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Hua Y, Cai D, Shirley CA, Mo S, Chen R, Gao F, Chen F. A prognostic model for ovarian neoplasms established by an integrated analysis of 1580 transcriptomic profiles. Sci Rep 2023; 13:19429. [PMID: 37940688 PMCID: PMC10632395 DOI: 10.1038/s41598-023-45410-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Even after debulking surgery combined with chemotherapy or new adjuvant chemotherapy paired with internal surgery, the average year of disease free survival in advanced ovarian cancer was approximately 1.7 years1. The development of a molecular predictor of early recurrence would allow for the identification of ovarian cancer (OC) patients with high risk of relapse. The Ovarian Cancer Disease Free Survival Predictor (ODFSP), a predictive model constructed from a special set of 1580 OC tumors in which gene expression was assessed using both microarray and sequencing platforms, was created by our team. To construct gene expression barcodes that were resistant to biases caused by disparate profiling platforms and batch effects, we employed a meta-analysis methodology that was based on the binary gene pair technique. We demonstrate that ODFSP is a reliable single-sample predictor of early recurrence (1 year or less) using the largest pool of OC transcriptome data sets available to date. The ODFSP model showed significantly high prognostic value for binary recurrence prediction unaffected by clinicopathologic factors, with a meta-estimate of the area under the receiver operating curve of 0.64 (P = 4.6E-05) and a D-index (robust hazard ratio) of 1.67 (P = 9.2E-06), respectively. GO analysis of ODFSP's 2040 gene pairs (collapsed to 886 distinct genes) revealed the involvement in small molecular catabolic process, sulfur compound metabolic process, organic acid catabolic process, sulfur compound biosynthetic process, glycosaminoglycan metabolic process and aminometabolic process. Kyoto encyclopedia of genes and genomes pathway analysis of ODFSP's signature genes identified prominent pathways that included cAMP signaling pathway and FoxO signaling pathway. By identifying individuals who might benefit from a more aggressive treatment plan or enrolment in a clinical trial but who will not benefit from standard surgery or chemotherapy, ODFSP could help with treatment decisions.
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Affiliation(s)
- Yanjiao Hua
- The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong Province, China
| | - Cole Andrea Shirley
- Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Sien Mo
- The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Ruyun Chen
- Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong Province, China
| | - Fangying Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, People's Republic of China.
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Imyanitov EN, Kuligina ES, Sokolenko AP, Suspitsin EN, Yanus GA, Iyevleva AG, Ivantsov AO, Aleksakhina SN. Hereditary cancer syndromes. World J Clin Oncol 2023; 14:40-68. [PMID: 36908677 PMCID: PMC9993141 DOI: 10.5306/wjco.v14.i2.40] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 02/15/2023] [Indexed: 02/21/2023] Open
Abstract
Hereditary cancer syndromes (HCSs) are arguably the most frequent category of Mendelian genetic diseases, as at least 2% of presumably healthy subjects carry highly-penetrant tumor-predisposing pathogenic variants (PVs). Hereditary breast-ovarian cancer and Lynch syndrome make the highest contribution to cancer morbidity; in addition, there are several dozen less frequent types of familial tumors. The development of the majority albeit not all hereditary malignancies involves two-hit mechanism, i.e. the somatic inactivation of the remaining copy of the affected gene. Earlier studies on cancer families suggested nearly fatal penetrance for the majority of HCS genes; however, population-based investigations and especially large-scale next-generation sequencing data sets demonstrate that the presence of some highly-penetrant PVs is often compatible with healthy status. Hereditary cancer research initially focused mainly on cancer detection and prevention. Recent studies identified multiple HCS-specific drug vulnerabilities, which translated into the development of highly efficient therapeutic options.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekaterina S Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Grigoriy A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
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3
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Alenezi WM, Fierheller CT, Serruya C, Revil T, Oros KK, Subramanian DN, Bruce J, Spiegelman D, Pugh T, Campbell IG, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Rouleau G, Bouchard L, Greenwood CMT, Ragoussis J, Tonin PN. Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases. Front Oncol 2023; 13:1111191. [PMID: 36969007 PMCID: PMC10030840 DOI: 10.3389/fonc.2023.1111191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Kathleen K. Oros
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jeffrey Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dan Spiegelman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Trevor Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Departement of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Guy Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medical Biology, Centres intégrés universitaires de santé et de services sociaux du Saguenay-Lac-Saint-Jean hôpital Universitaire de Chicoutimi, Saguenay, QC, Canada
- Centre de Recherche du Centre hospitalier l’Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: Patricia N. Tonin,
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do Canto LM, da Silva JM, Castelo-Branco PV, da Silva IM, Nogueira L, Fonseca-Alves CE, Khayat A, Birbrair A, Pereira SR. Mutational Signature and Integrative Genomic Analysis of Human Papillomavirus-Associated Penile Squamous Cell Carcinomas from Latin American Patients. Cancers (Basel) 2022; 14:cancers14143514. [PMID: 35884575 PMCID: PMC9316960 DOI: 10.3390/cancers14143514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary DNA sequencing has been crucial to comprehending cancer mutational patterns, leading to the identification of driver genes and altered signaling pathways. Thus, identifying new pathogenic variants and their impact on tumor onset, progression, and treatment response has fueled tumor biology research. Here, we present novel findings addressing the first whole-exome sequencing (WES) of human papillomavirus (HPV)-associated penile squamous cell carcinoma (PSCC) from Latin Americans and its association with pathogenesis. We also compared the molecular profile of the tumors to that of three previous studies from populations with different genetic and socioeconomic backgrounds, the majority of which was HPV-negative. We describe the most altered genes and the main pathogenic variants found in the Latin Americans, ten of which are exclusive to our study sample. The data allowed us to identify molecular pathways and druggable targets with potential treatment value for this still-neglected HPV-associated carcinoma. Abstract High-throughput DNA sequencing has allowed for the identification of genomic alterations and their impact on tumor development, progression, and therapeutic responses. In PSCC, for which the incidence has progressively increased worldwide, there are still limited data on the molecular mechanisms involved in the disease pathogenesis. In this study, we characterized the mutational signature of 30 human papillomavirus (HPV)-associated PSCC cases from Latin Americans, using whole-exome sequencing. Copy number variations (CNVs) were also identified and compared to previous array-generated data. Enrichment analyses were performed to reveal disrupted pathways and to identify alterations mapped to HPV integration sites (HPVis) and miRNA–mRNA hybridization regions. Among the most frequently mutated genes were NOTCH1, TERT, TTN, FAT1, TP53, CDKN2A, RYR2, CASP8, FBXW7, HMCN2, and ITGA8. Of note, 92% of these altered genes were localized at HPVis. We also found mutations in ten novel genes (KMT2C, SMARCA4, PTPRB, AJUBA, CR1, KMT2D, NBEA, FAM135B, GTF2I, and CIC), thus increasing our understanding of the potential HPV-disrupted pathways. Therefore, our study reveals innovative targets with potential therapeutic benefits for HPV-associated PSCCs. The CNV analysis by sequencing (CNV-seq) revealed five cancer-associated genes as the most frequent with gains (NOTCH1, MYC, NUMA1, PLAG1, and RAD21), while 30% of the tumors showed SMARCA4 with loss. Additionally, four cancer-associated genes (CARD11, CSMD3, KDR, and TLX3) carried untranslated regions (UTRs) variants, which may impact gene regulation by affecting the miRNAs hybridization regions. Altogether, these data contribute to the characterization of the mutational spectrum and its impact on cellular signaling pathways in PSCC, thus reinforcing the pivotal role of HPV infection in the molecular pathogenesis of these tumors.
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Affiliation(s)
- Luisa Matos do Canto
- Clinical Genetics Department, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Jenilson Mota da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís 65080-805, MA, Brazil;
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | - Patrícia Valèria Castelo-Branco
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | - Ingrid Monteiro da Silva
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | | | | | - André Khayat
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil;
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Department of Radiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
- Correspondence: ; Tel.: +55-98-32728543
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5
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Zhu Q, Wang J, Yu H, Hu Q, Bateman NW, Long M, Rosario S, Schultz E, Dalgard CL, Wilkerson MD, Sukumar G, Huang RY, Kaur J, Lele SB, Zsiros E, Villella J, Lugade A, Moysich K, Conrads TP, Maxwell GL, Odunsi K. Whole-Genome Sequencing Identifies PPARGC1A as a Putative Modifier of Cancer Risk in BRCA1/2 Mutation Carriers. Cancers (Basel) 2022; 14:2350. [PMID: 35625955 PMCID: PMC9139302 DOI: 10.3390/cancers14102350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
While BRCA1 and BRCA2 mutations are known to confer the largest risk of breast cancer and ovarian cancer, the incomplete penetrance of the mutations and the substantial variability in age at cancer onset among carriers suggest additional factors modifying the risk of cancer in BRCA1/2 mutation carriers. To identify genetic modifiers of BRCA1/2, we carried out a whole-genome sequencing study of 66 ovarian cancer patients that were enriched with BRCA carriers, followed by validation using data from the Pan-Cancer Analysis of Whole Genomes Consortium. We found PPARGC1A, a master regulator of mitochondrial biogenesis and function, to be highly mutated in BRCA carriers, and patients with both PPARGC1A and BRCA1/2 mutations were diagnosed with breast or ovarian cancer at significantly younger ages, while the mutation status of each gene alone did not significantly associate with age of onset. Our study suggests PPARGC1A as a possible BRCA modifier gene. Upon further validation, this finding can help improve cancer risk prediction and provide personalized preventive care for BRCA carriers.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Han Yu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
| | - Mark Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Spencer Rosario
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Emily Schultz
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Ruea-Yea Huang
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Jasmine Kaur
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Shashikant B. Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Emese Zsiros
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Jeannine Villella
- Division of Gynecologic Oncology, Lenox Hill Hospital/Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY 11549, USA;
| | - Amit Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL 60637, USA
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Wang L, Sun X, Jin C, Fan Y, Xue F. Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study. Front Genet 2021; 12:625145. [PMID: 34149794 PMCID: PMC8211425 DOI: 10.3389/fgene.2021.625145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/11/2021] [Indexed: 02/01/2023] Open
Abstract
Ovarian serous cancer (OSC) is one of the leading causes of death across the world. The role of the tumor microenvironment (TME) in OSC has received increasing attention. Targeted maximum likelihood estimation (TMLE) is developed under a counterfactual framework to produce effect estimation for both the population level and individual level. In this study, we aim to identify TME-related genes and using the TMLE method to estimate their effects on the 3-year mortality of OSC. In total, 285 OSC patients from the TCGA database constituted the studying population. ESTIMATE algorithm was implemented to evaluate immune and stromal components in TME. Differential analysis between high-score and low-score groups regarding ImmuneScore and StromalScore was performed to select shared differential expressed genes (DEGs). Univariate logistic regression analysis was followed to evaluate associations between DEGs and clinical pathologic factors with 3-year mortality. TMLE analysis was conducted to estimate the average effect (AE), individual effect (IE), and marginal odds ratio (MOR). The validation was performed using three datasets from Gene Expression Omnibus (GEO) database. Additionally, 355 DEGs were selected after differential analysis, and 12 genes from DEGs were significant after univariate logistic regression. Four genes remained significant after TMLE analysis. In specific, ARID3C and FREM2 were negatively correlated with OSC 3-year mortality. CROCC2 and PTF1A were positively correlated with OSC 3-year mortality. Combining of ESTIMATE algorithm and TMLE algorithm, we identified four TME-related genes in OSC. AEs were estimated to provide averaged effects based on the population level, while IEs were estimated to provide individualized effects and may be helpful for precision medicine.
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Affiliation(s)
- Lu Wang
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoru Sun
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chuandi Jin
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yue Fan
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Xi’an Jiaotong University, Xi’an, China
| | - Fuzhong Xue
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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7
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Song H, Dicks EM, Tyrer J, Intermaggio M, Chenevix-Trench G, Bowtell DD, Traficante N, Group A, Brenton J, Goranova T, Hosking K, Piskorz A, van Oudenhove E, Doherty J, Harris HR, Rossing MA, Duerst M, Dork T, Bogdanova NV, Modugno F, Moysich K, Odunsi K, Ness R, Karlan BY, Lester J, Jensen A, Krüger Kjaer S, Høgdall E, Campbell IG, Lázaro C, Pujara MA, Cunningham J, Vierkant R, Winham SJ, Hildebrandt M, Huff C, Li D, Wu X, Yu Y, Permuth JB, Levine DA, Schildkraut JM, Riggan MJ, Berchuck A, Webb PM, Group OS, Cybulski C, Gronwald J, Jakubowska A, Lubinski J, Alsop J, Harrington P, Chan I, Menon U, Pearce CL, Wu AH, de Fazio A, Kennedy CJ, Goode E, Ramus S, Gayther S, Pharoah P. Population-based targeted sequencing of 54 candidate genes identifies PALB2 as a susceptibility gene for high-grade serous ovarian cancer. J Med Genet 2021; 58:305-313. [PMID: 32546565 PMCID: PMC8086250 DOI: 10.1136/jmedgenet-2019-106739] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 05/12/2020] [Indexed: 11/19/2022]
Abstract
PURPOSE The known epithelial ovarian cancer (EOC) susceptibility genes account for less than 50% of the heritable risk of ovarian cancer suggesting that other susceptibility genes exist. The aim of this study was to evaluate the contribution to ovarian cancer susceptibility of rare deleterious germline variants in a set of candidate genes. METHODS We sequenced the coding region of 54 candidate genes in 6385 invasive EOC cases and 6115 controls of broad European ancestry. Genes with an increased frequency of putative deleterious variants in cases versus controls were further examined in an independent set of 14 135 EOC cases and 28 655 controls from the Ovarian Cancer Association Consortium and the UK Biobank. For each gene, we estimated the EOC risks and evaluated associations between germline variant status and clinical characteristics. RESULTS The ORs associated for high-grade serous ovarian cancer were 3.01 for PALB2 (95% CI 1.59 to 5.68; p=0.00068), 1.99 for POLK (95% CI 1.15 to 3.43; p=0.014) and 4.07 for SLX4 (95% CI 1.34 to 12.4; p=0.013). Deleterious mutations in FBXO10 were associated with a reduced risk of disease (OR 0.27, 95% CI 0.07 to 1.00, p=0.049). However, based on the Bayes false discovery probability, only the association for PALB2 in high-grade serous ovarian cancer is likely to represent a true positive. CONCLUSIONS We have found strong evidence that carriers of PALB2 deleterious mutations are at increased risk of high-grade serous ovarian cancer. Whether the magnitude of risk is sufficiently high to warrant the inclusion of PALB2 in cancer gene panels for ovarian cancer risk testing is unclear; much larger sample sizes will be needed to provide sufficiently precise estimates for clinical counselling.
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Affiliation(s)
- Honglin Song
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Ed M Dicks
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Maria Intermaggio
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Georgia Chenevix-Trench
- Cancer Genetics, Queensland Institute of Medical Research-QIMR, Herston, Queensland, Australia
| | - David D Bowtell
- Cancer Genomics and Genetics and Women's Cancer Programs, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nadia Traficante
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aocs Group
- QIMR Berghofer Department of Genetics and Computational Biology, Herston, Queensland, Australia
- Department of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - James Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Teodora Goranova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Karen Hosking
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Elke van Oudenhove
- Laura and Isaac Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Jen Doherty
- Huntsman Institute, University of Utah, Salt Lake City, Utah, USA
| | - Holly R Harris
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Mary Anne Rossing
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Matthias Duerst
- Department of Gynaecology, Jena University Hospital, Friedrich Schiller University Jena, Jena, Thüringen, Germany
| | - Thilo Dork
- Gynaecology Research Unit, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Niedersachsen, Germany
- Department of Gynaecology, NN Alexandrov National Cancer Centre, Minsk, Minsk, Belarus
| | - Francesmary Modugno
- Womens Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kirsten Moysich
- Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Roberta Ness
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Beth Y Karlan
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jenny Lester
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Kobenhavn, Denmark
| | - Susanne Krüger Kjaer
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Kobenhavn, Denmark
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Kobenhavn, Denmark
- Department of Pathology, Herlev Hospital, University of Copenhagen, Kobenhavn, Denmark
| | - Ian G Campbell
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Research, Cancer Genomics and Genetics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Barcelona, Catalunya, Spain
| | - Miguel Angel Pujara
- Translational Research Laboratory, Catalan Institute of Oncology, Barcelona, Catalunya, Spain
| | - Julie Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert Vierkant
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Stacey J Winham
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle Hildebrandt
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chad Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Donghui Li
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Douglas A Levine
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gynecologic Oncology, Laura and Isaac Pearlmutter Cancer Center, New York University, New York, New York, USA
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Marjorie J Riggan
- Department of Gynecologic Oncology, Duke University Hospital, Durham, North Carolina, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, North Carolina, USA
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Opal Study Group
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Jennifer Alsop
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Patricia Harrington
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Isaac Chan
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, London, UK
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna de Fazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Catherine J Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ellen Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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8
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Zhou Y, Liu J, Chu L, Dong M, Feng L. Whole-Exome Sequencing Reveals Novel Variations in Patients with Familial Von Hippel-Lindau Syndrome. World Neurosurg 2021; 150:e696-e704. [PMID: 33774214 DOI: 10.1016/j.wneu.2021.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Von Hippel-Lindau (VHL) syndrome is a rare disease that occurs in an autosomal-dominant genetic pattern. Due to the high genetic variability of VHL diseases, current studies have limited clinical value. Moreover, casual genetic variations in patients with VHL syndrome are still unclear. METHODS Here, we performed whole-exome sequencing of 25 individuals to identify reliable disease-related variations. Systemic computational analysis was performed for variant detection, and Sanger sequencing was used to validate detected mutations. RESULTS Most of the known mutations in the VHL gene were observed in the studied population. In addition, a large fragment deletion in VHL exon 2 in the immediate family members of the last family was detected. This had not been reported earlier. Moreover, we identified 3 novel mutation sites in the MAP2K3 gene that may be involved in the occurrence and development of the VHL disease. CONCLUSIONS These results demonstrated that the heterogeneous nature of VHL syndrome and novel mutational signatures may help to improve the diagnostic ability of VHL syndrome.
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Affiliation(s)
- Yuhao Zhou
- Guizhou Medical University, Affiliated Hospital, Guizhou Medical University, Guiyang, Guizhou, P. R. China
| | - Jian Liu
- Guizhou Medical University, Affiliated Hospital, Guizhou Medical University, Guiyang, Guizhou, P. R. China.
| | - Liangzhao Chu
- Department of Neurosurgery, Affiliated Hospital, Guizhou Medical University, Guiyang, Guizhou, P. R. China
| | - Minghao Dong
- Department of Neurosurgery, Affiliated Hospital, Guizhou Medical University, Guiyang, Guizhou, P. R. China
| | - Luqian Feng
- Department of Neurosurgery, Affiliated Hospital, Guizhou Medical University, Guiyang, Guizhou, P. R. China
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9
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Jung Y, Hur S, Liu J, Lee S, Kang BS, Kim M, Choi YJ. Peripheral blood BRCA1 methylation profiling to predict familial ovarian cancer. J Gynecol Oncol 2021; 32:e23. [PMID: 33470065 PMCID: PMC7930454 DOI: 10.3802/jgo.2021.32.e23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/12/2020] [Accepted: 11/29/2020] [Indexed: 01/13/2023] Open
Abstract
Objective Familial cancer appears at a young age and its incidence is increasing. About 12% of familial ovarian cancer cases are associated with BRCA1/2 mutations (BRCAm). In this study, we investigated BRCA1 methylation may predict ovarian cancer in those with a family history of cancer (FHC) but without BRCA1/2 mutations (BRCAwt). Methods Using peripheral blood DNA from 55 subjects without a history of cancer [cancer(−)] and 52 ovarian cancer patients, we examined BRCA1 promoter methylation through bisulfite sequencing of the promoter and expressed the results as the cumulative methylation index. Then, we evaluated the BRCA1 promoter methylation according to BRCA1/2 germline mutations. Results BRCA1 methylation was more prevalent in the BRCAm cancer(−) group than in the BRCAwt cancer(−) group and ovarian cancer patients (p=0.031 and p=0.019, respectively). In the BRCAwt cancer(−) group, BRCA1 methylation was more prevalent in those with an FHC than in those without one and in the BRCAm cancer(−) group with an FHC (p=0.001 and p<0.001, respectively). Conclusion Our data suggest a predictive role of BRCA1 methylation profile for ovarian cancer in those without a history of cancer but with an FHC. BRCA1 methylation has important implications for diagnostic and predictive testing of those with BRCAwt cancer(−) status with FHC.
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Affiliation(s)
- Yuyeon Jung
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sooyoung Hur
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - JingJing Liu
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Obstetrics and Gynecology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Sanha Lee
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byung Soo Kang
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Youn Jin Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
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10
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Alexandrova E, Pecoraro G, Sellitto A, Melone V, Ferravante C, Rocco T, Guacci A, Giurato G, Nassa G, Rizzo F, Weisz A, Tarallo R. An Overview of Candidate Therapeutic Target Genes in Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12061470. [PMID: 32512900 PMCID: PMC7352306 DOI: 10.3390/cancers12061470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Ovarian cancer (OC) shows the highest mortality rate among gynecological malignancies and, because of the absence of specific symptoms, it is frequently diagnosed at an advanced stage, mainly due to the lack of specific and early biomarkers, such as those based on cancer molecular signature identification. Indeed, although significant progress has been made toward improving the clinical outcome of other cancers, rates of mortality for OC are essentially unchanged since 1980, suggesting the need of new approaches to identify and characterize the molecular mechanisms underlying pathogenesis and progression of these malignancies. In addition, due to the low response rate and the high frequency of resistance to current treatments, emerging therapeutic strategies against OC focus on targeting single factors and pathways specifically involved in tumor growth and metastasis. To date, loss-of-function screenings are extensively applied to identify key drug targets in cancer, seeking for more effective, disease-tailored treatments to overcome lack of response or resistance to current therapies. We review here the information relative to essential genes and functional pathways recently discovered in OC, often strictly interconnected with each other and representing promising biomarkers and molecular targets to treat these malignancies.
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Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Viola Melone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Anna Guacci
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
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11
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Subramanian DN, Zethoven M, McInerny S, Morgan JA, Rowley SM, Lee JEA, Li N, Gorringe KL, James PA, Campbell IG. Exome sequencing of familial high-grade serous ovarian carcinoma reveals heterogeneity for rare candidate susceptibility genes. Nat Commun 2020; 11:1640. [PMID: 32242007 PMCID: PMC7118163 DOI: 10.1038/s41467-020-15461-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 03/12/2020] [Indexed: 01/31/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) has a significant hereditary component, approximately half of which cannot be explained by known genes. To discover genes, we analyse germline exome sequencing data from 516 BRCA1/2-negative women with HGSOC, focusing on genes enriched with rare, protein-coding loss-of-function (LoF) variants. Overall, there is a significant enrichment of rare protein-coding LoF variants in the cases (p < 0.0001, chi-squared test). Only thirty-four (6.6%) have a pathogenic variant in a known or proposed predisposition gene. Few genes have LoF mutations in more than four individuals and the majority are detected in one individual only. Forty-three highly-ranked genes are identified with three or more LoF variants that are enriched by three-fold or more compared to GnomAD. These genes represent diverse functional pathways with relatively few involved in DNA repair, suggesting that much of the remaining heritability is explained by previously under-explored genes and pathways.
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Affiliation(s)
- Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Magnus Zethoven
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Simone McInerny
- The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia
| | - James A Morgan
- The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Jue Er Amanda Lee
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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