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Rehman K, Iqbal Z, Zhiqin D, Ayub H, Saba N, Khan MA, Yujie L, Duan L. Analysis of genetic biomarkers, polymorphisms in ADME-related genes and their impact on pharmacotherapy for prostate cancer. Cancer Cell Int 2023; 23:247. [PMID: 37858151 PMCID: PMC10585889 DOI: 10.1186/s12935-023-03084-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
Prostate cancer (PCa) is a non-cutaneous malignancy in males with wide variation in incidence rates across the globe. It is the second most reported cause of cancer death. Its etiology may have been linked to genetic polymorphisms, which are not only dominating cause of malignancy casualties but also exerts significant effects on pharmacotherapy outcomes. Although many therapeutic options are available, but suitable candidates identified by useful biomarkers can exhibit maximum therapeutic efficacy. The single-nucleotide polymorphisms (SNPs) reported in androgen receptor signaling genes influence the effectiveness of androgen receptor pathway inhibitors and androgen deprivation therapy. Furthermore, SNPs located in genes involved in transport, drug metabolism, and efflux pumps also influence the efficacy of pharmacotherapy. Hence, SNPs biomarkers provide the basis for individualized pharmacotherapy. The pharmacotherapeutic options for PCa include hormonal therapy, chemotherapy (Docetaxel, Mitoxantrone, Cabazitaxel, and Estramustine, etc.), and radiotherapy. Here, we overview the impact of SNPs reported in various genes on the pharmacotherapy for PCa and evaluate current genetic biomarkers with an emphasis on early diagnosis and individualized treatment strategy in PCa.
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Affiliation(s)
- Khurram Rehman
- Faculty of Pharmacy, Gomal University, D.I.Khan, Pakistan
| | - Zoya Iqbal
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Deng Zhiqin
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Hina Ayub
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | - Naseem Saba
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | | | - Liang Yujie
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518035, Guangdong, China.
| | - Li Duan
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China.
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
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2
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Srinivasan S, Kryza T, Bock N, Tse BWC, Sokolowski KA, Panchadsaram J, Moya L, Stephens C, Dong Y, Röhl J, Alinezhad S, Vela I, Perry-Keene JL, Buzacott K, Gago-Dominguez M, Schleutker J, Maier C, Muir K, Tangen CM, Gronberg H, Pashayan N, Albanes D, Wolk A, Stanford JL, Berndt SI, Mucci LA, Koutros S, Cussenot O, Sorensen KD, Grindedal EM, Key TJ, Haiman CA, Giles GG, Vega A, Wiklund F, Neal DE, Kogevinas M, Stampfer MJ, Nordestgaard BG, Brenner H, Gamulin M, Claessens F, Melander O, Dahlin A, Stattin P, Hallmans G, Häggström C, Johansson R, Thysell E, Rönn AC, Li W, Brown N, Dimeski G, Shepherd B, Dadaev T, Brook MN, Spurdle AB, Stenman UH, Koistinen H, Kote-Jarai Z, Klein RJ, Lilja H, Ecker RC, Eeles R, Clements J, Batra J. Biochemical activity induced by a germline variation in KLK3 (PSA) associates with cellular function and clinical outcome in prostate cancer. RESEARCH SQUARE 2023:rs.3.rs-2650312. [PMID: 37034758 PMCID: PMC10081352 DOI: 10.21203/rs.3.rs-2650312/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility. The non-synonymous KLK3 SNP, rs17632542 (c.536T>C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity as a previously undescribed function mediating prostate cancer pathogenesis. The 'Thr' PSA variant led to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displayed higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterization of this PSA variant demonstrated markedly reduced proteolytic activity that correlated with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele had reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Thomas Kryza
- Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Nathalie Bock
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Brian WC Tse
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Kamil A. Sokolowski
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Janaththani Panchadsaram
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Carson Stephens
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ying Dong
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Joan Röhl
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Saeid Alinezhad
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ian Vela
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Department of Urology, Princess Alexandra Hospital, Brisbane, Woolloongabba, Brisbane, QLD, Australia
| | - Joanna L. Perry-Keene
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - Katie Buzacott
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - The IMPACT Study
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, IDIS, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - The PROFILE Study Steering Committee
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
- Ronald and Rita McAulay Foundation, London, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- University of Oxford, Oxford, UK
- Queen Mary University of London, London, UK
| | - Johanna Schleutker
- Institute of Biomedicine, Kiinamyllynkatu 10, FI-20014 University of Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521 Turku, Finland
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076 Tuebingen, Germany
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Catherine M. Tangen
- SWOG Statistical Center, Division of Public Health Sciences
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Lorelei A. Mucci
- Department of Epidemiology,Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Olivier Cussenot
- CeRePP and Sorbonne Universite, GRC N°5 AP-HP, Tenon Hospital, Paris, France
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University & Department of Molecular Medicine (MOMA), Aarhus University Hospital, DK-8200 Aarhus N., Denmark
| | | | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, USA
| | - Graham G. Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
- Biomedical Network on Rare Diseases (CIBERER), Santiago de Compostela, Spain
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, England
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Meir J. Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Børge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Anders Dahlin
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Sweden
| | - Christel Häggström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Ann-Charlotte Rönn
- Clinical Research Center, Karolinska University Hospital, Huddinge, Sweden
| | - Weiqiang Li
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nigel Brown
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Goce Dimeski
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Benjamin Shepherd
- Department of Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark N. Brook
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Robert J. Klein
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans Lilja
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Departments of Laboratory Medicine, Surgery (Urology Service) and Medicine (Genitourinary Oncology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | - The Australian Prostate Cancer BioResource
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD
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3
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Song X, Ru M, Steinsnyder Z, Tkachuk K, Kopp RP, Sullivan J, Gümüş ZH, Offit K, Joseph V, Klein RJ. SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiol Biomarkers Prev 2022; 31:1466-1472. [PMID: 35511739 PMCID: PMC9250608 DOI: 10.1158/1055-9965.epi-22-0053] [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: 01/14/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown. METHODS These variants were genotyped in a cohort of 1,298 patients. Samples were linked with age, PSA level, Gleason score, cancer stage at surgery, and times from surgery to biochemical recurrence to death from prostate cancer. SNPs rs2702185 and rs73055188 were tested for association with prostate cancer-specific survival time using a multivariate Cox proportional hazard model. SNP rs2702185 was further tested for association with time to biochemical recurrence and time from biochemical recurrence to death with a multi-state model. RESULTS SNP rs2702185 at SMG7 was associated with prostate cancer-specific survival time, specifically the time from biochemical recurrence to prostate cancer death (HR, 2.5; 95% confidence interval, 1.4-4.5; P = 0.0014). Nine variants were in linkage disequilibrium (LD) with rs2702185; one, rs10737246, was found to be most likely to be functional based on LD patterns and overlap with open chromatin. Patterns of open chromatin and correlation with gene expression suggest that this SNP may affect expression of SMG7 in T cells. CONCLUSIONS The SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional. IMPACT These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.
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Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Meng Ru
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Ryan P. Kopp
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239 USA
| | - John Sullivan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zeynep H. Gümüş
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Robert J. Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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KLK3 germline mutation I179T complements DNA repair genes for predicting prostate cancer progression. Prostate Cancer Prostatic Dis 2022; 25:749-754. [PMID: 35149774 DOI: 10.1038/s41391-021-00466-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Germline mutations in DNA repair genes and KLK3 have been associated with adverse prostate cancer (PCa) outcomes in separate studies but never jointly. The objective of this study is to simultaneously assess these two types of germline mutations. METHODS Germline rare pathogenic mutations (RPMs) in 9 commonly tested DNA repair genes and KLK3 variants were tested for their associations with PCa progression in two PCa cohorts: (1) hospital-based PCa patients treated with radical surgery at the Johns Hopkins Hospital (JHH, N = 1943), and (2) population-based PCa patients in the UK Biobank (UKB, N = 10,224). Progression was defined as metastasis and/or PCa-specific death (JHH) and PCa-specific death (UKB). RPMs of DNA repair genes were annotated using the American College of Medical Genetics recommendations. Known KLK3 variants were genotyped. Associations were tested using a logistic regression model adjusting for genetic background (top ten principal components). RESULTS In the JHH, 3.2% (59/1,843) of patients had RPMs in 9 DNA repair genes; odds ratio (OR, 95% confidence interval) for progression was 2.99 (1.6-5.34), P < 0.001. In comparison, KLK3 I179T mutation was more common; 9.7% (189/1,943) carried the mutation, OR = 1.6 (1.05-2.37), P = 0.02. Similar results were found in the UKB. Both types of mutations remained statistically significant in multivariable analyses. In the combined cohort, compared to patients without any mutations (RPMs-/KLK3-), RPMs-/KLK3+ patients had modestly increased risk for progression [OR = 1.54 (1.15-2.02), P = 0.003], and RPMs+/KLK3+ patients had greatly increased risk for progression [OR = 5.41 (2.04-12.99), P < 0.001]. Importantly, associations of mutations with PCa progression were found in patients with clinically defined low- or intermediate risk for disease progression. CONCLUSIONS Two different cohorts consistently demonstrate that KLK3 I179T and RPMs of nine commonly tested DNA repair genes are complementary for predicting PCa progression. These results are highly relevant to PCa germline testing and provide critical information for KLK3 I179T to be considered in guidelines.
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Lin HY, Huang PY, Cheng CH, Tung HY, Fang Z, Berglund AE, Chen A, French-Kwawu J, Harris D, Pow-Sang J, Yamoah K, Cleveland JL, Awasthi S, Rounbehler RJ, Gerke T, Dhillon J, Eeles R, Kote-Jarai Z, Muir K, Schleutker J, Pashayan N, Neal DE, Nielsen SF, Nordestgaard BG, Gronberg H, Wiklund F, Giles GG, Haiman CA, Travis RC, Stanford JL, Kibel AS, Cybulski C, Khaw KT, Maier C, Thibodeau SN, Teixeira MR, Cannon-Albright L, Brenner H, Kaneva R, Pandha H, Srinivasan S, Clements J, Batra J, Park JY. KLK3 SNP-SNP interactions for prediction of prostate cancer aggressiveness. Sci Rep 2021; 11:9264. [PMID: 33927218 PMCID: PMC8084951 DOI: 10.1038/s41598-021-85169-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
Risk classification for prostate cancer (PCa) aggressiveness and underlying mechanisms remain inadequate. Interactions between single nucleotide polymorphisms (SNPs) may provide a solution to fill these gaps. To identify SNP-SNP interactions in the four pathways (the angiogenesis-, mitochondria-, miRNA-, and androgen metabolism-related pathways) associated with PCa aggressiveness, we tested 8587 SNPs for 20,729 cases from the PCa consortium. We identified 3 KLK3 SNPs, and 1083 (P < 3.5 × 10-9) and 3145 (P < 1 × 10-5) SNP-SNP interaction pairs significantly associated with PCa aggressiveness. These SNP pairs associated with PCa aggressiveness were more significant than each of their constituent SNP individual effects. The majority (98.6%) of the 3145 pairs involved KLK3. The 3 most common gene-gene interactions were KLK3-COL4A1:COL4A2, KLK3-CDH13, and KLK3-TGFBR3. Predictions from the SNP interaction-based polygenic risk score based on 24 SNP pairs are promising. The prevalence of PCa aggressiveness was 49.8%, 21.9%, and 7.0% for the PCa cases from our cohort with the top 1%, middle 50%, and bottom 1% risk profiles. Potential biological functions of the identified KLK3 SNP-SNP interactions were supported by gene expression and protein-protein interaction results. Our findings suggest KLK3 SNP interactions may play an important role in PCa aggressiveness.
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Affiliation(s)
- Hui-Yi Lin
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA.
| | - Po-Yu Huang
- Computational Intelligence Technology Center, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Chia-Ho Cheng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Heng-Yuan Tung
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Zhide Fang
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Jennifer French-Kwawu
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Darian Harris
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Julio Pow-Sang
- Department of Genitourinary Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Kosj Yamoah
- Department of Radiation Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Travis Gerke
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Jasreman Dhillon
- Department of Pathology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | - Kenneth Muir
- Division of Population Health, Health Services Research, and Primary Care, University of Manchester, Oxford Road, Manchester, M139PT, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20014, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521, Turku, Finland
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Room 6603, Level 6, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Box 279, Cambridge, CB2 0QQ, UK
| | - Sune F Nielsen
- Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Børge G Nordestgaard
- Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, 72076, Tuebingen, Germany
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University of Sofia, Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Hardev Pandha
- University of Surrey, Guildford, GU2 7XH, Surrey, UK
| | - Srilakshmi Srinivasan
- Translational Research Institute, Brisbane, QLD, 4102, Australia
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Judith Clements
- Translational Research Institute, Brisbane, QLD, 4102, Australia
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Jyotsna Batra
- Translational Research Institute, Brisbane, QLD, 4102, Australia
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
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6
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Bicak M, Wang X, Gao X, Xu X, Väänänen RM, Taimen P, Lilja H, Pettersson K, Klein RJ. Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB. Hum Mol Genet 2020; 29:1581-1591. [PMID: 32065238 PMCID: PMC7526792 DOI: 10.1093/hmg/ddaa026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/25/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
How genome-wide association studies-identified single-nucleotide polymorphisms (SNPs) affect remote genes remains unknown. Expression quantitative trait locus (eQTL) association meta-analysis on 496 prostate tumor and 602 normal prostate samples with 117 SNPs revealed novel cis-eQTLs and trans-eQTLs. Mediation testing and colocalization analysis demonstrate that MSMB is a cis-acting mediator for SNHG11 (P < 0.01). Removing rs10993994 in LNCaP cell lines by CRISPR/Cas9 editing shows that the C-allele corresponds with an over 100-fold increase in MSMB expression and 5-fold increase in SNHG11 compared with the T-allele. Colocalization analysis confirmed that the same set of SNPs associated with MSMB expression is associated with SNHG11 expression (posterior probability of shared variants is 66.6% in tumor and 91.4% in benign). These analyses further demonstrate variants driving MSMB expression differ in tumor and normal, suggesting regulatory network rewiring during tumorigenesis.
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Affiliation(s)
- Mesude Bicak
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xing Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoni Gao
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xing Xu
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Pekka Taimen
- Department of Pathology, University of Turku, 20014 Turku, and Turku University Hospital, 20521 Turku, Finland
| | - Hans Lilja
- Department of Laboratory Medicine, Surgery and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, UK
- Department of Translational Medicine, Lund University, Malmö 205 02, Sweden
| | - Kim Pettersson
- Division of Biotechnology, University of Turku, Turku, Finland
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genome Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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7
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Zhang L, Walsh MF, Jairam S, Mandelker D, Zhong Y, Kemel Y, Chen YB, Musheyev D, Zehir A, Jayakumaran G, Brzostowski E, Birsoy O, Yang C, Li Y, Somar J, DeLair D, Pradhan N, Berger MF, Cadoo K, Carlo MI, Robson ME, Stadler ZK, Iacobuzio-Donahue CA, Joseph V, Offit K. Fumarate hydratase FH c.1431_1433dupAAA (p.Lys477dup) variant is not associated with cancer including renal cell carcinoma. Hum Mutat 2019; 41:103-109. [PMID: 31444830 DOI: 10.1002/humu.23900] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 01/25/2023]
Abstract
Fumarate hydratase (FH) mutations underpin the autosomal recessive syndrome. FH deficiency and the autosomal dominant syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC). The FH c.1431_1433dupAAA (p.Lys477dup) genomic alteration has been conclusively shown to contribute to FH deficiency when occurring with another FH germline alteration. However, a sufficiently large dataset has been lacking to conclusively determine its clinical significance to cancer predisposition in the heterozygous state. We reviewed a series of 7,571 patients with cancer who received germline results through MSK-IMPACT testing at the Memorial Sloan Kettering Cancer Center. The FH c.1431_1433dupAAA (p.Lys477dup) variant was detected in 24 individuals, none of whom was affected with renal cancer. Eleven of the 372 patients with renal cancer were identified to carried pathogenic FH variants associated with HLRCC. None of these 372 patients with renal cancer carried the FH c.1431_1433dupAAA variant. Our data indicate the FH c.1431_1433dupAAA is not associated with cancer including renal cell carcinoma.
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Affiliation(s)
- Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yi Zhong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Edyta Brzostowski
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ozge Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Joshua Somar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Deborah DeLair
- Department of Pathology, New York University Medical Center, New York City, New York
| | - Nisha Pradhan
- University of Colorado School of Medicine, Aurora, Colorado
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
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8
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Li W, Middha M, Bicak M, Sjoberg DD, Vertosick E, Dahlin A, Häggström C, Hallmans G, Rönn AC, Stattin P, Melander O, Ulmert D, Lilja H, Klein RJ. Genome-wide Scan Identifies Role for AOX1 in Prostate Cancer Survival. Eur Urol 2018; 74:710-719. [PMID: 30289108 PMCID: PMC6287611 DOI: 10.1016/j.eururo.2018.06.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/13/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Most men diagnosed with prostate cancer have low-risk cancers. How to predict prostate cancer progression at the time of diagnosis remains challenging. OBJECTIVE To identify single nucleotide polymorphisms (SNPs) associated with death from prostate cancer. DESIGN, SETTING, AND PARTICIPANTS Blood samples from 11 506 men in Sweden were collected during 1991-1996. Of these, 1053 men were diagnosed with prostate cancer and 245 died from the disease. Stage and grade at diagnosis and outcome information were obtained, and DNA from all cases was genotyped. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS A total of 6 126 633 SNPs were tested for association with prostate-cancer-specific survival time using a Cox proportional hazard model, adjusted for age, stage, and grade at diagnosis. A value of 1×10-6 was used as suggestive significance threshold. Positive candidate SNPs were tested for association with gene expression using expression quantitative trait locus analysis. RESULTS AND LIMITATIONS We found 12 SNPs at seven independent loci associated with prostate-cancer-specific survival time. One of 6 126 633 SNPs tested reached genome-wide significance (p<5×10-8) and replicated in an independent cohort: rs73055188 (p=5.27×10-9, per-allele hazard ratio [HR]=2.27, 95% confidence interval [CI] 1.72-2.98) in the AOX1 gene. A second SNP reached a suggestive level of significance (p<1×10-6) and replicated in an independent cohort: rs2702185 (p=7.1×10-7, per-allele HR=2.55, 95% CI=1.76-3.69) in the SMG7 gene. The SNP rs73055188 is correlated with AOX1 expression levels, which is associated with biochemical recurrence of prostate cancer in independent cohorts. This association is yet to be validated in other ethnic groups. CONCLUSIONS The SNP rs73055188 at the AOX1 locus is associated with prostate-cancer-specific survival time, and AOX1 gene expression level is correlated with biochemical recurrence of prostate cancer. PATIENT SUMMARY We identify two genetic markers that are associated with prostate-cancer-specific survival time.
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Affiliation(s)
- Weiqiang Li
- Icahn Institute for Genomics and Multiscale Biology and
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount
Sinai, New York, NY USA
| | - Mridu Middha
- Icahn Institute for Genomics and Multiscale Biology and
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount
Sinai, New York, NY USA
| | - Mesude Bicak
- Icahn Institute for Genomics and Multiscale Biology and
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount
Sinai, New York, NY USA
| | - Daniel D. Sjoberg
- Department of Epidemiology and Biostatistics, Memorial
Sloan Kettering Cancer Center, New York, NY USA
| | - Emily Vertosick
- Department of Epidemiology and Biostatistics, Memorial
Sloan Kettering Cancer Center, New York, NY USA
| | - Anders Dahlin
- Department of Clinical Sciences, Malmö, Lund
University, Malmö, Sweden
| | | | - Göran Hallmans
- Department of Public Health and Clinical Medicine,
Nutritional Research, Umeå University, Umeå, Sweden
| | - Ann-Charlotte Rönn
- Clinical Research Center, Karolinska University Hospital,
Huddinge, Sweden
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University,
Uppsala, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Malmö, Lund
University, Malmö, Sweden
| | - David Ulmert
- Molecular Pharmacology Program, Sloan Kettering Institute,
New York, NY USA
| | - Hans Lilja
- Departments of Laboratory Medicine, Surgery, and Medicine,
Memorial Sloan Kettering Cancer Center, New York, NY USA; Nuffield Department of
Surgical Sciences, University of Oxford, Oxford, UK; Department of Translational
Medicine, Lund University, Malmö, Sweden
| | - Robert J. Klein
- Icahn Institute for Genomics and Multiscale Biology and
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount
Sinai, New York, NY USA
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9
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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10
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Vaidyanathan V, Naidu V, Kao CHJ, Karunasinghe N, Bishop KS, Wang A, Pallati R, Shepherd P, Masters J, Zhu S, Goudie M, Krishnan M, Jabed A, Marlow G, Narayanan A, Ferguson LR. Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men - a genotypic approach. MOLECULAR BIOSYSTEMS 2017; 13:681-698. [PMID: 28252132 DOI: 10.1039/c6mb00873a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs. By using this method, we identified the susceptible alleles in a New Zealand population, and examined the interaction with environmental factors. We have identified a number of SNPs that have risk associations both with and without environmental interaction. The results indicate that certain SNPs are associated with disease vulnerability based on behavioral factors. The list of genes with SNPs identified as being associated with the risk of PCa in a New Zealand population is provided in the graphical abstract.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Vijay Naidu
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Chi Hsiu-Juei Kao
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | | | - Karen S Bishop
- Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Alice Wang
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Phillip Shepherd
- Sequenom Facility, Liggins Institute, University of Auckland, Auckland 1023, New Zealand.
| | - Jonathan Masters
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Shuotun Zhu
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Megan Goudie
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Mohanraj Krishnan
- Department of Obstetrics and Gynaecology, FMHS, University of Auckland, Auckland 1023, New Zealand.
| | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ajit Narayanan
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
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11
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Dmitriev AA, Rosenberg EE, Krasnov GS, Gerashchenko GV, Gordiyuk VV, Pavlova TV, Kudryavtseva AV, Beniaminov AD, Belova AA, Bondarenko YN, Danilets RO, Glukhov AI, Kondratov AG, Alexeyenko A, Alekseev BY, Klein G, Senchenko VN, Kashuba VI. Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. DISEASE MARKERS 2015; 2015:241301. [PMID: 26491211 PMCID: PMC4602334 DOI: 10.1155/2015/241301] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 12/30/2022]
Abstract
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - Eugenia E. Rosenberg
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ganna V. Gerashchenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Vasily V. Gordiyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anastasia A. Belova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Bondarenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Rostislav O. Danilets
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Alexander I. Glukhov
- Department of Molecular Biology, Kurchatov NBIC Centre NRC “Kurchatov Institute”, Moscow 123182, Russia
| | - Aleksandr G. Kondratov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Andrey Alexeyenko
- Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden
| | - Boris Y. Alekseev
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - George Klein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Vera N. Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
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12
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