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Witjes VM, Hermkens DMA, Swillens JEM, Smolders YHCM, Mourits MJE, Ausems MGEM, de Hullu JA, Ligtenberg MJL, Hoogerbrugge N. Optimizing the detection of hereditary predisposition in women with epithelial ovarian cancer: nationwide implementation of the Tumor-First workflow. Fam Cancer 2024:10.1007/s10689-024-00398-9. [PMID: 38811422 DOI: 10.1007/s10689-024-00398-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]
Abstract
Genetic testing in patients with ovarian carcinoma (OC) is crucial, as around 10-15% of these women have a genetic predisposition to OC. Although guidelines have recommended universal germline testing for all patients with OC for a decade, implementation has proved challenging, thus resulting in low germline-testing rates (around 30-50%). Many new initiatives to improve genetic-testing rates have emerged, but most have been carried out at the local level, leading to differences in workflows within and between countries. We present an example of a nationwide implementation project that has successfully led to a uniform, high-quality genetic-testing workflow for women with OC. Nationwide multidisciplinary meetings generated consensus on the preferred workflow for OC genetic testing: the "Tumor-First" workflow. This workflow means starting by testing the tumor DNA for the presence of pathogenic variants in OC-risk genes, thus providing a prescreen to germline testing while yielding information on the effectiveness of treatment with PARP inhibitors. This new workflow efficiently stratifies genetic counseling and germline testing and reduces healthcare costs. Although challenging, the nationwide implementation of this workflow was successful, resulting in tumor-DNA testing rates exceeding 80%. In this article, we present our structured implementation approach, illustrate our implementation strategies-which were tailored to identified factors important to implementation-and share the lessons learned from the Tumor-First implementation project. This knowledge could facilitate the future implementation of workflows aimed at optimizing the recognition of hereditary cancers.
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Affiliation(s)
- Vera M Witjes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dorien M A Hermkens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie E M Swillens
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- IQ Health Science Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yvonne H C M Smolders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marian J E Mourits
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Margreet G E M Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joanne A de Hullu
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands.
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McDevitt T, Durkie M, Arnold N, Burghel GJ, Butler S, Claes KBM, Logan P, Robinson R, Sheils K, Wolstenholme N, Hanson H, Turnbull C, Hume S. EMQN best practice guidelines for genetic testing in hereditary breast and ovarian cancer. Eur J Hum Genet 2024; 32:479-488. [PMID: 38443545 PMCID: PMC11061103 DOI: 10.1038/s41431-023-01507-5] [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: 06/08/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 03/07/2024] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) is a genetic condition associated with increased risk of cancers. The past decade has brought about significant changes to hereditary breast and ovarian cancer (HBOC) diagnostic testing with new treatments, testing methods and strategies, and evolving information on genetic associations. These best practice guidelines have been produced to assist clinical laboratories in effectively addressing the complexities of HBOC testing, while taking into account advancements since the last guidelines were published in 2007. These guidelines summarise cancer risk data from recent studies for the most commonly tested high and moderate risk HBOC genes for laboratories to refer to as a guide. Furthermore, recommendations are provided for somatic and germline testing services with regards to clinical referral, laboratory analyses, variant interpretation, and reporting. The guidelines present recommendations where 'must' is assigned to advocate that the recommendation is essential; and 'should' is assigned to advocate that the recommendation is highly advised but may not be universally applicable. Recommendations are presented in the form of shaded italicised statements throughout the document, and in the form of a table in supplementary materials (Table S4). Finally, for the purposes of encouraging standardisation and aiding implementation of recommendations, example report wording covering the essential points to be included is provided for the most common HBOC referral and reporting scenarios. These guidelines are aimed primarily at genomic scientists working in diagnostic testing laboratories.
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Affiliation(s)
- Trudi McDevitt
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland.
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust Western Bank, Sheffield, UK
| | - Norbert Arnold
- UKSH Campus Kiel, Gynecology and Obstetrics, Institut of Clinical Chemistry, Institut of Clinical Molecular Biology, Kiel, Germany
| | - George J Burghel
- Manchester University NHS Foundation Trust, North West Genomic Laboratory Hub, Manchester, UK
| | - Samantha Butler
- Central and South Genomic Laboratory Hub, West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Peter Logan
- HSCNI / Belfast Trust Laboratories, Regional Molecular Diagnostics Service, Belfast, Northern Ireland
| | - Rachel Robinson
- Leeds Teaching Hospitals NHS Trust, Genetics Department, Leeds, UK
| | | | | | - Helen Hanson
- St George's University Hospitals NHS Foundation Trust, Clinical Genetics, London, UK
| | | | - Stacey Hume
- University of British Columbia, Pathology and Laboratory Medicine, Vancouver, British Columbia, Canada
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3
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Torres-Esquius S, Llop-Guevara A, Gutiérrez-Enríquez S, Romey M, Teulé À, Llort G, Herrero A, Sánchez-Henarejos P, Vallmajó A, González-Santiago S, Chirivella I, Cano JM, Graña B, Simonetti S, Díaz de Corcuera I, Ramon y Cajal T, Sanz J, Serrano S, Otero A, Churruca C, Sánchez-Heras AB, Servitja S, Guillén-Ponce C, Brunet J, Denkert C, Serra V, Balmaña J. Prevalence of Homologous Recombination Deficiency Among Patients With Germline RAD51C/D Breast or Ovarian Cancer. JAMA Netw Open 2024; 7:e247811. [PMID: 38648056 PMCID: PMC11036141 DOI: 10.1001/jamanetworkopen.2024.7811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Importance RAD51C and RAD51D are involved in DNA repair by homologous recombination. Germline pathogenic variants (PVs) in these genes are associated with an increased risk of ovarian and breast cancer. Understanding the homologous recombination deficiency (HRD) status of tumors from patients with germline PVs in RAD51C/D could guide therapeutic decision-making and improve survival. Objective To characterize the clinical and tumor characteristics of germline RAD51C/D PV carriers, including the evaluation of HRD status. Design, Setting, and Participants This retrospective cohort study included 91 index patients plus 90 relatives carrying germline RAD51C/D PV (n = 181) in Spanish hospitals from January 1, 2014, to December 31, 2021. Genomic and functional HRD biomarkers were assessed in untreated breast and ovarian tumor samples (n = 45) from June 2022 to February 2023. Main Outcomes and Measures Clinical and pathologic characteristics were assessed using descriptive statistics. Genomic HRD by genomic instability scores, functional HRD by RAD51, and gene-specific loss of heterozygosity were analyzed. Associations between HRD status and tumor subtype, age at diagnosis, and gene-specific loss of heterozygosity in RAD51C/D were investigated using logistic regression or the t test. Results A total of 9507 index patients were reviewed, and 91 patients (1.0%) were found to carry a PV in RAD51C/D; 90 family members with a germline PV in RAD51C/D were also included. A total of 157 of carriers (86.7%) were women and 181 (55.8%) had received a diagnosis of cancer, mainly breast cancer or ovarian cancer. The most prevalent PVs were c.1026+5_1026+7del (11 of 56 [19.6%]) and c.709C>T (9 of 56 [16.1%]) in RAD51C and c.694C>T (20 of 35 [57.1%]) in RAD51D. In untreated breast cancer and ovarian cancer, the prevalence of functional and genomic HRD was 55.2% (16 of 29) and 61.1% (11 of 18) for RAD51C, respectively, and 66.7% (6 of 9) and 90.0% (9 of 10) for RAD51D. The concordance between HRD biomarkers was 91%. Tumors with the same PV displayed contrasting HRD status, and age at diagnosis did not correlate with the occurrence of HRD. All breast cancers retaining the wild-type allele were estrogen receptor positive and lacked HRD. Conclusions and Relevance In this cohort study of germline RAD51C/D breast cancer and ovarian cancer, less than 70% of tumors displayed functional HRD, and half of those that did not display HRD were explained by retention of the wild-type allele, which was more frequent among estrogen receptor-positive breast cancers. Understanding which tumors are associated with RAD51C/D and HRD is key to identify patients who can benefit from targeted therapies, such as PARP (poly [adenosine diphosphate-ribose] polymerase) inhibitors.
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Affiliation(s)
- Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Translational Medicine, DNA Damage Response Department, AstraZeneca, Barcelona, Spain
| | | | - Marcel Romey
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Gemma Llort
- Department of Medical Oncology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Ana Herrero
- Department of Medical Oncology, Hospital Miguel Servet de Zaragoza, Zaragoza, Spain
| | | | - Anna Vallmajó
- Genetic Counseling Unit, Arnau de Vilanova University Hospital, Lleida, Spain
| | | | - Isabel Chirivella
- Cancer Genetic Counseling, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Juana Maria Cano
- Department of Medical Oncology, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | - Begoña Graña
- Department of Medical Oncology, Xerencia de Xestión Integrada de A Coruña, Coruña, Spain
| | - Sara Simonetti
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | | | - Teresa Ramon y Cajal
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Judit Sanz
- Unidad de Cáncer Familiar y Hereditario, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Sara Serrano
- Department of Medical Oncology, Institute of Oncology of Southern Catalonia (IOCS), Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - Andrea Otero
- Institute of Oncology and Molecular Medicine of Asturias (IMOMA) S. A., Oviedo, Spain
| | - Cristina Churruca
- Department of Medical Oncology, Hospital Universitario Donostia, San Sebastián, Gipuzkoa, Spain
| | - Ana Beatriz Sánchez-Heras
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, Elche, Spain
| | - Sonia Servitja
- Department of Medical Oncology, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Carmen Guillén-Ponce
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona, Spain
- Precision Oncology Group (OncoGIR-Pro), Institut d’Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Medical Oncology Department, Hospital Universitari Vall d’Hebron, Barcelona, Spain
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Barili V, Ambrosini E, Bortesi B, Minari R, De Sensi E, Cannizzaro IR, Taiani A, Michiara M, Sikokis A, Boggiani D, Tommasi C, Serra O, Bonatti F, Adorni A, Luberto A, Caggiati P, Martorana D, Uliana V, Percesepe A, Musolino A, Pellegrino B. Genetic Basis of Breast and Ovarian Cancer: Approaches and Lessons Learnt from Three Decades of Inherited Predisposition Testing. Genes (Basel) 2024; 15:219. [PMID: 38397209 PMCID: PMC10888198 DOI: 10.3390/genes15020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Germline variants occurring in BRCA1 and BRCA2 give rise to hereditary breast and ovarian cancer (HBOC) syndrome, predisposing to breast, ovarian, fallopian tube, and peritoneal cancers marked by elevated incidences of genomic aberrations that correspond to poor prognoses. These genes are in fact involved in genetic integrity, particularly in the process of homologous recombination (HR) DNA repair, a high-fidelity repair system for mending DNA double-strand breaks. In addition to its implication in HBOC pathogenesis, the impairment of HR has become a prime target for therapeutic intervention utilizing poly (ADP-ribose) polymerase (PARP) inhibitors. In the present review, we introduce the molecular roles of HR orchestrated by BRCA1 and BRCA2 within the framework of sensitivity to PARP inhibitors. We examine the genetic architecture underneath breast and ovarian cancer ranging from high- and mid- to low-penetrant predisposing genes and taking into account both germline and somatic variations. Finally, we consider higher levels of complexity of the genomic landscape such as polygenic risk scores and other approaches aiming to optimize therapeutic and preventive strategies for breast and ovarian cancer.
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Affiliation(s)
- Valeria Barili
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Beatrice Bortesi
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Antonietta Taiani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Maria Michiara
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Angelica Sikokis
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Daniela Boggiani
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Chiara Tommasi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Olga Serra
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Francesco Bonatti
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Alessia Adorni
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Anita Luberto
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonio Percesepe
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonino Musolino
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Benedetta Pellegrino
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
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5
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Dai Y, Xu J, Gong X, Wei J, Gao Y, Chai R, Lu C, Zhao B, Kang Y. Human Fallopian Tube-Derived Organoids with TP53 and RAD51D Mutations Recapitulate an Early Stage High-Grade Serous Ovarian Cancer Phenotype In Vitro. Int J Mol Sci 2024; 25:886. [PMID: 38255960 PMCID: PMC10815309 DOI: 10.3390/ijms25020886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
RAD51D mutations have been implicated in the transformation of normal fallopian tube epithelial (FTE) cells into high-grade serous ovarian cancer (HGSOC), one of the most prevalent and aggressive gynecologic malignancies. Currently, no suitable model exists to elucidate the role of RAD51D in disease initiation and progression. Here, we established organoids from primary human FTE and introduced TP53 as well as RAD51D knockdown to enable the exploration of their mutational impact on FTE lesion generation. We observed that TP53 deletion rescued the adverse effects of RAD51D deletion on the proliferation, stemness, senescence, and apoptosis of FTE organoids. RAD51D deletion impaired the homologous recombination (HR) function and induced G2/M phase arrest, whereas concurrent TP53 deletion mitigated G0/G1 phase arrest and boosted DNA replication when combined with RAD51D mutation. The co-deletion of TP53 and RAD51D downregulated cilia assembly, development, and motility, but upregulated multiple HGSOC-associated pathways, including the IL-17 signaling pathway. IL-17A treatment significantly improved cell viability. TP53 and RAD51D co-deleted organoids exhibited heightened sensitivity to platinum, poly-ADP ribose polymerase inhibitors (PARPi), and cell cycle-related medication. In summary, our research highlighted the use of FTE organoids with RAD51D mutations as an invaluable in vitro platform for the early detection of carcinogenesis, mechanistic exploration, and drug screening.
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Affiliation(s)
- Yilin Dai
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Jing Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Xiaofeng Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Jinsong Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yi Gao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Ranran Chai
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Chong Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yu Kang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
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6
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Sokolenko AP, Bakaeva EK, Venina AR, Kuligina ES, Romanko AA, Aleksakhina SN, Belysheva YV, Belogubova EV, Stepanov IA, Zaitseva OA, Yatsuk OS, Togo AV, Khamgokov ZM, Kadyrova AO, Pirmagomedov AS, Bolieva MB, Epkhiev AA, Tsutsaev AK, Chakhieva MD, Khabrieva KM, Khabriev IM, Murachuev MA, Buttaeva BN, Baboshkina LS, Bayramkulova FI, Katchiev IR, Alieva LK, Raskin GA, Orlov SV, Khachmamuk ZK, Levonyan KR, Gichko DM, Kirtbaya DV, Degtyariov AM, Sultanova LV, Musayeva HS, Belyaev AM, Imyanitov EN. Ethnicity-specific BRCA1, BRCA2, PALB2, and ATM pathogenic alleles in breast and ovarian cancer patients from the North Caucasus. Breast Cancer Res Treat 2024; 203:307-315. [PMID: 37851290 DOI: 10.1007/s10549-023-07135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Mountain areas of the North Caucasus host several large ethnic communities that have preserved their national identity over the centuries. METHODS This study involved high-grade serous ovarian cancer (HGSOC) and breast cancer (BC) patients from Dagestan (HGSOC: 37; BC: 198), Kabardino-Balkaria (HGSOC: 68; BC: 155), North Ossetia (HGSOC: 51; BC: 104), Chechnya (HGSOC: 68; BC: 79), Ingushetia (HGSOC: 19; BC: 103), Karachay-Cherkessia (HGSOC: 13; BC: 47), and several Armenian settlements (HGSOC: 16; BC: 101). The group of BC patients was enriched by young-onset and/or family history-positive and/or bilateral and/or receptor triple-negative cases. The entire coding region of BRCA1, BRCA2, PALB2, and ATM genes was analyzed by next-generation sequencing. RESULTS A significant contribution of BRCA1/2 pathogenic variants (PVs) to HGSOC and BC development was observed across all North Caucasus regions (HGSOC: 19-39%; BC: 6-13%). Founder alleles were identified in all ethnic groups studied, e.g., BRCA1 c.3629_3630delAG in Chechens, BRCA2 c.6341delC in North Ossetians, BRCA2 c.5351dupA in Ingush, and BRCA1 c.2907_2910delTAAA in Karachays. Some BRCA1/2 alleles, particularly BRCA2 c.9895C > T, were shared by several nationalities. ATM PVs were detected in 14 patients, with c.1673delG and c.8876_8879delACTG alleles occurring twice each. PALB2 heterozygosity was observed in 5 subjects, with one variant seen in 2 unrelated women. CONCLUSION This study adds to the evidence for the global-wide contribution of BRCA1/2 genes to HGSOC and BC morbidity, although the spectrum of their PVs is a subject of ethnicity-specific variations. The data on founder BRCA1/2 alleles may be considered when adjusting the BRCA1/2 testing procedure to the ethnic origin of patients.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758.
- St. Petersburg Pediatric Medical University, St. Petersburg, Russia.
| | - Elvina Kh Bakaeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Aigul R Venina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Ekaterina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Alexandr A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Yana V Belysheva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Evgeniya V Belogubova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Ilya A Stepanov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Olga A Zaitseva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Olga S Yatsuk
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Alexandr V Togo
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Zaur M Khamgokov
- Republican Cancer Center, The Kabardino-Balkarian Republic, Nalchik, Russia
| | - Azinat O Kadyrova
- Republican Cancer Center, The Kabardino-Balkarian Republic, Nalchik, Russia
| | | | - Marina B Bolieva
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | - Alexandr A Epkhiev
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | - Aslan K Tsutsaev
- Republican Cancer Center, The Republic of North Ossetia-Alania, Vladikavkaz, Russia
| | | | | | - Idris M Khabriev
- Republican Cancer Center, The Republic of Ingushetia, Pliyevo, Russia
| | - Mirza A Murachuev
- Republican Cancer Center, The Republic of Dagestan, Makhachkala, Russia
| | - Bella N Buttaeva
- Republican Bureau of Pathology, The Republic of Dagestan, Makhachkala, Russia
| | - Liliya S Baboshkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | | | - Islam R Katchiev
- Republican Cancer Center, The Karachay-Cherkess Republic, Cherkessk, Russia
| | - Lina Kh Alieva
- Republican Cancer Center, The Karachay-Cherkess Republic, Cherkessk, Russia
| | - Grigory A Raskin
- Dr. Sergey Berezin Medical Institute of Biological Systems, St. Petersburg, Russia
| | - Sergey V Orlov
- I.P. Pavlov St.-Petersburg State Medical University, St. Petersburg, Russia
| | | | | | | | | | | | | | - Hedi S Musayeva
- Republican Cancer Center, Grozny, The Chechen Republic, Russia
| | - Alexey M Belyaev
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
- St. Petersburg Pediatric Medical University, St. Petersburg, Russia
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7
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D'Angelo E, Espinosa I, Felicioni L, Buttitta F, Prat J. Ovarian high-grade serous carcinoma with transitional-like (SET) morphology: a homologous recombination-deficient tumor. Hum Pathol 2023; 141:15-21. [PMID: 37673346 DOI: 10.1016/j.humpath.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
Thirteen years ago, we pointed out that ovarian transitional cell carcinomas (TCCs) and conventional high-grade serous carcinomas (HGSCs) had similar genetic alterations and clinical behavior. Consequently, ovarian TCC is now classified as a morphologic variant of HGSC. Defective homologous recombination, resulting from genetic or epigenetic inactivation of DNA damage repair genes, such as BRCA1/2, occurs in approximately 50% of the HGSCs. Although BRCA mutations have been associated with HGSCs with solid, pseudoendometrioid or transitional (SET) features, little is known about the role of non-BRCA homologous recombinationrepair (HRR) genes and the HRR status in these tumors. Using two commercially available assays (Myriad Genetics MyChoice CDx Plus test and SOPHiA Dx Homologous Recombination Deficiency Solution), we study mutations of BRCA1/2 and non-BRCA HRR genes (ATM, BARD1, BRIP1, CDK12, CHEK1/2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, and RAD54L), and the HRR status in 19 HGSCs with SET features and 20 HGSCs with classic morphology. We also studied, as control cases, 5 endometrioid carcinomas, 1 clear cell carcinoma, 2 low-grade serous carcinomas, and 1 malignant Brenner tumor. Seven HGSCs with SET features (7/19; 37%) showed BRCA mutations (4 BRCA1, 2 BRCA2, and 1 BRCA1/2). Mutations in non-BRCA HRR genes were found in ATM (1/15; 7%), BARD1 (1/15; 7%), and BRIP1 (1/19; 5%). Most HGSCs with SET features (17/19; 90%) were considered to be homologous recombination-deficient tumors. Three HGSCs with classic morphology (3/20; 15%) showed BRCA2 mutations. Mutations in non-BRCA HRR genes were found in CDK12 (2/14; 14%), FANCL (1/14; 7%), RAD51B (1/14; 7%), and RAD54L (1/14; 7%). Eleven HGSCs with classical morphology (11/20; 55%) were considered to be homologous recombination deficient. In contrast, all ovarian carcinoma control cases (5 endometrioid carcinomas, 1 clear cell carcinoma, 2 low-grade serous carcinomas, and 1 malignant Brenner tumor) were homologous recombination proficient and did not have BRCA mutations. Our results show that the majority of HGSCs with SET features are homologous recombination-deficient tumors independently of the BRCA status and highlight the importance of the HRR tumor testing, especially in BRCA wild-type tumors. Recognition of transitional cell variant of HGSCs may help to identify patients most likely to benefit from PARP inhibitors.
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Affiliation(s)
- Emanuela D'Angelo
- Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio", 66100 Italy; Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), Chieti-Pescara, 66100 Italy
| | - Iñigo Espinosa
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, 08041 Spain
| | - Lara Felicioni
- Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), Chieti-Pescara, 66100 Italy
| | - Fiamma Buttitta
- Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio", 66100 Italy; Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), Chieti-Pescara, 66100 Italy
| | - Jaime Prat
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, 08041 Spain.
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8
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Rein HL, Bernstein KA. Finding significance: New perspectives in variant classification of the RAD51 regulators, BRCA2 and beyond. DNA Repair (Amst) 2023; 130:103563. [PMID: 37651978 PMCID: PMC10529980 DOI: 10.1016/j.dnarep.2023.103563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
For many individuals harboring a variant of uncertain functional significance (VUS) in a homologous recombination (HR) gene, their risk of developing breast and ovarian cancer is unknown. Integral to the process of HR are BRCA1 and regulators of the central HR protein, RAD51, including BRCA2, PALB2, RAD51C and RAD51D. Due to advancements in sequencing technology and the continued expansion of cancer screening panels, the number of VUS identified in these genes has risen significantly. Standard practices for variant classification utilize different types of predictive, population, phenotypic, allelic and functional evidence. While variant analysis is improving, there remains a struggle to keep up with demand. Understanding the effects of an HR variant can aid in preventative care and is critical for developing an effective cancer treatment plan. In this review, we discuss current perspectives in the classification of variants in the breast and ovarian cancer genes BRCA1, BRCA2, PALB2, RAD51C and RAD51D.
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Affiliation(s)
- Hayley L Rein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, USA
| | - Kara A Bernstein
- University of Pennsylvania School of Medicine, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA.
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9
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El Gazzar WB, Albakri KA, Hasan H, Badr AM, Farag AA, Saleh OM. Poly(ADP-ribose) polymerase inhibitors in the treatment landscape of triple-negative breast cancer (TNBC). J Oncol Pharm Pract 2023; 29:1467-1479. [PMID: 37559370 DOI: 10.1177/10781552231188903] [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: 08/11/2023]
Abstract
OBJECTIVE Chemotherapy is the mainstay for triple-negative breast cancer (TNBC) patients. Over the years, the use of chemotherapy for these patients has demonstrated many adversities, including toxicity and resistance, which suggested the need to develop novel alternative therapeutic options, such as poly(ADP-ribose) polymerase inhibitors (PARPi). Herein, we provide an overview on PARPi, mechanisms of action and the role of biomarkers in PARPi sensitivity trials, clinical advances in PARPi therapy for TNBC patients based on the most recent studies and findings of clinical trials, and challenges that prevent PARP inhibitors from achieving high efficacy such as resistance and overlapping toxicities with other chemotherapies. DATA SOURCES Searching for relevant articles was done using PubMed and Cochrane Library databases by using the keywords including TNBC; chemotherapy; PARPi; BRCA; homologous recombination repair (HRR). Studies had to be published in full-text in English in order to be considered. DATA SUMMARY Although PARPi have been used in the treatment of local/metastatic breast malignancies that are HER2 negative and has a germline BRCA mutation, several questions are still to be answered in order to maximize the clinical benefit of PARP inhibitors in TNBC treatment, such as questions related to the optimal use in the neoadjuvant and metastatic settings as well as the best combinations with various chemotherapies. CONCLUSIONS PARPi are emerging treatment options for patients with gBRCA1/2 mutations. Determining patients that are most likely to benefit from PARPi and identifying the optimal treatment combinations with high efficacy and fewer side effects are currently ongoing.
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Affiliation(s)
- Walaa Bayoumie El Gazzar
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Benha University, Benha City, Egypt
| | | | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Amira M Badr
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmacology and Toxicology, College of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Amina A Farag
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Benha University, Benha City, Egypt
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O'Brien TD, Potter AB, Driscoll CC, Goh G, Letaw JH, McCabe S, Thanner J, Kulkarni A, Wong R, Medica S, Week T, Buitrago J, Larson A, Camacho KJ, Brown K, Crist R, Conrad C, Evans-Dutson S, Lutz R, Mitchell A, Anur P, Serrato V, Shafer A, Marriott LK, Hamman KJ, Mulford A, Wiszniewski W, Sampson JE, Adey A, O'Roak BJ, Harrington CA, Shannon J, Spellman PT, Richards CS. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon. Am J Hum Genet 2023; 110:1249-1265. [PMID: 37506692 PMCID: PMC10432140 DOI: 10.1016/j.ajhg.2023.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
The Healthy Oregon Project (HOP) is a statewide effort that aims to build a large research repository and influence the health of Oregonians through providing no-cost genetic screening to participants for a next-generation sequencing 32-gene panel comprising genes related to inherited cancers and familial hypercholesterolemia. This type of unbiased population screening can detect at-risk individuals who may otherwise be missed by conventional medical approaches. However, challenges exist for this type of high-throughput testing in an academic setting, including developing a low-cost high-efficiency test and scaling up the clinical laboratory for processing large numbers of samples. Modifications to our academic clinical laboratory including efficient test design, robotics, and a streamlined analysis approach increased our ability to test more than 1,000 samples per month for HOP using only one dedicated HOP laboratory technologist. Additionally, enrollment using a HIPAA-compliant smartphone app and sample collection using mouthwash increased efficiency and reduced cost. Here, we present our experience three years into HOP and discuss the lessons learned, including our successes, challenges, opportunities, and future directions, as well as the genetic screening results for the first 13,670 participants tested. Overall, we have identified 730 pathogenic/likely pathogenic variants in 710 participants in 24 of the 32 genes on the panel. The carrier rate for pathogenic/likely pathogenic variants in the inherited cancer genes on the panel for an unselected population was 5.0% and for familial hypercholesterolemia was 0.3%. Our laboratory experience described here may provide a useful model for population screening projects in other states.
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Affiliation(s)
- Timothy D O'Brien
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amiee B Potter
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Catherine C Driscoll
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Gregory Goh
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - John H Letaw
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sarah McCabe
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jane Thanner
- Information Technology Group, Oregon Health & Science University, Portland, OR 97201, USA
| | - Arpita Kulkarni
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rossana Wong
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samuel Medica
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tiana Week
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jacob Buitrago
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aaron Larson
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Katie Johnson Camacho
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kim Brown
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Rachel Crist
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Casey Conrad
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Sara Evans-Dutson
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Ryan Lutz
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Asia Mitchell
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Pavana Anur
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Vanessa Serrato
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Autumn Shafer
- University of Oregon, School of Journalism and Communication, Portland, OR 97209, USA
| | | | - K J Hamman
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amelia Mulford
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Wojciech Wiszniewski
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jone E Sampson
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andrew Adey
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina A Harrington
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jackilen Shannon
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - C Sue Richards
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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11
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Burke W, Barkley J, Barrows E, Brooks R, Gecsi K, Huber-Keener K, Jeudy M, Mei S, O'Hara JS, Chelmow D. Executive Summary of the Ovarian Cancer Evidence Review Conference. Obstet Gynecol 2023; 142:179-195. [PMID: 37348094 DOI: 10.1097/aog.0000000000005211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/19/2023] [Indexed: 06/24/2023]
Abstract
The Centers for Disease Control and Prevention awarded funding to the American College of Obstetricians and Gynecologists to develop educational materials for clinicians on gynecologic cancers. The American College of Obstetricians and Gynecologists convened a panel of experts in evidence review from the Society for Academic Specialists in General Obstetrics and Gynecology and content experts from the Society of Gynecologic Oncology to review relevant literature, best practices, and existing practice guidelines as a first step toward developing evidence-based educational materials for women's health care clinicians about ovarian cancer. Panel members conducted structured literature reviews, which were then reviewed by other panel members and discussed at a virtual meeting of stakeholder professional and patient advocacy organizations in February 2022. This article is the executive summary of the relevant literature and existing recommendations to guide clinicians in the prevention, early diagnosis, and special considerations of ovarian cancer. Substantive knowledge gaps are noted and summarized to provide guidance for future research.
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Affiliation(s)
- William Burke
- Departments of Obstetrics and Gynecology, Stony Brook University Hospital, New York, New York, Creighton University School of Medicine, Phoenix, Arizona, Virginia Commonwealth University School of Medicine, Richmond, Virginia, the University of California, Davis, Davis, California, the Medical College of Wisconsin, Milwaukee, Wisconsin, the University of Iowa Hospitals and Clinics, Iowa City, Iowa, and New York University Langone School of Medicine, New York; and the American College of Obstetricians and Gynecologists, Washington, DC
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12
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Bouras A, Guidara S, Leone M, Buisson A, Martin-Denavit T, Dussart S, Lasset C, Giraud S, Bonnet-Dupeyron MN, Kherraf ZE, Sanlaville D, Fert-Ferrer S, Lebrun M, Bonadona V, Calender A, Boutry-Kryza N. Overview of the Genetic Causes of Hereditary Breast and Ovarian Cancer Syndrome in a Large French Patient Cohort. Cancers (Basel) 2023; 15:3420. [PMID: 37444530 DOI: 10.3390/cancers15133420] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The use of multigene panel testing for patients with a predisposition to Hereditary Breast and Ovarian Cancer syndrome (HBOC) is increasing as the identification of mutations is useful for diagnosis and disease management. Here, we conducted a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in 4630 French HBOC suspected patients. Patients were investigated using a germline cancer panel including the 13 genes defined by The French Genetic and Cancer Group (GGC)-Unicancer. In the patients analyzed, 528 pathogenic and likely pathogenic variants (P/LP) were identified, including BRCA1 (n = 203, 38%), BRCA2 (n = 198, 37%), PALB2 (n = 46, 9%), RAD51C (n = 36, 7%), TP53 (n = 16, 3%), and RAD51D (n = 13, 2%). In addition, 35 novel (P/LP) variants, according to our knowledge, were identified, and double mutations in two distinct genes were found in five patients. Interestingly, retesting a subset of BRCA1/2-negative individuals with an expanded panel produced clinically relevant results in 5% of cases. Additionally, combining in silico (splicing impact prediction tools) and in vitro analyses (RT-PCR and Sanger sequencing) highlighted the deleterious impact of four candidate variants on splicing and translation. Our results present an overview of pathogenic variations of HBOC genes in the southeast of France, emphasizing the clinical relevance of cDNA analysis and the importance of retesting BRCA-negative individuals with an expanded panel.
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Affiliation(s)
- Ahmed Bouras
- Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, 69008 Lyon, France
- Team 'Endocrine Resistance, Methylation and Breast Cancer' Research Center of Lyon-CRCL, UMR Inserm 1052 CNRS 5286, 69008 Lyon, France
| | - Souhir Guidara
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Department of Genetics, CHU Hédi Chaker, Sfax 3027, Tunisia
| | - Mélanie Leone
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Adrien Buisson
- Department of Biopathology, Centre Léon Bérard, 69008 Lyon, France
| | - Tanguy Martin-Denavit
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
- Center for Medical Genetics, Alpigène, 69007 Lyon, France
| | - Sophie Dussart
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Christine Lasset
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Sophie Giraud
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | | | - Zine-Eddine Kherraf
- Institute for Advanced Biosciences, University Grenoble Alpes, INSERM, CNRS, 38000 Grenoble, France
- UM GI-DPI, University Hospital Grenoble Alpes, 38000 Grenoble, France
| | - Damien Sanlaville
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Sandra Fert-Ferrer
- Genetics Departement, Centre Hospitalier Métropole Savoie, 73011 Chambery, France
| | - Marine Lebrun
- Department of Genetics, Saint Etienne University Hospital, 42270 Saint Priez en Jarez, France
| | - Valerie Bonadona
- Centre Léon Bérard, Unité de Prévention et Epidémiologie Génétique, 69008 Lyon, France
| | - Alain Calender
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
| | - Nadia Boutry-Kryza
- Department of Genetics, Groupement Hospitalier EST, Hospices Civils de Lyon, 69500 Bron, France
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Gunawardena K, Sirisena ND, Anandagoda G, Neththikumara N, Dissanayake VHW. Germline variants of uncertain significance, their frequency, and clinico-pathological features in a cohort of Sri Lankan patients with hereditary breast cancer. BMC Res Notes 2023; 16:95. [PMID: 37277882 DOI: 10.1186/s13104-023-06365-4] [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: 10/21/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS)-based testing in cancer patients has led to increased detection of variants of uncertain significance (VUS). VUS are genetic variants whose impact on protein function is unknown. VUS pose a challenge to clinicians and patients due to uncertainty regarding their cancer predisposition risk. Paucity of data exists on the pattern of VUS in under-represented populations. This study describes the frequency of germline VUS and clinico-pathological features in Sri Lankan hereditary breast cancer patients. METHODS Data of 72 hereditary breast cancer patients who underwent NGS-based testing between January 2015 and December 2021 were maintained prospectively in a database and analyzed retrospectively. Data were subjected to bioinformatics analysis and variants were classified according to international guidelines. RESULTS Germline variants were detected in 33/72(45.8%) patients, comprising 16(48.5%) pathogenic/likely pathogenic variants and 17(51.5%) VUS. Distribution of VUS in breast cancer predisposing genes were :APC:1(5.8%), ATM:2(11.7%), BRCA1:1(5.8%), BRCA2:5(29.4%), BRIP1:1(5.8%), CDKN2A:1(5.8%), CHEK2:2(11.7%), FANC1:1(5.8%), MET:1(5.8%), STK11:1(5.8%), NF2:1(5.8%). Mean age at cancer diagnosis in patients with VUS was 51.2 years. Most common tumour histopathology was ductal carcinoma 11(78.6%). 50% of tumours in patients having VUS in BRCA1/2 genes were hormone receptor negative. 73.3% patients had family history of breast cancer. CONCLUSIONS A significant portion of patients had a germline VUS. Highest frequency was in BRCA2 gene. Majority had family history of breast cancer. This highlights the need to undertake functional genomic studies to determine the biological effects of VUS and identify potentially clinically actionable variants that would be useful for decision-making and patient management.
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Affiliation(s)
- Kawmadi Gunawardena
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Nirmala D Sirisena
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka.
| | - Gayani Anandagoda
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Nilaksha Neththikumara
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Vajira H W Dissanayake
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
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14
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Witjes VM, Ligtenberg MJL, Vos JR, Braspenning JCC, Ausems MGEM, Mourits MJE, de Hullu JA, Adang EMM, Hoogerbrugge N. The most efficient and effective BRCA1/2 testing strategy in epithelial ovarian cancer: Tumor-First or Germline-First? Gynecol Oncol 2023; 174:121-128. [PMID: 37182432 DOI: 10.1016/j.ygyno.2023.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/29/2023] [Indexed: 05/16/2023]
Abstract
OBJECTIVE Genetic testing in epithelial ovarian cancer (OC) is essential to identify a hereditary cause like a germline BRCA1/2 pathogenic variant (PV). An efficient strategy for genetic testing in OC is highly desired. We evaluated costs and effects of two strategies; (i) Tumor-First strategy, using a tumor DNA test as prescreen to germline testing, and (ii) Germline-First strategy, referring all patients to the clinical geneticist for germline testing. METHODS Tumor-First and Germline-First were compared in two scenarios; using real-world uptake of testing and setting implementation to 100%. Decision analytic models were built to analyze genetic testing costs (including counseling) per OC patient and per family as well as BRCA1/2 detection probabilities. With a Markov model, the life years gained among female relatives with a germline BRCA1/2 PV was investigated. RESULTS Focusing on real-world uptake, with the Tumor-First strategy more OC patients and relatives with a germline BRCA1/2 PV are detected (70% versus 49%), at lower genetic testing costs (€1898 versus €2502 per patient, and €2511 versus €2930 per family). Thereby, female relatives with a germline BRCA1/2 PV can live on average 0.54 life years longer with Tumor-First compared to Germline-First. Focusing on 100% uptake, the genetic testing costs per OC patient are substantially lower in the Tumor-First strategy (€2257 versus €4986). CONCLUSIONS The Tumor-First strategy in OC patients is more effective in identifying germline BRCA1/2 PV at lower genetic testing costs per patient and per family. Optimal implementation of Tumor-First can further improve detection of heredity in OC patients.
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Affiliation(s)
- Vera M Witjes
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands; Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Janet R Vos
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands
| | - Jozé C C Braspenning
- Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands; Department of IQ Healthcare, Radboud university medical center, Nijmegen, the Netherlands
| | - Margreet G E M Ausems
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marian J E Mourits
- Department of Gynecology, University Medical Center Groningen, Groningen, the Netherlands
| | - Joanne A de Hullu
- Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands; Department of Obstetrics and Gynecology, Radboud university medical center, Nijmegen, the Netherlands
| | - Eddy M M Adang
- Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands; Department for Health Evidence, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands.
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15
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Long G, Hu K, Zhang X, Zhou L, Li J. Spectrum of BRCA1 interacting helicase 1 aberrations and potential prognostic and therapeutic implication: a pan cancer analysis. Sci Rep 2023; 13:4435. [PMID: 36932143 PMCID: PMC10023799 DOI: 10.1038/s41598-023-31109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
BRCA1 interacting helicase 1 (BRIP1) alteration was crucial in tumors and it was a potential therapeutic target in ovarian serous cystadenocarcinoma (OV). Although a small number of studies had focused on BRIP1, an extensive study of BRIP1 genetic mutation and its clinical application in different cancer types had not been analyzed. In the current study, we analyzed BRIP1 abnormal expression, methylation, mutation, and their clinical application via several extensive datasets, which covered over 10,000 tumor samples across more than 30 cancer types. The total mutation rate of BRIP1 was rare in pan cancer. Its alteration frequency, oncogenic effects, mutation, and therapeutic implications were different in each cancer. 242 BRIP1 mutations were found across 32 cancer types. UCEC had the highest alteration (mutation and CNV) frequency. In addition, BRIP1 was a crucial oncogenic factor in OV and BRCA. BRIP1 mutation in PRAD was targetable, and FDA had approved a new drug. Moreover, Kaplan-Meier curve analysis showed that BRIP1 expression and genetic aberrations were closely related to patient survival in several cancers, indicating their potential for application as new tumor markers and therapeutic targets. The current study profiled the total BRIP1 mutation spectrum and offered an extensive molecular outlook of BRIP1 in a pan cancer analysis. And it suggested a brand-new perspective for clinical cancer therapy.
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Affiliation(s)
- Guo Long
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaofang Zhang
- Departments of Burn and Plastic, Ningxiang People's Hospital, Hunan University of Chinese Medicine, Changsha, 410600, Hunan, China
| | - Ledu Zhou
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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16
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Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K, Tithi SS, Goldin LR, Rotunno M, Caporaso N, Vogt A, Flamish D, Wyatt K, Liu J, Tucker M, Hahn CN, Brown AL, Scott HS, Mullighan C, Nichols KE, Metzger ML, McMaster ML, Yang JJ, Rampersaud E. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood 2023; 141:1293-1307. [PMID: 35977101 PMCID: PMC10082357 DOI: 10.1182/blood.2022016056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Familial aggregation of Hodgkin lymphoma (HL) has been demonstrated in large population studies, pointing to genetic predisposition to this hematological malignancy. To understand the genetic variants associated with the development of HL, we performed whole genome sequencing on 234 individuals with and without HL from 36 pedigrees that had 2 or more first-degree relatives with HL. Our pedigree selection criteria also required at least 1 affected individual aged <21 years, with the median age at diagnosis of 21.98 years (3-55 years). Family-based segregation analysis was performed for the identification of coding and noncoding variants using linkage and filtering approaches. Using our tiered variant prioritization algorithm, we identified 44 HL-risk variants in 28 pedigrees, of which 33 are coding and 11 are noncoding. The top 4 recurrent risk variants are a coding variant in KDR (rs56302315), a 5' untranslated region variant in KLHDC8B (rs387906223), a noncoding variant in an intron of PAX5 (rs147081110), and another noncoding variant in an intron of GATA3 (rs3824666). A newly identified splice variant in KDR (c.3849-2A>C) was observed for 1 pedigree, and high-confidence stop-gain variants affecting IRF7 (p.W238∗) and EEF2KMT (p.K116∗) were also observed. Multiple truncating variants in POLR1E were found in 3 independent pedigrees as well. Whereas KDR and KLHDC8B have previously been reported, PAX5, GATA3, IRF7, EEF2KMT, and POLR1E represent novel observations. Although there may be environmental factors influencing lymphomagenesis, we observed segregation of candidate germline variants likely to predispose HL in most of the pedigrees studied.
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Affiliation(s)
- Jamie E. Flerlage
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Sara R. Rashkin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yawei Hui
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kayla Hamilton
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Saima S. Tithi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Lynn R. Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | - Jia Liu
- Leidos Biomedical, Inc, Frederick, MD
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christopher N. Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Anna L. Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Monika L. Metzger
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN
| | - Mary L. McMaster
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
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17
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Bertozzi S, Londero AP, Xholli A, Azioni G, Di Vora R, Paudice M, Bucimazza I, Cedolini C, Cagnacci A. Risk-Reducing Breast and Gynecological Surgery for BRCA Mutation Carriers: A Narrative Review. J Clin Med 2023; 12:jcm12041422. [PMID: 36835955 PMCID: PMC9967164 DOI: 10.3390/jcm12041422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
This narrative review aims to clarify the role of breast and gynecological risk-reduction surgery in BRCA mutation carriers. We examine the indications, contraindications, complications, technical aspects, timing, economic impact, ethical issues, and prognostic benefits of the most common prophylactic surgical options from the perspectives of a breast surgeon and a gynecologist. A comprehensive literature review was conducted using the PubMed/Medline, Scopus, and EMBASE databases. The databases were explored from their inceptions to August 2022. Three independent reviewers screened the items and selected those most relevant to this review's scope. BRCA1/2 mutation carriers are significantly more likely to develop breast, ovarian, and serous endometrial cancer. Because of the Angelina effect, there has been a significant increase in bilateral risk-reducing mastectomy (BRRM) since 2013. BRRM and risk-reducing salpingo-oophorectomy (RRSO) significantly reduce the risk of developing breast and ovarian cancer. RRSO has significant side effects, including an impact on fertility and early menopause (i.e., vasomotor symptoms, cardiovascular disease, osteoporosis, cognitive impairment, and sexual dysfunction). Hormonal therapy can help with these symptoms. Because of the lower risk of developing breast cancer in the residual mammary gland tissue after BRRM, estrogen-only treatments have an advantage over an estrogen/progesterone combined treatment. Risk-reducing hysterectomy allows for estrogen-only treatments and lowers the risk of endometrial cancer. Although prophylactic surgery reduces the cancer risk, it has disadvantages associated with early menopause. A multidisciplinary team must carefully inform the woman who chooses this path of the broad spectrum of implications, from cancer risk reduction to hormonal therapies.
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Affiliation(s)
- Serena Bertozzi
- Breast Unit, University Hospital of Udine, 33100 Udine, UD, Italy
- Ennergi Research (Non-Profit Organisation), 33050 Lestizza, UD, Italy
| | - Ambrogio P. Londero
- Ennergi Research (Non-Profit Organisation), 33050 Lestizza, UD, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Infant Health, University of Genoa, 16132 Genova, GE, Italy
- Correspondence:
| | - Anjeza Xholli
- Academic Unit of Obstetrics and Gynecology, IRCCS Ospedale San Martino, 16132 Genoa, GE, Italy
| | - Guglielmo Azioni
- Academic Unit of Obstetrics and Gynecology, IRCCS Ospedale San Martino, 16132 Genoa, GE, Italy
| | - Roberta Di Vora
- Breast Unit, University Hospital of Udine, 33100 Udine, UD, Italy
| | - Michele Paudice
- Anatomic Pathology Unit, Department of Surgical Sciences, and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, GE, Italy
- Anatomic Pathology Unit, IRCCS Ospedale San Martino, 16132 Genoa, GE, Italy
| | - Ines Bucimazza
- Department of Surgery, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban 4001, South Africa
| | - Carla Cedolini
- Breast Unit, University Hospital of Udine, 33100 Udine, UD, Italy
- Ennergi Research (Non-Profit Organisation), 33050 Lestizza, UD, Italy
| | - Angelo Cagnacci
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Infant Health, University of Genoa, 16132 Genova, GE, Italy
- Academic Unit of Obstetrics and Gynecology, IRCCS Ospedale San Martino, 16132 Genoa, GE, Italy
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18
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Pujade-Lauraine E, Brown J, Barnicle A, Wessen J, Lao-Sirieix P, Criscione SW, du Bois A, Lorusso D, Romero I, Petru E, Yoshida H, Vergote I, Colombo N, Hietanen S, Provansal M, Schmalfeldt B, Pignata S, Martín Lorente C, Berton D, Runnebaum IB, Ray-Coquard I. Homologous Recombination Repair Gene Mutations to Predict Olaparib Plus Bevacizumab Efficacy in the First-Line Ovarian Cancer PAOLA-1/ENGOT-ov25 Trial. JCO Precis Oncol 2023; 7:e2200258. [PMID: 36716415 PMCID: PMC9928987 DOI: 10.1200/po.22.00258] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PURPOSE The PAOLA-1/ENGOT-ov25 trial of maintenance olaparib plus bevacizumab for newly diagnosed advanced high-grade ovarian cancer demonstrated a significant progression-free survival (PFS) benefit over placebo plus bevacizumab, particularly in patients with homologous recombination deficiency (HRD)-positive tumors. We explored whether mutations in non-BRCA1 or BRCA2 homologous recombination repair (non-BRCA HRRm) genes predicted benefit from olaparib plus bevacizumab in PAOLA-1. METHODS Eight hundred and six patients were randomly assigned (2:1). Tumors were analyzed using the Myriad MyChoice HRD Plus assay to assess non-BRCA HRRm and HRD status; HRD was based on a genomic instability score (GIS) of ≥ 42. In this exploratory analysis, PFS was assessed in patients harboring deleterious mutations using six non-BRCA HRR gene panels, three devised for this analysis and three previously published. RESULTS The non-BRCA HRRm prevalence ranged from 30 of 806 (3.7%) to 79 of 806 (9.8%) depending on the gene panel used, whereas 152 of 806 (18.9%) had non-BRCA1 or BRCA2 mutation HRD-positive tumors. The majority of tumors harboring non-BRCA HRRm had a low median GIS; however, a GIS of > 42 was observed for tumors with mutations in five HRR genes (BLM, BRIP1, RAD51C, PALB2, and RAD51D). Rates of gene-specific biallelic loss were variable (0% to 100%) in non-BRCA HRRm tumors relative to BRCA1-mutated (99%) or BRCA2-mutated (86%) tumors. Across all gene panels tested, hazard ratios for PFS (95% CI) ranged from 0.92 (0.51 to 1.73) to 1.83 (0.76 to 5.43). CONCLUSION Acknowledging limitations of small subgroup sizes, non-BRCA HRRm gene panels were not predictive of PFS benefit with maintenance olaparib plus bevacizumab versus placebo plus bevacizumab in PAOLA-1, irrespective of the gene panel tested. Current gene panels exploring HRRm should not be considered a substitute for HRD determined by BRCA mutation status and genomic instability testing in first-line high-grade ovarian cancer.
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Affiliation(s)
- Eric Pujade-Lauraine
- ARCAGY-GINECO, Paris, France,Eric Pujade-Lauraine, MD, 8 rue Lamennais, 75008 Paris, France; e-mail:
| | | | | | | | | | | | | | - Domenica Lorusso
- Fondazione IRCCS Istituto Nazionale Tumori, Milan and MITO, Italy
| | - Ignacio Romero
- Instituto Valenciano de Oncología, Valencia and GEICO, Spain
| | - Edgar Petru
- Universitätsklinik für Frauenheilkunde und Geburtshilfe der Med, Universität Graz, Graz and AGO, Austria
| | - Hiroyuki Yoshida
- Saitama Medical University International Medical Center, Saitama and GOTIC, Japan
| | - Ignace Vergote
- University Hospital Leuven, Leuven Cancer Institute, Leuven and BGOG, Belgium
| | - Nicoletta Colombo
- University of Milan-Bicocca and Istituto Europeo di Oncologia IRCCS, Milan and MANGO, Italy
| | | | | | | | - Sandro Pignata
- Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, Naples and MITO, Italy
| | | | - Dominique Berton
- L'Institut de Cancérologie de l'Ouest (ICO), Center René Gauducheau, Saint Herblain and GINECO, France
| | - Ingo B. Runnebaum
- Jena University Hospital, Universitaets-Frauenklinik Jena and AGO, Germany
| | - Isabelle Ray-Coquard
- Center Léon Bérard and University Claude Bernard Lyon 1, Lyon and GINECO, France
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19
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Liu Y, Wu X, Feng Y, Jiang Q, Zhang S, Wang Q, Yang A. Insights into the Oncogenic, Prognostic, and Immunological Role of BRIP1 in Pan-Cancer: A Comprehensive Data-Mining-Based Study. JOURNAL OF ONCOLOGY 2023; 2023:4104639. [PMID: 37153833 PMCID: PMC10162871 DOI: 10.1155/2023/4104639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/14/2023] [Accepted: 04/08/2023] [Indexed: 05/10/2023]
Abstract
Background BRCA1 interacting helicase 1 (BRIP1), an ATP-dependent DNA helicase which belongs to an Iron-Sulfur (Fe-S) helicase cluster family with a DEAH domain, plays a key role in DNA damage and repair, Fanconi anemia, and development of several cancers including breast and ovarian cancer. However, its role in pan-cancer remains largely unknown. Methods BRIP1 expression data of tumor and normal tissues were downloaded from the Cancer Genome Atlas, Genotype-Tissue Expression, and Human Protein Atlas databases. Correlation between BRIP1 and prognosis, genomic alterations, and copy number variation (CNV) as well as methylation in pan-cancer were further analyzed. Protein-protein interaction (PPI) and gene set enrichment and variation analysis (GSEA and GSVA) were performed to identify the potential pathways and functions of BRIP1. Besides, BRIP1 correlations with tumor microenvironment (TME), immune infiltration, immune-related genes, tumor mutation burden (TMB), microsatellite instability (MSI), and immunotherapy as well as antitumor drugs were explored in pan-cancer. Results Differential analyses showed an increased expression of BRIP1 in 28 cancer types and its aberrant expression could be an indicator for prognosis in most cancers. Among the various mutation types of BRIP1 in pan-cancer, amplification was the most common type. BRIP1 expression had a significant correlation with CNV and DNA methylation in 23 tumor types and 16 tumor types, respectively. PPI, GSEA, and GSVA results validated the association between BRIP1 and DNA damage and repair, cell cycle, and metabolism. In addition, the expression of BRIP1 and its correlation with TME, immune-infiltrating cells, immune-related genes, TMB, and MSI as well as a variety of antitumor drugs and immunotherapy were confirmed. Conclusions Our study indicates that BRIP1 plays an imperative role in the tumorigenesis and immunity of various tumors. It may not only serve as a diagnostic and prognostic biomarker but also can be a predictor for drug sensitivity and immunoreaction during antitumor treatment in pan-cancer.
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Affiliation(s)
- Yongru Liu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xi Wu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yunlu Feng
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qingwei Jiang
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shengyu Zhang
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qiang Wang
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Aiming Yang
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
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20
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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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21
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Yao H, Li N, Yuan H. Clinical characteristics and survival analysis of Chinese ovarian cancer patients with RAD51D germline mutations. BMC Cancer 2022; 22:1337. [PMID: 36544182 PMCID: PMC9768941 DOI: 10.1186/s12885-022-10456-z] [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: 09/06/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES We aimed to describe the behavior among Chinese ovarian cancer patients with RAD51D germline mutations at our institution. METHODS Next-generation sequencing (NGS) was conducted for the entire coding regions and exon/intron boundaries of the RAD51D genes in 781 Chinese ovarian cancer patients treated at our institution from January 1, 2015 to August 1, 2021. Clinicopathological characteristics, treatment modalities, and outcomes were assessed for ovarian cancer patients with RAD51D germline mutations. RESULTS RAD51D germline pathogenic mutations were detected in 1.7% (13/781) of patients in this cohort. RAD51D c. 270_271dup (p. Lys91fs) mutation was the most common mutation which was found in 7 patients (7/13, 53.1%). Patients median age at diagnosis was 58 years (range: 45-69 years). 46.2% (6/13) of them were diagnosed after 60 years. Only 1 patient (1/13, 7.7%) had a family history of ovarian or breast cancer. And 1 patient (1/13, 7.7%) had a personal history of breast cancer. The FIGO 2014 distribution by stage was: stage II in 1 patient (7.7%), stage III in 9 patients (69.2%) and stage IV in 3 patient (23.1%). 92.3% (12/13) patients had high-grade serous carcinoma. 2 patients (2/13, 15.4%) had a primary peritoneal cancer. The majority of patients in the entire cohort were reported to be platinum sensitive (92.3%, 12/13) with a platinum-free interval (PFI) of > 6 months. For patients who received PARPis for 2nd line maintenance treatment (n = 5), 2 patients discontinued PARPis treatment after 33.5 and 8.1 months of duration. Other 3 patients are still on therapy with a duration of 2.4, 13.8 and 30.1 months at the date of data cutoff. 1 patient received PARPi as salvage treatment with a duration of only 1.2 months. Nine patients (9/13, 69.2%) relapsed during follow up and all of them relapsed within 2 years after diagnosis, among which 88.9% (8/9) were classified as platinum-sensitive recurrence (PSR), and only 1 patient was classified as platinum-resistant recurrence (PRR). Median PFS for the entire cohort was 17.3 months. Median PFS for the PSR subgroup was 15.9 months. 2 patients died during follow-up. The OS of these 2 patients was 17.2 and 39.6 months. The 5-year OS rate was 67.5%. CONCLUSIONS RAD51D germline mutations are more frequent in Chinese ovarian cancer patients than other population. Few patients have a family history of ovarian or breast cancer, and personal history of breast cancer. Most patients are diagnosed after 50 years. The sensitivity to PARP inhibitors of patients with RAD51D germline mutations need a further analysis.
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Affiliation(s)
- Hongwen Yao
- grid.506261.60000 0001 0706 7839Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Ning Li
- grid.506261.60000 0001 0706 7839Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Hua Yuan
- grid.506261.60000 0001 0706 7839Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
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Nurmi AK, Suvanto M, Dennis J, Aittomäki K, Blomqvist C, Nevanlinna H. Pathogenic Variant Spectrum in Breast Cancer Risk Genes in Finnish Patients. Cancers (Basel) 2022; 14:cancers14246158. [PMID: 36551643 PMCID: PMC9776204 DOI: 10.3390/cancers14246158] [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: 11/08/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Recurrent pathogenic variants have been detected in several breast and ovarian cancer (BC/OC) risk genes in the Finnish population. We conducted a gene-panel sequencing and copy number variant (CNV) analysis to define a more comprehensive spectrum of pathogenic variants in BRCA1, BRCA2, PALB2, CHEK2, ATM, BARD1, RAD51C, RAD51D, BRIP1, and FANCM genes in Finnish BC patients. The combined frequency of pathogenic variants in the BRCA1/2 genes was 1.8% in 1356 unselected patients, whereas variants in the other genes were detected altogether in 8.3% of 1356 unselected patients and in 12.9% of 699 familial patients. CNVs were detected in 0.3% of both 1137 unselected and 612 familial patients. A few variants covered most of the pathogenic burden in the studied genes. Of the BRCA1/2 carriers, 70.8% had 1 of 10 recurrent variants. In the other genes combined, 92.1% of the carrier patients had at least 1 of 11 recurrent variants. In particular, PALB2 c.1592delT and CHEK2 c.1100delC accounted for 88.9% and 82.9%, respectively, of the pathogenic variation in each gene. Our results highlight the importance of founder variants in the BC risk genes in the Finnish population and could be used in the designing of population screening for the risk variants.
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Affiliation(s)
- Anna K. Nurmi
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Maija Suvanto
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
- Correspondence:
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Hanson H, Kulkarni A, Loong L, Kavanaugh G, Torr B, Allen S, Ahmed M, Antoniou AC, Cleaver R, Dabir T, Evans DG, Golightly E, Jewell R, Kohut K, Manchanda R, Murray A, Murray J, Ong KR, Rosenthal AN, Woodward ER, Eccles DM, Turnbull C, Tischkowitz M, Lalloo F. UK consensus recommendations for clinical management of cancer risk for women with germline pathogenic variants in cancer predisposition genes: RAD51C, RAD51D, BRIP1 and PALB2. J Med Genet 2022; 60:417-429. [PMID: 36411032 PMCID: PMC10176381 DOI: 10.1136/jmg-2022-108898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2022]
Abstract
Germline pathogenic variants (GPVs) in the cancer predisposition genes BRCA1, BRCA2, MLH1, MSH2, MSH6, BRIP1, PALB2, RAD51D and RAD51C are identified in approximately 15% of patients with ovarian cancer (OC). While there are clear guidelines around clinical management of cancer risk in patients with GPV in BRCA1, BRCA2, MLH1, MSH2 and MSH6, there are few guidelines on how to manage the more moderate OC risk in patients with GPV in BRIP1, PALB2, RAD51D and RAD51C, with clinical questions about appropriateness and timing of risk-reducing gynaecological surgery. Furthermore, while recognition of RAD51C and RAD51D as OC predisposition genes has been established for several years, an association with breast cancer (BC) has only more recently been described and clinical management of this risk has been unclear. With expansion of genetic testing of these genes to all patients with non-mucinous OC, new data on BC risk and improved estimates of OC risk, the UK Cancer Genetics Group and CanGene-CanVar project convened a 2-day meeting to reach a national consensus on clinical management of BRIP1, PALB2, RAD51D and RAD51C carriers in clinical practice. In this paper, we present a summary of the processes used to reach and agree on a consensus, as well as the key recommendations from the meeting.
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Affiliation(s)
- Helen Hanson
- South West Thames Regional Genetic Services, St George's University Hospitals NHS Foundation Trust, London, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Anjana Kulkarni
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lucy Loong
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Grace Kavanaugh
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Sophie Allen
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ruth Cleaver
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ellen Golightly
- Lothian Menopause Service, Chalmers Sexual Health Centre, Edinburgh, UK
| | - Rosalyn Jewell
- Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kelly Kohut
- South West Thames Regional Genetic Services, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, London, UK
- Department of Health Services Research and Policy, London School of Hygiene & Tropical Medicine, London, UK
- Department of Gynaecological Oncology, Barts Health NHS Trust, London, UK
| | - Alex Murray
- All Wales Medical Genomics Services, University Hospital of Wales, Cardiff, UK
| | - Jennie Murray
- South East Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - Adam N Rosenthal
- Department of Gynaecological Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Emma Roisin Woodward
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Central Manchester NHS Foundation Trust, Manchester, UK
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Central Manchester NHS Foundation Trust, Manchester, UK
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Dong C, Cheng W, Zhang M, Li S, Zhao L, Chen D, Qin Y, Xiao M, Fang S. Genomic profiling of non-small cell lung cancer with the rare pulmonary lymphangitic carcinomatosis and clinical outcome of the exploratory anlotinib treatment. Front Oncol 2022; 12:992596. [PMID: 36324591 PMCID: PMC9620420 DOI: 10.3389/fonc.2022.992596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background To evaluate the potential treatment for patients with non-small cell lung cancer (NSCLC) and rare malignant pulmonary lymphangitis carcinomatosis (PLC), our study provided a genomic profile and clinical outcome of this group of patients. Methods We retrospectively reviewed patients with NSCLC who developed PLC. The genomic alterations, tumor mutation burden (TMB), and microsatellite instability (MSI) based on DNA-based next-generation sequencing were reviewed and compared in a Chinese population with lung adenocarcinomas (Chinese-LUAD cohort). Clinical outcomes after exploratory anlotinib treatment and factors influencing survival are summarized. Results A total of 564 patients with stage IV NSCLC were reviewed, and 39 patients with PLC were included. Genomic profiling of 17 adenocarcinoma patients with PLC (PLC-LUAD cohort) revealed TP53, EGFR, and LRP1B as the three most frequently altered genes. EGFR was less mutated in PLC-LUAD than Chinese-LUAD cohort of 778 patients (35.3% vs. 60.9%, P = 0.043). BRIP1 was mutated more often in the PLC-LUAD cohort (11.8% vs. 1.8%, P= 0.043). Two patients presented with high tumor mutational burden (TMB-H, 10 mutations/MB). Combing alterations in the patient with squamous cell carcinoma, the most altered pathways of PLC included cell cycle/DNA damage, chromatin modification, the RTK/Ras/MAPK pathway and VEGF signaling changes. Fourteen of the participants received anlotinib treatment. The ORR and DCR were 57.1% and 92.9%, respectively. Patients achieved a median progression-free survival of 4.9 months and a median overall survival of 7 months. The adverse effects were manageable. In patients with adenocarcinoma, the mPFS (5.3 months vs. 2.6 months) and mOS (9.9 months vs. 4.5 months) were prolonged in patients receiving anlotinib treatment compared to those receiving other treatment strategies (P < 0.05). Conclusion Patients with PLC in NSCLC demonstrated distinct genetic alterations. The results improve our understanding of the plausible genetic underpinnings of tumorigenesis in PLC and potential treatment strategies. Exploratory anlotinib treatment achieved considerable benefits and demonstrated manageable safety.
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Affiliation(s)
- Changqing Dong
- Department of Thoracic Surgery, Nanjing Chest hospital, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Wanwan Cheng
- Department of Respiratory Medicine, Nanjing Chest hospital, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Meiling Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Si Li
- Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Lele Zhao
- Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Dongsheng Chen
- Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Yong Qin
- Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Mingzhe Xiao
- Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Shencun Fang
- Department of Respiratory Medicine, Nanjing Chest hospital, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Shencun Fang,
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Shah S, Cheung A, Kutka M, Sheriff M, Boussios S. Epithelial Ovarian Cancer: Providing Evidence of Predisposition Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19138113. [PMID: 35805770 PMCID: PMC9265838 DOI: 10.3390/ijerph19138113] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/19/2022]
Abstract
Epithelial ovarian cancer (EOC) is one of the cancers most influenced by hereditary factors. A fourth to a fifth of unselected EOC patients carry pathogenic variants (PVs) in a number of genes, the majority of which encode for proteins involved in DNA mismatch repair (MMR) pathways. PVs in BRCA1 and BRCA2 genes are responsible for a substantial fraction of hereditary EOC. In addition, PV genes involved in the MMR pathway account for 10–15% of hereditary EOC. The identification of women with homologous recombination (HR)-deficient EOCs has significant clinical implications, concerning chemotherapy regimen planning and development as well as the use of targeted therapies such as poly(ADP-ribose) polymerase (PARP) inhibitors. With several genes involved, the complexity of genetic testing increases. In this context, next-generation sequencing (NGS) allows testing for multiple genes simultaneously with a rapid turnaround time. In this review, we discuss the EOC risk assessment in the era of NGS.
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Affiliation(s)
- Sidrah Shah
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
| | - Alison Cheung
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Mikolaj Kutka
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Matin Sheriff
- Department of Urology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK;
| | - Stergios Boussios
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
- King’s College London, Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, London SE1 9RT, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence: or or
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Li X, Wang Y, Xu C, Reheman X, Wang Y, Xu R, Fan J, Huang X, Long L, Yu S, Huang H. Analysis of Competitive Endogenous Mechanism and Survival Prognosis of Serum Exosomes in Ovarian Cancer Patients Based on Sequencing Technology and Bioinformatics. Front Genet 2022; 13:850089. [PMID: 35910206 PMCID: PMC9337233 DOI: 10.3389/fgene.2022.850089] [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: 01/07/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background: We determined the competitive endogenous in serum exosomes of ovarian cancer patients via sequencing technology and raw signal analysis. We performed an in-depth study of the potential mechanisms of ovarian cancer, predicted potential therapeutic targets and performed survival analysis of the potential targets. Methods: Serum exosomes from three ovarian cancer patients were used as the experimental group, serum exosomes from three patients with uterine fibroids were used as the control group, and whole transcriptome analysis of serum exosomes was performed to identify differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in ovarian cancer. The miRcode database and miRNA target gene prediction website were used to predict the target genes. Cytoscape software was used to generate a competing endogenous RNA (ceRNA) network of competitive endogenous mechanism of serum exosomes in ovarian cancer, and the R language was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the target genes. Finally, the TCGA website was used to download clinical and expression data related to ovarian cancer, and the common potential target genes obtained previously were analyzed for survival. Results: A total of 117 differentially expressed lncRNAs as well as 513 differentially expressed mRNAs (p < 0.05, |log2 fold change (FC)|≥ 1.0) were obtained by combining sequencing data and raw signal analysis, and 841 predicted target genes were reciprocally mapped by combining the data from the miRcode database and miRNA target gene prediction website, resulting in 11 potential target genes related to ovarian cancer (FGFR3, BMPR1B, TRIM29, FBN2, PAPPA, CCDC58, IGSF3, FBXO10, GPAM, HOXA10, and LHFPL4). Survival analysis of the above 11 target genes revealed that the survival curve was statistically significant (p < 0.05) for HOXA10 but not for the other genes. Through enrichment analysis, we found that the above target genes were mainly involved in biological processes such as regulation of transmembrane receptor protein kinase activity, structural molecule activity with elasticity, transforming growth factor-activated receptor activity, and GABA receptor binding and were mainly enriched in signaling pathways regulating stem cell pluripotency, bladder cancer, glycerolipid metabolism, central carbon metabolism of cancer, and tyrosine stimulation to EGFR in signaling pathways such as resistance to enzyme inhibitors. Conclusions: The serum exosomal DIO3OS-hsa-miR-27a-3p-HOXA10 competitive endogenous signaling axis affects ovarian cancer development and disease survival by targeting dysregulated transcriptional pathways in cancer.
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Affiliation(s)
- Xia Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Yurong Wang
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Chunju Xu
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Xirenguli Reheman
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Yuxi Wang
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Rong Xu
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
| | - Jiahui Fan
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
| | - Xueying Huang
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
| | - Linna Long
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
| | - Siying Yu
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
| | - He Huang
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, Hunan China
- *Correspondence: He Huang,
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Minigene Splicing Assays Identify 20 Spliceogenic Variants of the Breast/Ovarian Cancer Susceptibility Gene RAD51C. Cancers (Basel) 2022; 14:cancers14122960. [PMID: 35740625 PMCID: PMC9221245 DOI: 10.3390/cancers14122960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
RAD51C loss-of-function variants are associated with an increased risk of breast and ovarian cancers. Likewise, splicing disruptions are a frequent mechanism of gene inactivation. Taking advantage of a previous splicing-reporter minigene with exons 2-8 (mgR51C_ex2-8), we proceeded to check its impact on the splicing of candidate ClinVar variants. A total of 141 RAD51C variants at the intron/exon boundaries were analyzed with MaxEntScan. Twenty variants were selected and genetically engineered into the wild-type minigene. All the variants disrupted splicing, and 18 induced major splicing anomalies without any trace or minimal amounts (<2.4%) of the minigene full-length (FL) transcript. Twenty-seven transcripts (including the wild-type and r.904A FL transcripts) were identified by fluorescent fragment electrophoresis; of these, 14 were predicted to truncate the RAD51C protein, 3 kept the reading frame, and 8 minor isoforms (1.1−4.7% of the overall expression) could not be characterized. Finally, we performed a tentative interpretation of the variants according to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, classifying 16 variants as likely pathogenic. Minigene assays have been proven as valuable tools for the initial characterization of potential spliceogenic variants. Hence, minigene mgR51C_ex2-8 provided useful splicing data for 40 RAD51C variants.
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Assidi M. High N-Cadherin Protein Expression in Ovarian Cancer Predicts Poor Survival and Triggers Cell Invasion. Front Oncol 2022; 12:870820. [PMID: 35574323 PMCID: PMC9096138 DOI: 10.3389/fonc.2022.870820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/04/2022] [Indexed: 12/05/2022] Open
Abstract
Ovarian cancer (OC) is among the most lethal cancer among all gynaecological malignancies. Since most OC patients are diagnosed only at advanced stages mainly because of their imperceptible/nonspecific symptoms, survival rates are low. Therefore, more molecular biomarkers are needed to achieve more effective molecular stratification for better prognostic and theranostic outcomes. The cadherin family, particularly N-cadherin (N-CAD; also known as CDH2), is critical for cell-cell adhesion and epithelial- mesenchymal transition (EMT) of cancer. N-CAD protein has also been shown to be overexpressed in many advanced carcinomas. The aim of this study was to investigate the expression patterns of N-CAD protein, determine their correlations with the clinicopathological features of OC patients, and evaluate its prognostic value and involvement in EMT and metastasis. Protein expression of N-CAD was studied in 117 formalin-fixed and paraffin-embedded (FFPE) blocks from patients diagnosed with OC using Tissue Microarray and immunohistochemistry techniques. The N-CAD protein was overexpressed in 58% of our OC cohort. Furthermore, its cytoplasmic overexpression was significantly correlated with tumor grade (p= 0.05), tumor subtype (p= 0.05), tumor necrosis (p= 0.01), and age at menarche (p= 0.002). Interestingly, Kaplan-Meier analysis showed a significant correlation of disease-free survival (DFS) with OC patients with cytoplasmic N-CAD overexpression (p< 0.03, log rank). Patients with high N-CAD expression have approximately twice the recurrence rate at 5-year follow-up. The results of this study demonstrate a poor prognostic role of N-CAD overexpression in OC, which is reflected in higher recurrence and death rates of OC and its molecular contribution to EMT and distant metastasis. Therefore, OC patients with overexpressed N-CAD need to be monitored more frequently and closely. Further studies with larger patient cohorts are needed to validate these findings, demystify the role of N-CAD in OC pathophysiology, and further investigate its role as a potential therapeutic target.
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Affiliation(s)
- Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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The Genetic and Molecular Analyses of RAD51C and RAD51D Identifies Rare Variants Implicated in Hereditary Ovarian Cancer from a Genetically Unique Population. Cancers (Basel) 2022; 14:cancers14092251. [PMID: 35565380 PMCID: PMC9104874 DOI: 10.3390/cancers14092251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
To identify candidate variants in RAD51C and RAD51D ovarian cancer (OC) predisposing genes by investigating French Canadians (FC) exhibiting unique genetic architecture. Candidates were identified by whole exome sequencing analysis of 17 OC families and 53 early-onset OC cases. Carrier frequencies were determined by the genetic analysis of 100 OC or HBOC families, 438 sporadic OC cases and 1025 controls. Variants of unknown function were assayed for their biological impact and/or cellular sensitivity to olaparib. RAD51C c.414G>C;p.Leu138Phe and c.705G>T;p.Lys235Asn and RAD51D c.137C>G;p.Ser46Cys, c.620C>T;p.Ser207Leu and c.694C>T;p.Arg232Ter were identified in 17.6% of families and 11.3% of early-onset cases. The highest carrier frequency was observed in OC families (1/44, 2.3%) and sporadic cases (15/438, 3.4%) harbouring RAD51D c.620C>T versus controls (1/1025, 0.1%). Carriers of c.620C>T (n = 7), c.705G>T (n = 2) and c.137C>G (n = 1) were identified in another 538 FC OC cases. RAD51C c.705G>T affected splicing by skipping exon four, while RAD51D p.Ser46Cys affected protein stability and conferred olaparib sensitivity. Genetic and functional assays implicate RAD51C c.705G>T and RAD51D c.137C>G as likely pathogenic variants in OC. The high carrier frequency of RAD51D c.620C>T in FC OC cases validates previous findings. Our findings further support the role of RAD51C and RAD51D in hereditary OC.
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Sherill-Rofe D, Raban O, Findlay S, Rahat D, Unterman I, Samiei A, Yasmeen A, Kaiser Z, Kuasne H, Park M, Foulkes WD, Bloch I, Zick A, Gotlieb WH, Tabach Y, Orthwein A. Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair. NAR Cancer 2022; 4:zcac013. [PMID: 35399185 PMCID: PMC8991968 DOI: 10.1093/narcan/zcac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).
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Affiliation(s)
- Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oded Raban
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Amber Yasmeen
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Zafir Kaiser
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - William D Foulkes
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Ein-Kerem, Jerusalem 91120, Israel
| | - Walter H Gotlieb
- Division of Gynecology Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
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Abstract
DNA repair and DNA damage signaling pathways are critical for the maintenance of genomic stability. Defects of DNA repair and damage signaling contribute to tumorigenesis, but also render cancer cells vulnerable to DNA damage and reliant on remaining repair and signaling activities. Here, we review the major classes of DNA repair and damage signaling defects in cancer, the genomic instability that they give rise to, and therapeutic strategies to exploit the resulting vulnerabilities. Furthermore, we discuss the impacts of DNA repair defects on both targeted therapy and immunotherapy, and highlight emerging principles for targeting DNA repair defects in cancer therapy.
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Affiliation(s)
- Jessica L Hopkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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32
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Kandettu A, Adiga D, Devi V, Suresh PS, Chakrabarty S, Radhakrishnan R, Kabekkodu SP. Deregulated miRNA clusters in ovarian cancer: Imperative implications in personalized medicine. Genes Dis 2022; 9:1443-1465. [PMID: 36157483 PMCID: PMC9485269 DOI: 10.1016/j.gendis.2021.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/04/2021] [Accepted: 12/31/2021] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer (OC) is one of the most common and fatal types of gynecological cancer. OC is usually detected at the advanced stages of the disease, making it highly lethal. miRNAs are single-stranded, small non-coding RNAs with an approximate size ranging around 22 nt. Interestingly, a considerable proportion of miRNAs are organized in clusters with miRNA genes placed adjacent to one another, getting transcribed together to result in miRNA clusters (MCs). MCs comprise two or more miRNAs that follow the same orientation during transcription. Abnormal expression of the miRNA cluster has been identified as one of the key drivers in OC. MC exists both as tumor-suppressive and oncogenic clusters and has a significant role in OC pathogenesis by facilitating cancer cells to acquire various hallmarks. The present review summarizes the regulation and biological function of MCs in OC. The review also highlights the utility of abnormally expressed MCs in the clinical management of OC.
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33
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Ogawa C, Hirasawa A, Ida N, Nakamura K, Masuyama H. Hereditary gynecologic tumors and precision cancer medicine. J Obstet Gynaecol Res 2022; 48:1076-1090. [PMID: 35229413 DOI: 10.1111/jog.15197] [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: 11/30/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
Gynecologic cancers are more often caused by genetic factors than other cancers. Genetic testing has become a promising avenue for the prevention, prognosis, and treatment of cancers. This review describes molecular features of gynecologic tumors linked to hereditary syndromes, gives an overview of the current state of clinical management, and clarifies the role of gynecology in the treatment of hereditary tumors. Typical hereditary gynecologic tumors include hereditary breast and ovarian cancer, Lynch syndrome, Peutz-Jeghers syndrome, and Cowden syndrome. Multigene panel testing, which analyzes a preselected subset of genes for genetic variants, has recently become the first-choice test because it can provide more accurate risk assessment than a single test. Furthermore, comprehensive genomic cancer profiling enables personalized cancer treatment and aids in germline findings.
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Affiliation(s)
- Chikako Ogawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naoyuki Ida
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Keiichiro Nakamura
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hisashi Masuyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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34
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Beyond BRCA1/2: Homologous Recombination Repair Genetic Profile in a Large Cohort of Apulian Ovarian Cancers. Cancers (Basel) 2022; 14:cancers14020365. [PMID: 35053526 PMCID: PMC8773795 DOI: 10.3390/cancers14020365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/29/2021] [Accepted: 01/07/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Ovarian cancer (OC) is the second most common gynecologic malignancy and the most common cause of death among women with gynecologic cancer. Despite significant improvements having been made over the past decades, OC remains one of the most challenging malignancies to treat. Targeted therapies, such as PARPi, have emerged as one of the most interesting treatments for OC, particularly in women with BRCA1 or BRCA2 mutations. or those with a dysfunctional homologous recombination repair pathway. The purpose of our study is to address the role of NGS-targeted resequencing in the clinical routine of OC, focusing not only on BRCA1/2 but also on the homologous recombination repair genetic profile. Abstract Background: Pathogenic variants in homologous recombination repair (HRR) genes other than BRCA1/2 have been associated with a high risk of ovarian cancer (OC). In current clinical practice, genetic testing is generally limited to BRCA1/2. Herein, we investigated the mutational status of both BRCA1/2 and 5 HRR genes in 69 unselected OC, evaluating the advantage of multigene panel testing in everyday clinical practice. Methods: We analyzed 69 epithelial OC samples using an NGS custom multigene panel of the 5 HRR pathways genes, beyond the genetic screening routine of BRCA1/2 testing. Results: Overall, 19 pathogenic variants (27.5%) were detected. The majority (21.7%) of patients displayed a deleterious mutation in BRCA1/2, whereas 5.8% harbored a pathogenic variant in one of the HRR genes. Additionally, there were 14 (20.3%) uncertain significant variants (VUS). The assessment of germline mutational status showed that a small number of variants (five) were not detected in the corresponding blood sample. Notably, we detected one BRIP1 and four BRCA1/2 deleterious variants in the low-grade serous and endometrioid histology OC, respectively. Conclusion: We demonstrate that using a multigene panel beyond BRCA1/2 improves the diagnostic yield in OC testing, and it could produce clinically relevant results.
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Hospital-based ovarian cancer patient traceback program results in minimal genetic testing uptake. Gynecol Oncol 2022; 164:615-621. [PMID: 34998598 DOI: 10.1016/j.ygyno.2021.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To determine the feasibility of hospital-based genetic counseling and testing (GC/T) Traceback for Ovarian Cancer (OC) patients, as proposed by the Division of Cancer Prevention and the Division of Cancer Control and Population Sciences, National Cancer Institute. METHODS Living patients with OC were sent a letter explaining the availability of guideline-supported GC/T for at least BRCA1/2 and surrogates of deceased patients were called on the telephone. Outcomes of contact attempts were systematically recorded and statistically described. RESULTS 598 Traceback-eligible OC patients diagnosed from 2006 to 2016 were identified (163 presumed-living and 435 deceased). Two living patients called our office and scheduled an appointment for GC/T after receiving a letter. For surrogates of prior patients, successful contact occurred in 25% of call attempts. Fourteen individuals (2 living patients and 12 surrogates) underwent genetic counseling. Of those 14, 10 individuals consented to genetic testing and 5 followed through with sample collection. None of these individuals had pathogenic variants (PVs). When surrogate call notes were reviewed, 58% reflected positive responses to contact, however 42% were noted to have negative or indifferent responses, which were most common among spouses. Total time spent for hospital-based Traceback was 109 h. CONCLUSIONS Overall, hospital-based Traceback via letter and telephone contact of surrogates is time-intensive and results in minimal uptake of GC/T. To practically execute this type of outreach program, health systems should consider collection of alternative contact information to allow for electronic communication of patient surrogates. Our study also underscores the importance of timely GC/T while patients are in active cancer care.
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36
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Yamamoto H, Hirasawa A. Homologous Recombination Deficiencies and Hereditary Tumors. Int J Mol Sci 2021; 23:348. [PMID: 35008774 PMCID: PMC8745585 DOI: 10.3390/ijms23010348] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination (HR) is a vital process for repairing DNA double-strand breaks. Germline variants in the HR pathway, comprising at least 10 genes, such as BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK2, NBS1(NBN), PALB2, RAD51C, and RAD51D, lead to inherited susceptibility to specific types of cancers, including those of the breast, ovaries, prostate, and pancreas. The penetrance of germline pathogenic variants of each gene varies, whereas all their associated protein products are indispensable for maintaining a high-fidelity DNA repair system by HR. The present review summarizes the basic molecular mechanisms and components that collectively play a role in maintaining genomic integrity against DNA double-strand damage and their clinical implications on each type of hereditary tumor.
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Affiliation(s)
- Hideki Yamamoto
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
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37
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A Review of Breast Cancer Risk Factors in Adolescents and Young Adults. Cancers (Basel) 2021; 13:cancers13215552. [PMID: 34771713 PMCID: PMC8583289 DOI: 10.3390/cancers13215552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Cancer diagnosed in patients between the ages of 15 and 39 deserves special consideration. Diagnoses within this cohort of adolescents and young adults include childhood cancers which present at an older age than expected, or an early presentation of cancers that are typically observed in older adults, such as breast cancer. Cancers within this age group are associated with worse disease-free and overall survival rates, and the incidence of these cases are rising. Knowing an individual’s susceptibility to disease can change their clinical management and allow for the risk-testing of relatives. This review discusses the risk factors that contribute to breast cancer in this unique cohort of patients, including inherited genetic risk factors, as well as environmental and lifestyle factors. We also describe risk models that allow clinicians to quantify a patient’s lifetime risk of developing disease. Abstract Cancer in adolescents and young adults (AYAs) deserves special consideration for several reasons. AYA cancers encompass paediatric malignancies that present at an older age than expected, or early-onset of cancers that are typically observed in adults. However, disease diagnosed in the AYA population is distinct to those same cancers which are diagnosed in a paediatric or older adult setting. Worse disease-free and overall survival outcomes are observed in the AYA setting, and the incidence of AYA cancers is increasing. Knowledge of an individual’s underlying cancer predisposition can influence their clinical care and may facilitate early tumour surveillance strategies and cascade testing of at-risk relatives. This information can further influence reproductive decision making. In this review we discuss the risk factors contributing to AYA breast cancer, such as heritable predisposition, environmental, and lifestyle factors. We also describe a number of risk models which incorporate genetic factors that aid clinicians in quantifying an individual’s lifetime risk of disease.
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38
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Tang J, Casey PJ, Wang M. Suppression of isoprenylcysteine carboxylmethyltransferase compromises DNA damage repair. Life Sci Alliance 2021; 4:4/12/e202101144. [PMID: 34610973 PMCID: PMC8500237 DOI: 10.26508/lsa.202101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Inhibition of isoprenylcysteine carboxylmethyltransferase reduces cancer cells’ ability to repair DNA damage by suppressing the expression of critical DNA damage repair pathway genes, hence increasing their vulnerability to DNA damaging insults such as PARP inhibitors and other DNA damage agents. DNA damage is a double-edged sword for cancer cells. On the one hand, DNA damage–induced genomic instability contributes to cancer development; on the other hand, accumulating damage compromises proliferation and survival of cancer cells. Understanding the key regulators of DNA damage repair machinery would benefit the development of cancer therapies that induce DNA damage and apoptosis. In this study, we found that isoprenylcysteine carboxylmethyltransferase (ICMT), a posttranslational modification enzyme, plays an important role in DNA damage repair. We found that ICMT suppression consistently reduces the activity of MAPK signaling, which compromises the expression of key proteins in the DNA damage repair machinery. The ensuing accumulation of DNA damage leads to cell cycle arrest and apoptosis in multiple breast cancer cells. Interestingly, these observations are more pronounced in cells grown under anchorage-independent conditions or grown in vivo. Consistent with the negative impact on DNA repair, ICMT inhibition transforms the cancer cells into a “BRCA-like” state, hence sensitizing cancer cells to the treatment of PARP inhibitor and other DNA damage–inducing agents.
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Affiliation(s)
- Jingyi Tang
- Duke-NUS Medical School, Program in Cancer and Stem Cell, Singapore, Singapore
| | - Patrick J Casey
- Duke-NUS Medical School, Program in Cancer and Stem Cell, Singapore, Singapore.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Mei Wang
- Duke-NUS Medical School, Program in Cancer and Stem Cell, Singapore, Singapore .,Department of Biochemistry, National University of Singapore, Singapore 117596
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39
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Gjorgoska M, Rižner TL. Estrogens and the Schrödinger's Cat in the Ovarian Tumor Microenvironment. Cancers (Basel) 2021; 13:cancers13195011. [PMID: 34638494 PMCID: PMC8508344 DOI: 10.3390/cancers13195011] [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: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Ovarian cancer is a complex pathology for which we require effective screening and therapeutical strategies. Apart from the cancer cell portion, there exist plastic immune and non-immune cell populations, jointly constituting the context-adaptive tumor microenvironment, which is pivotal in tumorigenesis. Estrogens might be synthesized in the ovarian tumor tissue and actively contribute to the shaping of an immunosuppressive microenvironment. Current immune therapies have limited effectiveness as a multitude of factors influence the outcome. A thorough understanding of the ovarian cancer biology is crucial in the efforts to reestablish homeostasis. Abstract Ovarian cancer is a heterogeneous disease affecting the aging ovary, in concert with a complex network of cells and signals, together representing the ovarian tumor microenvironment. As in the “Schrödinger’s cat” thought experiment, the context-dependent constituents of the—by the time of diagnosis—well-established tumor microenvironment may display a tumor-protective and -destructive role. Systemic and locally synthesized estrogens contribute to the formation of a pro-tumoral microenvironment that enables the sustained tumor growth, invasion and metastasis. Here we focus on the estrogen biosynthetic and metabolic pathways in ovarian cancer and elaborate their actions on phenotypically plastic, estrogen-responsive, aging immune cells of the tumor microenvironment, altogether highlighting the multicomponent-connectedness and complexity of cancer, and contributing to a broader understanding of the ovarian cancer biology.
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40
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Flaum N, van Veen EM, Smith O, Amico S, Newman WG, Crosbie EJ, Edmondson R, Smith MJ, Evans DG. Dominant-negative pathogenic variant BRIP1 c.1045G>C is a high-risk allele for non-mucinous epithelial ovarian cancer: A case-control study. Clin Genet 2021; 101:48-54. [PMID: 34585738 DOI: 10.1111/cge.14068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 11/28/2022]
Abstract
BRIP1 is a moderate susceptibility epithelial ovarian cancer (EOC) gene. Having identified the BRIP1 c.1045G>C missense variant in a number of families with EOC, we aimed to investigate the frequency of this and BRIP1.2392C>T pathogenic variant in patients with breast cancer (BC) and/or EOC. A case-control study of 3767 cases and 2043 controls was undertaken investigating the presence of these variants using Sanger sequencing and gene panel data. Individuals with BC and/or EOC were grouped by family history. BRIP1 c.1045G>C was associated with increased risk of BC/EOC (OR = 37.7; 95% CI 5.3-444.2; P = 0.0001). The risk was highest for women with EOC (OR = 140.8; 95% CI 23.5-1723.0; P < 0.0001) and lower for BC (OR = 11.1; 95% CI 1.2-106.5; P = 0.1588). BRIP1 c.2392C>T was associated with smaller risks for BC/EOC (OR = 5.4; 95%CI 2.4-12.7; P = 0.0003), EOC (OR = 5.9; 95% CI 1.3-23.0; p = 0.0550) and BC (OR = 5.3; 95%CI 2.3-12.9; P = 0.0009). Our study highlights the importance of BRIP1 as an EOC susceptibility gene, especially in familial EOC. The variant BRIP1 c.1045G>C, rs149364097, is of particular interest as its dominant-negative effect may confer a higher risk of EOC than that of the previously reported BRIP1 c.2392C>T nonsense variant. Dominant-negative missense variants may confer higher risks than their loss-of-function counterparts.
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Affiliation(s)
- Nicola Flaum
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Elke M van Veen
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Olivia Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Stephanie Amico
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard Edmondson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.,Prevention Breast Cancer Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester, UK.,The Christie NHS Foundation Trust, Manchester, UK.,Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, UK
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41
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Shin J, Ding Q, Wang L, Cui Y, Baljinnyam E, Guvenek A, Tian B. CRISPRpas: programmable regulation of alternative polyadenylation by dCas9. Nucleic Acids Res 2021; 50:e25. [PMID: 34244761 PMCID: PMC8934653 DOI: 10.1093/nar/gkab519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/14/2022] Open
Abstract
Most human protein-coding genes produce alternative polyadenylation (APA) isoforms that differ in 3' UTR size or, when coupled with splicing, have variable coding sequences. APA is an important layer of gene expression program critical for defining cell identity. Here, by using a catalytically dead Cas9 and coupling its target site with polyadenylation site (PAS), we develop a method, named CRISPRpas, to alter APA isoform abundance. CRISPRpas functions by enhancing proximal PAS usage, whose efficiency is influenced by several factors, including targeting strand of DNA, distance between PAS and target sequence and strength of the PAS. For intronic polyadenylation (IPA), splicing features, such as strengths of 5' splice site and 3' splice site, also affect CRISPRpas efficiency. We show modulation of APA of multiple endogenous genes, including IPA of PCF11, a master regulator of APA and gene expression. In sum, CRISPRpas offers a programmable tool for APA regulation that impacts gene expression.
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Affiliation(s)
- Jihae Shin
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Qingbao Ding
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Program in Gene Expression and Regulation, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Luyang Wang
- Program in Gene Expression and Regulation, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Yange Cui
- Program in Gene Expression and Regulation, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Erdene Baljinnyam
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Rutgers School of Graduate Studies, Newark, NJ 07103, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Program in Gene Expression and Regulation, the Wistar Institute, Philadelphia, PA 19104, USA.,Center for Systems and Computational Biology, the Wistar Institute, Philadelphia, PA 19104, USA
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42
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Liu CL, Yuan RH, Mao TL. The Molecular Landscape Influencing Prognoses of Epithelial Ovarian Cancer. Biomolecules 2021; 11:998. [PMID: 34356623 PMCID: PMC8301761 DOI: 10.3390/biom11070998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/26/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the major increasing lethal malignancies of the gynecological tract, mostly due to delayed diagnosis and chemoresistance, as well as its very heterogeneous genetic makeup. Application of high-throughput molecular technologies, gene expression microarrays, and powerful preclinical models has provided a deeper understanding of the molecular characteristics of EOC. Therefore, molecular markers have become a potent tool in EOC management, including prediction of aggressiveness, prognosis, and recurrence, and identification of novel therapeutic targets. In addition, biomarkers derived from genomic/epigenomic alterations (e.g., gene mutations, copy number aberrations, and DNA methylation) enable targeted treatment of affected signaling pathways in advanced EOC, thereby improving the effectiveness of traditional treatments. This review outlines the molecular landscape and discusses the impacts of biomarkers on the detection, diagnosis, surveillance, and therapeutic targets of EOC. These findings focus on the necessity to translate these potential biomarkers into clinical practice.
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Affiliation(s)
- Chao-Lien Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Ray-Hwang Yuan
- Department of Surgery, National Taiwan University Hospital, Taipei 10002, Taiwan;
- Department of Surgery, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Tsui-Lien Mao
- Department of Pathology, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Department of Pathology, National Taiwan University Hospital, Taipei 10002, Taiwan
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Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study. NPJ Breast Cancer 2021; 7:76. [PMID: 34117267 PMCID: PMC8196173 DOI: 10.1038/s41523-021-00279-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/03/2021] [Indexed: 01/19/2023] Open
Abstract
Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.
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Robson M. Management of Women With Breast Cancer and Pathogenic Variants in Genes Other Than BRCA1 or BRCA2. J Clin Oncol 2021; 39:2528-2534. [PMID: 34106763 DOI: 10.1200/jco.21.00999] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Oncology Grand Rounds series is designed to place original reports published in the Journal into clinical context. A case presentation is followed by a description of diagnostic and management challenges, a review of the relevant literature, and a summary of the authors' suggested management approaches. The goal of this series is to help readers better understand how to apply the results of key studies, including those published in the Journal of Clinical Oncology, to patients seen in their own clinical practice.
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Affiliation(s)
- Mark Robson
- Breast Cancer Medicine and Clinical Genetics Services, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Sullivan MR, Prakash R, Rawal Y, Wang W, Sung P, Radke MR, Kaufmann SH, Swisher EM, Bernstein KA, Jasin M. Long-term survival of an ovarian cancer patient harboring a RAD51C missense mutation. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006083. [PMID: 33832919 PMCID: PMC8040731 DOI: 10.1101/mcs.a006083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/28/2021] [Indexed: 11/30/2022] Open
Abstract
Mutations in homologous recombination (HR) genes predispose to cancer but also sensitize to chemotherapeutics. Although therapy can initially be effective, cancers frequently cease responding, leading to recurrence and poor prognosis. Here we identify a germline mutation in RAD51C, a critical HR factor and known tumor suppressor, in an ovarian cancer patient with exceptionally long, progression-free survival. The RAD51C–T132P mutation is in a highly conserved residue within the nucleotide-binding site and interferes with single-strand DNA binding of the RAD51 paralog complex RAD51B–RAD51C–RAD51D–XRCC2 and association with another RAD51 paralog XRCC3. These biochemical defects lead to highly defective HR and drug sensitivity in tumor cells, ascribing RAD51C–T132P as a deleterious mutation that was likely causal for tumor formation. Conversely, its position within a critical site suggests that it is refractory to secondary mutations that would restore RAD51C gene function and lead to therapy resistance. A need for a greater understanding of the relationship between mutation position and reversion potential of HR genes is underscored, as it may help predict the effectiveness of therapies in patients with HR-deficient cancers.
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Affiliation(s)
- Meghan R Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology, UT Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Weibin Wang
- Department of Radiation Medicine, Peking University Health Science Center, Beijing, 100191, China
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, UT Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Marc R Radke
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Elizabeth M Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Kara A Bernstein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
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Kiyozawa D, Kohashi K, Takamatsu D, Yamamoto T, Eto M, Iwasaki T, Motoshita J, Shimokama T, Kinjo M, Oshiro Y, Yonemasu H, Oda Y. Morphological, immunohistochemical, and genomic analyses of papillary renal neoplasm with reverse polarity. Hum Pathol 2021; 112:48-58. [PMID: 33811832 DOI: 10.1016/j.humpath.2021.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 01/27/2023]
Abstract
Papillary renal neoplasm with reverse polarity (PRNRP) is a recently proposed entity of renal tumor. It shows a far better prognosis than papillary renal cell carcinoma (PRCC) and frequently has KRAS missense mutation. In this study, we compared 14 cases of PRNRP and 10 cases of PRCC type 1 (PRCC1) and type 2 (PRCC2) from clinical, morphological, immunohistochemical, and molecular biological perspectives. We subjected all PRNRP and PRCC cases to immunohistochemical analysis. Whole-exome sequencing using next-generation sequencing (NGS) was performed for six cases of PRNRP, three cases of PRCC1, and four cases of PRCC2. A search for KRAS gene mutation in the remaining eight cases of PRNRP was performed by polymerase chain reaction (PCR) sequencing. The results showed that all cases of PRNRP were pT1N0M0, none of which followed a course of recurrence or tumor-related death. Immunohistochemical analysis revealed diffuse staining of CK7, EMA, PAX8, and GATA3 but weak or negative staining of CD10, CD15, and AMACR in PRNRP. By NGS and PCR, KRAS missense mutation was detected in 11 of 14 PRNRP cases, although pathogenic KRAS mutation was not observed in PRCC1 and PRCC2. NGS analysis revealed less tumor mutation burden in PRNRP than in PRCC. PRNRP also showed no specific chromosomal copy number abnormalities, including gains of 7 and 17. In conclusion, we propose that PRNRP is a distinct condition from PRCC.
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Affiliation(s)
- Daisuke Kiyozawa
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Dai Takamatsu
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takeo Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takeshi Iwasaki
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan; Department of Pathology, JCHO Kyushu Hospital, Kitakyushu, 806-8501, Japan
| | - Junichi Motoshita
- Department of Pathology, JCHO Kyushu Hospital, Kitakyushu, 806-8501, Japan
| | - Tatsuro Shimokama
- Department of Pathology, Steel Memorial Yawata Hospital, Kitakyushu, 805-8508, Japan
| | - Mitsuru Kinjo
- Department of Pathology, Steel Memorial Yawata Hospital, Kitakyushu, 805-8508, Japan
| | - Yumi Oshiro
- Department of Pathology, Matsuyama Red Cross Hospital, Matsuyama, 790-8524, Japan
| | | | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
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Recurrent Mutations in BRCA1, BRCA2, RAD51C, PALB2 and CHEK2 in Polish Patients with Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13040849. [PMID: 33670479 PMCID: PMC7921976 DOI: 10.3390/cancers13040849] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of the study was to analyze the frequency and magnitude of association of 21 recurrent founder germline mutations in BRCA1, BRCA2, PALB2, RAD51C, and CHEK2 genes with ovarian cancer risk among unselected patients in Poland. We genotyped 21 recurrent germline mutations in BRCA1 (9 mutations), BRCA2 (4 mutations), RAD51C (3 mutations), PALB2 (2 mutations), and CHEK2 (3 mutations) among 2270 Polish ovarian cancer patients and 1743 healthy controls, and assessed the odds ratios (OR) for developing ovarian cancer for each gene. Mutations were detected in 369 out of 2095 (17.6%) unselected ovarian cancer cases and 117 out of 1743 (6.7%) unaffected controls. The ovarian cancer risk was associated with mutations in BRCA1 (OR = 40.79, 95% CI: 18.67-114.78; p = 0.29 × 10-15), in BRCA2 (OR = 25.98; 95% CI: 1.55-434.8; p = 0.001), in RAD51C (OR = 6.28; 95% CI 1.77-39.9; p = 0.02), and in PALB2 (OR 3.34; 95% CI: 1.06-14.68; p = 0.06). There was no association found for CHEK2. We found that pathogenic mutations in BRCA1, BRCA2, RAD51C or PALB2 are responsible for 12.5% of unselected cases of ovarian cancer. We recommend that all women with ovarian cancer in Poland and first-degree female relatives should be tested for this panel of 18 mutations.
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Polaczek R, Schürmann P, Speith LM, Geffers R, Dürst M, Hillemanns P, Park-Simon TW, Liebrich C, Dörk T. Germline variation of Ribonuclease H2 genes in ovarian cancer patients. J Ovarian Res 2020; 13:146. [PMID: 33353557 PMCID: PMC7756920 DOI: 10.1186/s13048-020-00753-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 12/02/2022] Open
Abstract
Epithelial ovarian carcinoma (EOC) is a genetically heterogeneous disease that is partly driven by molecular defects in mismatch repair (MMR) or homology-directed DNA repair (HDR). Ribonuclease H2 serves to remove mis-incorporated ribonucleotides from DNA which alleviates HDR mechanisms and guides the MMR machinery. Although Ribonuclease H2 has been implicated in cancer, the role of germline variants for ovarian cancer is unknown. In the present case-control study, we sequenced the coding and flanking untranslated regions of the RNASEH2A, RNASEH2B and RNASEH2C genes, encoding all three subunits of Ribonuclease H2, in a total of 602 German patients with EOC and of 940 healthy females from the same population. We identified one patient with a truncating variant in RNASEH2B, p.C44X, resulting in a premature stop codon. This patient had high-grade serous EOC with an 8 years survival after platinum/taxane-based therapy. Subsequent analysis of TCGA data similarly showed a significantly longer progression-free survival in ovarian cancer patients with low RNASEH2B or RNASEH2C expression levels. In conclusion, loss-of-function variants in Ribonuclease H2 genes are not common predisposing factors in ovarian cancer but the possibility that they modulate therapeutic platinum response deserves further investigation.
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Affiliation(s)
- Rahel Polaczek
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Peter Schürmann
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Lisa-Marie Speith
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Robert Geffers
- Genome Analytics Unit, Helmholtz Institute for Infection Research, Braunschweig, Germany
| | - Matthias Dürst
- Department of Gynaecology and Obstetrics, University Clinics Jena, Jena, Germany
| | - Peter Hillemanns
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Tjoung-Won Park-Simon
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Clemens Liebrich
- Department of Gynaecology and Obstetrics, Hospital Wolfsburg, Wolfsburg, Germany
| | - Thilo Dörk
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany.
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
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50
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Owiti NA, Nagel ZD, Engelward BP. Fluorescence Sheds Light on DNA Damage, DNA Repair, and Mutations. Trends Cancer 2020; 7:240-248. [PMID: 33203608 DOI: 10.1016/j.trecan.2020.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
DNA damage can lead to carcinogenic mutations and toxicity that promotes diseases. Therefore, having rapid assays to quantify DNA damage, DNA repair, mutations, and cytotoxicity is broadly relevant to health. For example, DNA damage assays can be used to screen chemicals for genotoxicity, and knowledge about DNA repair capacity has applications in precision prevention and in personalized medicine. Furthermore, knowledge of mutation frequency has predictive power for downstream cancer, and assays for cytotoxicity can predict deleterious health effects. Tests for all of these purposes have been rendered faster and more effective via adoption of fluorescent readouts. Here, we provide an overview of established and emerging cell-based assays that exploit fluorescence for studies of DNA damage and its consequences.
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Affiliation(s)
- Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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