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Chailapakul P, Maeda J, Kato TA. ATM dysfunction in Chinese hamster XRCC8 mutants. Biochem Biophys Res Commun 2024; 736:150491. [PMID: 39142236 DOI: 10.1016/j.bbrc.2024.150491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
XRCC8 is a member of the X-ray cross-complementing (XRCC) family, whose responsible gene has not been identified. Previous studies suggested ATM and other genes were potential candidates for XRCC8, but this was not confirmed. In this study, we characterized three V79-derived XRCC8 mutant cells: V-C4, V-E5, and V-G8. Western blot analysis showed reduced expression of the ATM protein in three XRCC8 mutants, and radiation-induced phosphorylated ATM foci were not detected by fluorescence immunocytochemistry. Both ATM knockout cells and XRCC8 mutants exhibited hypersensitivity to camptothecin. Through a cell fusion-based complementation test, we found that XRCC8 mutants were complemented by ATM-proficient cells, but not by ATM knockout cells, in terms of camptothecin sensitivity. Comprehensive sequencing of the ATM genome in XRCC8 mutants revealed unique mutations in each mutant. These results suggest that XRCC8 mutants carry ATM mutations, and their ATM is not properly functional, despite protein expression being detected. This is similar to missense mutations in some Ataxia Telangiectasia patients.
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Affiliation(s)
- Piyawan Chailapakul
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Junko Maeda
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Takamitsu A Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Amandi ARD, Jabbarpour N, Shiva S, Bonyadi M. Identification of Two Novel Pathogenic Variants of the ATM Gene in the Iranian-Azeri Turkish Ethnic Group by Applying Whole Exome Sequencing. Curr Genomics 2023; 24:345-353. [PMID: 38327652 PMCID: PMC10845066 DOI: 10.2174/0113892029268949231104165301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 02/09/2024] Open
Abstract
Background The ATM gene encodes a multifunctional kinase involved in important cellular functions, such as checkpoint signaling and apoptosis, in response to DNA damage. Bi-allelic pathogenic variants in this gene cause Ataxia Telangiectasia (AT), while carriers of ATM pathogenic variants are at increased risk of cancer depending on the pathogenicity of the variant they carry. Identifying pathogenic variants can aid in the management of the disease in carriers. Methods Whole-exome sequencing (WES) was performed on three unrelated patients from the Iranian-Azeri Turkish ethnic group referred to a genetic center for analysis. WES was also conducted on 400 individuals from the same ethnic group to determine the frequencies of all ATM variants. Blood samples were collected from the patients and their family members for DNA extraction, and PCR-Sanger sequencing was performed to confirm the WES results. Results The first proband with AT disease had two novel compound heterozygote variants (c.2639-2A>T, c.8708delC) in the ATM gene revealed by WES analysis, which was potentially/likely pathogenic. The second proband with bi-lateral breast cancer had a homozygous pathogenic variant (c.6067G>A) in the ATM gene identified by WES analysis. The third case with a family history of cancer had a heterozygous synonymous pathogenic variant (c.7788G>A) in the ATM gene found by WES analysis. Sanger sequencing confirmed the WES results, and bioinformatics analysis of the mutated ATM RNA and protein structure added evidence for the potential pathogenicity of the novel variants. WES analysis of the cohort revealed 38 different variants, including a variant (rs1800057, ATM:c.3161C>G, p.P1054R) associated with prostate cancer that had a higher frequency in our cohort. Conclusion Genetic analysis of three unrelated families with ATM-related disorders discovered two novel pathogenic variants. A homozygous missense pathogenic variant was identified in a woman with bi-lateral breast cancer, and a synonymous but pathogenic variant was found in a family with a history of different cancers.
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Affiliation(s)
- Amir-Reza Dalal Amandi
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Neda Jabbarpour
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Shadi Shiva
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Bonyadi
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
- Center of Excellence for Biodiversity, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Stratification of Oligometastatic Prostate Cancer Patients by Liquid Biopsy: Clinical Insights from a Pilot Study. Biomedicines 2022; 10:biomedicines10061321. [PMID: 35740343 PMCID: PMC9219949 DOI: 10.3390/biomedicines10061321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/29/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023] Open
Abstract
We propose a pilot, prospective, translational study with the aim of identifying possible molecular markers underlying metastatic prostate cancer (PC) evolution with the use of liquid biopsy. Twenty-eight castrate sensitive, oligometastatic PC patients undergoing bone and/or nodal stereotactic body radiotherapy (SBRT) were recruited. Peripheral blood samples were collected before the commencement of SBRT, then they were processed for circulating cell free DNA (cfDNA) extraction. Deep targeted sequencing was performed using a custom gene panel. The primary endpoint was to identify differences in the molecular contribution between the oligometastatic and polymetastatic evolution of PC to same-first oligo-recurrent disease presentation. Seventy-seven mutations were detected in 25/28 cfDNA samples: ATM in 14 (50%) cases, BRCA2 11 (39%), BRCA1 6 (21%), AR 13 (46%), ETV4, and ETV6 2 (7%). SBRT failure was associated with an increased risk of harboring the BRCA1 mutation (OR 10.5) (p = 0.043). The median cfDNA concentration was 24.02 ng/mL for ATM mutation carriers vs. 40.04 ng/mL for non-carriers (p = 0.039). Real-time molecular characterization of oligometastatic PC may allow for the identification of a true oligometastatic phenotype, with a stable disease over a long time being more likely to benefit from local, curative treatments or the achievement of long-term disease control. A prospective validation of our promising findings is desirable for a better understanding of the real impact of liquid biopsy in detecting tumor aggressiveness and clonal evolution.
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Clinical Multigene Testing for Prostate Cancer. Urol Clin North Am 2021; 48:297-309. [PMID: 34210486 DOI: 10.1016/j.ucl.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Germline genetic testing for prostate cancer (PC) is increasingly important as the clinical utility of germline variants in this patient population is understood better. To better characterize the clinical landscape of germline testing in PC, published clinical cohorts of PC who underwent clinical germline genetic analysis at point of care are reviewed. Limitations and heterogeneity of these cohorts are highlighted and pathogenic results with established or potential clinical utility in PC noted. The need for additional germline genetic studies is underscored, because the number of PC patients studied lags greatly behind the high prevalence of the disease.
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The association of three DNA repair genes polymorphisms on the frequency of chromosomal alterations detected by fluorescence in situ hybridization. Int Arch Occup Environ Health 2021; 94:1567-1577. [PMID: 33778923 PMCID: PMC8384795 DOI: 10.1007/s00420-021-01652-8] [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: 06/19/2020] [Accepted: 01/07/2021] [Indexed: 10/26/2022]
Abstract
PURPOSE Gas station workers (GSWs) are exposed to carcinogenic agents. The aim was to study the association of high somatic chromosome alterations (CAs) rates in the blood of GSWs and the polymorphisms of three genes playing a role in DNA double-strand break repair. METHODS This is a cross-sectional study with 114 GSWs and 115 age-matched controls. Cytogenetic analyses, blood exams, medical interviews and genotypes for RAD51/G135C (rs1801320), ATM/P1054R (rs1800057) and CHEK2/T470C (rs17879961) genes were performed. RESULTS The CA rate in GSWs was 9.8 CAs/1000 metaphases, and 19.1% of the workers had > 10 CAs per 1000 metaphases (group two). GSWs had decreased levels of monocytes (P = 0.024) in their blood exams. The number of variant alleles of the RAD51/G135C polymorphism was higher in GSWs (P = 0.011) compared to the controls, and were associated with enhanced number of CAs per worker (P = 0.008). No allele variant was found for CHEK2/T470C in this study. CONCLUSION The RAD51/G135C polymorphism appears to be related to genome instability in gas station workers. Increasing the knowledge of DNA repair gene variations involved in maintaining genomic stability in GSWs may be crucial for future cancer prevention.
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Bensouilah FZ, Chellat-Rezgoune D, Garcia-Gonzalez MA, Carrera N, Abadi N, Dahdouh A, Satta D. Association of single nucleotide polymorphisms with renal cell carcinoma in Algerian population. AFRICAN JOURNAL OF UROLOGY 2020. [DOI: 10.1186/s12301-020-00055-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Renal cell carcinoma (RCC) is a common malignant tumor of the urinary system. The etiology of RCC is a complex interaction between environmental and multigenetic factors. Genome-wide association studies have identified new susceptibility risk loci for RCC. We examined associations of genetic variants of genes that are involved in metabolism, DNA repair and oncogenes with renal cancer risk. A total of 14 single nucleotide polymorphisms (SNPs) in 11 genes (VEGF, VHL, ATM, FAF1, LRRIQ4, RHOBTB2, OBFC1, DPF3, ALDH9A1 and EPAS1) were examined.
Methods
The current case–control study included 87 RCC patients and 114 controls matched for age, gender and ethnic origin. The 14 tag-SNPs were genotyped by Sequenom MassARRAY® iPLEX using blood genomic DNA.
Results
Genotype CG and allele G of ATM rs1800057 were significantly associated with RCC susceptibility (p = 0.043; OR = 8.47; CI = 1.00–71.76). Meanwhile, we found that genotype AA of rs67311347 polymorphism could increase the risk of RCC (p = 0.03; OR = 2.95; IC = 1.10–7.89). While, genotype TT and T allele of ALDH9A1 rs3845536 were observed to approach significance for a protective role against RCC (p = 0.007; OR = 0.26; CI = 0.09–0.70).
Conclusion
Our results indicate that ATM rs1800057 may have an effect on the risk of RCC, and suggest that ALDH9A1 was a protective factor against RCC in Algerian population.
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Giri VN, Knudsen KE, Kelly WK, Cheng HH, Cooney KA, Cookson MS, Dahut W, Weissman S, Soule HR, Petrylak DP, Dicker AP, AlDubayan SH, Toland AE, Pritchard CC, Pettaway CA, Daly MB, Mohler JL, Parsons JK, Carroll PR, Pilarski R, Blanco A, Woodson A, Rahm A, Taplin ME, Polascik TJ, Helfand BT, Hyatt C, Morgans AK, Feng F, Mullane M, Powers J, Concepcion R, Lin DW, Wender R, Mark JR, Costello A, Burnett AL, Sartor O, Isaacs WB, Xu J, Weitzel J, Andriole GL, Beltran H, Briganti A, Byrne L, Calvaresi A, Chandrasekar T, Chen DYT, Den RB, Dobi A, Crawford ED, Eastham J, Eggener S, Freedman ML, Garnick M, Gomella PT, Handley N, Hurwitz MD, Izes J, Karnes RJ, Lallas C, Languino L, Loeb S, Lopez AM, Loughlin KR, Lu-Yao G, Malkowicz SB, Mann M, Mille P, Miner MM, Morgan T, Moreno J, Mucci L, Myers RE, Nielsen SM, O’Neil B, Pinover W, Pinto P, Poage W, Raj GV, Rebbeck TR, Ryan C, Sandler H, Schiewer M, Scott EMD, Szymaniak B, Tester W, Trabulsi EJ, Vapiwala N, Yu EY, Zeigler-Johnson C, Gomella LG. Implementation of Germline Testing for Prostate Cancer: Philadelphia Prostate Cancer Consensus Conference 2019. J Clin Oncol 2020; 38:2798-2811. [PMID: 32516092 PMCID: PMC7430215 DOI: 10.1200/jco.20.00046] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Germline testing (GT) is a central feature of prostate cancer (PCA) treatment, management, and hereditary cancer assessment. Critical needs include optimized multigene testing strategies that incorporate evolving genetic data, consistency in GT indications and management, and alternate genetic evaluation models that address the rising demand for genetic services. METHODS A multidisciplinary consensus conference that included experts, stakeholders, and national organization leaders was convened in response to current practice challenges and to develop a genetic implementation framework. Evidence review informed questions using the modified Delphi model. The final framework included criteria with strong (> 75%) agreement (Recommend) or moderate (50% to 74%) agreement (Consider). RESULTS Large germline panels and somatic testing were recommended for metastatic PCA. Reflex testing-initial testing of priority genes followed by expanded testing-was suggested for multiple scenarios. Metastatic disease or family history suggestive of hereditary PCA was recommended for GT. Additional family history and pathologic criteria garnered moderate consensus. Priority genes to test for metastatic disease treatment included BRCA2, BRCA1, and mismatch repair genes, with broader testing, such as ATM, for clinical trial eligibility. BRCA2 was recommended for active surveillance discussions. Screening starting at age 40 years or 10 years before the youngest PCA diagnosis in a family was recommended for BRCA2 carriers, with consideration in HOXB13, BRCA1, ATM, and mismatch repair carriers. Collaborative (point-of-care) evaluation models between health care and genetic providers was endorsed to address the genetic counseling shortage. The genetic evaluation framework included optimal pretest informed consent, post-test discussion, cascade testing, and technology-based approaches. CONCLUSION This multidisciplinary, consensus-driven PCA genetic implementation framework provides novel guidance to clinicians and patients tailored to the precision era. Multiple research, education, and policy needs remain of importance.
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Affiliation(s)
- Veda N. Giri
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - William K. Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Heather H. Cheng
- Department of Medicine, University of Washington, and Fred Hutchinson Cancer Research Center, Division of Clinical Research, Seattle, WA
| | - Kathleen A. Cooney
- Duke University School of Medicine and Duke Cancer Institute, Durham, NC
| | | | - William Dahut
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | - Adam P. Dicker
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Amanda E. Toland
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Colin C. Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | | | | | | | - Peter R. Carroll
- Department of Urology, University of California, San Francisco, San Francisco, CA
| | - Robert Pilarski
- James Comprehensive Cancer Center and Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Amie Blanco
- University of California, San Francisco, Cancer Genetics and Prevention Program, San Francisco, CA
| | - Ashley Woodson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alanna Rahm
- Center for Health Research, Genomic Medicine Institute, Geisinger, Danville, PA
| | | | | | | | - Colette Hyatt
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Felix Feng
- Departments of Radiation Oncology, Urology, and Medicine, University of California, San Francisco, San Francisco, CA
| | | | - Jacqueline Powers
- University of Pennsylvania, Basser Center for BRCA, Philadelphia, PA
| | | | | | | | - James Ryan Mark
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Anthony Costello
- Urology at Royal Melbourne Hospital, North Melbourne, VIC, Australia
| | | | | | | | - Jianfeng Xu
- North Shore University Health System, Evanston, IL
| | | | | | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alberto Briganti
- Unit of Urology, Division of Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Anne Calvaresi
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Thenappan Chandrasekar
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Robert B. Den
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Albert Dobi
- Henry Jackson Foundation for the Advancement of Military Medicine, Center for Prostate Disease Research, Department of Surgery, Uniformed Services University and the Walter Reed National Military Medical Center, Bethesda, MD
| | | | - James Eastham
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Marc Garnick
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | | | - Nathan Handley
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Mark D. Hurwitz
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Joseph Izes
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Costas Lallas
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Lucia Languino
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Stacy Loeb
- Department of Urology and Population Health, New York University and Manhattan Veterans Affairs, New York, NY
| | - Ana Maria Lopez
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Grace Lu-Yao
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Mark Mann
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Patrick Mille
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | | | | | - Lorelei Mucci
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston MA
| | - Ronald E. Myers
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Brock O’Neil
- University of Utah, Huntsman Cancer Institute, Salt Lake City, UT
| | | | - Peter Pinto
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Wendy Poage
- Prostate Conditions Education Council, Elizabeth, CO
| | - Ganesh V. Raj
- University of Texas Southwestern Medical Center at Dallas, Dallas, TX
| | - Timothy R. Rebbeck
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston MA
| | - Charles Ryan
- University of Minnesota and Masonic Cancer Center, Madison, WI
| | | | - Matthew Schiewer
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | | | - William Tester
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Edouard J. Trabulsi
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Evan Y. Yu
- University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Charnita Zeigler-Johnson
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Leonard G. Gomella
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
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Swift SL, Lang SH, White H, Misso K, Kleijnen J, Quek RG. Effect of DNA damage response mutations on prostate cancer prognosis: a systematic review. Future Oncol 2019; 15:3283-3303. [PMID: 31535940 DOI: 10.2217/fon-2019-0298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The prognosis of men with prostate cancer (PC) with mutations in DNA damage response (DDR) genes undergoing different treatments is unclear. This systematic review compared clinical outcomes in PC patients with DDR mutations (DDR+) versus no mutations (DDR-). 14 resources plus gray literature were searched for studies in PC and subgroups (castration-resistant PC, metastatic PC and metastatic castration-resistant PC) by DDR gene (ATM, ATR, BRCA1, BRCA2, CHEK2, FANCA, MLH1, MRE11A, NBN, PALB2, RAD51C) mutation status. From 11,648 records, 26 studies were included. For mCRPC, six studies reported comparative efficacy for key outcomes. Improvements in several clinical outcomes were observed for DDR+ (vs DDR-) after PARP inhibitor therapy or immunotherapy. DDR+ PC patients may have improved outcomes depending on the treatment they undergo.
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Affiliation(s)
| | - Shona H Lang
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Heath White
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Kate Misso
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Jos Kleijnen
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK.,School for Public Health & Primary Care, Maastricht University, Maastricht, 6211 LK, The Netherlands
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Lang SH, Swift SL, White H, Misso K, Kleijnen J, Quek RG. A systematic review of the prevalence of DNA damage response gene mutations in prostate cancer. Int J Oncol 2019; 55:597-616. [PMID: 31322208 PMCID: PMC6685596 DOI: 10.3892/ijo.2019.4842] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023] Open
Abstract
Several ongoing international prostate cancer (PC) clinical trials are exploring therapies that target the DNA damage response (DDR) pathway. This systematic review summarizes the prevalence of DDR mutation carriers in the unselected (general) PC and familial PC populations. A total of 11 electronic databases, 10 conference proceedings, and grey literature sources were searched from their inception to December 2017. Studies reporting the prevalence of somatic and/or germline DDR mutations were summarized. Metastatic PC (mPC), castration‑resistant PC (CRPC) and metastatic CRPC (mCRPC) subgroups were included. A total of 11,648 records were retrieved, and 80 studies (103 records) across all PC populations were included; 59 records were of unselected PC and 13 records of familial PC. Most data were available for DDR panels (n=12 studies), ataxia telangiectasia mutated (ATM; n=13), breast cancer susceptibility gene (BRCA)1 (n=14) and BRCA2 (n=20). ATM, BRCA2 and partner and localizer of BRCA2 (PALB2) had the highest mutation rates (≥4%). Median prevalence rates for DDR germline mutations were 18.6% in PC (range, 17.2‑19%; three studies, n=1,712), 11.6% in mPC (range, 11.4‑11.8%; two studies, n=1,261) and 8.3% in mCRPC (range, 7.5‑9.1%; two studies, n=738). Median prevalence rates for DDR somatic mutations were 10.7% in PC (range, 4.9‑22%; three studies, n=680), 13.2% in mPC (range, 10‑16.4%; two studies, n=105) and not reported (NR) in mCRPC. The prevalence of DDR germline and/or somatic mutations was 27% in PC (one study, n=221), 22.67% in mCRPC (one study, n=150) and NR in mPC. In familial PC, median mutation prevalence was 12.1% (range, 7.3‑16.9%) for germline DDR (two studies, n=315) and 3.7% (range, 1.3‑7.9%) for BRCA2 (six studies, n=945). In total, 88% of studies were at a high risk of bias. The prevalence of DDR gene mutations in PC varied widely within somatic subgroups depending on study size, genetic screening techniques, DDR mutation definition and PC diagnosis; somatic and/or germline DDR mutation prevalence was in the range of 23‑27% in PC. These findings support DDR mutation testing for all patients with PC (including those with mCRPC). With the advent of the latest clinical practice PC guidelines highlighting the importance of DDR mutation screening, and ongoing mCRPC clinical trials evaluating DDR mutation‑targeted drugs, future larger epidemiological studies are warranted to further quantify the international burden of DDR mutations in PC.
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Affiliation(s)
| | | | | | - Kate Misso
- Information Department, Kleijnen Systematic Reviews Ltd., Escrick, York YO19 6FD, UK
| | - Jos Kleijnen
- Reviews Department
- School for Public Health and Primary Care, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Ruben G.W. Quek
- Health Economics and Outcomes Research, Pfizer Inc., San Francisco, CA 94105, USA
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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Schumacher FR, Al Olama AA, Berndt SI, Benlloch S, Ahmed M, Saunders EJ, Dadaev T, Leongamornlert D, Anokian E, Cieza-Borrella C, Goh C, Brook MN, Sheng X, Fachal L, Dennis J, Tyrer J, Muir K, Lophatananon A, Stevens VL, Gapstur SM, Carter BD, Tangen CM, Goodman PJ, Thompson IM, Batra J, Chambers S, Moya L, Clements J, Horvath L, Tilley W, Risbridger GP, Gronberg H, Aly M, Nordström T, Pharoah P, Pashayan N, Schleutker J, Tammela TLJ, Sipeky C, Auvinen A, Albanes D, Weinstein S, Wolk A, Håkansson N, West CML, Dunning AM, Burnet N, Mucci LA, Giovannucci E, Andriole GL, Cussenot O, Cancel-Tassin G, Koutros S, Beane Freeman LE, Sorensen KD, Orntoft TF, Borre M, Maehle L, Grindedal EM, Neal DE, Donovan JL, Hamdy FC, Martin RM, Travis RC, Key TJ, Hamilton RJ, Fleshner NE, Finelli A, Ingles SA, Stern MC, Rosenstein BS, Kerns SL, Ostrer H, Lu YJ, Zhang HW, Feng N, Mao X, Guo X, Wang G, Sun Z, Giles GG, Southey MC, MacInnis RJ, FitzGerald LM, Kibel AS, Drake BF, Vega A, Gómez-Caamaño A, Szulkin R, Eklund M, Kogevinas M, Llorca J, Castaño-Vinyals G, Penney KL, Stampfer M, Park JY, Sellers TA, Lin HY, Stanford JL, Cybulski C, Wokolorczyk D, Lubinski J, Ostrander EA, Geybels MS, Nordestgaard BG, Nielsen SF, Weischer M, Bisbjerg R, Røder MA, Iversen P, Brenner H, Cuk K, Holleczek B, Maier C, Luedeke M, Schnoeller T, Kim J, Logothetis CJ, John EM, Teixeira MR, Paulo P, Cardoso M, Neuhausen SL, Steele L, Ding YC, De Ruyck K, De Meerleer G, Ost P, Razack A, Lim J, Teo SH, Lin DW, Newcomb LF, Lessel D, Gamulin M, Kulis T, Kaneva R, Usmani N, Singhal S, Slavov C, Mitev V, Parliament M, Claessens F, Joniau S, Van den Broeck T, Larkin S, Townsend PA, Aukim-Hastie C, Gago-Dominguez M, Castelao JE, Martinez ME, Roobol MJ, Jenster G, van Schaik RHN, Menegaux F, Truong T, Koudou YA, Xu J, Khaw KT, Cannon-Albright L, Pandha H, Michael A, Thibodeau SN, McDonnell SK, Schaid DJ, Lindstrom S, Turman C, Ma J, Hunter DJ, Riboli E, Siddiq A, Canzian F, Kolonel LN, Le Marchand L, Hoover RN, Machiela MJ, Cui Z, Kraft P, Amos CI, Conti DV, Easton DF, Wiklund F, Chanock SJ, Henderson BE, Kote-Jarai Z, Haiman CA, Eeles RA. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. Nat Genet 2018; 50:928-936. [PMID: 29892016 PMCID: PMC6568012 DOI: 10.1038/s41588-018-0142-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/05/2018] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data from a custom high-density array of 46,939 PrCa cases and 27,910 controls of European ancestry with previously genotyped data of 32,255 PrCa cases and 33,202 controls of European ancestry. Our analysis identified 62 novel loci associated (P < 5.0 × 10-8) with PrCa and one locus significantly associated with early-onset PrCa (≤55 years). Our findings include missense variants rs1800057 (odds ratio (OR) = 1.16; P = 8.2 × 10-9; G>C, p.Pro1054Arg) in ATM and rs2066827 (OR = 1.06; P = 2.3 × 10-9; T>G, p.Val109Gly) in CDKN1B. The combination of all loci captured 28.4% of the PrCa familial relative risk, and a polygenic risk score conferred an elevated PrCa risk for men in the ninetieth to ninety-ninth percentiles (relative risk = 2.69; 95% confidence interval (CI): 2.55-2.82) and first percentile (relative risk = 5.71; 95% CI: 5.04-6.48) risk stratum compared with the population average. These findings improve risk prediction, enhance fine-mapping, and provide insight into the underlying biology of PrCa1.
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Affiliation(s)
- Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA.
| | - Ali Amin Al Olama
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sara Benlloch
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Institute of Cancer Research, London, UK
| | | | | | | | | | | | | | - Chee Goh
- Institute of Cancer Research, London, UK
| | | | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
- Department of Oncology, Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jonathan Tyrer
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Brian D Carter
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital-Medical Center, San Antonio, TX, USA
| | - Jyotsna Batra
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Qld, Translational Research Institute, Brisbane, Queensland, Australia
| | - Suzanne Chambers
- Menzies Health Institute of Queensland, Griffith University, Nathan, Queensland, Australia
- Cancer Council Queensland, Fortitude Valley, Queensland, Australia
| | - Leire Moya
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Qld, Translational Research Institute, Brisbane, Queensland, Australia
| | - Judith Clements
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Qld, Translational Research Institute, Brisbane, Queensland, Australia
| | - Lisa Horvath
- Chris O'Brien Lifehouse (COBLH), Camperdown, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Centre, University of Adelaide, Adelaide, South Australia, Australia
| | - Gail P Risbridger
- Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Program, Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Markus Aly
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Nordström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences at Danderyds Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Paul Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge, UK
| | - Nora Pashayan
- Department of Oncology, Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, Turku, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences, University of Tampere, Tampere, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Catharine M L West
- Division of Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Science Centre and Christie NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge, UK
| | - Neil Burnet
- Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, University of Cambridge, Cambridge, UK
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Olivier Cussenot
- UPMC Sorbonne Universités, GRC no. 5 ONCOTYPE-URO, Tenon Hospital, Paris, France
- CeRePP, Tenon Hospital, Paris, France
| | - Géraldine Cancel-Tassin
- UPMC Sorbonne Universités, GRC no. 5 ONCOTYPE-URO, Tenon Hospital, Paris, France
- CeRePP, Tenon Hospital, Paris, France
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Torben Falck Orntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK, Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK, Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Richard M Martin
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Robert J Hamilton
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Neil E Fleshner
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sue Ann Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Barry S Rosenstein
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Xin Guo
- Department of Urology, First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Guomin Wang
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, China
| | - Zan Sun
- People's Hospital of Liaoning Province, People's Hospital of China Medical University, Shenyang, China
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J MacInnis
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | - Bettina F Drake
- Washington University School of Medicine, St. Louis, MO, USA
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Robert Szulkin
- Division of Family Medicine, Department of Neurobiology, Care Science and Society, Karolinska, Institutet, Huddinge, Sweden
- Scandinavian Development Services, Danderyd, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Javier Llorca
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Kathryn L Penney
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meir Stampfer
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 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, Denmark
| | - Sune F Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Rasmus Bisbjerg
- Department of Urology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Martin Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Iversen
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christiane Maier
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Manuel Luedeke
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany
| | | | - Jeri Kim
- Department of Genitourinary Medical Oncology, University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research & Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Marta Cardoso
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Kim De Ruyck
- Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Gert De Meerleer
- Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Piet Ost
- Department of Radiotherapy, Ghent University Hospital, Ghent, Belgium
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Selangor, Malaysia
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Lisa F Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marija Gamulin
- Department of Oncology, Division of Medical Oncology, Urogenital Unit, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Samantha Larkin
- University of Southampton, Southampton General Hospital, Southampton, UK
| | - Paul A Townsend
- Division of Cancer Sciences, Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Center, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, University of Manchester, Manchester, UK
| | | | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Instituto de Investigación Biomédica Galicia Sur (IISGS), Complexo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Maria Elena Martinez
- Department of Family Medicine and Public Health, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | | | | | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shannon K McDonnell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Sara Lindstrom
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jing Ma
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Afshan Siddiq
- Genomics England, Queen Mary University of London, London, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Zuxi Cui
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge, UK
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Rosalind A Eeles
- Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London, UK.
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12
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Ivanov M, Laktionov K, Breder V, Chernenko P, Novikova E, Telysheva E, Musienko S, Baranova A, Mileyko V. Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions. J Transl Med 2017; 15:22. [PMID: 28137276 PMCID: PMC5282851 DOI: 10.1186/s12967-017-1125-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/19/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Next generation sequencing has a potential to revolutionize the management of cancer patients within the framework of precision oncology. Nevertheless, lack of standardization decelerated entering of the technology into the clinical testing space. Here we dissected a number of common problems of NGS diagnostics in oncology and introduced ways they can be resolved. METHODS DNA was extracted from 26 formalin fixed paraffin embedded (FFPE) specimens and processed with the TrueSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) targeting 48 cancer-related genes and sequenced in single run. Sequencing data were comparatively analyzed by several bioinformatics pipelines. RESULTS Libraries yielded sufficient coverage to detect even low prevalent mutations. We found that the number of FFPE sequence artifacts significantly correlates with pre-normalization concentration of libraries (rank correlation -0.81; p < 1e-10), thus, contributing to sample-specific variant detection cut-offs. Surprisingly, extensive validation of EGFR mutation calls by a combination of aligners and variant callers resulted in identification of two false negatives and one false positive that were due to complexity of underlying genomic change, confirmed by Sanger sequencing. Additionally, the study of the non-EGFR amplicons revealed 33 confirmed unique mutations in 17 genes, with TP53 being the most frequently mutated. Clinical relevance of these finding is discussed. CONCLUSIONS Reporting of entire mutational spectrum revealed by targeted sequencing is questionable, at least until the clinically-driven guidelines on reporting of somatic mutations are established. The standardization of sequencing protocols, especially their data analysis components, requires assay-, disease-, and, in many cases, even sample-specific customization that could be performed only in cooperation with clinicians.
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Affiliation(s)
- Maxim Ivanov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700 Russia
- Atlas Biomed Group, Moscow, 121069 Russia
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, 630090 Russia
| | - Konstantin Laktionov
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Valery Breder
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Polina Chernenko
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Ekaterina Novikova
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology (RSCRR) of the Ministry of Healthcare of the Russian Federation (Russian Scientific Center of Roentgenoradiology), Moscow, 117485 Russia
| | - Ekaterina Telysheva
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology (RSCRR) of the Ministry of Healthcare of the Russian Federation (Russian Scientific Center of Roentgenoradiology), Moscow, 117485 Russia
| | | | - Ancha Baranova
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700 Russia
- Atlas Biomed Group, Moscow, 121069 Russia
- Research Centre for Medical Genetics, Moscow, 115478 Russia
- Center for the Study of Chronic Metabolic and Rare Diseases, School of System Biology, George Mason University, Fairfax, VA USA
| | - Vladislav Mileyko
- Atlas Biomed Group, Moscow, 121069 Russia
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, 630090 Russia
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13
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Walsh MF, Nathanson KL, Couch FJ, Offit K. Genomic Biomarkers for Breast Cancer Risk. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:1-32. [PMID: 26987529 DOI: 10.1007/978-3-319-22909-6_1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clinical risk assessment for cancer predisposition includes a three-generation pedigree and physical examination to identify inherited syndromes. Additionally genetic and genomic biomarkers may identify individuals with a constitutional basis for their disease that may not be evident clinically. Genomic biomarker testing may detect molecular variations in single genes, panels of genes, or entire genomes. The strength of evidence for the association of a genomic biomarker with disease risk may be weak or strong. The factors contributing to clinical validity and utility of genomic biomarkers include functional laboratory analyses and genetic epidemiologic evidence. Genomic biomarkers may be further classified as low, moderate or highly penetrant based on the likelihood of disease. Genomic biomarkers for breast cancer are comprised of rare highly penetrant mutations of genes such as BRCA1 or BRCA2, moderately penetrant mutations of genes such as CHEK2, as well as more common genomic variants, including single nucleotide polymorphisms, associated with modest effect sizes. When applied in the context of appropriate counseling and interpretation, identification of genomic biomarkers of inherited risk for breast cancer may decrease morbidity and mortality, allow for definitive prevention through assisted reproduction, and serve as a guide to targeted therapy .
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Affiliation(s)
- Michael F Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 10065, New York, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 19104, Philadelphia, PA, USA
| | - Fergus J Couch
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, 55905, Rochester, MN, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 10065, New York, NY, USA.
- Program in Cancer Biology and Genetics, Sloan Kettering Institute; Departments of Medicine and Public Health, Weill Cornell Medical College, 10065, New York, NY, USA.
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Berlin A, Lalonde E, Sykes J, Zafarana G, Chu KC, Ramnarine VR, Ishkanian A, Sendorek DHS, Pasic I, Lam WL, Jurisica I, van der Kwast T, Milosevic M, Boutros PC, Bristow RG. NBN gain is predictive for adverse outcome following image-guided radiotherapy for localized prostate cancer. Oncotarget 2015; 5:11081-90. [PMID: 25415046 PMCID: PMC4294365 DOI: 10.18632/oncotarget.2404] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/26/2014] [Indexed: 12/31/2022] Open
Abstract
Despite the use of clinical prognostic factors (PSA, T-category and Gleason score), 20-60% of localized prostate cancers (PCa) fail primary local treatment. Herein, we determined the prognostic importance of main sensors of the DNA damage response (DDR): MRE11A, RAD50, NBN, ATM, ATR and PRKDC. We studied copy number alterations in DDR genes in localized PCa treated with image-guided radiotherapy (IGRT; n=139) versus radical prostatectomy (RadP; n=154). In both cohorts, NBN gains were the most frequent genomic alteration (14.4 and 11% of cases, respectively), and were associated with overall tumour genomic instability (p<0.0001). NBN gains were the only significant predictor of 5yrs biochemical relapse-free rate (bRFR) following IGRT (46% versus 77%; p=0.00067). On multivariate analysis, NBN gain remained a significant independent predictor of bRFR after adjusting for known clinical prognostic variables (HR=3.28, 95% CI 1.56–6.89, Wald p-value=0.0017). No DDR-sensing gene was prognostic in the RadP cohort. In vitro studies correlated NBN gene overexpression with PCa cells radioresistance. In conclusion, NBN gain predicts for decreased bRFR in IGRT, but not in RadP patients. If validated independently, Nibrin gains may be the first PCa predictive biomarker to facilitate local treatment decisions using precision medicine approaches with surgery or radiotherapy.
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Affiliation(s)
- Alejandro Berlin
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Emilie Lalonde
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jenna Sykes
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada
| | - Gaetano Zafarana
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada
| | - Kenneth C Chu
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Varune R Ramnarine
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adrian Ishkanian
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dorota H S Sendorek
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada
| | - Ivan Pasic
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada
| | - Wan L Lam
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada. Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Igor Jurisica
- The Techna Institute, University Health Network, Toronto, ON, Canada
| | - Theo van der Kwast
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada
| | - Michael Milosevic
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Robert G Bristow
- Departments of Radiation Oncology, Medical Biophysics, Medical Oncology, Laboratory Medicine and Pathology, Pharmacology & Toxicology and Biostatistics, Computer Science, University of Toronto, Toronto, ON, Canada. Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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15
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Felgueiras J, Fardilha M. Phosphoprotein phosphatase 1-interacting proteins as therapeutic targets in prostate cancer. World J Pharmacol 2014; 3:120-139. [DOI: 10.5497/wjp.v3.i4.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer is a major public health concern worldwide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still an urgent need for reliable biomarkers that could overcome the lack of cancer-specificity of prostate-specific antigen, as well as alternative therapeutic targets for advanced metastatic cases. Reversible phosphorylation of proteins is a post-translational modification critical to the regulation of numerous cellular processes. Phosphoprotein phosphatase 1 (PPP1) is a major serine/threonine phosphatase, whose specificity is determined by its interacting proteins. These interactors can be PPP1 substrates, regulators, or even both. Deregulation of this protein-protein interaction network alters cell dynamics and underlies the development of several cancer hallmarks. Therefore, the identification of PPP1 interactome in specific cellular context is of crucial importance. The knowledge on PPP1 complexes in prostate cancer remains scarce, with only 4 holoenzymes characterized in human prostate cancer models. However, an increasing number of PPP1 interactors have been identified as expressed in human prostate tissue, including the tumor suppressors TP53 and RB1. Efforts should be made in order to identify the role of such proteins in prostate carcinogenesis, since only 26 have yet well-recognized roles. Here, we revise literature and human protein databases to provide an in-depth knowledge on the biological significance of PPP1 complexes in human prostate carcinogenesis and their potential use as therapeutic targets for the development of new therapies for prostate cancer.
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16
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Gu Y, Yu Y, Ai L, Shi J, Liu X, Sun H, Liu Y. Association of the ATM gene polymorphisms with papillary thyroid cancer. Endocrine 2014; 45:454-61. [PMID: 23925578 DOI: 10.1007/s12020-013-0020-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/18/2013] [Indexed: 01/02/2023]
Abstract
Papillary thyroid cancer (PTC) is the most common type of thyroid cancer, yet few genetic markers of PTC risk useful for screening exist. Our study aimed to evaluate the association between single nucleotide polymorphisms (SNPs) of the ataxia telangiectasia mutated (ATM) gene and PTC risk. 358 patients with PTC and 360 healthy controls were included in the case-control study. Four ATM SNPs (rs664677, rs373759, rs4988099, and rs189037) were genotyped by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). The analysis of genetic data was performed using the SNPStats program. The allele frequencies and genotype distributions of the four ATM SNPs were not different between PTC patients and controls. We did not observe any tendency of increasing the frequency of the risk allele from controls, patients without metastasis to patients with metastasis (P(trend) > 0.05). Interestingly, the AG genotype of rs373759 was associated with PTC risk under an overdominant model of inheritance (adjusted OR = 1.38; 95 % CI, 1.03-1.87; P = 0.03). No haplotype was observed to be significantly associated with PTC risk. Our results suggest that heterozygosity for the ATM rs373759 polymorphism may be a potential risk factor for PTC.
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Affiliation(s)
- Yulu Gu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
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17
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Proud C. Radiogenomics: The Promise of Personalized Treatment in Radiation Oncology? Clin J Oncol Nurs 2014; 18:185-9. [DOI: 10.1188/14.cjon.185-189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Gu Y, Liu X, Yu Y, Shi J, Ai L, Sun H, Kanu JS, Wang C, Liu Y. Association of ATM Gene Polymorphism with PTC Metastasis in Female Patients. Int J Endocrinol 2014; 2014:370825. [PMID: 25386189 PMCID: PMC4216711 DOI: 10.1155/2014/370825] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/30/2014] [Indexed: 11/30/2022] Open
Abstract
Ataxia telangiectasia mutated (ATM) gene is critical in the process of recognizing and repairing DNA lesions and is related to invasion and metastasis of malignancy. The incidence rate of papillary thyroid cancer (PTC) has increased for several decades and is higher in females than males. In this study, we want to investigate whether ATM polymorphisms are associated with gender-specific metastasis of PTC. 358 PTC patients in Northern China, including 109 males and 249 females, were included in our study. Four ATM single nucleotide polymorphisms (SNPs) were genotyped using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). Association between genotypes and the gender-specific risk of metastasis was assessed by odds ratios (OR) and 95% confidence intervals (CI) under the unconditional logistic regression analysis. Significant associations were observed between rs189037 and metastasis of PTC in females under different models of inheritance (codominant model: OR = 0.15, 95% CI 0.04-0.56, P = 0.01 for GA versus GG and OR = 0.08, 95% CI 0.01-0.74, P = 0.03 for AA versus GG, resp.; dominant model: OR = 0.49, 95% CI 0.25-0.98, P = 0.04; overdominant model: OR = 0.47, 95% CI 0.25-0.89, P = 0.02). However, no association remained significant after Bonferroni correction. Our findings suggest a possible association between ATM rs189037 polymorphisms and metastasis in female PTCs.
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Affiliation(s)
- Yulu Gu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Xiaoli Liu
- Jilin Provincial Key Laboratory of Surgical Translational Medicine, Department of Thyroid and Parathyroid Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, China
| | - Yaqin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Jieping Shi
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Lizhe Ai
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Hui Sun
- Jilin Provincial Key Laboratory of Surgical Translational Medicine, Department of Thyroid and Parathyroid Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, China
| | - Joseph Sam Kanu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Chong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Molecular Epidemiology, School of Public Health, Jilin University, Changchun 130021, China
- *Yawen Liu:
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Chiu YT, Liu J, Tang K, Wong YC, Khanna KK, Ling MT. Inactivation of ATM/ATR DNA damage checkpoint promotes androgen induced chromosomal instability in prostate epithelial cells. PLoS One 2012; 7:e51108. [PMID: 23272087 PMCID: PMC3525593 DOI: 10.1371/journal.pone.0051108] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
The ATM/ATR DNA damage checkpoint functions in the maintenance of genetic stability and some missense variants of the ATM gene have been shown to confer a moderate increased risk of prostate cancer. However, whether inactivation of this checkpoint contributes directly to prostate specific cancer predisposition is still unknown. Here, we show that exposure of non-malignant prostate epithelial cells (HPr-1AR) to androgen led to activation of the ATM/ATR DNA damage response and induction of cellular senescence. Notably, knockdown of the ATM gene expression in HPr-1AR cells can promote androgen-induced TMPRSS2: ERG rearrangement, a prostate-specific chromosome translocation frequently found in prostate cancer cells. Intriguingly, unlike the non-malignant prostate epithelial cells, the ATM/ATR DNA damage checkpoint appears to be defective in prostate cancer cells, since androgen treatment only induced a partial activation of the DNA damage response. This mechanism appears to preserve androgen induced autophosphorylation of ATM and phosphorylation of H2AX, lesion processing and repair pathway yet restrain ATM/CHK1/CHK2 and p53 signaling pathway. Our findings demonstrate that ATM/ATR inactivation is a crucial step in promoting androgen-induced genomic instability and prostate carcinogenesis.
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Affiliation(s)
- Yung-Tuen Chiu
- Department of Anatomy, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Ji Liu
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Kaidun Tang
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Yong-Chuan Wong
- Department of Pathology, Faculty of Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Kum Kum Khanna
- Signal Transduction Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Ming-Tat Ling
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
- * E-mail:
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20
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Chen J, Pande M, Huang YJ, Wei C, Amos CI, Talseth-Palmer BA, Meldrum CJ, Chen WV, Gorlov IP, Lynch PM, Scott RJ, Frazier ML. Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. Carcinogenesis 2012; 34:299-306. [PMID: 23125224 DOI: 10.1093/carcin/bgs344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Heterogeneity in age of onset of colorectal cancer in individuals with mutations in DNA mismatch repair genes (Lynch syndrome) suggests the influence of other lifestyle and genetic modifiers. We hypothesized that genes regulating the cell cycle influence the observed heterogeneity as cell cycle-related genes respond to DNA damage by arresting the cell cycle to provide time for repair and induce transcription of genes that facilitate repair. We examined the association of 1456 single nucleotide polymorphisms (SNPs) in 128 cell cycle-related genes and 31 DNA repair-related genes in 485 non-Hispanic white participants with Lynch syndrome to determine whether there are SNPs associated with age of onset of colorectal cancer. Genotyping was performed on an Illumina GoldenGate platform, and data were analyzed using Kaplan-Meier survival analysis, Cox regression analysis and classification and regression tree (CART) methods. Ten SNPs were independently significant in a multivariable Cox proportional hazards regression model after correcting for multiple comparisons (P < 5 × 10(-4)). Furthermore, risk modeling using CART analysis defined combinations of genotypes for these SNPs with which subjects could be classified into low-risk, moderate-risk and high-risk groups that had median ages of colorectal cancer onset of 63, 50 and 42 years, respectively. The age-associated risk of colorectal cancer in the high-risk group was more than four times the risk in the low-risk group (hazard ratio = 4.67, 95% CI = 3.16-6.92). The additional genetic markers identified may help in refining risk groups for more tailored screening and follow-up of non-Hispanic white patients with Lynch syndrome.
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Affiliation(s)
- Jinyun Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Xu L, Morari EC, Wei Q, Sturgis EM, Ward LS. Functional variations in the ATM gene and susceptibility to differentiated thyroid carcinoma. J Clin Endocrinol Metab 2012; 97:1913-21. [PMID: 22438227 PMCID: PMC3387410 DOI: 10.1210/jc.2011-3299] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT ATM is critical in response to ionizing radiation-induced DNA damage. OBJECTIVE Variations in ATM are hypothesized to affect individual susceptibility to thyroid cancer. Our objective was to evaluate the association between ATM polymorphisms and thyroid cancer risk. DESIGN, PARTICIPANTS, AND METHODS Six ATM single nucleotide polymorphisms (SNP) were genotyped in two independent case-control series including 592 patients with differentiated thyroid carcinoma (DTC) and 885 healthy individuals. An unconditional logistic regression model was applied to calculate odds ratios (OR) and 95% confidence intervals (CI) for each SNP with respect to risk of DTC and the combination effect of SNP on cancer risk. RESULTS The risk-allele frequencies of all the SNP were similar in the two case-control populations. Under a dominant model of inheritance, the G allele of ATM rs189037 exhibited a protective effect against DTC (adjusted OR = 0.8; 95% CI, 0.6-1.0; P = 0.04), and the G allele of rs1800057 was associated with increased risk of DTC (adjusted OR = 1.9; 95% CI, 1.1-3.1; P = 0.02). A protective haplotype (A-G-C-T-C-A) was associated with decreased risk of DTC in non-Hispanic whites (adjusted OR = 0.2; 95% CI, 0.0-0.8; P = 0.03). A significant dose-response relationship was observed between the total number of risk alleles of ATM and DTC risk (P = 0.01). Carriers of a combination of six to seven and eight to 10 risk alleles were at 30% (adjusted OR = 1.3; 95% CI, 1.0-1.7) and 50% (adjusted OR = 1.5; 95% CI, 1.1-2.1) increased risk of DTC, respectively. CONCLUSION Individual susceptibility to DTC may be attributable to polymorphisms of ATM, and the associations warrant confirmation in independent studies.
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Affiliation(s)
- Li Xu
- Departments of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Upon the tightrope in prostate cancer: two acrobats on the same tightrope to cross the finishline. Mol Cell Biochem 2011; 364:53-7. [PMID: 22200977 DOI: 10.1007/s11010-011-1204-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/15/2011] [Indexed: 01/03/2023]
Abstract
Prostate cancer is a multifactorial, multistep progressive disorder that is undruggable to date because of stumbling blocks in the standardization of therapy. It is triggered by a broad range of proteins, signaling networks and DNA damage response modulators. It is becoming increasingly apparent that DNA repair mediators have split personalities, as they are instrumental in suppressing and promoting carcinogenesis. In this article, we discuss on post-transcriptional processing of regulators of DNA damage response, and how DNA repair proteins trigger shuttling of androgen receptor. Substantial fraction of information has been added into the existing literature of ATM biology; however, the particular area of post-transcriptional processing errors and gene therapy for reprogramming of ATM has been left unaddressed in prostate cancer. It is therefore noteworthy that the facet of targeting strategy, antisense morpholino oligonucleotides chemistry, and systematic delivery of AOs has promising outlook in splice-targeted antisense-mediated therapy.
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23
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Rosenstein BS. Identification of SNPs associated with susceptibility for development of adverse reactions to radiotherapy. Pharmacogenomics 2011; 12:267-75. [PMID: 21332318 DOI: 10.2217/pgs.10.186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although cancer treatment with radiation can produce high cure rates, adverse effects often result from radiotherapy. These toxicities are manifested as damage to normal tissues and organs in the radiation field. In recognition of the substantial variation in the intrinsic response of individuals to radiation, an effort began approximately 10 years ago to discover the genetic markers, primarily SNPs, which are associated with susceptibility for the development of these adverse responses to radiation therapy. The goal of this research is to identify the SNPs that could serve as the basis of an assay to predict which cancer patients are most likely to develop complications resulting from radiotherapy. This would permit personalization and optimization of the treatment plan for each cancer patient.
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Affiliation(s)
- Barry S Rosenstein
- Department of Radiation Oncology, Mount Sinai School of Medicine, New York, NY 10029, USA.
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Meyer A, Coinac I, Bogdanova N, Dubrowinskaja N, Turmanov N, Haubold S, Schürmann P, Imkamp F, von Klot C, Merseburger AS, Machtens S, Bremer M, Hillemanns P, Kuczyk MA, Karstens JH, Serth J, Dörk T. Apoptosis gene polymorphisms and risk of prostate cancer: a hospital-based study of German patients treated with brachytherapy. Urol Oncol 2011; 31:74-81. [PMID: 21396839 DOI: 10.1016/j.urolonc.2010.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/15/2010] [Accepted: 09/21/2010] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVES Prostate cancer has a genetic component, and single nucleotide polymorphisms (SNPs) can contribute to the risk. We aimed to investigate the role of polymorphisms in 10 candidate genes with a key function in apoptosis. METHODS AND MATERIALS Eight coding SNPs were chosen in ATM (Ser49Cys), BID (Ser56Cys), CASP8 (Asp302His), CASP10 (Val410Ile), LGALS3 (Pro64His), RASSF1 (Ser133Ala), TP53 (Arg72Pro), and TP53AIP1 (Ala7Val), and two non-coding SNPs were selected in BCL2 (-938C/A) and HDM2 (SNP309). A hospital-based case-control series of 510 prostate cancer patients and 490 healthy males from Northern Germany were genotyped for these polymorphisms. RESULTS SNP rs4644 in LGALS3 showed evidence for a protective effect of the minor allele, encoding the His64 variant (OR 0.82, 95% CI 0.69;0.99, P = 0.04). Carriers were underrepresented among cases under a dominant model (OR 0.71; 95% CI 0.54;0.92; P = 0.01), and the effect appeared more pronounced in patients diagnosed before the age of 60 years (OR 0.52; 95% CI 0.31;0.85, P = 0.01). The other nine polymorphisms did not vary significantly between cases and controls, though subtle trends were noted for BCL2 (P = 0.07) and CASP10 (P = 0.08). The Asp302His variant of CASP8 tended to associate with a protective effect in the group with higher Gleason score under a dominant model (P = 0.03). Carriers of either the CASP8 or the CASP10 variants were underrepresented in the prostate cancer series (P = 0.02). CONCLUSIONS These results provide first evidence to implicate the functional Pro64His variant of galectin-3 (LGALS3) in the genetic susceptibility towards prostate cancer. The potential role of polymorphisms in BCL2, CASP8, and CASP10 merits further investigation.
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Affiliation(s)
- Andreas Meyer
- Clinic of Radiation Oncology, Hannover Medical School, Hannover, Germany
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25
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Yano K. Gene expression correlation analysis predicts involvement of high- and low-confidence risk genes in different stages of prostate carcinogenesis. Prostate 2010; 70:1746-59. [PMID: 20564324 DOI: 10.1002/pros.21210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Whole genome association studies have identified many loci associated with the risk of prostate cancer (PC). However, very few of the genes associated with these loci have been related to specific processes of prostate carcinogenesis. Therefore I inferred biological functions associated with these risk genes using gene expression correlation analysis. METHODS PC risk genes reported in the literature were classified as having high (P<10(-6)), medium (P<10(-4)), or low (P<10(-2)) statistical confidence. Correlation coefficients of the expression levels between the risk genes and other genes in cancerous prostates samples were compared against those in normal prostates using a microarray dataset from Gene Expression Omnibus. RESULTS Overall, significant decrease of correlations in PC was observed between the levels of expression of the high-confidence genes and other genes in the microarray dataset, whereas correlation between low-confidence genes and other genes in PC showed smaller decrease. Genes involved in developmental processes were significantly correlated with all risk gene categories. Ectoderm development genes, which may be related to squamous metaplasia, and genes enriched in fetal prostate stem cells (PSCs) showed strong association with the high-confidence genes. The association between the PSC genes and the low-confidence genes was weak, but genes related to neural system genes showed strong association with low-confidence genes. CONCLUSIONS The high-confidence risk genes may be associated with an early stage of prostate carcinogenesis, possibly involving PSCs and squamous metaplasia. The low-confidence genes may be involved in a later stage of carcinogenesis.
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Affiliation(s)
- Kojiro Yano
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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Borgmann K, Raabe A, Reuther S, Szymczak S, Schlomm T, Isbarn H, Gomolka M, Busjahn A, Bonin M, Ziegler A, Dikomey E. The potential role of G2- but not of G0-radiosensitivity for predisposition of prostate cancer. Radiother Oncol 2010; 96:19-24. [DOI: 10.1016/j.radonc.2010.04.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 04/09/2010] [Accepted: 04/12/2010] [Indexed: 11/30/2022]
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Deng Q, Sheng L, Su D, Zhang L, Liu P, Lu K, Ma S. Genetic polymorphisms in ATM, ERCC1, APE1 and iASPP genes and lung cancer risk in a population of southeast China. Med Oncol 2010; 28:667-72. [PMID: 20354815 DOI: 10.1007/s12032-010-9507-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 03/17/2010] [Indexed: 11/29/2022]
Abstract
Polymorphisms in DNA repair and apoptosis genes are suspected to alter the individual susceptibility to develop lung cancer. We investigated the relationship between polymorphisms in ATM (A60G), ERCC1 (Asn118Asn), APE1 (Asn148Glu) and iASPP (A67T) and the risk of developing lung cancer. A case-control study was conducted with 315 patients with lung cancer and 315 cancer-free controls, matched on age and sex. Genotypes were detected using the ABI 7500 real-time PCR system. The T/T homozygote in ERCC1 (Asn118Asn) was correlated with a strong statistically significant increased risk of developing lung cancer (adjusted OR=2.44; 95% CI=1.13-5.28; P=0.023), especially lung adenocarcinoma (adjusted OR=3.18) and small cell lung cancer (adjusted OR=6.08). For iASPP (A67T), smokers with at least one T allele (A/T+T/T) were more likely to develop lung cancer (95% CI, 1.07-2.84, P=0.026). Subjects carrying the G allele in APE1 (Asn148Glu) had a decreased risk of lung cancer (P<0.05), which showing a protective effect. Our results suggest that polymorphism Asn118Asn in ERCC1, A67T in iASPP and Asn148Glu in APE1 may associated with early onset of lung cancer as well as some specific subtype of lung cancer. Detection of these biomarkers may be helpful for screening this high-risk population for primary preventing.
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Affiliation(s)
- Qinghua Deng
- Department of Radiation Oncology, Zhejiang Cancer Hospital, 38 Banshan Road, Hangzhou, 310022, China
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28
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Rodemann HP. Molecular radiation biology: Perspectives for radiation oncology. Radiother Oncol 2009; 92:293-8. [PMID: 19726094 DOI: 10.1016/j.radonc.2009.08.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 08/15/2009] [Indexed: 12/27/2022]
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Pugh TJ, Keyes M, Barclay L, Delaney A, Krzywinski M, Thomas D, Novik K, Yang C, Agranovich A, McKenzie M, Morris WJ, Olive PL, Marra MA, Moore RA. Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients. Clin Cancer Res 2009; 15:5008-16. [PMID: 19638463 DOI: 10.1158/1078-0432.ccr-08-3357] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The presence of intrinsic radiosensitivity within prostate cancer patients may be an important factor contributing to development of radiation toxicity. We investigated whether variants in genes responsible for detecting and repairing DNA damage independently contribute to toxicity following prostate brachytherapy. EXPERIMENTAL DESIGN Genomic DNA was extracted from blood samples of 41 prostate brachytherapy patients, 21 with high and 20 with low late toxicity scores. For each patient, 242 PCR amplicons were generated containing 173 exons of eight candidate genes: ATM, BRCA1, ERCC2, H2AFX, LIG4, MDC1, MRE11A, and RAD50. These amplicons were sequenced and all sequence variants were subjected to statistical analysis to identify those associated with late radiation toxicity. RESULTS Across 41 patients, 239 sites differed from the human genome reference sequence; 170 of these corresponded to known polymorphisms. Sixty variants, 14 of them novel, affected protein coding regions and 43 of these were missense mutations. In our patient population, the high toxicity group was enriched for individuals with at least one LIG4 coding variant (P = 0.028). One synonymous variant in MDC1, rs28986317, was associated with increased radiosensitivity (P = 0.048). A missense variant in ATM, rs1800057, associated with increased prostate cancer risk, was found exclusively in two high toxicity patients but did not reach statistical significance for association with radiosensitivity (P = 0.488). CONCLUSIONS Our data revealed new germ-line sequence variants, indicating that existing sequence databases do not fully represent the full extent of sequence variation. Variants in three DNA repair genes were linked to increased radiosensitivity but require validation in larger populations.
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Affiliation(s)
- Trevor J Pugh
- Genome Sciences Centre, Provincial Prostate Brachytherapy Program, and Medical Biophysics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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Meyer A, Dörk T, Bogdanova N, Brinkhaus MJ, Wiese B, Hagemann J, Serth J, Bremer M, Baumann R, Karstens JH, Machtens S. TGFB1 gene polymorphism Leu10Pro (c.29T>C), prostate cancer incidence and quality of life in patients treated with brachytherapy. World J Urol 2008; 27:371-7. [PMID: 19039592 DOI: 10.1007/s00345-008-0354-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 10/29/2008] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Transforming growth factor beta1 gene (TGFB1) variant Leu10Pro (L10P) has previously been implicated in prostate cancer risk and radiation-induced side-effects. We investigated whether prevalence of this polymorphism is increased in prostate cancer patients and whether carriers are at increased risk for treatment-related side effects. METHODS A series of 445 consecutive patients treated for early-stage prostate cancer receiving definitive I-125 brachytherapy (permanent seed implantation) between 10/2000 and 10/2007 at our institution and a comparison group of 457 healthy male control individuals were screened for TGFB1 L10P (869T>C) polymorphism. Morbidity was assessed prospectively and compared between carriers versus non-carriers using International Prostate Symptom Score (IPSS), disease-specific Quality-of-Life single question added to the IPSS and International Index of Erectile Function with its subgroups. RESULTS The Leu/Leu genotype was found in 150 patients (34%) versus 180 controls (39%), the Pro/Pro genotype in 75 patients (17%) versus 65 controls (14%) and the Leu/Pro genotype in 220 patients (49%) versus 212 controls (46%) without any statistically significant differences between the two groups. There was a trend towards an increased prevalence of the L10P substitution among patients with a per allele odds ratio of 1.19 (95% CI 0.99-1.44; P = 0.08). After a median follow-up of 18 months (range 1-60 months) there were no statistically significant differences regarding morbidity. CONCLUSIONS TGFB1 polymorphism L10P is not strongly associated with prostate cancer risk. After 18 months, there was no evidence for increased adverse radiotherapy responses in heterozygote or rare homozygote carriers. Longer follow-up may be necessary to detect a statistically significant difference.
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Affiliation(s)
- Andreas Meyer
- Clinics of Radiation Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany.
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Association of chromosomal locus 8q24 and risk of prostate cancer: a hospital-based study of German patients treated with brachytherapy. Urol Oncol 2008; 27:373-6. [PMID: 18625567 DOI: 10.1016/j.urolonc.2008.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 04/07/2008] [Accepted: 04/08/2008] [Indexed: 11/24/2022]
Abstract
BACKGROUND Genetic susceptibility contributes to the risk of prostate cancer but the underlying genes are largely unknown. Polymorphic loci on chromosome 8q24 have emerged as possible risk factors for breast and prostate cancer from genome-wide association studies. OBJECTIVE We aimed to define the risks associated with two single nucleotide polymorphisms, rs1447295 and rs13281615, in a hospital-based series of prostate cancer patients treated with brachytherapy. MATERIAL AND METHODS We analyzed genomic DNA samples of 488 prostate cancer cases undergoing brachytherapy at Hannover Medical School, and of 462 male controls from the same location. Genotyping was performed using 5'-exonuclease allelic discrimination assays, and results were evaluated with chi(2) tests and logistic regression analyses. RESULTS We investigated whether rs1447295 and rs13281615 are associated with disease risk in a hospital-based prostate cancer case-control series from Northern Germany. The rare allele of rs1447295 was observed at higher frequency among cases than among hospital-based controls (13.9% vs. 10.2%, P = 0.01), and there was a dose-dependent trend towards a higher prevalence of heterozygous and homozygous carriers among the prostate cancer patients (per allele OR 1.42, 95% CI 1.07; 1.87, P = 0.02). By contrast, the rare allele of rs13281615 did not predispose to prostate cancer (per allele OR 0.84, 95% CI 0.70; 1.00, P = 0.05). The distribution of combined 8q24 genotypes was significantly different between cases and controls (P = 0.01). CONCLUSION Our results corroborate previous reports of 8q24 as a prostate cancer susceptibility locus and provide evidence for rs1447295 as a potentially important genetic marker. Further studies are required to confirm whether the adjacent breast cancer-associated variant rs13281615 may be inversely associated with prostate cancer risk.
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Begg A, van der Kogel A. Clinical radiobiology in 2008. Radiother Oncol 2008; 86:295-9. [PMID: 18313778 DOI: 10.1016/j.radonc.2008.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 02/01/2008] [Accepted: 02/01/2008] [Indexed: 11/18/2022]
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Lavelle C, Salles B, Wiesmüller L. DNA repair, damage signaling and carcinogenesis. DNA Repair (Amst) 2008; 7:670-80. [PMID: 18221920 DOI: 10.1016/j.dnarep.2007.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2007] [Indexed: 12/14/2022]
Abstract
The First joint meeting of the German DGDR (German Society for Research on DNA Repair) and the French SFTG (French Society of Genotoxicology) on DNA Repair was held in Toulouse, France, from September 15 to 19, 2007. It was organized by Lisa Wiesmüller and Bernard Salles together with the scientific committee consisting of Gilbert de Murcia, Jean-Marc Egly, Frank Grosse, Karl-Peter Hopfner, Georges Iliakis, Bernd Kaina, Markus Löbrich, Bernard Lopez, Daniel Marzin and Alain Sarasin. This report summarizes information presented by the speakers (invited lectures and oral communications) during the seven plenary sessions, which include (1) excision repair, (2) DNA repair and carcinogenesis, (3) double-strand break repair, (4) replication in repair and lesion bypass, (5) cellular responses to genotoxic stress, (6) DNA repair machinery within the chromatin context and (7) genotoxicology and testing. A total of 23 plenary lectures, 32 oral communications and 66 posters were presented in this rather intense 4 days meeting, which stimulated extensive discussions and highly interdisciplinary scientific exchanges among the approximately 250 participants.
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