1
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yoshimura S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. Nat Commun 2024; 15:3681. [PMID: 38693155 PMCID: PMC11063049 DOI: 10.1038/s41467-024-48124-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robert J Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kelly R Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Baranda S Hansen
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Satoshi Yoshimura
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristine R Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Christopher S Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jun J Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Jeon S, Lo YC, Morimoto LM, Metayer C, Ma X, Wiemels JL, de Smith AJ, Chiang CWK. Evaluating genomic polygenic risk scores for childhood acute lymphoblastic leukemia in Latinos. HGG ADVANCES 2023; 4:100239. [PMID: 37710962 PMCID: PMC10550840 DOI: 10.1016/j.xhgg.2023.100239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023] Open
Abstract
The utility of polygenic risk score (PRS) models has not been comprehensively evaluated for childhood acute lymphoblastic leukemia (ALL), the most common type of cancer in children. Previous PRS models for ALL were based on significant loci observed in genome-wide association studies (GWASs), even though genomic PRS models have been shown to improve prediction performance for a number of complex diseases. In the United States, Latino (LAT) children have the highest risk of ALL, but the transferability of PRS models to LAT children has not been studied. In this study, we constructed and evaluated genomic PRS models based on either non-Latino White (NLW) GWAS or a multi-ancestry GWAS. We found that the best PRS models performed similarly between held-out NLW and LAT samples (PseudoR2 = 0.086 ± 0.023 in NLW vs. 0.060 ± 0.020 in LAT), and can be improved for LAT if we performed GWAS in LAT-only (PseudoR2 = 0.116 ± 0.026) or multi-ancestry samples (PseudoR2 = 0.131 ± 0.025). However, the best genomic models currently do not have better prediction accuracy than a conventional model using all known ALL-associated loci in the literature (PseudoR2 = 0.166 ± 0.025), which includes loci from GWAS populations that we could not access to train genomic PRS models. Our results suggest that larger and more inclusive GWASs may be needed for genomic PRS to be useful for ALL. Moreover, the comparable performance between populations may suggest a more oligogenic architecture for ALL, where some large effect loci may be shared between populations. Future PRS models that move away from the infinite causal loci assumption may further improve PRS for ALL.
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Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ying Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M Morimoto
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA, USA.
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Jeon S, Lo YC, Morimoto LM, Metayer C, Ma X, Wiemels JL, de Smith AJ, Chiang CW. Evaluating Genomic Polygenic Risk Scores for Childhood Acute Lymphoblastic Leukemia in Latinos. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291167. [PMID: 37398036 PMCID: PMC10312899 DOI: 10.1101/2023.06.08.23291167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The utility of polygenic risk score (PRS) models has not been comprehensively evaluated for childhood acute lymphoblastic leukemia (ALL), the most common type of cancer in children. Previous PRS models for ALL were based on significant loci observed in genome-wide association studies (GWAS), even though genomic PRS models have been shown to improve prediction performance for a number of complex diseases. In the United States, Latino (LAT) children have the highest risk of ALL, but the transferability of PRS models to LAT children has not been studied. In this study we constructed and evaluated genomic PRS models based on either non-Latino white (NLW) GWAS or a multi-ancestry GWAS. We found that the best PRS models performed similarly between held-out NLW and LAT samples (PseudoR 2 = 0.086 ± 0.023 in NLW vs. 0.060 ± 0.020 in LAT), and can be improved for LAT if we performed GWAS in LAT-only (PseudoR 2 = 0.116 ± 0.026) or multi-ancestry samples (PseudoR 2 = 0.131 ± 0.025). However, the best genomic models currently do not have better prediction accuracy than a conventional model using all known ALL-associated loci in the literature (PseudoR 2 = 0.166 ± 0.025), which includes loci from GWAS populations that we could not access to train genomic PRS models. Our results suggest that larger and more inclusive GWAS may be needed for genomic PRS to be useful for ALL. Moreover, the comparable performance between populations may suggest a more oligo-genic architecture for ALL, where some large effect loci may be shared between populations. Future PRS models that move away from the infinite causal loci assumption may further improve PRS for ALL.
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Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ying Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M. Morimoto
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charleston W.K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.10.23285762. [PMID: 36798219 PMCID: PMC9934807 DOI: 10.1101/2023.02.10.23285762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although acute lymphoblastic leukemia (ALL) is the most common childhood cancer, there is limited understanding of the contribution of inherited genetic variation on inter-individual differences in chemotherapy response. Defining genetic factors impacting therapy failure can help better predict response and identify drug resistance mechanisms. We therefore mapped inherited noncoding variants associated with chemotherapeutic drug resistance and/or treatment outcome to ALL cis-regulatory elements and investigated their gene regulatory potential and genomic connectivity using massively parallel reporter assays and promoter capture Hi-C, respectively. We identified 53 variants with reproducible allele-specific effects on transcription and high-confidence gene targets. Subsequent functional interrogation of the top variant (rs1247117) determined that it disrupted a PU.1 consensus motif and PU.1 binding affinity. Importantly, deletion of the genomic interval containing rs1247117 sensitized ALL cells to vincristine. Together, these data demonstrate that noncoding regulatory variation associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to chemotherapeutic agents in ALL.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel C. Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Baranda S. Hansen
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
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5
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Haas OA, Borkhardt A. Hyperdiploidy: the longest known, most prevalent, and most enigmatic form of acute lymphoblastic leukemia in children. Leukemia 2022; 36:2769-2783. [PMID: 36266323 PMCID: PMC9712104 DOI: 10.1038/s41375-022-01720-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Hyperdiploidy is the largest genetic entity B-cell precursor acute lymphoblastic leukemia in children. The diagnostic hallmark of its two variants that will be discussed in detail herein is a chromosome count between 52 and 67, respectively. The classical HD form consists of heterozygous di-, tri-, and tetrasomies, whereas the nonclassical one (usually viewed as "duplicated hyperhaploid") contains only disomies and tetrasomies. Despite their apparently different clinical behavior, we show that these two sub-forms can in principle be produced by the same chromosomal maldistribution mechanism. Moreover, their respective array, gene expression, and mutation patterns also indicate that they are biologically more similar than hitherto appreciated. Even though in-depth analyses of the genomic intricacies of classical HD leukemias are indispensable for the elucidation of the disease process, the ensuing results play at present surprisingly little role in treatment stratification, a fact that can be attributed to the overall good prognoses and low relapse rates of the concerned patients and, consequently, their excellent treatment outcome. Irrespective of this underutilization, however, the detailed genetic characterization of HD leukemias may, especially in planned treatment reduction trials, eventually become important for further treatment stratification, patient management, and the clinical elucidation of outcome data. It should therefore become an integral part of all upcoming treatment studies.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Hospital, Pediatric Clinic, Medical University, Vienna, Austria.
- Labdia Labordiagnostik, Vienna, Austria.
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Düsseldorf, Germany.
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Sattarzadeh Bardsiri M, Zehtab S, Karami N, Farsinejad A, Ehsan M, Fatemi A. Association of IKZF1 and CDKN2A gene polymorphisms with childhood acute lymphoblastic leukemia: a high-resolution melting analysis. BMC Med Genomics 2022; 15:171. [PMID: 35932035 PMCID: PMC9354342 DOI: 10.1186/s12920-022-01325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Acute lymphoblastic leukemia is the most prevailing pediatric hematologic malignancy, and various factors such as environmental exposures and genetic variation affect ALL susceptibility and patients outcome. According to genome-wide association studies, several single nucleotide polymorphisms (SNPs) in IKZF1 (rs4132601) and CDKN2A (rs3731249 and rs3731217) genes are associated with ALL susceptibility. Hereupon, this study aimed to discover the association between these SNPs and the risk of childhood ALL among a sample of the Iranian population.
Methods A total of fifty children with ALL were included in this case–control study, along with an additional fifty healthy children, matched for age and gender. High-resolution melting (HRM) analysis was employed to genotyping rs4132601, rs3731249, and rs3731217.
Results In the patient group, the CT genotype and T allele frequency of rs3731249 were significantly greater than controls (p = 0.01 and p = 0.005, respectively). Moreover, the positive association of CT and dominant model (CT + TT) genotypes and T allele at rs3731249 with the risk of ALL was confirmed (OR = 9.56, OR = 10.76 and OR = 11.00, respectively). There was no significant relation between rs4132601 (IKZF1), rs3731217 (CDKN2A), and childhood ALL. Conclusion The present study indicates that CT genotype and T allele at rs3731249 (CDKN2A) can significantly increase the risk of ALL among children.
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Affiliation(s)
- Mahla Sattarzadeh Bardsiri
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahrzad Zehtab
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Najibe Karami
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Farsinejad
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Ehsan
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran
| | - Ahmad Fatemi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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7
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Sardarzadeh N, Khojasteh-Leylakoohi F, Damavandi S, Khalili-Tanha G, Dashtiahangar M, Khalili-Tanha N, Avan A, Amoueian S, Hassanian SM, Esmaily H, Khazaei M, Ferns G, Khooei A, Aliakbarian M. Association of a Genetic Variant in the Cyclin-Dependent Kinase Inhibitor 2B with Risk of Pancreatic Cancer. Rep Biochem Mol Biol 2022; 11:336-343. [PMID: 36164638 PMCID: PMC9455181 DOI: 10.52547/rbmb.11.2.336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pancreatic cancer (PC) is among the most aggressive tumors with a poor prognosis, indicating the need for the identification of a novel prognostic biomarker for risk stratifications. Recent genome-wide association studies have demonstrated common genetic variants in a region on chromosome 9p21 associated with an increased risk of different malignancies. METHODS In the present study, we explore the possible relationship between genetic variant, rs10811661, and gene expression of CDKN2B in 75 pancreatic cancer patients, and 188 healthy individuals. DNAs were extracted and genotyping and gene expression were performed by TaqMan real-time PCR and RT-PCR, respectively. Logistic regression was used to assess the association between risk and genotypes, while the significant prognostic variables in the univariate analysis were included in multivariate analyses. RESULTS The patients with PDAC had a higher frequency of a TT genotype for rs10811661 than the control group. Also, PDAC patients with dominant genetic model, (TT + TC), was associated with increased risk of developing PDAC (OR= 14.71, 95% CI [1.96-110.35], p= 0.009). Moreover, patients with CC genotype had a higher expression of CDKN2B, in comparison with TT genotype. CONCLUSION Our findings demonstrated that CDKN2A/B was associated with the risk of developing PDAC, supporting further investigations in the larger and multicenter setting to validate the potential value of this gene as an emerging marker for PDAC.
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Affiliation(s)
- Newsha Sardarzadeh
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Sedigheh Damavandi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Ghazaleh Khalili-Tanha
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Dashtiahangar
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Nima Khalili-Tanha
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Sakineh Amoueian
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Habibollah Esmaily
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gordon Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK.
| | - Alireza Khooei
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohsen Aliakbarian
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Towards prevention of childhood ALL by early-life immune training. Blood 2021; 138:1412-1428. [PMID: 34010407 PMCID: PMC8532195 DOI: 10.1182/blood.2020009895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/21/2021] [Indexed: 11/21/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of childhood cancer. Chemotherapy is associated with life-long health sequelae and fails in ∼20% of cases. Thus, prevention of leukemia would be preferable to treatment. Childhood leukemia frequently starts before birth, during fetal hematopoiesis. A first genetic hit (eg, the ETV6-RUNX1 gene fusion) leads to the expansion of preleukemic B-cell clones, which are detectable in healthy newborn cord blood (up to 5%). These preleukemic clones give rise to clinically overt leukemia in only ∼0.2% of carriers. Experimental evidence suggests that a major driver of conversion from the preleukemic to the leukemic state is exposure to immune challenges. Novel insights have shed light on immune host responses and how they shape the complex interplay between (1) inherited or acquired genetic predispositions, (2) exposure to infection, and (3) abnormal cytokine release from immunologically untrained cells. Here, we integrate the recently emerging concept of “trained immunity” into existing models of childhood BCP-ALL and suggest future avenues toward leukemia prevention.
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9
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Vijayakrishnan J, Qian M, Studd JB, Yang W, Kinnersley B, Law PJ, Broderick P, Raetz EA, Allan J, Pui CH, Vora A, Evans WE, Moorman A, Yeoh A, Yang W, Li C, Bartram CR, Mullighan CG, Zimmerman M, Hunger SP, Schrappe M, Relling MV, Stanulla M, Loh ML, Houlston RS, Yang JJ. Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk. Nat Commun 2019; 10:5348. [PMID: 31767839 PMCID: PMC6877561 DOI: 10.1038/s41467-019-13069-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10-8), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10-8) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10-8), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10-8). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - James B Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Elizabeth A Raetz
- Division of Pediatric Hematology and Oncology, New York University Langone Health, New York, New York, USA
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anthony Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Allen Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Charles G Mullighan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Stephen P Hunger
- Department of Paediatrics and Centre for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Martin Schrappe
- Department of Paediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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10
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Brown AL, de Smith AJ, Gant VU, Yang W, Scheurer ME, Walsh KM, Chernus JM, Kallsen NA, Peyton SA, Davies GE, Ehli EA, Winick N, Heerema NA, Carroll AJ, Borowitz MJ, Wood BL, Carroll WL, Raetz EA, Feingold E, Devidas M, Barcellos LF, Hansen HM, Morimoto L, Kang AY, Smirnov I, Healy J, Laverdière C, Sinnett D, Taub JW, Birch JM, Thompson P, Spector LG, Pombo-de-Oliveira MS, DeWan AT, Mullighan CG, Hunger SP, Pui CH, Loh ML, Zwick ME, Metayer C, Ma X, Mueller BA, Sherman SL, Wiemels JL, Relling MV, Yang JJ, Lupo PJ, Rabin KR. Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome. Blood 2019; 134:1227-1237. [PMID: 31350265 PMCID: PMC6788009 DOI: 10.1182/blood.2018890764] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/14/2019] [Indexed: 02/07/2023] Open
Abstract
Children with Down syndrome (DS) have a 20-fold increased risk of acute lymphoblastic leukemia (ALL) and distinct somatic features, including CRLF2 rearrangement in ∼50% of cases; however, the role of inherited genetic variation in DS-ALL susceptibility is unknown. We report the first genome-wide association study of DS-ALL, comprising a meta-analysis of 4 independent studies, with 542 DS-ALL cases and 1192 DS controls. We identified 4 susceptibility loci at genome-wide significance: rs58923657 near IKZF1 (odds ratio [OR], 2.02; Pmeta = 5.32 × 10-15), rs3731249 in CDKN2A (OR, 3.63; Pmeta = 3.91 × 10-10), rs7090445 in ARID5B (OR, 1.60; Pmeta = 8.44 × 10-9), and rs3781093 in GATA3 (OR, 1.73; Pmeta = 2.89 × 10-8). We performed DS-ALL vs non-DS ALL case-case analyses, comparing risk allele frequencies at these and other established susceptibility loci (BMI1, PIP4K2A, and CEBPE) and found significant association with DS status for CDKN2A (OR, 1.58; Pmeta = 4.1 × 10-4). This association was maintained in separate regression models, both adjusting for and stratifying on CRLF2 overexpression and other molecular subgroups, indicating an increased penetrance of CDKN2A risk alleles in children with DS. Finally, we investigated functional significance of the IKZF1 risk locus, and demonstrated mapping to a B-cell super-enhancer, and risk allele association with decreased enhancer activity and differential protein binding. IKZF1 knockdown resulted in significantly higher proliferation in DS than non-DS lymphoblastoid cell lines. Our findings demonstrate a higher penetrance of the CDKN2A risk locus in DS and serve as a basis for further biological insights into DS-ALL etiology.
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Affiliation(s)
- Austin L Brown
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Adam J de Smith
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Vincent U Gant
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC
| | - Jonathan M Chernus
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD
| | - Naomi Winick
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Michael J Borowitz
- Department of Pathology and
- Department of Oncology, Johns Hopkins Hospital, Baltimore, MD;
| | - Brent L Wood
- Department of Pathology and
- Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - William L Carroll
- Department of Pediatrics, Perlmutter Cancer Center, New York University, New York, NY
| | - Elizabeth A Raetz
- Department of Pediatrics, Perlmutter Cancer Center, New York University, New York, NY
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Meenakshi Devidas
- Department of Biostatistics, College of Medicine, Public Health and Health Professions, University of Florida, Gainesville, FL
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Libby Morimoto
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Alice Y Kang
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Jasmine Healy
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Caroline Laverdière
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Jeffrey W Taub
- Division of Hematology Oncology, Department of Oncology, Wayne State University, Detroit, MI
| | - Jillian M Birch
- Department of Paediatric and Adolescent Oncology, University of Manchester, Manchester, United Kingdom
| | - Pamela Thompson
- Department of Paediatric and Adolescent Oncology, University of Manchester, Manchester, United Kingdom
| | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | | | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, GA; and
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | - Beth A Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Joseph L Wiemels
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
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11
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Haas OA. Primary Immunodeficiency and Cancer Predisposition Revisited: Embedding Two Closely Related Concepts Into an Integrative Conceptual Framework. Front Immunol 2019; 9:3136. [PMID: 30809233 PMCID: PMC6379258 DOI: 10.3389/fimmu.2018.03136] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
Common understanding suggests that the normal function of a "healthy" immune system safe-guards and protects against the development of malignancies, whereas a genetically impaired one might increase the likelihood of their manifestation. This view is primarily based on and apparently supported by an increased incidence of such diseases in patients with specific forms of immunodeficiencies that are caused by high penetrant gene defects. As I will review and discuss herein, such constellations merely represent the tip of an iceberg. The overall situation is by far more varied and complex, especially if one takes into account the growing difficulties to define what actually constitutes an immunodeficiency and what defines a cancer predisposition. The enormous advances in genome sequencing, in bioinformatic analyses and in the functional in vitro and in vivo assessment of novel findings together with the availability of large databases provide us with a wealth of information that steadily increases the number of sequence variants that concur with clinically more or less recognizable immunological problems and their consequences. Since many of the newly identified hard-core defects are exceedingly rare, their tumor predisposing effect is difficult to ascertain. The analyses of large data sets, on the other hand, continuously supply us with low penetrant variants that, at least in statistical terms, are clearly tumor predisposing, although their specific relevance for the respective carriers still needs to be carefully assessed on an individual basis. Finally, defects and variants that affect the same gene families and pathways in both a constitutional and somatic setting underscore the fact that immunodeficiencies and cancer predisposition can be viewed as two closely related errors of development. Depending on the particular genetic and/or environmental context as well as the respective stage of development, the same changes can have either a neutral, predisposing and, in some instances, even a protective effect. To understand the interaction between the immune system, be it "normal" or "deficient" and tumor predisposition and development on a systemic level, one therefore needs to focus on the structure and dynamic functional organization of the entire immune system rather than on its isolated individual components alone.
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Affiliation(s)
- Oskar A. Haas
- Department of Clinical Genetics, Children's Cancer Research Institute, Vienna, Austria
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12
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Abstract
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.
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13
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Abstract
In this Review, I present evidence supporting a multifactorial causation of childhood acute lymphoblastic leukaemia (ALL), a major subtype of paediatric cancer. ALL evolves in two discrete steps. First, in utero initiation by fusion gene formation or hyperdiploidy generates a covert, pre-leukaemic clone. Second, in a small fraction of these cases, the postnatal acquisition of secondary genetic changes (primarily V(D)J recombination-activating protein (RAG) and activation-induced cytidine deaminase (AID)-driven copy number alterations in the case of ETS translocation variant 6 (ETV6)-runt-related transcription factor 1 (RUNX1)+ ALL) drives conversion to overt leukaemia. Epidemiological and modelling studies endorse a dual role for common infections. Microbial exposures earlier in life are protective but, in their absence, later infections trigger the critical secondary mutations. Risk is further modified by inherited genetics, chance and, probably, diet. Childhood ALL can be viewed as a paradoxical consequence of progress in modern societies, where behavioural changes have restrained early microbial exposure. This engenders an evolutionary mismatch between historical adaptations of the immune system and contemporary lifestyles. Childhood ALL may be a preventable cancer.
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Affiliation(s)
- Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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14
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Association of the independent polymorphisms in CDKN2A with susceptibility of acute lymphoblastic leukemia. Biosci Rep 2018; 38:BSR20180331. [PMID: 29654170 PMCID: PMC6019384 DOI: 10.1042/bsr20180331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and alterations in CDKN2A were considered to play an important role on leukemogenesis. Two single nucleotide polymorphisms (SNPs) at CDKN2A locus were identified to impact on ALL susceptibility via genome wide association studies, and followed by multiple subsequent replication studies at the specific hits. Here, we conducted a systematic review and meta-analysis to re-evaluate the association of both SNPs (rs3731217 and rs3731249) with ALL susceptibility by gathering the data from 24 independent studies, totally containing 7922 cases/21503 controls for rs3731217 and 6295 cases/24191 controls for rs3731249. Both SNPs were significantly associated with ALL risk (odds ratio [OR] = 0.72 and 2.26 respectively), however, exhibit race-specific pattern. In summary, our meta-analysis indicated that two SNPs at CDKN2A locus are associated with ALL susceptibility independently mainly in Caucasians. Future large-scale studies are required to validate the associations in other ethnicities.
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15
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Vijayakrishnan J, Studd J, Broderick P, Kinnersley B, Holroyd A, Law PJ, Kumar R, Allan JM, Harrison CJ, Moorman AV, Vora A, Roman E, Rachakonda S, Kinsey SE, Sheridan E, Thompson PD, Irving JA, Koehler R, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Easton DF, Pharaoh PDP, Dunning AM, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai ZS, Muir K, Pashayan N, Greaves M, Zimmerman M, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia. Nat Commun 2018; 9:1340. [PMID: 29632299 PMCID: PMC5890276 DOI: 10.1038/s41467-018-03178-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/25/2018] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - James Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Christine J Harrison
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony V Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, WC1N 3JH, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | | | - Sally E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Eamonn Sheridan
- Medical Genetics Research Group, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Pamela D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Julie A Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Rolf Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Per Hoffmann
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital and University of Basel, 4031, Basel, Switzerland
| | - Markus M Nöthen
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Department of Genomics, Institute of Human Genetics, Life & Brain Centre, University of Bonn, D-53012, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D P Pharaoh
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Laboratory, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Frederico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Claus R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 221 00, Lund, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK.
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16
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Wiemels JL, Walsh KM, de Smith AJ, Metayer C, Gonseth S, Hansen HM, Francis SS, Ojha J, Smirnov I, Barcellos L, Xiao X, Morimoto L, McKean-Cowdin R, Wang R, Yu H, Hoh J, DeWan AT, Ma X. GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. Nat Commun 2018; 9:286. [PMID: 29348612 PMCID: PMC5773513 DOI: 10.1038/s41467-017-02596-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) (age 0-14 years) is 20% more common in Latino Americans than non-Latino whites. We conduct a genome-wide association study in a large sample of 3263 Californian children with ALL (including 1949 of Latino heritage) and 3506 controls matched on month and year of birth, sex, and ethnicity, and an additional 12,471 controls from the Kaiser Resource for Genetic Epidemiology Research on Aging Cohort. Replication of the strongest genetic associations is performed in two independent datasets from the Children's Oncology Group and the California Childhood Leukemia Study. Here we identify new risk loci on 17q12 near IKZF3/ZPBP2/GSDMB/ORMDL3, a locus encompassing a transcription factor important for lymphocyte development (IKZF3), and at an 8q24 region known for structural contacts with the MYC oncogene. These new risk loci may impact gene expression via local (four 17q12 genes) or long-range (8q24) interactions, affecting function of well-characterized hematopoietic and growth-regulation pathways.
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Affiliation(s)
- Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA.
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Semira Gonseth
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Epidemiology, School of Community Health Sciences, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Juhi Ojha
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Lisa Barcellos
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Xiaorong Xiao
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Roberta McKean-Cowdin
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA
| | - Rong Wang
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Herbert Yu
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Josephine Hoh
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Andrew T DeWan
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA.
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17
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Urayama KY, Takagi M, Kawaguchi T, Matsuo K, Tanaka Y, Ayukawa Y, Arakawa Y, Hasegawa D, Yuza Y, Kaneko T, Noguchi Y, Taneyama Y, Ota S, Inukai T, Yanagimachi M, Keino D, Koike K, Toyama D, Nakazawa Y, Kurosawa H, Nakamura K, Moriwaki K, Goto H, Sekinaka Y, Morita D, Kato M, Takita J, Tanaka T, Inazawa J, Koh K, Ishida Y, Ohara A, Mizutani S, Matsuda F, Manabe A. Regional evaluation of childhood acute lymphoblastic leukemia genetic susceptibility loci among Japanese. Sci Rep 2018; 8:789. [PMID: 29335448 PMCID: PMC5768812 DOI: 10.1038/s41598-017-19127-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) performed mostly in populations of European and Hispanic ancestry have confirmed an inherited genetic basis for childhood acute lymphoblastic leukemia (ALL), but these associations are less clear in other races/ethnicities. DNA samples from ALL patients (aged 0–19 years) previously enrolled onto a Tokyo Children’s Cancer Study Group trial were collected during 2013–2015, and underwent single nucleotide polymorphism (SNP) microarray genotyping resulting in 527 B-cell ALL for analysis. Cases and control data for 3,882 samples from the Nagahama Study Group and Aichi Cancer Center Study were combined, and association analyses across 10 previous GWAS-identified regions were performed after targeted SNP imputation. Linkage disequilibrium (LD) patterns in Japanese and other populations were evaluated using the varLD score based on 1000 Genomes data. Risk associations for ARID5B (rs10821936, OR = 1.84, P = 6 × 10−17) and PIP4K2A (rs7088318, OR = 0.76, P = 2 × 10−4) directly transferred to Japanese, and the IKZF1 association was detected by an alternate SNP (rs1451367, OR = 1.52, P = 2 × 10−6). Marked regional LD differences between Japanese and Europeans was observed for most of the remaining loci for which associations did not transfer, including CEBPE, CDKN2A, CDKN2B, and ELK3. This study represents a first step towards characterizing the role of genetic susceptibility in childhood ALL risk in Japanese.
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Affiliation(s)
- Kevin Y Urayama
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, Japan. .,Graduate School of Public Health, St. Luke's International University, Tokyo, Japan.
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoichi Tanaka
- Department of Clinical Pharmacy, Center for Clinical Pharmacy and Sciences, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Yoko Ayukawa
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Yuki Yuza
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Takashi Kaneko
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Yuichi Taneyama
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Setsuo Ota
- Department of Pediatrics, Teikyo University Chiba Medical Center, Chiba, Japan
| | - Takeshi Inukai
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan
| | - Masakatsu Yanagimachi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Dai Keino
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kazutoshi Koike
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito, Japan
| | - Daisuke Toyama
- Division of Pediatrics, Showa University Fujigaoka Hospital, Yokohama, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Kozue Nakamura
- Department of Pediatrics, Teikyo University Hospital, Tokyo, Japan
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology & Regenerative Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yujin Sekinaka
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Daisuke Morita
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Tokyo Medical Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Yasushi Ishida
- Pediatric Medical Center, Ehime Prefectural Central Hospital, Matsuyama, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University, Tokyo, Japan
| | - Shuki Mizutani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
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18
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Sud A, Kinnersley B, Houlston RS. Genome-wide association studies of cancer: current insights and future perspectives. Nat Rev Cancer 2017; 17:692-704. [PMID: 29026206 DOI: 10.1038/nrc.2017.82] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) provide an agnostic approach for investigating the genetic basis of complex diseases. In oncology, GWAS of nearly all common malignancies have been performed, and over 450 genetic variants associated with increased risks have been identified. As well as revealing novel pathways important in carcinogenesis, these studies have shown that common genetic variation contributes substantially to the heritable risk of many common cancers. The clinical application of GWAS is starting to provide opportunities for drug discovery and repositioning as well as for cancer prevention. However, deciphering the functional and biological basis of associations is challenging and is in part a barrier to fully unlocking the potential of GWAS.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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19
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Genetic susceptibility in childhood acute lymphoblastic leukemia. Med Oncol 2017; 34:179. [PMID: 28905228 DOI: 10.1007/s12032-017-1038-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading cause of death due to disease in children. The genetic basis of ALL susceptibility has been supported by its association with certain congenital disorders and, more recently, by several genome-wide association studies (GWAS). These GWAS identified common variants in ARID5B, IKZF1, CEBPE, CDKN2A, PIP4K2A, LHPP and ELK3 influencing ALL risk. However, the risk variants of these SNPs were not validated in all populations, suggesting that some of the loci could be population specific. On the other hand, the currently identified risk SNPs in these genes only account for 19% of the additive heritable risk. This estimation indicates that additional susceptibility variants could be discovered. In this review, we will provide an overview of the most important findings carried out in genetic susceptibility of childhood ALL in all GWAS and subsequent studies and we will also point to future directions that could be explored in the near future.
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20
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Gutierrez-Camino A, Martin-Guerrero I, Garcia de Andoin N, Sastre A, Carbone Bañeres A, Astigarraga I, Navajas A, Garcia-Orad A. Confirmation of involvement of new variants at CDKN2A/B in pediatric acute lymphoblastic leukemia susceptibility in the Spanish population. PLoS One 2017; 12:e0177421. [PMID: 28481918 PMCID: PMC5421813 DOI: 10.1371/journal.pone.0177421] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/26/2017] [Indexed: 01/12/2023] Open
Abstract
The locus CDKN2A/B (9p21.3), which comprises the tumor suppressors genes CDKN2A and CDKN2B and the long noncoding RNA (lncRNA) known as ANRIL (or CDKN2B-AS), was associated with childhood acute lymphoblastic leukemia (ALL) susceptibility in several genome wide association studies (GWAS). However, the variants associated in the diverse studies were different. Recently, new and independent SNPs deregulating the locus function were also identified in association with ALL risk. This diversity in the results may be explained because different variants in each population could alter CDKN2A/B locus function through diverse mechanisms. Therefore, the aim of this study was to determine whether the annotated risk variants in the CDKN2A/B locus affect the susceptibility of B cell precursor ALL (B-ALL) in our Spanish population and explore if other SNPs altering additional regulatory mechanisms could be also involved. We analyzed the four SNPs proposed by GWAs and two additional SNPs in miRNA binding sites in 217 pediatric patients with B-ALL and 330 healthy controls. The SNPs rs2811712, rs3731249, rs3217992 and rs2811709 were associated with B-ALL susceptibility in our Spanish population. ALL subtypes analyses showed that rs2811712 was associated with B-hyperdiploid ALL. These results provide evidence for the influence of genetic variants at CDKN2A/B locus with the risk of developing B-ALL.
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Affiliation(s)
- Angela Gutierrez-Camino
- Department of Genetics, Physic Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physic Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Nagore Garcia de Andoin
- Department of Pediatrics, University Hospital Donostia, San Sebastian, Spain
- BioDonostia Health Research Institute, San Sebastian, Spain
| | - Ana Sastre
- Department of Oncohematology, University Hospital La Paz, Madrid, Spain
| | - Ana Carbone Bañeres
- Department of Pediatrics, University Hospital Miguel Servet, Zaragoza, Spain
| | - Itziar Astigarraga
- Department of Pediatrics, University Hospital Cruces, Barakaldo, Spain
- BioCruces Health Research Institute, Barakaldo, Spain
| | | | - Africa Garcia-Orad
- Department of Genetics, Physic Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
- BioCruces Health Research Institute, Barakaldo, Spain
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21
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Vijayakrishnan J, Kumar R, Henrion MYR, Moorman AV, Rachakonda PS, Hosen I, da Silva Filho MI, Holroyd A, Dobbins SE, Koehler R, Thomsen H, Irving JA, Allan JM, Lightfoot T, Roman E, Kinsey SE, Sheridan E, Thompson PD, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Greaves M, Harrison CJ, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. Leukemia 2017; 31:573-579. [PMID: 27694927 PMCID: PMC5336191 DOI: 10.1038/leu.2016.271] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype of ALL, B-cell precursor ALL (BCP-ALL), we conducted a meta-analysis of two GWASs with imputation using 1000 Genomes and UK10K Project data as reference (totaling 1658 cases and 7224 controls). After genotyping an additional 2525 cases and 3575 controls, we identify new susceptibility loci for BCP-ALL mapping to 10q26.13 (rs35837782, LHPP, P=1.38 × 10-11) and 12q23.1 (rs4762284, ELK3, P=8.41 × 10-9). We also provide confirmatory evidence for the existence of independent risk loci at 9p21.3, but show that the association marked by rs77728904 can be accounted for by linkage disequilibrium with the rare high-impact CDKN2A p.Ala148Thr variant rs3731249. Our data provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- J Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M Y R Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - A V Moorman
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - P S Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - I Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M I da Silva Filho
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - A Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - S E Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - H Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - J A Irving
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - J M Allan
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - T Lightfoot
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - E Roman
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - S E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, UK
| | - E Sheridan
- Medical Genetics Research Group, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - P D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, University of Manchester, St Mary's Hospital, Manchester, UK
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital Basel, Basel, Switzerland
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - K H Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - M Greaves
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Sutton, UK
| | - C J Harrison
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - C R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - M Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany
| | - K Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - R S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
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22
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Campa D, Capurso G, Pastore M, Talar-Wojnarowska R, Milanetto AC, Landoni L, Maiello E, Lawlor RT, Malecka-Panas E, Funel N, Gazouli M, De Bonis A, Klüter H, Rinzivillo M, Delle Fave G, Hackert T, Landi S, Bugert P, Bambi F, Archibugi L, Scarpa A, Katzke V, Dervenis C, Liço V, Furlanello S, Strobel O, Tavano F, Basso D, Kaaks R, Pasquali C, Gentiluomo M, Rizzato C, Canzian F. Common germline variants within the CDKN2A/2B region affect risk of pancreatic neuroendocrine tumors. Sci Rep 2016; 6:39565. [PMID: 28008994 PMCID: PMC5180167 DOI: 10.1038/srep39565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/23/2016] [Indexed: 01/14/2023] Open
Abstract
Pancreatic neuroendocrine tumors (PNETs) are heterogeneous neoplasms which represent only 2% of all pancreatic neoplasms by incidence, but 10% by prevalence. Genetic risk factors could have an important role in the disease aetiology, however only a small number of case control studies have been performed yet. To further our knowledge, we genotyped 13 SNPs belonging to the pleiotropic CDKN2A/B gene region in 320 PNET cases and 4436 controls, the largest study on the disease so far. We observed a statistically significant association between the homozygotes for the minor allele of the rs2518719 SNP and an increased risk of developing PNET (ORhom = 2.08, 95% CI 1.05-4.11, p = 0.035). This SNP is in linkage disequilibrium with another polymorphic variant associated with increased risk of several cancer types. In silico analysis suggested that the SNP could alter the sequence recognized by the Neuron-Restrictive Silencer Factor (NRSF), whose deregulation has been associated with the development of several tumors. The mechanistic link between the allele and the disease has not been completely clarified yet but the epidemiologic evidences that link the DNA region to increased cancer risk are convincing. In conclusion, our results suggest rs2518719 as a pleiotropic CDKN2A variant associated with the risk of developing PNETs.
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Affiliation(s)
- Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, S. Andrea Hospital, 'Sapienza' University of Rome, Rome, Italy
| | - Manuela Pastore
- Department of Biology, University of Pisa, Pisa, Italy.,Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Anna Caterina Milanetto
- Department of Surgery, Oncology and Gastroenterology (DISCOG), Pancreatic and Digestive Endocrine Surgery, University of Padova, Padova, Italy
| | - Luca Landoni
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Evaristo Maiello
- Department of Oncology, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Rita T Lawlor
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Ewa Malecka-Panas
- Dept of Digestive Tract Diseases, Medical University of Lodz, Poland
| | - Niccola Funel
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School National and Kapodistrian University of Athens, Greece
| | - Antonio De Bonis
- Department of Surgery, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Harald Klüter
- Mannheim Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Maria Rinzivillo
- Digestive and Liver Disease Unit, S. Andrea Hospital, 'Sapienza' University of Rome, Rome, Italy
| | - Gianfranco Delle Fave
- Digestive and Liver Disease Unit, S. Andrea Hospital, 'Sapienza' University of Rome, Rome, Italy
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Peter Bugert
- Mannheim Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Franco Bambi
- Blood Transfusion Service, Azienda Ospedaliero-Universitaria Meyer, Florence, Italy
| | - Livia Archibugi
- Digestive and Liver Disease Unit, S. Andrea Hospital, 'Sapienza' University of Rome, Rome, Italy
| | - Aldo Scarpa
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christos Dervenis
- Department of Surgery, Konstantopouleion General Hospital Nea Ionia, Greece
| | - Valbona Liço
- Department of Surgery, Oncology and Gastroenterology (DISCOG), Pancreatic and Digestive Endocrine Surgery, University of Padova, Padova, Italy
| | - Sara Furlanello
- Department of Medicine (DIMED), Laboratory Medicine, University of Padova, Padova, Italy
| | - Oliver Strobel
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Daniela Basso
- Department of Medicine (DIMED), Laboratory Medicine, University of Padova, Padova, Italy
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology (DISCOG), Pancreatic and Digestive Endocrine Surgery, University of Padova, Padova, Italy
| | | | - Cosmeri Rizzato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Gu J, Reynolds A, Fang L, DeGraffenreid C, Sterns K, Patel KP, Medeiros LJ, Lin P, Lu X. Coexistence of iAMP21 and ETV6-RUNX1 fusion in an adolescent with B cell acute lymphoblastic leukemia: literature review of six additional cases. Mol Cytogenet 2016; 9:84. [PMID: 27895713 PMCID: PMC5117506 DOI: 10.1186/s13039-016-0294-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 11/11/2016] [Indexed: 12/29/2022] Open
Abstract
Background Intrachromosomal amplification of chromosome 21 (iAMP21) results from breakage-fusion-bridge cycles and chromothripsis is a distinct marker of a subgroup of B cell acute lymphoblastic leukemia (B-ALL) cases associated with a poor prognosis. iAMP21 accounts for 2% of pediatric B-ALL and occurs predominantly in older children or adolescents. ETV6-RUNX1 fusion, resulting from t(12;21)(p13;q22), is associated with an excellent outcome in younger children with B-ALL. Coexistence of iAMP21 with ETV6-RUNX1 fusion is extremely rare with limited clinical information available. Results We report the case of an 18-year old Caucasian man diagnosed with ETV6-RUNX1 fusion positive B-ALL. He was treated with intensive chemotherapy and achieved remission for 6 months before relapse, 15 months after the initial diagnosis. G-band karyotyping and Fluorescence in situ hybridization (FISH) analyses performed on bone marrow revealed complex abnormalities: 41,X,-Y,der(3)t(3;20)(p11.2;q11.2),-4,t(5;22)(q32;q11.2),del(9)(p13),dic(9;17)(p13;p11.2),t(12;21)(p13;q22),der(14)t(14;17)(p11.2;q11.2),der(17;22)(q11.2;q11.2),-20,add(21)(q22),-22[4]/46,XY[15] with an iAMP21 and an ETV6-RUNX1. Additional molecular studies confirmed ETV6-RUNX1 fusion and with a TP53 mutation. High-resolution single nucleotide polymorphism microarray (SNP array) revealed the iAMP21 to be chromothripsis of 21q and subsequent metaphase FISH further delineated complex genomic aberrations. Although the patient received intensive chemotherapy with allogenic stem cell transplant, he died 26 months after initial diagnosis. We searched the literature and identified six cases showing coexisting iAMP21 and ETV6-RUNX1. The median age for these six patients was 10 years (range, 2–18) and males predominated. The median overall survival (OS) was 28 months. Conclusions Patients with B-ALL associated with both iAMP21 and ETV6-RUNX1 tend to be older children or adolescents and have a poor prognosis.
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Affiliation(s)
- Jun Gu
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Alexandra Reynolds
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0350, Houston, TX 77030 USA
| | - Lianghua Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0149, Houston, TX 77030 USA ; Department of Oncology, Jiangsu Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu China
| | - Corrie DeGraffenreid
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Kenneth Sterns
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0149, Houston, TX 77030 USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0072, Houston, TX 77030 USA
| | - Pei Lin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0072, Houston, TX 77030 USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0350, Houston, TX 77030 USA ; Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Tarry 7-723, Chicago, IL 60611 USA
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Campa D, Pastore M, Gentiluomo M, Talar-Wojnarowska R, Kupcinskas J, Malecka-Panas E, Neoptolemos JP, Niesen W, Vodicka P, Fave GD, Bueno-de-Mesquita HB, Gazouli M, Pacetti P, Di Leo M, Ito H, Klüter H, Soucek P, Corbo V, Yamao K, Hosono S, Kaaks R, Vashist Y, Gioffreda D, Strobel O, Shimizu Y, Dijk F, Andriulli A, Ivanauskas A, Bugert P, Tavano F, Vodickova L, Zambon CF, Lovecek M, Landi S, Key TJ, Boggi U, Pezzilli R, Jamroziak K, Mohelnikova-Duchonova B, Mambrini A, Bambi F, Busch O, Pazienza V, Valente R, Theodoropoulos GE, Hackert T, Capurso G, Cavestro GM, Pasquali C, Basso D, Sperti C, Matsuo K, Büchler M, Khaw KT, Izbicki J, Costello E, Katzke V, Michalski C, Stepien A, Rizzato C, Canzian F. Functional single nucleotide polymorphisms within the cyclin-dependent kinase inhibitor 2A/2B region affect pancreatic cancer risk. Oncotarget 2016; 7:57011-57020. [PMID: 27486979 PMCID: PMC5302969 DOI: 10.18632/oncotarget.10935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/13/2016] [Indexed: 02/05/2023] Open
Abstract
The CDKN2A (p16) gene plays a key role in pancreatic cancer etiology. It is one of the most commonly somatically mutated genes in pancreatic cancer, rare germline mutations have been found to be associated with increased risk of developing familiar pancreatic cancer and CDKN2A promoter hyper-methylation has been suggested to play a critical role both in pancreatic cancer onset and prognosis. In addition several unrelated SNPs in the 9p21.3 region, that includes the CDNK2A, CDNK2B and the CDNK2B-AS1 genes, are associated with the development of cancer in various organs. However, association between the common genetic variability in this region and pancreatic cancer risk is not clearly understood. We sought to fill this gap in a case-control study genotyping 13 single nucleotide polymorphisms (SNPs) in 2,857 pancreatic ductal adenocarcinoma (PDAC) patients and 6,111 controls in the context of the Pancreatic Disease Research (PANDoRA) consortium. We found that the A allele of the rs3217992 SNP was associated with an increased pancreatic cancer risk (ORhet=1.14, 95% CI 1.01-1.27, p=0.026, ORhom=1.30, 95% CI 1.12-1.51, p=0.00049). This pleiotropic variant is reported to be a mir-SNP that, by changing the binding site of one or more miRNAs, could influence the normal cell cycle progression and in turn increase PDAC risk. In conclusion, we observed a novel association in a pleiotropic region that has been found to be of key relevance in the susceptibility to various types of cancer and diabetes suggesting that the CDKN2A/B locus could represent a genetic link between diabetes and pancreatic cancer risk.
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Affiliation(s)
- Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Pastore
- Department of Biology, University of Pisa, Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuel Gentiluomo
- Department of Biology, University of Pisa, Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Juozas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ewa Malecka-Panas
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - John P. Neoptolemos
- Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Liverpool, United Kingdom
| | - Willem Niesen
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Pavel Vodicka
- Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
| | - Gianfranco Delle Fave
- Digestive and Liver Disease Unit, S. Andrea Hospital, ‘Sapienza’ University of Rome, Rome, Italy
| | - H. Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Paola Pacetti
- Oncological Department Massa Carrara Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Milena Di Leo
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hidemi Ito
- Division Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Harald Klüter
- Institute of Transfusion Medicine and Immunology, German Red Cross Blood Service Baden-Württemberg – Hessen gGmbH, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Pavel Soucek
- Laboratory of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Vincenzo Corbo
- ARC-Net Research Centre, and Department of Diagnostics and Public Health University and Hospital Trust of Verona, Verona, Italy
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Satoyo Hosono
- Division Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Yasuhiro Shimizu
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Frederike Dijk
- Department of Pathology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Angelo Andriulli
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Audrius Ivanauskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, German Red Cross Blood Service Baden-Württemberg – Hessen gGmbH, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Ludmila Vodickova
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Prague, Czech Republic
| | | | - Martin Lovecek
- Department of Surgery I, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Timothy J. Key
- Epidemiology Unit Nuffield Department of Population Health University of Oxford, Oxford, UK
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Raffaele Pezzilli
- Pancreas Unit, Department of Digestive System, Dant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Beatrice Mohelnikova-Duchonova
- Laboratory of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Andrea Mambrini
- Oncological Department Massa Carrara Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Franco Bambi
- Blood Transfusion Service, Azienda Ospedaliero Universitaria Meyer, Florence, Italy
| | - Olivier Busch
- Department of Surgery, Academic Medical Centre, Amsterdam, The Netherlands
| | - Valerio Pazienza
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Roberto Valente
- Digestive and Liver Disease Unit, S. Andrea Hospital, ‘Sapienza’ University of Rome, Rome, Italy
| | - George E. Theodoropoulos
- Colorectal Unit, First Department of Propaedeutic Surgery, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, S. Andrea Hospital, ‘Sapienza’ University of Rome, Rome, Italy
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | - Daniela Basso
- Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Cosimo Sperti
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Markus Büchler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, Addenbrooke's Hospital, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Jakob Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eithne Costello
- Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Liverpool, United Kingdom
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Michalski
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna Stepien
- Laboratory of Clinical, Transplant Immunology and Genetics, Copernicus Memorial Hospital, Lodz, Poland
| | - Cosmeri Rizzato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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