7, Canada
| | - Paul J Villeneuve
- School of Mathematics and Statistics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada
| | - Marie-Élise Parent
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boul des Prairies, Laval, QC, Canada
| | - Linda Kachuri
- Occupational Cancer Research Centre, Cancer Care Ontario, Ontario Health, 525 University Ave, Toronto, ON, Canada.,Department of Epidemiology & Biostatistics, University of California at San Francisco, San Francisco, CA, USA
| | | | - Shelley A Harris
- Occupational Cancer Research Centre, Cancer Care Ontario, Ontario Health, 525 University Ave, Toronto, ON, Canada. .,Dalla Lana School of Public Health, University of Toronto, 155 College St, 6th floor, Toronto, ON, M5T 3M7, Canada. .,School of Mathematics and Statistics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada.
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Kachuri L, Johansson M, Rashkin SR, Graff RE, Bossé Y, Manem V, Caporaso NE, Landi MT, Christiani DC, Vineis P, Liu G, Scelo G, Zaridze D, Shete SS, Albanes D, Aldrich MC, Tardón A, Rennert G, Chen C, Goodman GE, Doherty JA, Bickeböller H, Field JK, Davies MP, Dawn Teare M, Kiemeney LA, Bojesen SE, Haugen A, Zienolddiny S, Lam S, Le Marchand L, Cheng I, Schabath MB, Duell EJ, Andrew AS, Manjer J, Lazarus P, Arnold S, McKay JD, Emami NC, Warkentin MT, Brhane Y, Obeidat M, Martin RM, Relton C, Davey Smith G, Haycock PC, Amos CI, Brennan P, Witte JS, Hung RJ. Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility. Nat Commun 2020; 11:27. [PMID: 31911640 PMCID: PMC6946810 DOI: 10.1038/s41467-019-13855-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Impaired lung function is often caused by cigarette smoking, making it challenging to disentangle its role in lung cancer susceptibility. Investigation of the shared genetic basis of these phenotypes in the UK Biobank and International Lung Cancer Consortium (29,266 cases, 56,450 controls) shows that lung cancer is genetically correlated with reduced forced expiratory volume in one second (FEV1: rg = 0.098, p = 2.3 × 10-8) and the ratio of FEV1 to forced vital capacity (FEV1/FVC: rg = 0.137, p = 2.0 × 10-12). Mendelian randomization analyses demonstrate that reduced FEV1 increases squamous cell carcinoma risk (odds ratio (OR) = 1.51, 95% confidence intervals: 1.21-1.88), while reduced FEV1/FVC increases the risk of adenocarcinoma (OR = 1.17, 1.01-1.35) and lung cancer in never smokers (OR = 1.56, 1.05-2.30). These findings support a causal role of pulmonary impairment in lung cancer etiology. Integrative analyses reveal that pulmonary function instruments, including 73 novel variants, influence lung tissue gene expression and implicate immune-related pathways in mediating the observed effects on lung carcinogenesis.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Sara R Rashkin
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Venkata Manem
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Neil E Caporaso
- Division of Cancer Epidemiology & Genetics, US NCI, Bethesda, MD, USA
| | | | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Geoffrey Liu
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | | | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Sanjay S Shete
- Department of Biostatistics, Division of Basic Sciences, MD Anderson Cancer Center, Houston, TX, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology & Genetics, US NCI, Bethesda, MD, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adonina Tardón
- Faculty of Medicine, University of Oviedo and ISPA and CIBERESP, Campus del Cristo, Oviedo, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center, Technion Faculty of Medicine, Haifa, Israel
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary E Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-Universität Göttingen, Göttingen, Germany
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, London, UK
| | - Michael P Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, London, UK
| | - M Dawn Teare
- Biostatistics Research Group, Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Aage Haugen
- The National Institute of Occupational Health, Oslo, Norway
| | | | | | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Eric J Duell
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Jonas Manjer
- Skåne University Hospital, Lund University, Lund, Sweden
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Nima C Emami
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Matthew T Warkentin
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ma'en Obeidat
- University of British Columbia, Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - John S Witte
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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Peters CE, Parent MÉ, Harris SA, Bogaert L, Latifovic L, Kachuri L, Villeneuve PJ. Occupational Exposure to Diesel and Gasoline Engine Exhausts and the Risk of Kidney Cancer in Canadian Men. Ann Work Expo Health 2019; 62:978-989. [PMID: 30059990 PMCID: PMC6188530 DOI: 10.1093/annweh/wxy059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/05/2018] [Indexed: 11/17/2022] Open
Abstract
Introduction Kidney cancer is the fifth most common incident cancer in Canadian men. Diesel and gasoline exhausts are common workplace exposures that have been examined as risk factors for non-lung cancer sites, including the kidney, but limitations in exposure assessment methods have contributed to inconsistent findings. The objective of this study was to assess the relationship between occupational gasoline and diesel engine exhausts and the risk of kidney cancer in men. Methods The National Enhanced Cancer Surveillance System (NECSS) is a Canadian population-based case–control study conducted in 1994–1997. Incident kidney cancer cases were identified using provincial registries, while the control series was identified through random-digit dialing, or provincial administrative databases. Self-reported questionnaires were used to obtain information on lifetime occupational history and cancer risk factors. Two hygienists, blinded to case status, coded occupational histories for diesel and gasoline exhaust exposures using concentration, frequency, duration, and reliability. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) separately by exhaust type. The separate and combined impacts of both engine exhausts were also examined. ORs were adjusted for age, province, body mass index, occupational secondhand smoke exposure, and education. Results Of the kidney cancer cases (n = 712), 372 (52%) had exposure to both exhausts at some point, and 984 (40%) of the controls (n = 2457) were ever exposed. Workers who had ever been exposed to engine exhausts were more likely to have kidney cancer than those who were never exposed (OR diesel = 1.23, 95% CI = 0.99–1.53; OR gasoline = 1.51, 95% CI = 1.23–1.86). Exposure to gasoline exhaust was consistently associated with kidney cancer in a dose–response manner (P value for trends in highest attained and cumulative exposure both <0.0001). Those men with high cumulative exposure to both gasoline and diesel exhaust had a 76% increased odds of kidney cancer (95% CI = 1.27–2.43). Conclusions This study provides evidence that occupational gasoline, and to a lesser extent, diesel exhaust exposure may increase the risk of kidney cancer.
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Affiliation(s)
- Cheryl E Peters
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada.,Institut Armand-Frappier, Institut national de la recherche scientifique (IAF-INRS), Laval, Quebec, Canada
| | - Marie-Élise Parent
- Institut Armand-Frappier, Institut national de la recherche scientifique (IAF-INRS), Laval, Quebec, Canada
| | - Shelley A Harris
- Cancer Care Ontario, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Laura Bogaert
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | | | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Paul J Villeneuve
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
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Emami NC, Kachuri L, Meyers TJ, Das R, Hoffman JD, Hoffmann TJ, Hu D, Shan J, Feng FY, Ziv E, Van Den Eeden SK, Witte JS. Author Correction: Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun 2019; 10:3948. [PMID: 31462633 PMCID: PMC6713745 DOI: 10.1038/s41467-019-11810-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Nima C Emami
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Rajdeep Das
- Department of Urology, University of California San Francisco, San Francisco, CA, 94158, USA.,Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Donglei Hu
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jun Shan
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, 94612, USA
| | - Felix Y Feng
- Department of Urology, University of California San Francisco, San Francisco, CA, 94158, USA.,Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Stephen K Van Den Eeden
- Department of Urology, University of California San Francisco, San Francisco, CA, 94158, USA.,Division of Research, Kaiser Permanente, Northern California, Oakland, CA, 94612, USA
| | - John S Witte
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, 94158, USA. .,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, 94158, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA.
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46
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Peters CE, Bogaert L, Latifovic L, Kachuri L, Harris SA, Parent ME, Villeneuve PJ. Exposure to crystalline silica in Canadian workplaces and the risk of kidney cancer. Occup Environ Med 2019; 76:668-671. [PMID: 31413189 DOI: 10.1136/oemed-2019-105870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 11/04/2022]
Abstract
OBJECTIVES The causes of kidney cancer are not well understood though occupational exposures are thought to play a role. Crystalline silica is a known human carcinogen, and despite previous links with kidney disease, there have been few studies investigating its association with kidney cancer. We addressed this research gap using a population-based case-control study of Canadian men. METHODS Questionnaire data were obtained from individuals with histologically confirmed kidney cancer, and population-based controls recruited from eight Canadian provinces (1994-1997). An industrial hygienist characterised participants' lifetime occupational exposure, and their confidence in the assessment (possibly, probably or definitely exposed) to silica on three dimensions (intensity, frequency and duration), and cumulative exposure was estimated. Logistic regression was used to estimate ORs and 95% CIs, adjusting for potential confounders. RESULTS Nearly half of the 689 kidney cancer cases (49%) and 2369 controls (44%) had ever been occupationally exposed to crystalline silica. In a fully adjusted model, workers ever-exposed to silica had a slightly increased risk of kidney cancer relative to those who were unexposed (OR 1.10, 95% CI 0.92 to 1.32). Odds were modestly (and generally not statistically significantly) increased for models with duration of exposure and cumulative exposure, though exposure-response relationships were not evident. CONCLUSIONS Our findings do not provide evidence that occupational exposure to crystalline silica increases risk of kidney cancer in men.
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Affiliation(s)
- Cheryl E Peters
- Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Alberta, Canada .,Community Health Sciences and Oncology, University of Calgary, Calgary, Alberta, Canada.,Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Laura Bogaert
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Institute for Work and Health, Toronto, Ontario, Canada
| | - Lidija Latifovic
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Prevention, Screening & Cancer Control, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Linda Kachuri
- Department of Epidemiology and Biostatics, University of California San Francisco, San Francisco, California, USA
| | - Shelley A Harris
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Marie-Elise Parent
- INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Laval, Quebec, Canada
| | - Paul J Villeneuve
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
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47
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Koutros S, Harris SA, Spinelli JJ, Blair A, McLaughlin JR, Zahm SH, Kim S, Albert PS, Kachuri L, Pahwa M, Cantor KP, Weisenburger DD, Pahwa P, Pardo LA, Dosman JA, Demers PA, Beane Freeman LE. Non-Hodgkin lymphoma risk and organophosphate and carbamate insecticide use in the north American pooled project. Environ Int 2019; 127:199-205. [PMID: 30928843 PMCID: PMC6513687 DOI: 10.1016/j.envint.2019.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 05/07/2023]
Abstract
Organophosphates and carbamates have been among the most commonly used insecticides, with both agricultural and residential uses. Previous studies have suggested associations of non-Hodgkin lymphoma (NHL) with some of these chemicals; however, many studies have been limited in their ability to evaluate associations with lymphoma subtypes. We evaluated the use of eleven organophosphate and two carbamate insecticides in association with NHL in the North American Pooled Project, which includes data from case-control studies in the United States and Canada (1690 cases/5131 controls). We used unconditional logistic regression adjusting for potential confounders, including use of other pesticides, to estimate odds ratios (OR) and 95% confidence intervals (CI) for associations between these chemicals and NHL overall, and NHL subtypes, i.e., follicular (FL), diffuse large B-cell (DLBCL), small lymphocytic lymphoma (SLL) and others. Ever use of malathion was associated with increased risk of NHL overall (OR = 1.43; 95% CI: 1.14-1.81) compared with never users. Categories using tertiles of duration (<4 yrs., 4-12 yrs., and >12 yrs) also showed a significant exposure-response for increasing years of use of malathion and risk of NHL (OR<4vsUnex = 1.33 (0.88, 2.03), OR4-12vsUnex = 1.42 (1.02, 1.96), OR>12vsUnex = 1.55 (1.05, 2.28, p-trend < 0.01)). In addition, malathion use was statistically significantly associated with FL (OR = 1.58; 95% CI: 1.11-2.27) and DLBCL (OR = 1.61; 95% CI: 1.16-2.22) while there were no apparent associations with SLL or other subtypes, the p-value for heterogeneity across subtypes, however, was not significant. These results support previous studies suggesting an association between insecticide use and NHL overall, and provide new information on associations with NHL subtypes.
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Affiliation(s)
- Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA.
| | - Shelley A Harris
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Prevention and Cancer Control, Cancer Care Ontario, Toronto, Canada
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, Canada; School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Aaron Blair
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - John R McLaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Public Health Ontario, Toronto, Canada
| | | | - Sungduk Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Paul S Albert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Manisha Pahwa
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Canada
| | - Kenneth P Cantor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | | | - Punam Pahwa
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, Canada; Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Larissa A Pardo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - James A Dosman
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, Canada
| | - Paul A Demers
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
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48
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Kachuri L, Saarela O, Bojesen SE, Davey Smith G, Liu G, Landi MT, Caporaso NE, Christiani DC, Johansson M, Panico S, Overvad K, Trichopoulou A, Vineis P, Scelo G, Zaridze D, Wu X, Albanes D, Diergaarde B, Lagiou P, Macfarlane GJ, Aldrich MC, Tardón A, Rennert G, Olshan AF, Weissler MC, Chen C, Goodman GE, Doherty JA, Ness AR, Bickeböller H, Wichmann HE, Risch A, Field JK, Teare MD, Kiemeney LA, van der Heijden EHFM, Carroll JC, Haugen A, Zienolddiny S, Skaug V, Wünsch-Filho V, Tajara EH, Ayoub Moysés R, Daumas Nunes F, Lam S, Eluf-Neto J, Lacko M, Peters WHM, Le Marchand L, Duell EJ, Andrew AS, Franceschi S, Schabath MB, Manjer J, Arnold S, Lazarus P, Mukeriya A, Swiatkowska B, Janout V, Holcatova I, Stojsic J, Mates D, Lissowska J, Boccia S, Lesseur C, Zong X, McKay JD, Brennan P, Amos CI, Hung RJ. Mendelian Randomization and mediation analysis of leukocyte telomere length and risk of lung and head and neck cancers. Int J Epidemiol 2019; 48:751-766. [PMID: 30059977 PMCID: PMC6659464 DOI: 10.1093/ije/dyy140] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Evidence from observational studies of telomere length (TL) has been conflicting regarding its direction of association with cancer risk. We investigated the causal relevance of TL for lung and head and neck cancers using Mendelian Randomization (MR) and mediation analyses. METHODS We developed a novel genetic instrument for TL in chromosome 5p15.33, using variants identified through deep-sequencing, that were genotyped in 2051 cancer-free subjects. Next, we conducted an MR analysis of lung (16 396 cases, 13 013 controls) and head and neck cancer (4415 cases, 5013 controls) using eight genetic instruments for TL. Lastly, the 5p15.33 instrument and distinct 5p15.33 lung cancer risk loci were evaluated using two-sample mediation analysis, to quantify their direct and indirect, telomere-mediated, effects. RESULTS The multi-allelic 5p15.33 instrument explained 1.49-2.00% of TL variation in our data (p = 2.6 × 10-9). The MR analysis estimated that a 1000 base-pair increase in TL increases risk of lung cancer [odds ratio (OR) = 1.41, 95% confidence interval (CI): 1.20-1.65] and lung adenocarcinoma (OR = 1.92, 95% CI: 1.51-2.22), but not squamous lung carcinoma (OR = 1.04, 95% CI: 0.83-1.29) or head and neck cancers (OR = 0.90, 95% CI: 0.70-1.05). Mediation analysis of the 5p15.33 instrument indicated an absence of direct effects on lung cancer risk (OR = 1.00, 95% CI: 0.95-1.04). Analysis of distinct 5p15.33 susceptibility variants estimated that TL mediates up to 40% of the observed associations with lung cancer risk. CONCLUSIONS Our findings support a causal role for long telomeres in lung cancer aetiology, particularly for adenocarcinoma, and demonstrate that telomere maintenance partially mediates the lung cancer susceptibility conferred by 5p15.33 loci.
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Affiliation(s)
- Linda Kachuri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Olli Saarela
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev Ringvej 75, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - George Davey Smith
- Population Health Science, Bristol Medical School, MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Geoffrey Liu
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Institute, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David C Christiani
- Departments of Epidemiology and Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Kim Overvad
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus, Denmark
| | - Antonia Trichopoulou
- Hellenic Health Foundation, and WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Athens, Greece
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Paolo Vineis
- MRC/PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | | | - David Zaridze
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gary J Macfarlane
- The Institute of Applied Health Sciences, School of Medicine, University of Aberdeen, Aberdeen, UK
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adonina Tardón
- Faculty of Medicine, University of Oviedo and CIBERESP, Campus del Cristo, Oviedo, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark C Weissler
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary E Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Andrew R Ness
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University, Munich, Germany
| | - Angela Risch
- Division of Epigenomics & Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John K Field
- Roy Castle Lung Cancer Research Programme, University of Liverpool Cancer Research Centre Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - M Dawn Teare
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - June C Carroll
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Aage Haugen
- The National Institute of Occupational Health, Oslo, Norway
| | | | - Vidar Skaug
- The National Institute of Occupational Health, Oslo, Norway
| | | | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, São José do Rio Preto, Brazil
| | - Raquel Ayoub Moysés
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Disciplina de Cirurgia de Cabeça e Pescoço (LIM28), São Paulo, Brasil
| | - Fabio Daumas Nunes
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | | | - Jose Eluf-Neto
- Departamento de Medicina Preventiva, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Martin Lacko
- Department of Otorhinolaryngology, Head and Neck Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Wilbert H M Peters
- Department of Gastroenterology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Eric J Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jonas Manjer
- Skåne University Hospital, Lund University, Lund, Sweden
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Philip Lazarus
- College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Anush Mukeriya
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Beata Swiatkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Belgrade, Serbia
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Cancer Center Maria Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Stefania Boccia
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italia
- Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Corina Lesseur
- International Agency for Research on Cancer, Lyon, France
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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49
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Zhu Y, Wei Y, Zhang R, Dong X, Shen S, Zhao Y, Bai J, Albanes D, Caporaso NE, Landi MT, Zhu B, Chanock SJ, Gu F, Lam S, Tsao MS, Shepherd FA, Tardon A, Fernández-Somoano A, Fernandez-Tardon G, Chen C, Barnett MJ, Doherty J, Bojesen SE, Johansson M, Brennan P, McKay JD, Carreras-Torres R, Muley T, Risch A, Wichmann HE, Bickeboeller H, Rosenberger A, Rennert G, Saliba W, Arnold SM, Field JK, Davies MPA, Marcus MW, Wu X, Ye Y, Le Marchand L, Wilkens LR, Melander O, Manjer J, Brunnström H, Hung RJ, Liu G, Brhane Y, Kachuri L, Andrew AS, Duell EJ, Kiemeney LA, van der Heijden EH, Haugen A, Zienolddiny S, Skaug V, Grankvist K, Johansson M, Woll PJ, Cox A, Taylor F, Teare DM, Lazarus P, Schabath MB, Aldrich MC, Houlston RS, McLaughlin J, Stevens VL, Shen H, Hu Z, Dai J, Amos CI, Han Y, Zhu D, Goodman GE, Chen F, Christiani DC. Elevated Platelet Count Appears to Be Causally Associated with Increased Risk of Lung Cancer: A Mendelian Randomization Analysis. Cancer Epidemiol Biomarkers Prev 2019; 28:935-942. [PMID: 30700444 PMCID: PMC7075698 DOI: 10.1158/1055-9965.epi-18-0356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/11/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Platelets are a critical element in coagulation and inflammation, and activated platelets are linked to cancer risk through diverse mechanisms. However, a causal relationship between platelets and risk of lung cancer remains unclear. METHODS We performed single and combined multiple instrumental variable Mendelian randomization analysis by an inverse-weighted method, in addition to a series of sensitivity analyses. Summary data for associations between SNPs and platelet count are from a recent publication that included 48,666 Caucasian Europeans, and the International Lung Cancer Consortium and Transdisciplinary Research in Cancer of the Lung data consisting of 29,266 cases and 56,450 controls to analyze associations between candidate SNPs and lung cancer risk. RESULTS Multiple instrumental variable analysis incorporating six SNPs showed a 62% increased risk of overall non-small cell lung cancer [NSCLC; OR, 1.62; 95% confidence interval (CI), 1.15-2.27; P = 0.005] and a 200% increased risk for small-cell lung cancer (OR, 3.00; 95% CI, 1.27-7.06; P = 0.01). Results showed only a trending association with NSCLC histologic subtypes, which may be due to insufficient sample size and/or weak effect size. A series of sensitivity analysis retained these findings. CONCLUSIONS Our findings suggest a causal relationship between elevated platelet count and increased risk of lung cancer and provide evidence of possible antiplatelet interventions for lung cancer prevention. IMPACT These findings provide a better understanding of lung cancer etiology and potential evidence for antiplatelet interventions for lung cancer prevention.
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Affiliation(s)
- Ying Zhu
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts.,China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts.,China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Xuesi Dong
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing, China
| | - Sipeng Shen
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Jianling Bai
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Fangyi Gu
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Frances A Shepherd
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Oviedo, Spain
| | | | | | - Chu Chen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthew J Barnett
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jennifer Doherty
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Thomas Muley
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Angela Risch
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heunz-Erich Wichmann
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heike Bickeboeller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Walid Saliba
- Department of Community Medicine and Epidemiology, Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P A Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael W Marcus
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | | | - Jonas Manjer
- Faculty of Medicine, Lund University, Lund, Sweden
| | | | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Linda Kachuri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, Hanover, New Hampshire
| | - Eric J Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Erik Hfm van der Heijden
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | | | - Vidar Skaug
- National Institute of Occupational Health, Oslo, Norway
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Penella J Woll
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Dawn M Teare
- School of Health and Related Research, University of Sheffield, England, United Kingdom
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Younghun Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Dakai Zhu
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | | | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China. .,China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - David C Christiani
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China. .,Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts.,China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, China
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Graff RE, Kachuri L, Witte JS. Personalized Prostate Cancer Screening Based on a Single Midlife Prostate-specific Antigen Measurement. Eur Urol 2018; 75:408-409. [PMID: 30268658 DOI: 10.1016/j.eururo.2018.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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