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Xiao Q, Mao X, Ploner A, Grassmann F, Rodriguez J, Eriksson M, Hall P, Czene K. Cancer risks among first-degree relatives of women with a genetic predisposition to breast cancer. J Natl Cancer Inst 2024; 116:911-919. [PMID: 38366028 PMCID: PMC11160497 DOI: 10.1093/jnci/djae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Associations between germline alterations in women and cancer risks among their relatives are largely unknown. METHODS We identified women from 2 Swedish cohorts Karolinska Mammography Project for Risk Prediction of Breast Cancer (KARMA) and prevalent KARMA (pKARMA), including 28 362 women with genotyping data and 13 226 with sequencing data. Using Swedish Multi-Generation Register, we linked these women to 133 389 first-degree relatives. Associations between protein-truncating variants in 8 risk genes and breast cancer polygenic risk score in index women and cancer risks among their relatives were modeled via Cox regression. RESULTS Female relatives of index women who were protein-truncating variant carriers in any of the 8 risk genes had an increased breast cancer risk compared with those of noncarriers (hazard ratio [HR] = 1.85, 95% confidence interval [CI] = 1.52 to 2.27), with the strongest association found for protein-truncating variants in BRCA1 and 2. These relatives had a statistically higher risk of early onset than late-onset breast cancer (P = .001). Elevated breast cancer risk was also observed in female relatives of index women with higher polygenic risk score (HR per SD = 1.28, 95% CI = 1.23 to 1.32). The estimated lifetime risk was 22.3% for female relatives of protein-truncating variant carriers and 14.4% for those related to women in the top polygenic risk score quartile. Moreover, relatives of index women with protein-truncating variant presence (HR = 1.30, 95% CI = 1.06 to 1.59) or higher polygenic risk score (HR per SD = 1.04, 95% CI = 1.01 to 1.07) were also at higher risk of nonbreast hereditary breast and ovary cancer syndrome-related cancers. CONCLUSIONS Protein-truncating variants of risk genes and higher polygenic risk score in index women are associated with an increased risk of breast and other hereditary breast and ovary syndrome-related cancers among relatives.
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Affiliation(s)
- Qingyang Xiao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xinhe Mao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Felix Grassmann
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Juan Rodriguez
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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2
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Freire MV, Martin M, Segers K, Sepulchre E, Leroi N, Coupier J, Kalantari HR, Wolter P, Collignon J, Polus M, Plomteux O, Josse C, Bours V. Digenic Inheritance of Mutations in Homologous Recombination Genes in Cancer Patients. J Pers Med 2024; 14:584. [PMID: 38929805 PMCID: PMC11204488 DOI: 10.3390/jpm14060584] [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: 04/07/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND/OBJECTIVES BRCA1, BRCA2, ATM, and CHEK2 are known cancer predisposition genes (CPGs), but tumor risk in patients with simultaneous pathogenic variants (PVs) in CPGs remains largely unknown. In this study, we describe six patients from five families with multiple cancers who coinherited a combination of PVs in these genes. METHODS PVs were identified using NGS DNA sequencing and were confirmed by Sanger. RESULTS Families 1, 2, and 3 presented PVs in BRCA2 and ATM, family 4 in BRCA2 and BRCA1, and family 5 in BRCA2 and CHEK2. PVs were identified using NGS DNA sequencing and were confirmed by Sanger. The first family included patients with kidney, prostate, and breast cancer, in addition to pancreatic adenocarcinomas. In the second family, a female had breast cancer, while a male from the third family had prostate, gastric, and pancreatic cancer. The fourth family included a male with pancreatic cancer, and the fifth family a female with breast cancer. CONCLUSIONS The early age of diagnosis and the development of multiple cancers in the reported patients indicate a very high risk of cancer in double-heterozygous patients associated with PVs in HR-related CPGs. Therefore, in families with patients who differ from other family members in terms of phenotype, age of diagnosis, or type of cancer, the cascade testing needs to include the study of other CPGs.
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Affiliation(s)
- Maria Valeria Freire
- Department of Human Genetics, GIGA Research Center, University of Liège and CHU Liège, Av. Hippocrate 1/11, 4000 Liège, Belgium;
| | - Marie Martin
- Department of Human Genetics, CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (M.M.); (K.S.); (E.S.); (N.L.)
| | - Karin Segers
- Department of Human Genetics, CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (M.M.); (K.S.); (E.S.); (N.L.)
| | - Edith Sepulchre
- Department of Human Genetics, CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (M.M.); (K.S.); (E.S.); (N.L.)
| | - Natacha Leroi
- Department of Human Genetics, CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (M.M.); (K.S.); (E.S.); (N.L.)
| | - Jérôme Coupier
- Department of Human Genetics, CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (M.M.); (K.S.); (E.S.); (N.L.)
| | | | - Pascal Wolter
- Onco-Hematology Department, St Nikolaus Hospital, Hufengasse 4/8, 4700 Eupen, Belgium;
| | - Joëlle Collignon
- Department of Medical Oncology, GIGA Research Center, University of Liège and CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (J.C.); (C.J.)
| | - Marc Polus
- Department of Gastroenterology, CHU Liège, Av. Hippocrate 1/11, 4000 Liège, Belgium;
| | - Olivier Plomteux
- Gastro-Enterology Department, CHC, Boulevard Patience et Beaujonc 2, 4000 Liège, Belgium;
| | - Claire Josse
- Department of Medical Oncology, GIGA Research Center, University of Liège and CHU Liège, Domaine Universitaire, 4000 Liège, Belgium; (J.C.); (C.J.)
| | - Vincent Bours
- Department of Human Genetics, GIGA Research Center, University of Liège and CHU Liège, Av. Hippocrate 1/11, 4000 Liège, Belgium;
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3
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Tuncer SB, Celik B, Erciyas SK, Erdogan OS, Gültaslar BK, Odemis DA, Avsar M, Sen F, Saip PM, Yazici H. Germline mutational variants of Turkish ovarian cancer patients suspected of Hereditary Breast and Ovarian Cancer (HBOC) by next-generation sequencing. Pathol Res Pract 2024; 254:155075. [PMID: 38219492 DOI: 10.1016/j.prp.2023.155075] [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: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) syndrome is characterized by an increased risk of developing breast cancer (BC) and ovarian cancer (OC) due to inherited genetic mutations. Understanding the genetic variants associated with HBOC is crucial for identifying individuals at high risk and implementing appropriate preventive measures. The study included 630 Turkish OC patients with confirmed diagnostic criteria of The National Comprehensive Cancer Network (NCCN) concerning HBOC. Genomic DNA was extracted from peripheral blood samples, and targeted Next-generation sequencing (NGS) was performed. Bioinformatics analysis and variant interpretation were conducted to identify pathogenic variants (PVs). Our analysis revealed a spectrum of germline pathogenic variants associated with HBOC in Turkish OC patients. Notably, several pathogenic variants in BRCA1, BRCA2, and other DNA repair genes were identified. Specifically, we observed germline PVs in 130 individuals, accounting for 20.63% of the total cohort. 76 distinct PVs in genes, BRCA1 (40 PVs), BRCA2 (29 PVs), ATM (1 PV), CHEK2 (2 PVs), ERCC2 (1 PV), MUTYH (1 PV), RAD51C (1 PV), and TP53 (1PV) and also, two different PVs (i.e., c.135-2 A>G p.? in BRCA1 and c.6466_6469delTCTC in BRCA2) were detected in a 34-year-old OC patient. In conclusion, our study contributes to a better understanding of the genetic variants underlying HBOC in Turkish OC patients. These findings provide valuable insights into the genetic architecture of HBOC in the Turkish population and shed light on the potential contribution of specific germline PVs to the increased risk of OC.
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Affiliation(s)
- Seref Bugra Tuncer
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Betul Celik
- Erzincan Binali Yıldırım University, Department of Molecular Biology, Erzincan, Türkiye
| | - Seda Kilic Erciyas
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Ozge Sukruoglu Erdogan
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Busra Kurt Gültaslar
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Demet Akdeniz Odemis
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Mukaddes Avsar
- Health Services Vocational of Higher Education, T.C. Istanbul Aydın University, Istanbul, Türkiye
| | - Fatma Sen
- Clinic of Medical Oncology, Avrasya Hospital, Istanbul, Türkiye
| | - Pınar Mualla Saip
- Department of Medical Oncology, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Hulya Yazici
- Istanbul Arel University, Arel Medical Faculty, Department of Medical Biology and Genetics, Istanbul, Türkiye
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4
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Zhang Y, Wu H, Gan C, Rao H, Wang Q, Guo X. BRCA1 and BRCA2 germline mutations in Chinese Hakka breast cancer patients. BMC Med Genomics 2024; 17:3. [PMID: 38167124 PMCID: PMC10763220 DOI: 10.1186/s12920-023-01772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE To investigate the prevalence of BRCA1/2 gene variants and evaluate the clinical and pathological characteristics associated with these variants in Chinese Hakka breast cancer patients. METHODS A total of 409 breast cancer patients were analyzed based on next-generation sequencing results, with 337 categorized as non-carriers and 72 as carriers of BRCA1/2 variants. Data on the patients' BRCA1/2 gene mutation status, clinical and pathological characteristics, as well as menstrual and reproductive information, were collected, analyzed, compared, and tabulated. Logistic regression analysis was performed to explore the relationship between clinical characteristics and pathogenic variants. RESULTS Among the patients, 72 were identified as carriers of pathogenic or likely pathogenic variants in BRCA1/2, while 337 had likely benign or benign mutations. The BRCA1 c.2635G > T (p. Glu879*) variant was detected at a high frequency, accounting for 12.5% (4/32) of the BRCA1 mutations, while the c.5164_5165del (p.Ser1722Tyrfs*4) variant was common among the BRCA2 mutations, accounting for 17.5% (7/40). It was observed that a higher proportion of BRCA1 carriers had the triple-negative breast cancer subtype, whereas more BRCA2 carriers exhibited estrogen receptor (ER) + and progesterone receptor (PR) + subtypes. Multivariate logistic regression analysis revealed that a family history of cancer (OR = 2.36, 95% CI = 1.00-5.54), bilateral cancer (OR = 4.78, 95% CI 1.61-14.20), human epidermal growth factor receptor 2 (HER2)- (OR = 8.23, 95% CI 3.25-20.84), and Ki67 ≥ 15% (OR = 3.88, 95% CI 1.41-10.65) were associated with BRCA1/2 mutations, with the age at diagnosis, age at menarche, and premenopausal status serving as covariates. CONCLUSIONS The most common pathogenic variant of the BRCA1 and BRCA2 in breast cancer patients was c.2635G > T and c.5164_5165del, respectively. Additionally, a family history of cancer, bilateral cancer, HER2-, and Ki67 ≥ 15% were identified as independent predictors of BRCA1/2 pathogenic variants.
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Affiliation(s)
- Yinmei Zhang
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Caiyan Gan
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Hui Rao
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Qiuming Wang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, People's Republic of China
| | - Xueming Guo
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China.
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5
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Hughes T, Rose AM. The emergence of Fanconi anaemia type S: a phenotypic spectrum of biallelic BRCA1 mutations. Front Oncol 2023; 13:1278004. [PMID: 38146508 PMCID: PMC10749362 DOI: 10.3389/fonc.2023.1278004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/27/2023] Open
Abstract
BRCA1 is involved in the Fanconi anaemia (FA) pathway, which coordinates repair of DNA interstrand cross-links. FA is a rare genetic disorder characterised by bone marrow failure, cancer predisposition and congenital abnormalities, caused by biallelic mutations affecting proteins in the FA pathway. Germline monoallelic pathogenic BRCA1 mutations are known to be associated with hereditary breast/ovarian cancer, however biallelic mutations of BRCA1 were long predicted to be incompatible with embryonic viability, hence BRCA1 was not considered to be a canonical FA gene. Despite this, several patients with biallelic pathogenic BRCA1 mutations and FA-like phenotypes have been identified - defining a new FA type (FA-S) and designating BRCA1 as an FA gene. This report presents a scoping review of the cases of biallelic BRCA1 mutations identified to date, discusses the functional effects of the mutations identified, and proposes a phenotypic spectrum of BRCA1 mutations based upon available clinical and genetic data. We report that this FA-S cohort phenotype includes short stature, microcephaly, facial dysmorphisms, hypo/hyperpigmented lesions, intellectual disability, chromosomal sensitivity to crosslinking agents and predisposition to breast/ovarian cancer and/or childhood cancers, with some patients exhibiting sensitivity to chemotherapy. Unlike most other types of FA, FA-S patients lack bone marrow failure.
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Affiliation(s)
- Tirion Hughes
- University of Oxford Medical School, Oxford, United Kingdom
| | - Anna M. Rose
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
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6
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Erali RA, Pu T, Vu TM, Mangieri CW, Jee Y, Wise JS, Perry KC, Hsu FC, Levine EA, McNatt MH, Chiba A. Pivotal Role of Genetic Counselors in the Uptake of Germline Genetic Testing in Non-Metastatic Breast Cancer and the Impact of Testing on Surgical Decision Making. Am Surg 2023; 89:5842-5849. [PMID: 37183417 DOI: 10.1177/00031348231175097] [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] [Indexed: 05/16/2023]
Abstract
BACKGROUND Genetic testing is increasingly utilized in breast cancer patients; however, testing rates remain low. We aimed to evaluate the rate of genetic testing at a tertiary academic medical center utilizing a multidisciplinary clinic model including genetic counselor. METHODS A single-center retrospective chart review was performed on a cohort of newly diagnosed breast cancer patients from January 2018 through February 2019. Patients were reviewed for genetic screening eligibility, consultation with a genetic counselor, and test results. RESULTS Final analysis included 426 patients. 261 (61.3%) were found to meet National Comprehensive Cancer Network guidelines for genetic testing, of which 178 patient (68.2%) underwent testing and 32 patients (12.3%) declined testing. Of the 165 not eligible for testing, 5 patients were tested. A total of 183 patients underwent testing and 116 (63.4%) had a negative result, 17 (9.3%) were positive for at least one gene mutation and 50 (27.3%) were identified to have a variant of unknown significance (VUS). There was a positive association between those patients who met with a genetic counselor and eligibility for testing (OR 31.1, 95% CI 16.0-60.5). CONCLUSIONS Genetic testing result has become an increasingly important factor when defining optimal surgical treatment for breast cancer patients. Increasing the availability of genetic consultation for breast cancer patients can improve testing rates and patient selection.
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Affiliation(s)
- Richard A Erali
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Tracey Pu
- Department of Surgery, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Thuy M Vu
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Christopher W Mangieri
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yoonsun Jee
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jordan S Wise
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kathleen C Perry
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Fang-Chi Hsu
- Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Edward A Levine
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Marissa H McNatt
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Akiko Chiba
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
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7
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Han Y, Rovella V, Smirnov A, Buonomo OC, Mauriello A, Perretta T, Shi Y, Woodmsith J, Bischof J, Melino G, Candi E, Bernassola F. A BRCA2 germline mutation and high expression of immune checkpoints in a TNBC patient. Cell Death Discov 2023; 9:370. [PMID: 37813891 PMCID: PMC10562433 DOI: 10.1038/s41420-023-01651-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/23/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of mammary carcinoma. Here, we describe a case of an 81-year-old female diagnosed with ductal triple negative breast cancer with a germline pathogenic variant in BReast CAncer gene2 (BRCA2). Genetic testing also revealed the presence of four somatic mutations in the ephrin type-A receptor 3 (EphA3), TP53, BRCA1-associated protein (BAP1), and MYB genes. The BRCA2, TP53, and BAP1 gene mutations are highly predictive of a defective homologous recombination repair system and subsequent chromosomal instability in this patient. Coherently, the patient displayed a strong homologous recombination deficiency signature and high tumor mutational burden status, which are generally associated with increased probability of immune neoantigens formation and presentation, and with tumor immunogenicity. Analysis of immune checkpoint revealed high expression of programmed cell death ligand 1 (PD-L1), programmed cell death ligand 2 (PD-L2), programmed death 1 (PD1), and cytotoxic T-lymphocyte-associated protein 4 (CTLA 4), suggesting that the patient might likely benefit from immunotherapies. Altogether, these findings support an unveiled link between BRCA2 inactivation, HR deficiency and increased expression of immune checkpoints in TNBC. This clinical case highlights the importance of screening TNBC patients for genetic mutations and TMB biomarkers in order to predict the potential efficacy of immunotherapy.
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Affiliation(s)
- Yuyi Han
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Department of Ophthalmology, The Affiliated Hospital of Jiangnan University, 214000, Wuxi, China
| | - Valentina Rovella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Artem Smirnov
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy
| | - Oreste Claudio Buonomo
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Tommaso Perretta
- Department of Diagnostic Imaging and Interventional Radiology, Policlinico Tor Vergata University, Rome, 00133, Italy
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, Suzhou, 215000, China
| | | | - Julia Bischof
- Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy.
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
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8
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Bilyalov A, Nikolaev S, Danishevich A, Khatkov I, Makhmudov K, Isakova Z, Bakirov N, Omurbaev E, Osipova A, Ramaldanov R, Shagimardanova E, Kiyasov A, Gusev O, Bodunova N. The Spectrum of Germline Nucleotide Variants in Gastric Cancer Patients in the Kyrgyz Republic. Curr Issues Mol Biol 2023; 45:6383-6394. [PMID: 37623222 PMCID: PMC10453583 DOI: 10.3390/cimb45080403] [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: 06/08/2023] [Revised: 07/11/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023] Open
Abstract
Gastric cancer is a major challenge in modern oncology due to its high detection rate and prevalence. While sporadic cases make up the majority of gastric cancer, hereditary gastric cancer is caused by germline mutations in several genes linked to different syndromes. Thus, identifying hereditary forms of gastric cancer is considered crucial globally. A survey study using NGS-based analysis was conducted to determine the frequency of different types of hereditary gastric cancer in the yet-unstudied Kyrgyz population. The study cohort included 113 patients with diagnosed gastric cancer from Kyrgyzstan. The age of patients was 57.6 ± 8.9. Next-generation sequencing analysis of genomic DNA was performed using a custom Roche NimbleGen enrichment panel. The results showed that 6.2% (7/113) of the patients had pathogenic or likely pathogenic genetic variants. Additionally, 3.5% (4/113) of the patients carried heterozygous pathogenic/likely pathogenic variants in high penetrance genes, such as TP53, POLD1, RET, and BRCA2. Moreover, 2.7% (3/113) of the patients carried heterozygous mutations in genes linked to autosomal recessive conditions, specifically PALB2, FANCA, and FANCD2. We have not identified any genetic variants in hereditary GC-associated genes: CDH1, STK11, SMAD4, BMPRIA, APC, MLH1, and others. Our study included patients with sporadic features of GC. The use of recognized criteria (NCCN, Gastric Cancer, Version 2.2022) would increase the number of identified genetic variants in hereditary GC-associated genes. Further research is required to determine the clinical relevance of the genetic variants identified in the current study.
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Affiliation(s)
- Airat Bilyalov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (K.M.); (E.S.); (A.K.); (O.G.)
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
| | - Sergey Nikolaev
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
| | - Anastasiia Danishevich
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
| | - Igor Khatkov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
| | - Komron Makhmudov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (K.M.); (E.S.); (A.K.); (O.G.)
| | - Zhainagul Isakova
- Research Institute of Molecular Biology and Medicine, Bishkek 720005, Kyrgyzstan;
| | - Nurbek Bakirov
- National Center of Oncology and Hematology of the Ministry of Health of the Kyrgyz Republic, Bishkek 720055, Kyrgyzstan; (N.B.); (E.O.); (R.R.)
| | - Ernis Omurbaev
- National Center of Oncology and Hematology of the Ministry of Health of the Kyrgyz Republic, Bishkek 720055, Kyrgyzstan; (N.B.); (E.O.); (R.R.)
| | - Alena Osipova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
- Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ramaldan Ramaldanov
- National Center of Oncology and Hematology of the Ministry of Health of the Kyrgyz Republic, Bishkek 720055, Kyrgyzstan; (N.B.); (E.O.); (R.R.)
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (K.M.); (E.S.); (A.K.); (O.G.)
| | - Andrey Kiyasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (K.M.); (E.S.); (A.K.); (O.G.)
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (K.M.); (E.S.); (A.K.); (O.G.)
- Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Natalia Bodunova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia; (S.N.); (A.D.); (I.K.); (A.O.); (N.B.)
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9
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Mustafa Karim A, Eun Kwon J, Ali T, Jang J, Ullah I, Lee YG, Won Park D, Park J, Woo Jeang J, Chan Kang S. Triple-negative breast cancer: epidemiology, molecular mechanisms, and modern vaccine-based treatment strategies. Biochem Pharmacol 2023; 212:115545. [PMID: 37044296 DOI: 10.1016/j.bcp.2023.115545] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023]
Abstract
Long-standing scarcity of efficacious treatments and tumor heterogeneity have contributed to triple-negative breast cancer (TNBC), a subtype with a poor prognosis and aggressive behavior that accounts for 10-15% of all new cases of breast cancer. TNBC is characterized by the absence of progesterone and estrogen receptor expression and lacks gene amplification or overexpression of HER2. Genomic sequencing has detected that the unique mutational profile of both the somatic and germline modifications in TNBC is staggeringly dissimilar from other breast tumor subtypes. The clinical utility of sequencing germline BRCA1/2 genes has been well established in TNBC. Nevertheless, reports regarding the penetrance and risk of other susceptibility genes are relatively scarce. Recurring mutations (e.g., TP53 and PI3KCA mutations) occur together with rare mutations in TNBC, and the shared effects of genomic modifications drive its progression. Given the heterogeneity and complexity of this disease, a clinical understanding of the genomic modifications in TNBC can pave an innovative way toward its therapy. In this review, we summarized the most recent discoveries associated with the underlying biology of developmental signaling pathways in TNBC. We also summarize the recent advancements in genetics and epidemiology and discuss state-of-the-art vaccine-based therapeutic strategies for TNBC that will enable tailored therapeutics.
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Affiliation(s)
- Asad Mustafa Karim
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea.
| | - Jeong Eun Kwon
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Tanveer Ali
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Jinsoo Jang
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yeong-Geun Lee
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Dae Won Park
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Juha Park
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Jin Woo Jeang
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Se Chan Kang
- Department of Oriental Medicine and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea.
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10
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Sun J, Chu F, Pan J, Zhang Y, Yao L, Chen J, Hu L, Zhang J, Xu Y, Wang X, Cao W, Xie Y. BRCA-CRisk: A Contralateral Breast Cancer Risk Prediction Model for BRCA Carriers. J Clin Oncol 2023; 41:991-999. [PMID: 36480783 DOI: 10.1200/jco.22.00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The absolute cumulative risk of contralateral breast cancer (CBC) for patients with BRCA1/2 variants is unknown. The purpose of this study was to develop a CBC risk prediction model for assessing CBC risk for BRCA1/2 carriers. METHODS The primary cohort of 491 patients with BRCA1/2 variants was derived from a large series of unselected patients with breast cancer. A nomogram was established on the basis of the results of a multivariate Cox regression analysis from this cohort. This model, named BRCA-CRisk, was further validated by an independent cohort of 205 patients with BRCA1/2 variants. Discrimination and calibration of the model were assessed. RESULTS In the primary cohort of 491 patients, 66 developed contralateral breast cancer after a median follow-up of 7.0 years. Four variables were significantly associated with risk of CBC and were incorporated in the establishment of the BRCA-CRisk prediction model: younger age at first breast cancer (with continuous variable, P = .002), positive first-degree family history of breast and/or ovarian cancer (hazard ratio [HR], 1.89; 95% CI, 1.16 to 3.08; P = .011), variant located near the 3' region of BRCA (HR, 2.01; 95% CI, 1.23 to 3.30; P = .006), and endocrine therapy (HR, 0.54; 95% CI, 0.33 to 0.88; P = .013). The area under the time-dependent curves for the 5- and 10-year cumulative risks of CBC were 0.775 and 0.702, respectively. The model was well validated in the independent cohort of 205 BRCA1/2 carriers, with area under the curves of 0.750 and 0.691 for 5 and 10 years, respectively. CONCLUSION BRCA-CRisk model provides a useful tool for assessing the absolute cumulative risk of CBC for BRCA1/2 carriers and may help carriers and clinicians optimally select risk-reducing strategies on the basis of individual CBC risk.
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Affiliation(s)
- Jie Sun
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Futao Chu
- Department of Breast Surgery, Peking University International Hospital, Beijing, P. R. China
| | - Jiani Pan
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, P. R. China.,Zhejiang Chinese Medical University, Hangzhou, P. R. China
| | - Yaxin Zhang
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Lu Yao
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Jiuan Chen
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Li Hu
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Juan Zhang
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Ye Xu
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Xiaojia Wang
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, P. R. China
| | - Wenming Cao
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, P. R. China
| | - Yuntao Xie
- Familial & Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P. R. China.,Department of Breast Surgery, Peking University International Hospital, Beijing, P. R. China
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11
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Larionov A, Fewings E, Redman J, Goldgraben M, Clark G, Boice J, Concannon P, Bernstein J, Conti DV, Tischkowitz M. The Contribution of Germline Pathogenic Variants in Breast Cancer Genes to Contralateral Breast Cancer Risk in BRCA1/BRCA2/PALB2-Negative Women. Cancers (Basel) 2023; 15:cancers15020415. [PMID: 36672364 PMCID: PMC9856968 DOI: 10.3390/cancers15020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Contralateral breast cancer (CBC) is associated with younger age at first diagnosis, family history and pathogenic germline variants (PGVs) in genes such as BRCA1, BRCA2 and PALB2. However, data regarding genetic factors predisposing to CBC among younger women who are BRCA1/2/PALB2-negative remain limited. METHODS In this nested case-control study, participants negative for BRCA1/2/PALB2 PGVs were selected from the WECARE Study. The burden of PGVs in established breast cancer risk genes was compared in 357 cases with CBC and 366 matched controls with unilateral breast cancer (UBC). The samples were sequenced in two phases. Whole exome sequencing was used in Group 1, 162 CBC and 172 UBC (mean age at diagnosis: 42 years). A targeted panel of genes was used in Group 2, 195 CBC and 194 UBC (mean age at diagnosis: 50 years). Comparisons of PGVs burdens between CBC and UBC were made in these groups, and additional stratified sub-analysis was performed within each group according to the age at diagnosis and the time from first breast cancer (BC). RESULTS The PGVs burden in Group 1 was significantly higher in CBC than in UBC (p = 0.002, OR = 2.5, 95CI: 1.2-5.6), driven mainly by variants in CHEK2 and ATM. The proportions of PGVs carriers in CBC and UBC in this group were 14.8% and 5.8%, respectively. There was no significant difference in PGVs burden between CBC and UBC in Group 2 (p = 0.4, OR = 1.4, 95CI: 0.7-2.8), with proportions of carriers being 8.7% and 8.2%, respectively. There was a significant association of PGVs in CBC with younger age. Metanalysis combining both groups confirmed the significant association between the burden of PGVs and the risk of CBC (p = 0.006) with the significance driven by the younger cases (Group 1). CONCLUSION In younger BRCA1/BRCA2/PALB2-negative women, the aggregated burden of PGVs in breast cancer risk genes was associated with the increased risk of CBC and was inversely proportional to the age at onset.
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Affiliation(s)
- Alexey Larionov
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedford MK43 0AL, UK
- Correspondence: (A.L.); (M.T.)
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
| | - James Redman
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
| | - Mae Goldgraben
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
| | - Graeme Clark
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
| | - John Boice
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Patrick Concannon
- Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jonine Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - David V. Conti
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA
| | | | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridge CB2 0QQ, UK
- Correspondence: (A.L.); (M.T.)
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12
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McDonald JT, Ricks-Santi LJ. Hereditary variants of unknown significance in African American women with breast cancer. PLoS One 2022; 17:e0273835. [PMID: 36315513 PMCID: PMC9621418 DOI: 10.1371/journal.pone.0273835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/17/2022] [Indexed: 11/06/2022] Open
Abstract
Expanded implementation of genetic sequencing has precipitously increased the discovery of germline and somatic variants. The direct benefit of identifying variants in actionable genes may lead to risk reduction strategies such as increased surveillance, prophylactic surgery, as well as lifestyle modifications to reduce morbidity and mortality. However, patients with African ancestry are more likely to receive inconclusive genetic testing results due to an increased number of variants of unknown significance decreasing the utility and impact on disease management and prevention. This study examines whole exome sequencing results from germline DNA samples in African American women with a family history of cancer including 37 cases that were diagnosed with breast cancer and 51 family members. Self-identified ancestry was validated and compared to the 1000 genomes population. The analysis of sequencing results was limited to 85 genes from three clinically available common genetic screening platforms. This target region had a total of 993 variants of which 6 (<1%) were pathogenic or likely pathogenic, 736 (74.1%) were benign, and 170 (17.1%) were classified as a variant of unknown significance. There was an average of 3.4±1.8 variants with an unknown significance per individual and 85 of 88 individuals (96.6%) harbored at least one of these in the targeted genes. Pathogenic or likely pathogenic variants were only found in 6 individuals for the BRCA1 (p.R1726fs, rs80357867), BRCA2 (p.K589fs, rs397507606 & p.L2805fs, rs397507402), RAD50 (p.E995fs, rs587780154), ATM (p.V2424G, rs28904921), or MUTYH (p.G396D, rs36053993) genes. Strategies to functionally validate the remaining variants of unknown significance, especially in understudied and hereditary cancer populations, are greatly needed to increase the clinical utility and utilization of clinical genetic screening platforms to reduce cancer incidence and mortality.
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Affiliation(s)
- J. Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington, DC, United States of America
| | - Luisel J. Ricks-Santi
- Cancer Research Center, Hampton University, Hampton, VA, United States of America
- Department of Pharmacotherapy and Translational Research, College of Medicine, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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13
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Ferreira GM, Claro IM, Grosche VR, Cândido D, José DP, Rocha EC, de Moura Coletti T, Manuli ER, Gaburo N, Faria NR, Sabino EC, de Jesus JG, Jardim ACG. Molecular characterization and sequecing analysis of SARS-CoV-2 genome in Minas Gerais, Brazil. Biologicals 2022; 80:43-52. [PMID: 36175304 PMCID: PMC9436897 DOI: 10.1016/j.biologicals.2022.08.001] [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: 02/25/2022] [Revised: 06/14/2022] [Accepted: 08/21/2022] [Indexed: 11/05/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in Wuhan, China, is the causative agent of the coronavirus disease 2019 (COVID-19). Since its first notification in São Paulo state (SP) on 26th February 2020, more than 22,300,000 cases and 619,000 deaths were reported in Brazil. In early pandemic, SARS-CoV-2 spread locally, however, over time, this virus was disseminated to other regions of the country. Herein, we performed genomic sequencing and phylogenetic analysis of SARS-CoV-2 using 20 clinical samples of COVID-19 confirmed cases from 9 cities of Minas Gerais state (MG), in order to evaluate the molecular properties of circulating viral strains in this locality from March to May 2020. Our analyses demonstrated the circulation of B.1 lineage isolates in the investigated locations and nucleotide substitutions were observed into the genomic regions related to important viral structures. Additionally, sequences generated in this study clustered with isolates from SP, suggesting a dissemination route between these two states. Alternatively, monophyletic groups of sequences from MG and other states or country were observed, indicating independent events of virus introduction. These results reinforce the need of genomic surveillance for understand the ongoing spread of emerging viral pathogens.
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Affiliation(s)
| | - Ingra Morales Claro
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Victória Riquena Grosche
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, MG, Brazil; Institute of Bioscience, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Darlan Cândido
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Zoology, University of Oxford, Oxford, UK
| | | | - Esmenia Coelho Rocha
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Thaís de Moura Coletti
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Erika Regina Manuli
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Nuno Rodrigues Faria
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Zoology, University of Oxford, Oxford, UK; MCR Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Jaqueline Goes de Jesus
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, MG, Brazil; Institute of Bioscience, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
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14
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Shinde S, Satpute DP, Behera SK, Kumar D. Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification. ACS OMEGA 2022; 7:30447-30461. [PMID: 36061650 PMCID: PMC9434626 DOI: 10.1021/acsomega.2c03851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Male breast cancer (MBC) is a relatively rare disease, but emerging data recommend the development of novel therapeutics considering its alarming threats. Compared to female breast cancer (FBC), MBC is reportedly associated with inferior outcomes (poor survival) owing to their late diagnosis and lack of adequate treatment. Treatment typically correlates with FBC, involving surgical removal of the breast tissue along with chemo/hormonal/radiation therapy, the tamoxifen being a standard adjuvant. Considering the distinct immunophenotypic (implying different pathogenesis and progression) differences from FBC, the identification of diagnostics, prognostics, and therapeutics for MBC is highly desirable. In this context, we have analyzed the most deleterious nsSNPs of BRCA2, a human tumor suppressor gene constituting the potential biomarker for tumors including MBC, to predict the structural changes associated with the mutants hampering the normal protein-protein and protein-ligand interactions, resulting in MBC progression. Among 27 nsSNPs confined to 21 rsIDs pertaining to MBC, the 19 nsSNPs constituting 14 rsIDs have been predicted as highly deleterious. We believe that these nsSNPs could serve as potential biomarkers for diagnostic and prognostic purposes and could be the pivotal target for MBC drug discovery. Subsequently, the study highlights the exploration of the key nsSNPs (of BRCA2 associated with the MBC) and its applications toward the identification of therapeutic hit TIP006136 following the homology modeling, virtual screening of 5284 phytochemicals retrieved from the TIPdb (a database of phytochemicals from indigenous plants in Taiwan) database, molecular docking (against native and mutant BRCA2), dynamic simulations (against native and mutant BRCA2), density functional theory (DFT), and molecular electrostatic potential. To the best of our knowledge, this is the first report to use diverse computational modules to investigate the important nsSNPs of BRCA2 related to MBC, implying that TIP006136 could be a potential hit and must be studied further (in vitro and in vivo) to establish its anticancer property and efficacy against MBC.
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Affiliation(s)
- Sangita
Dattatray Shinde
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Parshuram Satpute
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Santosh Kumar Behera
- Department
of Biotechnology, National Institute of
Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Kumar
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
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15
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Sun X, Chen W, Qu X, Chen Y. Case Report: Fluzoparib for multiple lines of chemotherapy refractory in metastatic cutaneous squamous cell carcinoma with BRCA2 pathogenic mutation. Front Pharmacol 2022; 13:968060. [PMID: 36034850 PMCID: PMC9411933 DOI: 10.3389/fphar.2022.968060] [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: 06/13/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Poly ADP-ribose polymerase inhibitors (PARPis) are widely used for patients with BRCA1/2 mutations. However, until now, there is no available evidence reported for the efficiency of PARPis in cutaneous squamous cell carcinoma (cSCC). Case presentation: We presented a case of a 40-year-old man diagnosed with metastatic cSCC, relapsing after multiple lines of chemotherapy. Liquid biopsy detected a BRCA2 pathogenic germline mutation (c.3109C > T), indicating PARPis might be effective for this patient. The patient achieved tumor stability, and progression-free survival was five months without severe adverse effects after taking fluzoparib. Conclusion: This result confirmed that PARPis were effective for metastatic cSCC patients with germline BRCA2 pathogenic mutations and provided a new treatment option for this group of patients.
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Affiliation(s)
- Xin Sun
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China
| | - Wenjuan Chen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China
- Liaoning Province Clinical Research Center for Cancer, Shenyang, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Ying Chen, , orcid.org/0000-0002-0022-4034, Xiujuan Qu, , orcid.org/0000-0002-3135-8772
| | - Ying Chen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China
- Liaoning Province Clinical Research Center for Cancer, Shenyang, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Ying Chen, , orcid.org/0000-0002-0022-4034, Xiujuan Qu, , orcid.org/0000-0002-3135-8772
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16
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Paduano F, Colao E, Fabiani F, Rocca V, Dinatolo F, Dattola A, D’Antona L, Amato R, Trapasso F, Baudi F, Perrotti N, Iuliano R. Germline Testing in a Cohort of Patients at High Risk of Hereditary Cancer Predisposition Syndromes: First Two-Year Results from South Italy. Genes (Basel) 2022; 13:genes13071286. [PMID: 35886069 PMCID: PMC9319682 DOI: 10.3390/genes13071286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Germline pathogenic variants (PVs) in oncogenes and tumour suppressor genes are responsible for 5 to 10% of all diagnosed cancers, which are commonly known as hereditary cancer predisposition syndromes (HCPS). A total of 104 individuals at high risk of HCPS were selected by genetic counselling for genetic testing in the past 2 years. Most of them were subjects having a personal and family history of breast cancer (BC) selected according to current established criteria. Genes analysis involved in HCPS was assessed by next-generation sequencing (NGS) using a custom cancer panel with high- and moderate-risk susceptibility genes. Germline PVs were identified in 17 of 104 individuals (16.3%) analysed, while variants of uncertain significance (VUS) were identified in 21/104 (20.2%) cases. Concerning the germline PVs distribution among the 13 BC individuals with positive findings, 8/13 (61.5%) were in the BRCA1/2 genes, whereas 5/13 (38.4%) were in other high- or moderate-risk genes including PALB2, TP53, ATM and CHEK2. NGS genetic testing showed that 6/13 (46.1%) of the PVs observed in BC patients were detected in triple-negative BC. Interestingly, the likelihood of carrying the PVs in the moderate-to-high-risk genes calculated by the cancer risk model BOADICEA was significantly higher in pathogenic variant carriers than in negative subjects. Collectively, this study shows that multigene panel testing can offer an effective diagnostic approach for patients at high risk of hereditary cancers.
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Stem Cells and Medical Genetics Units, Tecnologica Research Institute and Marrelli Health, 88900 Crotone, Italy
- Correspondence: (F.P.); (R.I.)
| | - Emma Colao
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Fernanda Fabiani
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Valentina Rocca
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesca Dinatolo
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Adele Dattola
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Lucia D’Antona
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Francesco Trapasso
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesco Baudi
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Perrotti
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (F.P.); (R.I.)
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17
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Kiendrebeogo IT, Zoure AA, Zongo FI, Ouedraogo SY, Sawadogo AY, Amegnona J, Sombie HK, Bazie JTVE, Sorgho PA, Yonli AT, Ouedraogo MNL, Obiri-Yeboah D, Zongo N, Bambara HA, Simpore J. Screening of BRCA1 (c.5177_5180delGAAA rs80357867 and c.4986+6T>C rs80358086) and the BRCA2 (c.6445_6446delAT rs80359592) Genes for Breast Cancer Prevention in Burkina Faso. Ethiop J Health Sci 2022; 32:699-708. [PMID: 35950060 PMCID: PMC9341024 DOI: 10.4314/ejhs.v32i4.5] [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: 03/16/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background The objective of this study is to search for mutations in the BRCA1 (c.5177_5180delGAAA and c.4986+6T>C) and BRCA2 genes (c.6445_6446delAT) in a population of women diagnosed with breast cancer. Methods This is a case-control study that involved 140 participants, including 70 patients with histologically diagnosed breast cancer and 70 healthy women without breast cancer. Mutations in the BRCA1 (rs80357867, rs80358086) and BRCA2 (rs80359592) genes were tested by real-time PCR. The 95% confidence interval Odds Ratio (OR) was used to estimate the associations between specific genotypes and breast cancer. Results The study revealed that no mutations were detected for rs80359592. Similarly, no reference allele (TTTC/TTTC) of rs80357867 was found in this study. However, the homozygous double mutant (-/) genotype of this rs80357867 was observed in 11.43% and 1.43% of patients and controls respectively, while 88.57% of patients and 98.57% of controls had a heterozygous deletion (TTTC/-). Concerning rs80358086, 8.57% of the patients had a heterozygous mutation (A/G) with no significantly risk association with occurrence of breast cancer (OR = 6.46; 95% CI: 0.75-55.21; p = 0.11). In addition, this heterozygous mutation was significantly associated with a family history of breast cancer (OR=128; 95% CI: 9.46-1730.93) and breast cancer risk in nonmultiparous women (OR=6; 95% CI: 1-35.90; p= 0.05) but no association with overweight/obesity (OR=1.66; 95% CI: 0.18-15.35; p=1). Conclusion This study shows high frequencies of heterozygous mutation of rs80357867 and rs80358086 from patients. In Burkina Faso, these results could help with early diagnosis of breast cancer in patients.
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Affiliation(s)
- Isabelle T Kiendrebeogo
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Abdou A Zoure
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Institute of Health Sciences Research, Department of Biomedical and Public Health, Burkina Faso
| | - Fabienne I Zongo
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso
| | - Serge Y Ouedraogo
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Alexis Y Sawadogo
- Service of Gynecology, University Hospital Center Bogodogo, University Joseph KI-ZERBO, UFR/SDS, Burkina Faso
| | - Jospin Amegnona
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso
| | - Herman K Sombie
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Jean T Valérie Elvira Bazie
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Pegdwendé A Sorgho
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Albert T Yonli
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso
| | - Marie N Lamoussa Ouedraogo
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Faculty of Health Sciences, University Saint Thomas d'Aquin
| | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, School of Medical Sciences, University of Cape Coast
| | - Nayi Zongo
- Department of General and Digestive Surgery, University Hospital Center Yalgado Ouedraogo, University Joseph KI-ZERBO, UFR/SDS, Burkina Faso
| | - Hierrhum A Bambara
- Service of oncology, University Hospital Center Bogodogo, University Joseph KI-ZERBO, UFR/SDS, Burkina Faso
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics, UFR/SVT, University Joseph KI-ZERBO, Burkina Faso.,Pietro Annigoni Biomolecular Research Center, Burkina Faso.,Faculty of Health Sciences, University Saint Thomas d'Aquin
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18
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Discovery of BRCA1/BRCA2 Founder Variants by Haplotype Analysis. Cancer Genet 2022; 266-267:19-27. [DOI: 10.1016/j.cancergen.2022.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
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19
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Kaissarian NM, Meyer D, Kimchi-Sarfaty C. Synonymous Variants: Necessary Nuance in our Understanding of Cancer Drivers and Treatment Outcomes. J Natl Cancer Inst 2022; 114:1072-1094. [PMID: 35477782 PMCID: PMC9360466 DOI: 10.1093/jnci/djac090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Once called "silent mutations" and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.
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Affiliation(s)
- Nayiri M Kaissarian
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
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20
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Rajagopal T, Seshachalam A, Jothi A, Rathnam KK, Talluri S, Venkatabalasubranian S, Dunna NR. Analysis of pathogenic variants in BRCA1 and BRCA2 genes using next-generation sequencing in women with triple negative breast cancer from South India. Mol Biol Rep 2022; 49:3025-3032. [PMID: 35020120 DOI: 10.1007/s11033-022-07129-2] [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: 08/14/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND The frequency of triple-negative breast cancer (TNBC) incidence varies among different populations suggesting the involvement of genetic components towards TNBC development. Previous studies have reported that BRCA1/2 germline mutations confer a lifetime risk of developing TNBC. However, there is hardly any information regarding the common pathogenic variants (PVs) in BRCA1/2 genes that contribute to TNBC in the Indian population. Hence, we screened for PVs in BRCA1/2 and their association with clinico-pathological features in TNBC patients. METHODS AND RESULTS The study recruited 59 TNBC patients without hereditary breast and ovarian cancer (HBOC) from South India. The entire BRCA1 and BRCA2 genes were sequenced for the 59 patients using the Illumina HiSeq X Ten sequencer. Among the 59 TNBC genomic DNA samples sequenced, BRCA mutations were identified in 8 patients (13.6%), BRCA1 mutations in 6 patients, and BRCA2 mutations in 2 patients. Among the 6 BRCA1 mutations, three were c.68_69delAG (185delAG) mutation. Remarkably, all the TNBC patients with BRCA mutations exhibited higher-grade tumors (grade 2 or 3). However, among all the BRCA mutation carriers, only one patient with a BRCA2 mutation (p.Glu1879Lys) developed metastasis. CONCLUSION Our data advocates that South Indian women with higher grade TNBC tumors and without HBOC could be considered for BRCA mutation screening, thereby enabling enhanced decision-making and preventive therapy.
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Affiliation(s)
- Taruna Rajagopal
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA - Deemed University, Thanjavur, 613 401, India
| | - Arun Seshachalam
- Department of Medical and Paediatric Oncology, Dr.G.V.N Cancer Institute, Singarathope, Trichy, 620 008, India
| | - Arunachalam Jothi
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA - Deemed University, Thanjavur, 613 401, India
| | - Krishna Kumar Rathnam
- Department of Hemato Oncology - Medical Oncology and Bone Marrow Transplantation, Meenakshi Mission Hospital & Research Centre, Madurai, 625 107, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Sivaramakrishnan Venkatabalasubranian
- Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai, Tamil Nadu, 603 203, India
| | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA - Deemed University, Thanjavur, 613 401, India.
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21
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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22
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Kim DM, Feilotter HE, Davey SK. BRCA1 Variant Assessment Using a Simple Analytic Assay. J Appl Lab Med 2022; 7:674-688. [PMID: 35021209 DOI: 10.1093/jalm/jfab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND We previously developed a biological assay to accurately predict BRCA1 (BRCA1 DNA repair associated) mutation status, based on gene expression profiles of Epstein-Barr virus-transformed lymphoblastoid cell lines. The original work was done using whole genome expression microarrays, and nearest shrunken centroids analysis. While these approaches are appropriate for model building, they are difficult to implement clinically, where more targeted testing and analysis are required for time and cost savings. METHODS Here, we describe adaptation of the original predictor to use the NanoString nCounter platform for testing, with analysis based on the k-top scoring pairs (k-TSP) method. RESULTS Assessing gene expression using the nCounter platform on a set of lymphoblastoid cell lines yielded 93.8% agreement with the microarray-derived data, and 87.5% overall correct classification of BRCA1 carriers and controls. Using the original gene expression microarray data used to develop our predictor with nearest shrunken centroids, we rebuilt a classifier based on the k-TSP method. This classifier relies on the relative expression of 10 pairs of genes, compared to the original 43 identified by nearest shrunken centroids (NSC), and was 96.2% concordant with the original training set prediction, with a 94.3% overall correct classification of BRCA1 carriers and controls. CONCLUSIONS The k-TSP classifier was shown to accurately predict BRCA1 status using data generated on the nCounter platform and is feasible for initiating a clinical validation.
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Affiliation(s)
- Daniel M Kim
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Scott K Davey
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Departments of Oncology and Biomedical and Molecular Sciences, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
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23
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Resch LD, Hotz A, Zimmer AD, Komlosi K, Singh N, Tzschach A, Windfuhr-Blum M, Juhasz-Boess I, Erbes T, Fischer J, Alter S. The Importance of Extended Analysis Using Current Molecular Genetic Methods Based on the Example of a Cohort of 228 Patients with Hereditary Breast and Ovarian Cancer Syndrome. Genes (Basel) 2021; 12:1483. [PMID: 34680878 PMCID: PMC8535571 DOI: 10.3390/genes12101483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
In about 20-30% of all women with breast cancer, an increased number of cases of breast cancer can be observed in their family history. However, currently, only 5-10% of all breast cancer cases can be attributed to a pathogenic gene alteration. Molecular genetic diagnostics underwent enormous development within the last 10 years. Next-generation sequencing approaches allow increasingly extensive analyses resulting in the identification of additional candidate genes. In the present work, the germline molecular diagnostic analysis of a cohort of 228 patients with suspected hereditary breast and ovarian cancer syndrome (HBOC) was evaluated. The 27 pathogenic gene variants initially detected are listed, and their distribution in the high-risk BRCA1 and BRCA2 genes is presented in this study. In ten high-risk patients, in whom, to date, no pathogenic variant could be detected, an extended genetic analysis of previously not considered risk genes was performed. Three variants of uncertain significance and one pathogenic variant could be described. This proves the importance of extended analysis using current molecular genetic methods.
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Affiliation(s)
- Luise D. Resch
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Alrun Hotz
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Andreas D. Zimmer
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Katalin Komlosi
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Nina Singh
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Andreas Tzschach
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Marisa Windfuhr-Blum
- Radiology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
| | - Ingolf Juhasz-Boess
- Department of Obstetrics and Gynaecology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (I.J.-B.); (T.E.)
| | - Thalia Erbes
- Department of Obstetrics and Gynaecology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (I.J.-B.); (T.E.)
| | - Judith Fischer
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
| | - Svenja Alter
- Medical Center, Faculty of Medicine, Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany; (L.D.R.); (A.H.); (A.D.Z.); (K.K.); (N.S.); (A.T.); (J.F.)
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24
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Huszno J, Pigłowski W, Mazur M, Pamuła-Piłat J, Zajkowicz A, Kierzkowska AF, Wojciechowska MO. BRCA1/BRCA2 variants of uncertain significance in clinical practice: A case report. Mol Clin Oncol 2021; 15:222. [PMID: 34548921 DOI: 10.3892/mco.2021.2385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 05/11/2021] [Indexed: 11/05/2022] Open
Abstract
The influence of BRCA1/2 variants of uncertain significance (VUSs) on the cancer risk and their association with the response to treatment is uncertain. The aim of the present study was to evaluate the role of BRCA VUS in patients with breast cancer. A total of two cases of breast cancer patients with the BRCA VUS were described. The complete coding sequence of BRCA1/2 genes was analyzed from the genomic DNA material by next generation sequencing on the Ion Torrent platform. The presence of c.3454G>A (p.Asp1152Asn) VUS in the BRCA1 gene was reported in a 64-year-old woman with invasive breast carcinoma. The characteristics of the breast tumors were the following: moderately differentiated-intermediate grade (NG-2 G-2), HER2 (+), estrogen receptor (ER) (+++), progesterone receptor (PR) (+++), luminal A subtype and pT2 N1a Mx. The second detected VUS was the c.2374T>C (p.Tyr792His) variant in the BRCA2 gene. This variant was reported in a 33-year-old woman who was diagnosed with right breast cancer (cT2N1M0). The invasive breast carcinoma was characterized as follows: NG-2 G-2, ER (+++), PR (+++), Ki-67 10%, HER2 (+++) and luminal B subtype. The data demonstrated that patients with VUSs should be managed based on their family history of cancer and clinicopathological characteristics. The clinical significance of the VUS in BRCA1/2 may change over time and reclassification of the variant to 'pathogenic' or 'benign' should be undertaken. Patients with VUS should be followed up regularly.
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Affiliation(s)
- Joanna Huszno
- Genetic Outpatient Clinic, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Wojciech Pigłowski
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland.,Department of Tumor Pathology, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Magdalena Mazur
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Jolanta Pamuła-Piłat
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Artur Zajkowicz
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Anna Fiszer Kierzkowska
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Małgorzata Oczko Wojciechowska
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
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25
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Saied MH, Elkaffash D, Fadl R, Haleem RA, Refeat A, Ibrahim I, Tahoun M, Elkayal A, Tayae E. Preliminary results of targeted sequencing of BRCA1 and BRCA2 in a cohort of breast cancer families: New insight into pathogenic variants in patients and at‑risk relatives. Mol Med Rep 2021; 24:678. [PMID: 34296289 DOI: 10.3892/mmr.2021.12317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/24/2021] [Indexed: 11/06/2022] Open
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer worldwide and a major health concern in Egypt. There is a known association between pathogenic variants identified in breast cancer susceptibility gene (BRCA)1 and 2 and the risk of developing BC. However, the number of studies investigating mutations in BRCA1 and BRCA2 in Egypt remains limited. Thus, the aim of the present study was to investigate the frequency of BRCA1 and BRCA2 variants in patients with BC and their relatives. For this purpose, 11 families (11 patients and 16 relatives) were included in the present study. BRCA1 and BRCA2 variants were investigated using the Ion S5 next‑generation sequencer. It was found that pathogenic variants were more frequent in patients with familial BC (FBC) than in those with sporadic BC, with 71% of variants in BRCA2, including the first reported identification of c.9089del, c.5583_5584dup, c.8243G>A and c.7976G>A pathogenic variants in Egyptian patients with BC. Pathogenic variants in relatives were confined to FBC c.1278delA, c.1960_1961del, and c.1224delT, with a higher incidence of variants of uncertain significance (VUS), such as BRCA2 intron 2 c.68‑16delT. Of note, two cold spot benign variants, c.3113A>G and c.4837A>G, were repeatedly found (67%) in patients and relatives. In conclusion, to the best of our knowledge, novel pathogenic variants and VUS in Egyptian patients with BC and their high‑risk relatives were identified for the first time in the present study. These findings should be integrated with other genomic data concerning Egyptian families and carefully interpreted during genetic counseling.
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Affiliation(s)
- Marwa H Saied
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Dalal Elkaffash
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Reham Fadl
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Reham Abdel Haleem
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Amal Refeat
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Inas Ibrahim
- Department of Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Mona Tahoun
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Alyaa Elkayal
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Eman Tayae
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
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26
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Lazzari G, Buono G, Zannino B, Silvano G. Breast Cancer Adjuvant Radiotherapy in BRCA1/2, TP53, ATM Genes Mutations: Are There Solved Issues? BREAST CANCER-TARGETS AND THERAPY 2021; 13:299-310. [PMID: 34012291 PMCID: PMC8126701 DOI: 10.2147/bctt.s306075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/21/2021] [Indexed: 01/08/2023]
Abstract
BRCA1, BRCA2, TP53 and ATM gene mutations are the most studied tumour suppressor genes (TSGs) influencing the loco-regional approach to breast cancer (BC). Due to altered radio sensitivity of mutated cancer cells, mastectomy has always been advised in most patients with BC linked to TSGs mutations in order to avoid or minimize the use of adjuvant radiotherapy (ART). Whether ART is safe or not in these carriers is still debated. As a result, this issue has been widely discussed in the recent ASTRO and ASCO papers, yielding important and useful recommendations on the use of ART according to the mutational status. In this review, we have highlighted the impact of these mutations on local control, toxicities, second tumors, and contralateral breast cancers (CBCs) after ART to solve remaining doubts and encourage the safe use of ART when indicated.
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Affiliation(s)
- Grazia Lazzari
- Radiation Oncology Unit, San Giuseppe Moscati Hospital, Taranto, 74100, Italy
| | - Giuseppe Buono
- Medical Oncology Unit, San Rocco Hospital, Sessa Aurunca, Caserta, 81037, Italy
| | - Benedetto Zannino
- Medical Oncology Unit, San Rocco Hospital, Sessa Aurunca, Caserta, 81037, Italy
| | - Giovanni Silvano
- Radiation Oncology Unit, San Giuseppe Moscati Hospital, Taranto, 74100, Italy
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27
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Kim JH, Park S, Park HS, Park JS, Lee ST, Kim SW, Lee JW, Lee MH, Park SK, Noh WC, Choi DH, Han W, Jung SH. Analysis of BRCA1/2 variants of unknown significance in the prospective Korean Hereditary Breast Cancer study. Sci Rep 2021; 11:8485. [PMID: 33875706 PMCID: PMC8055990 DOI: 10.1038/s41598-021-87792-w] [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: 09/18/2020] [Accepted: 04/05/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic testing for BRCA1 and BRCA2 is crucial in diagnosing hereditary breast and ovarian cancer syndromes and has increased with the development of multigene panel tests. However, results classified as variants of uncertain significance (VUS) present challenges to clinicians in attempting to choose an appropriate management plans. We reviewed a total of 676 breast cancer patients included in the Korean Hereditary Breast Cancer (KOHBRA) study with a VUS on BRCA mutation tests between November 2007 and April 2013. These results were compared to the ClinVar database. We calculated the incidence and odds ratios for these variants using the Korean Reference Genome Database. A total of 58 and 91 distinct VUS in BRCA1 and BRCA2 were identified in the KOHBRA study (comprising 278 and 453 patients, respectively). A total of 27 variants in the KOHBRA study were not registered in the Single Nucleotide Polymorphism database. Among BRCA1 VUSs, 20 were reclassified as benign or likely benign, four were reclassified as pathogenic or likely pathogenic, and eight remained as VUSs according to the ClinVar database. Of the BRCA2 VUSs, 25 were reclassified as benign or likely benign, two were reclassified as pathogenic or likely pathogenic, and 33 remained as VUS according to the ClinVar database. There were 12 variants with conflicting interpretations of pathogenicity for BRCA1 and 18 for BRCA2. Among them, p.Leu1780Pro showed a particularly high odds ratio. Six pathogenic variants and one conflicting variant identified using ClinVar could be reclassified as pathogenic variants in this study. Using updated ClinVar information and calculating odds ratios can be helpful when reclassifying VUSs in BRCA1/2.
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Affiliation(s)
- Joo Heung Kim
- Department of Surgery, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Gyeonggi, Republic of Korea
| | - Sunggyun Park
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, 50-1 Yonseiro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Ji Soo Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonseiro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Republic of Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Woo-Chul Noh
- Department of Surgery, Korea Institute of Radiological & Medical Science, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Doo Ho Choi
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Hoo Jung
- Department of Surgery, Chonbuk National University Hospital, Jeonju, Jeollabuk, Republic of Korea
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28
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Leitsalu L, Palover M, Sikka TT, Reigo A, Kals M, Pärn K, Nikopensius T, Esko T, Metspalu A, Padrik P, Tõnisson N. Genotype-first approach to the detection of hereditary breast and ovarian cancer risk, and effects of risk disclosure to biobank participants. Eur J Hum Genet 2021; 29:471-481. [PMID: 33230308 PMCID: PMC7940387 DOI: 10.1038/s41431-020-00760-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/08/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Genotype-first approach allows to systematically identify carriers of pathogenic variants in BRCA1/2 genes conferring a high risk of familial breast and ovarian cancer. Participants of the Estonian biobank have expressed support for the disclosure of clinically significant findings. With an Estonian biobank cohort, we applied a genotype-first approach, contacted carriers, and offered return of results with genetic counseling. We evaluated participants' responses to and the clinical utility of the reporting of actionable genetic findings. Twenty-two of 40 contacted carriers of 17 pathogenic BRCA1/2 variants responded and chose to receive results. Eight of these 22 participants qualified for high-risk assessment based on National Comprehensive Cancer Network criteria. Twenty of 21 counseled participants appreciated being contacted. Relatives of 10 participants underwent cascade screening. Five of 16 eligible female BRCA1/2 variant carriers chose to undergo risk-reducing surgery, and 10 adhered to surveillance recommendations over the 30-month follow-up period. We recommend the return of results to population-based biobank participants; this approach could be viewed as a model for population-wide genetic testing. The genotype-first approach permits the identification of individuals at high risk who would not be identified by application of an approach based on personal and family histories only.
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Affiliation(s)
- Liis Leitsalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marili Palover
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Timo Tõnis Sikka
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mart Kals
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Tiit Nikopensius
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Peeter Padrik
- Hematology and Oncology Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.
- Dept. of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.
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29
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Butz H, Papp J, Bozsik A, Krokker L, Pócza T, Oláh E, Patócs A. Application of Multilayer Evidence for Annotation of C-Terminal BRCA2 Variants. Cancers (Basel) 2021; 13:cancers13040881. [PMID: 33672545 PMCID: PMC7923782 DOI: 10.3390/cancers13040881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The potential pathogenic role of germline BRCA2 c.9976A>T and c.10095delinsGAATTATATCT was evaluated in hereditary breast and ovarian cancer (HBOC) patients by investigating 2491 probands and verified in an independent cohort of 122,209 patients. Although the c.10095delinsGAATTATATCT variant was more prevalent among patients compared to control populations, no increased risk for cancer was found. No association between c.9976A>T and clinicopathological parameters or elevated risk for HBOC cases was detected. However, lung cancer was more prevalent in families carrying c.9976A>T compared to pathogenic BRCA1/BRCA2 carrier families. An increased frequency of pancreatic cancer was found in families where c.9976A>T occurred together with other pathogenic BRCA1 variants. The C-terminal stop codon variants showed no association with other pathogenic BRCA2 variants. No loss of heterozygosity (LOH) in tumor tissue and no allelic imbalance in RNA level were confirmed. The c.9976A>T variant may be considered as a potential risk for lung cancer, and a potential modifying factor in pancreatic cancer when it occurs along with the pathogenic BRCA1 variant, although this observation should be validated in a larger sample cohort. Abstract The clinical relevance of the BRCA2 C-terminal stop codon variants is controversial. The pathogenic role of the germline BRCA2 c.9976A>T and c.10095delinsGAATTATATCT variants in hereditary breast and ovarian cancer (HBOC) patients was evaluated. An association with clinicopathological parameters was performed in 2491 independent probands diagnosed with HBOC and in 122,209 cancer patients reported earlier. Loss-of-heterozygosity (LOH) in tumor samples and allelic imbalance in RNA extracted from peripheral blood cells were investigated. Neither c.10095delinsGAATTATATCT or c.9976A>T variants showed significant association with clinicopathological parameters or elevated risk for HBOC-associated tumors. Lung cancer was more prevalent in families carrying the c.9976A>T variant compared to pathogenic BRCA1 or BRCA2 carrier families. An increased prevalence of pancreatic cancer was found in families where c.9976A>T occurred together with other pathogenic BRCA1 variants. An increased risk for familial pancreatic, lung and upper aero-digestive tract cancers was confirmed in the validation set. Regarding BRCA2 C-terminal variants, no linkage with other pathogenic BRCA2 variants, no LOH in tumor tissue and no allelic imbalance in RNA level were confirmed. The c.9976A>T variant may be considered as a potential risk for lung cancer, and a potential modifying factor in pancreatic cancer when it occurs along with the pathogenic BRCA1 variant, although this observation should be validated in a larger sample cohort.
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Affiliation(s)
- Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
| | - Lilla Krokker
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
| | - Tímea Pócza
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
| | - Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Correspondence:
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30
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Moradian MM, Babikyan DT, Markarian S, Petrosyan JG, Avanesian N, Arutunyan T, Sarkisian TF. Germline mutational spectrum in Armenian breast cancer patients suspected of hereditary breast and ovarian cancer. Hum Genome Var 2021; 8:9. [PMID: 33558524 PMCID: PMC7870655 DOI: 10.1038/s41439-021-00140-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/09/2022] Open
Abstract
Hereditary breast and ovarian cancer (HBOC) can be identified by genetic testing of cancer-causing genes. In this study, we identified a spectrum of genetic variations among 76 individuals of Armenian descent either with a family history of cancer or breast cancer before the age of 40. We screened 76 suspected HBOC patients and family members as well as four healthy controls using a targeted and hereditary comprehensive cancer panel (127 genes). We found 26 pathogenic (path) and 6 likely pathogenic (LPath)variants in 6 genes in 44 patients (58%); these variants were found in BRCA1 (17), BRCA2 (19), CHEK2 (4), PALB2 (2), and NBN (1). A few different variants were found in unrelated individuals; most notably, variant p.Trp1815Ter in the BRCA1 gene occurred in four unrelated patients. We did not find any known significant variants in five patients. Comprehensive cancer panel testing revealed pathogenic variants in cancer genes other than BRCA1 and BRCA2, suggesting that testing only BRCA1 and BRCA2 would have missed 8 out of 44 suspected HBOC patients (18%). These data also confirm that a comprehensive cancer panel testing approach could be an appropriate way to identify most of the variants associated with hereditary breast cancer.
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Affiliation(s)
- Mike M Moradian
- Department of Medical Genetics, Yerevan State Medical University, Yerevan, Armenia. .,Department of Molecular Genetics, Morava Scientific & Technology Services, Glendale, CA, USA.
| | - Davit T Babikyan
- Department of Medical Genetics, Yerevan State Medical University, Yerevan, Armenia.,Department of Molecular Genetics, Center of Medical Genetics and Primary Health Care, Yerevan, Armenia
| | - Sione Markarian
- Department of Molecular Genetics, Morava Scientific & Technology Services, Glendale, CA, USA
| | - Jonny G Petrosyan
- Department of Molecular Genetics, Center of Medical Genetics and Primary Health Care, Yerevan, Armenia
| | - Nare Avanesian
- Department of Molecular Genetics, Morava Scientific & Technology Services, Glendale, CA, USA
| | - Tereza Arutunyan
- Department of Molecular Genetics, Morava Scientific & Technology Services, Glendale, CA, USA
| | - Tamara F Sarkisian
- Department of Medical Genetics, Yerevan State Medical University, Yerevan, Armenia.,Department of Molecular Genetics, Center of Medical Genetics and Primary Health Care, Yerevan, Armenia
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31
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Wang D, Guan R, Tao Q, Liu S, Yu M, Li X. A novel somatic BRCA2 point mutation in a metastatic pancreatic cancer patient: a case report. BMC Med Genomics 2021; 14:6. [PMID: 33407459 PMCID: PMC7788890 DOI: 10.1186/s12920-020-00850-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/06/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In addition to ovarian and breast cancers, loss-of-function mutations in BRCA1 and BRCA2 genes are also linked to an increased risk of pancreatic cancer, with ~ 4 to 7% of pancreatic cancer patients harboring germline BRCA mutations. Most BRCA alterations in pancreatic cancer are frame-shifting indels, stop-gain, and splice-site mutations, but single nucleotide substitutions are rare. Recent studies demonstrated a significant progression-free survival (PFS) benefit from maintenance olaparib, a poly (ADP-ribose) polymerase (PARP) inhibitor administered to patients with germline BRCA mutations and metastatic pancreatic cancer. CASE PRESENTATION Here, we report a metastatic pancreatic cancer case who harbored a novel somatic BRCA2 c.6944T > C (p. I2315T) point mutation. After 6 weeks first-line chemotherapy, the patient was refractory to treatment and had a progressive disease. Due to the novel nonsynonymous BRCA2 point mutation, we decided to change the strategy by administering olaparib. The patient benefited from olaparib therapy and achieved a PFS of ~ 6.5 months. CONCLUSIONS We describe a patient carrying a novel somatic BRCA2 p. I2315T point mutation, which is first reported in metastatic pancreatic cancer. This case report indicates that a gene mutation-based strategy should be considered in the clinic to provide more effective treatment.
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Affiliation(s)
- Deqiang Wang
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ruting Guan
- Department of Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Qing Tao
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Sisi Liu
- Department of Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Man Yu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Xiaoqin Li
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
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32
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Five Italian Families with Two Mutations in BRCA Genes. Genes (Basel) 2020; 11:genes11121451. [PMID: 33287145 PMCID: PMC7761639 DOI: 10.3390/genes11121451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Double heterozygosity (DH) in BRCA1 and BRCA2 genes and double mutation (DM) in BRCA1 or BRCA2 are extremely rare events in the general population, and few cases have been reported worldwide so far. Here, we describe five probands, all women, with breast and/or ovarian cancer and their families. Particularly, we identified two probands with DH in the BRCA1/2 genes with a frequency of 0.3% and three probands with DM in the BRCA2 gene with a frequency of 0.5%. The DH BRCA1 c.547+2T>A (IVS8+2T>A)/BRCA2 c.2830A>T (p.Lys944Ter) and BRCA1 c.3752_3755GTCT (p.Ser1253fs)/BRCA2 c.425+2T>C (IVS4+2T>C) have not been described together so far. The DM in BRCA2, c.631G>A (p.Val211Ile) and c.7008-2A>T (IVS13-2A>T), found in three unrelated probands, was previously reported in further unrelated patients. Due to its peculiarity, it is likely that both pathogenic variants descend from a common ancestor and, therefore, are founder mutations. Interestingly, analyzing the tumor types occurring in DH and DM families, we observed ovarian cancer only in DH families, probably due to the presence in DH patients of BRCA1 pathogenic variants, which predispose one more to ovarian cancer onset. Furthermore, male breast cancer and pancreatic cancer ensued in families with DM but not with DH. These data confirm that BRCA2 pathogenic variants have greater penetrance to develop breast cancer in men and are associated with an increased risk of pancreatic cancer.
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33
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Trusler O, Goodwin J, Laslett AL. BRCA1 and BRCA2 associated breast cancer and the roles of current modelling systems in drug discovery. Biochim Biophys Acta Rev Cancer 2020; 1875:188459. [PMID: 33129865 DOI: 10.1016/j.bbcan.2020.188459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 02/08/2023]
Abstract
For a drug candidate to be fully developed takes years and investment of hundreds of millions of dollars. There is no doubt that drug development is difficult and risky, but vital to protecting against devastating disease. This difficulty is clearly evident in BRCA1 and BRCA2 related breast cancer, with current treatment options largely confined to invasive surgical procedures, as well as chemotherapy and radiotherapy regimes which damage healthy tissue and can leave remnant disease. Consequently, patient survival and relapse rates are far from ideal, and new candidate treatments are needed. The preclinical stages of drug discovery are crucial to get right for translation to hospital beds. Disease models must take advantage of current technologies and be accurate for rapid and translatable treatments. Careful selection of cell lines must be coupled with high throughput techniques, with promising results trialled further in highly accurate humanised patient derived xenograft models. Traditional adherent drug screening should transition to 3D culture systems amenable to high throughput techniques if the gap between in vitro and in vivo studies is to be partially bridged. The possibility of organoid, induced pluripotent stem cell, and conditionally reprogrammed in vitro models is tantalising, however protocols are yet to be fully established. This review of BRCA1 and BRCA2 cancer biology and current modelling systems will hopefully guide the design of future drug discovery endeavours and highlight areas requiring improvement.
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Affiliation(s)
- Oliver Trusler
- CSIRO Manufacturing, Clayton, Victoria 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Victoria 3800, Australia
| | - Jacob Goodwin
- CSIRO Manufacturing, Clayton, Victoria 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Victoria 3800, Australia
| | - Andrew L Laslett
- CSIRO Manufacturing, Clayton, Victoria 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Victoria 3800, Australia.
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34
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Chirita-Emandi A, Andreescu N, Popa C, Mihailescu A, Riza AL, Plesea R, Ioana M, Arghirescu S, Puiu M. Biallelic variants in BRCA1 gene cause a recognisable phenotype within chromosomal instability syndromes reframed as BRCA1 deficiency. J Med Genet 2020; 58:648-652. [PMID: 32843487 PMCID: PMC8394758 DOI: 10.1136/jmedgenet-2020-107198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/05/2022]
Abstract
Pathogenic variants in BRCA1 gene in heterozygous state are known to be associated with breast-ovarian cancer susceptibility; however, biallelic variants cause a phenotype recognised as Fanconi anaemia complementation group S. Due to its rarity, medical management and preventive screening measures are insufficiently understood. Here, we present nine individuals (one new and eight previously presented) with biallelic variants in BRCA1 gene, to delineate clinical features in comparison with other chromosome instability syndromes and understand the patients’ health risk. Features seen in these 9 individuals (7 females/2 males) include prenatal and postnatal growth failure (9/9), microcephaly (9/9), hypo/hyperpigmented lesions (9/9), facial dysmorphism (9/9), mild developmental delay (8/9) and early-onset solid tumours (5/9). None presented bone marrow failure or immunodeficiency. Individuals with biallelic variants in BRCA1 also showed chromosomal instability by mitomycin and diepoxybutane test. The phenotype caused by biallelic BRCA1 variants is best framed between Fanconi anaemia and Nijmegen syndrome, yet distinct due to lack of bone marrow failure and immunodeficiency. We hypothesise that disease class should be reframed and medical management in people with biallelic variants in BRCA1 should emphasise on detection of solid tumour development and avoiding exposure to ionising radiation.
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Affiliation(s)
- Adela Chirita-Emandi
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Romania .,Regional Center of Medical Genetics Timis, Genetics, Emergency Hospital for Children Louis Turcanu Timisoara, Timisoara, Romania
| | - Nicoleta Andreescu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Romania.,Regional Center of Medical Genetics Timis, Genetics, Emergency Hospital for Children Louis Turcanu Timisoara, Timisoara, Romania
| | - Cristina Popa
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Alexandra Mihailescu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Anca-Lelia Riza
- Human Genomics Laboratory, Genetics, University of Medicine and Pharmacy of Craiova, Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, Craiova, Romania
| | - Razvan Plesea
- Human Genomics Laboratory, Genetics, University of Medicine and Pharmacy of Craiova, Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, Craiova, Romania
| | - Mihai Ioana
- Human Genomics Laboratory, Genetics, University of Medicine and Pharmacy of Craiova, Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, Craiova, Romania
| | - Smaranda Arghirescu
- Pediatric Department - Pediatric Discipline III, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Timis, Romania.,Onco-Hematology Department, Emergency Hospital for Children Louis Turcanu Timisoara, Timisoara, Timis, Romania
| | - Maria Puiu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, Timisoara, Romania.,Regional Center of Medical Genetics Timis, Genetics, Emergency Hospital for Children Louis Turcanu Timisoara, Timisoara, Romania
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35
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Malhotra H, Kowtal P, Mehra N, Pramank R, Sarin R, Rajkumar T, Gupta S, Bapna A, Bhattacharyya GS, Gupta S, Maheshwari A, Mannan AU, Reddy Kundur R, Sekhon R, Singhal M, Smruti B, SP S, Suryavanshi M, Verma A. Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology. JCO Glob Oncol 2020; 6:991-1008. [PMID: 32628584 PMCID: PMC7392772 DOI: 10.1200/jgo.19.00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Affiliation(s)
- Hemant Malhotra
- Department of Medical Oncology, Sri Ram Cancer Center, Mahatma Gandhi Medical College Hospital, Jaipur, India
| | - Pradnya Kowtal
- Sarin Laboratory and OIC Sanger Sequencing Facility, Advanced Centre for Treatment Research, and Education in Cancer, Navi Mumbai, India
| | - Nikita Mehra
- Department of Medical Oncology, Cancer Institute (WIA), Chennai, India
| | - Raja Pramank
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajiv Sarin
- Radiation Oncology, Cancer Genetics Unit, Tata Memorial Centre and PI Sarin Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | | | - Sudeep Gupta
- Tata Memorial Centre Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ajay Bapna
- Department of Medical Oncology, Bhagwan Mahavir Cancer Hospital Research Center, Jaipur, India
| | | | - Sabhyata Gupta
- Department of Gynae Oncology, Medanta-The Medicity, Gurgaon, India
| | - Amita Maheshwari
- Department of Gynecologic Oncology, Tata Memorial Centre, Mumbai, India
| | - Ashraf U. Mannan
- Clinical Diagnostics, Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Rupinder Sekhon
- Gynae Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - B.K. Smruti
- Bombay Hospital and Medical Research Centre, Mumbai, India
| | - Somashekhar SP
- Manipal Comprehensive Cancer Center, Manipal Hospital, Bengaluru, India
| | - Moushumi Suryavanshi
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Amit Verma
- Molecular Oncology and Cancer Genetics, Max Hospital, New Delhi, India
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36
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Carlson P, Wojczynski MK, Druley T, Lee JH, Zmuda JM, Thyagarajan B. Prevalence of clinically actionable disease variants in exceptionally long-lived families. BMC Med Genomics 2020; 13:61. [PMID: 32272925 PMCID: PMC7146901 DOI: 10.1186/s12920-020-0710-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Phenotypic expression of pathogenic variants in individuals with no family history of inherited disorders remains unclear. Methods We evaluated the prevalence of pathogenic variants in 25 genes associated with Mendelian-inherited disorders in 3015 participants from 485 families in the Long Life Family Study (LLFS). Boot-strapping and Fisher’s exact test were used to determine whether allele frequencies in LLFS were significantly different from the allele frequencies reported in publicly available genomic databases. Results The proportions of pathogenic autosomal dominant mutation carriers in BRCA1 and SDHC in LLFS study participants were similar to those reported in publicly available genomic databases (0.03% vs. 0.0008%, p = 1 for BRCA1, and 0.08% vs. 0.003%, p = 0.05 for SDHC). The frequency of carriers of pathogenic autosomal recessive variants in CPT2, ACADM, SUMF1, WRN, ATM, and ACADVL were also similar in LLFS as compared to those reported in genomic databases. The lack of clinical disease among LLFS participants with well-established pathogenic variants in BRCA1 and SDHC suggests that penetrance of pathogenic variants may be different in long lived families. Conclusion Further research is needed to better understand the penetrance of pathogenic variants before expanding large scale genomic testing to asymptomatic individuals.
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Affiliation(s)
- Paige Carlson
- University of Minnesota Medical School, Duluth, MN, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Todd Druley
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO, 63108, USA.,Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO, 63108, USA
| | - Joseph H Lee
- Sergievsky Center, College of Physicians and Surgeons, Columbia University New York, New York, NY, USA.,Taub Institute, College of Physicians and Surgeons, Columbia University New York, New York, NY, USA.,Departments of Epidemiology and Neurology, Columbia University New York, New York, NY, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 609, 420 Delaware street, Minneapolis, MN, 55455, USA.
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37
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Ren Y, Cherukuri Y, Wickland DP, Sarangi V, Tian S, Carter JM, Mansfield AS, Block MS, Sherman ME, Knutson KL, Lin Y, Asmann YW. HLA class-I and class-II restricted neoantigen loads predict overall survival in breast cancer. Oncoimmunology 2020; 9:1744947. [PMID: 32523802 PMCID: PMC7255108 DOI: 10.1080/2162402x.2020.1744947] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/21/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
Tumors acquire numerous mutations during development and progression. When translated into proteins, these mutations give rise to neoantigens that can be recognized by T cells and generate antibodies, representing an exciting direction of cancer immunotherapy. While neoantigens have been reported in many cancer types, the profiling of neoantigens often focused on the class-I subtype that are presented to CD8 + T cells, and the relationship between neoantigen load and clinical outcomes was often inconsistent among cancer types. In this study, we described an informatics workflow, REAL-neo, for identification, quality control (QC), and prioritization of both class-I and class-II human leukocyte antigen (HLA) bound neoantigens that arise from somatic single nucleotide mutations (SNM), small insertions and deletions (INDEL), and gene fusions. We applied REAL-neo to 835 primary breast tumors in the Cancer Genome Atlas (TCGA) and performed comprehensive profiling and characterization of the detected neoantigens. We found recurrent HLA class-I and class-II restricted neoantigens across breast cancer cases, and uncovered associations between neoantigen load and clinical traits. Both class-I and class-II neoantigen loads from SNM and INDEL were found to predict overall survival independent of tumor mutational burden (TMB), breast cancer subtypes, tumor-infiltrating lymphocyte (TIL) levels, tumor stage, and age at diagnosis. Our study highlighted the importance of accurate and comprehensive neoantigen profiling and QC, and is the first to report the predictive value of neoantigen load for overall survival in breast cancer.
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Affiliation(s)
- Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Yesesri Cherukuri
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Daniel P Wickland
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jodi M Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Matthew S Block
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Mark E Sherman
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Keith L Knutson
- Department of Immunology, Mayo Clinic, Jacksonville, FL, USA
| | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
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38
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Su L, Xu Y, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Xie Y. Contralateral breast cancer risk in
BRCA1
and
BRCA2
mutation carriers in a large cohort of unselected Chinese breast cancer patients. Int J Cancer 2020; 146:3335-3342. [PMID: 32037537 DOI: 10.1002/ijc.32918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Liming Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Ye Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Tao Ouyang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Jinfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Tianfeng Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Zhaoqing Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Tie Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Benyao Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
| | - Yuntao Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center Beijing Cancer Hospital & Institute, Peking University Cancer Hospital Beijing People's Republic of China
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Cao CX, Sharib JM, Blanco AM, Goldberg D, Bracci P, Mukhtar RA, Esserman LJ, Kirkwood KS. Abdominal Imaging of Pancreatic Cysts and Cyst-Associated Pancreatic Cancer in BRCA1/2 Mutation Carriers: A Retrospective Cross-Sectional Study. J Am Coll Surg 2019; 230:53-63.e1. [PMID: 31672679 DOI: 10.1016/j.jamcollsurg.2019.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/30/2019] [Accepted: 09/16/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Direct-to-consumer BRCA testing will increase BRCA diagnoses and subsequent abdominal imaging. It is unclear whether BRCA carriers are at higher risk of developing pancreatic cysts (PCs) or cyst-associated pancreatic ductal adenocarcinoma (PDAC). We investigated the prevalence of PCs in BRCA-tested patients, and whether BRCA-carriers have higher rates of PDAC when PCs are found. STUDY DESIGN This is a retrospective cross-sectional study of patients with BRCA testing and abdominal imaging between 1996 and 2018. Pancreatic cysts were identified on original imaging reports. Prevalence and risk characteristics of PCs, as well as incidence of PDAC, were compared between BRCA+, BRCA-, and BRCA-untested patients. RESULTS Pancreatic cysts were identified in 4,045 patients among 128,164 unique patients with abdominal imaging, including 33 patients with PCs in 1,113 BRCA-tested patients. There was no difference in PC prevalence between BRCA+, BRCA-, and untested patients (3.6%, 2.6%, 3.2%, respectively; p = 0.64). Pancreatic cysts were diagnosed in BRCA+ patients at a younger age (57.1 vs 65.3 years, p < 0.001); however, there was no difference in risk stratification compared with BRCA- or untested patients by consensus criteria. Across the population of imaged patients, patients with PCs had significantly higher rates of PDAC compared with those without PCs (18.2% vs 2.4%, p < 0.001). Incidence of cyst-associated PDAC was similar in BRCA+ and BRCA- patients (13.3% vs 22.2%, p = 0.84). CONCLUSIONS BRCA+ patients have similar rates of PCs, high-risk features in their cysts, and PDAC as BRCA- and untested patients. BRCA+ patients likely do not require dedicated abdominal imaging to evaluate for PCs and should follow management guidelines similar to those as the untested general population if an incidental PC is identified.
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Affiliation(s)
- Carrie X Cao
- Department of Surgery, University of California San Francisco, San Francisco, CA
| | - Jeremy M Sharib
- Department of Surgery, University of California San Francisco, San Francisco, CA.
| | - Amie M Blanco
- University of California San Francisco Cancer Genetics and Prevention Program, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Dena Goldberg
- University of California San Francisco Cancer Genetics and Prevention Program, San Francisco, CA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
| | - Rita A Mukhtar
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Laura J Esserman
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Kimberly S Kirkwood
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
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40
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Arason A, Agnarsson BA, Johannesdottir G, Johannsson OT, Hilmarsdottir B, Reynisdottir I, Barkardottir RB. The BRCA1 c.4096+3A>G Variant Displays Classical Characteristics of Pathogenic BRCA1 Mutations in Hereditary Breast and Ovarian Cancers, But Still Allows Homozygous Viability. Genes (Basel) 2019; 10:E882. [PMID: 31683985 PMCID: PMC6896150 DOI: 10.3390/genes10110882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Mutations in BRCA1 result in predisposal to breast and ovarian cancers, but many variants exist with unknown clinical significance (VUS). One is BRCA1 c.4096+3A>G, which affects production of the full-length BRCA1 transcript, while augmenting transcripts lacking most or all of exon 11. Nonetheless, homozygosity of this variant has been reported in a healthy woman. We saw this variant cosegregate with breast and ovarian cancer in several family branches of four Icelandic pedigrees, with instances of phenocopies and a homozygous woman with lung cancer. We found eight heterozygous carriers (0.44%) in 1820 unselected breast cancer cases, and three (0.15%) in 1968 controls (p = 0.13). Seeking conclusive evidence, we studied tumors from carriers in the pedigrees for wild-type-loss of heterozygosity (wtLOH) and BRCA1-characteristic prevalence of estrogen receptor (ER) negativity. Of 15 breast and six ovarian tumors, wtLOH occurred in nine breast and all six ovarian tumours, and six of the nine breast tumors with wtLOH were ER-negative. These data accord with a pathogenic BRCA1-mutation. Our findings add to the current knowledge of BRCA1, and the role of its exon 11 in cancer pathogenicity, and will be of use in clinical genetic counselling.
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Affiliation(s)
- Adalgeir Arason
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Gudrun Johannesdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
| | - Oskar Th Johannsson
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
- Department of Oncology, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland.
| | - Bylgja Hilmarsdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Inga Reynisdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
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Terashima T, Umemoto K, Takahashi H, Hosoi H, Takai E, Kondo S, Sakamoto Y, Mitsunaga S, Ohno I, Hashimoto Y, Sasaki M, Ikeda M, Shimada K, Kaneko S, Yachida S, Sugano K, Okusaka T, Morizane C. Germline mutations in cancer-predisposition genes in patients with biliary tract cancer. Oncotarget 2019; 10:5949-5957. [PMID: 31666926 PMCID: PMC6800267 DOI: 10.18632/oncotarget.27224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/10/2019] [Indexed: 01/07/2023] Open
Abstract
The prevalence of germline mutations in patients with biliary tract carcinoma (BTC) remains unclear. Here, we investigated the prevalence and types of germline mutations in patients with BTC. We reviewed 269 patients with pathologically proven BTC and collected clinical characteristics, including medical and family histories. Additionally, we evaluated germline variants in 21 genes associated with hereditary predisposition for cancer by targeted sequencing in patients meeting ≥1 of the following criteria: 1) hereditary breast and/or ovarian cancer (HBOC) testing criteria modified for BTC, 2) Revised Bethesda Guidelines (RBGs) modified for BTC (modified RBG), 3) familial BTC criteria, or 4) young BTC criteria. Among the 269 patients, 80 met at least one criterion. Three pathogenic mutations in three patients were identified: two in BRCA2 and one in BRCA1. Among the 16 patients meeting modified HBOC testing criteria, 2 harbored germline BRCA2 mutations, and 1 harbored a germline BRCA1 mutation. However, no mutation in mismatch-repair genes were detected, despite 63 patients meeting modified RBG screening criteria and 18 qualifying as young BTC patients. We detected high prevalence of pathogenic germline mutations in BRCA1/2 and none in mismatch-repair genes in BTC patients following enrichment according to family or medical history in this study.
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Affiliation(s)
- Takeshi Terashima
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan.,Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kumiko Umemoto
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Takahashi
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroko Hosoi
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shunsuke Kondo
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasunari Sakamoto
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Shuichi Mitsunaga
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Izumi Ohno
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yusuke Hashimoto
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Mitsuhito Sasaki
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Masafumi Ikeda
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kazuaki Shimada
- Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kokichi Sugano
- Oncogene Research Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute, Tochigi, Japan.,Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
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42
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Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women. Int J Mol Sci 2019; 20:ijms20194828. [PMID: 31569399 PMCID: PMC6801521 DOI: 10.3390/ijms20194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022] Open
Abstract
This study suggests that two newly discovered variants in the MSH2 gene, which codes for a DNA mismatch repair (MMR) protein, can be associated with a high risk of breast cancer. While variants in the MSH2 gene are known to be linked with an elevated cancer risk, the MSH2 gene is not a part of the standard kit for testing patients for elevated breast cancer risk. Here we used the results of genetic testing of women diagnosed with breast cancer, but who did not have variants in BRCA1 and BRCA2 genes. Instead, the test identified four variants with unknown significance (VUS) in the MSH2 gene. Here, we carried in silico analysis to develop a classifier that can distinguish pathogenic from benign mutations in MSH2 genes taken from ClinVar. The classifier was then used to classify VUS in MSH2 genes, and two of them, p.Ala272Val and p.Met592Val, were predicted to be pathogenic mutations. These two mutations were found in women with breast cancer who did not have mutations in BRCA1 and BRCA2 genes, and thus they are suggested to be considered as new bio-markers for the early detection of elevated breast cancer risk. However, before this is done, an in vitro validation of mutation pathogenicity is needed and, moreover, the presence of these mutations should be demonstrated in a higher number of patients or in families with breast cancer history.
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43
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Shariff MZ, Curras-Martin D, Campbell N, Gupta V, Mikhail JD, Levitt MJ, Hossain MA. Carcinoid tumor of lung and BRCA mutation: a case report. J Med Case Rep 2019; 13:132. [PMID: 31039815 PMCID: PMC6492413 DOI: 10.1186/s13256-019-2052-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/14/2019] [Indexed: 11/29/2022] Open
Abstract
Background A BRCA mutation is a mutation in either of the BRCA1 or BRCA2 genes, which are tumor suppressor genes. Hundreds of different types of mutations in these genes have been identified, some of which have been determined to be harmful, whereas others have no proven impact. BRCA mutations are well known to be associated with breast, uterine, and ovarian cancers along with some nongynecological malignancies involving the peritoneum, prostate, pancreas, skin, stomach, and rectum. However, there are no reported cases to date of an association between carcinoid tumors and a BRCA mutation. Case presentation Our patient was a 33-year-old White woman with BRCA2 mutation who presented to her primary care physician for evaluation of abdominal pain. She underwent computed tomography of her abdomen and pelvis, which showed an incidental finding of infrahilar mass along with renal stones. Further workup with bronchoscopy and biopsy of the mass confirmed it to be a carcinoid tumor of the lung. Conclusions No literature thus far exists describing a connection between BRCA mutations and carcinoid tumors. Early diagnosis and prompt treatment of carcinoid tumors are proven to have impact on survival and prognosis of these patients.
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Affiliation(s)
- Mohammed Z Shariff
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA.
| | - Diana Curras-Martin
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
| | - Natasha Campbell
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
| | - Varsha Gupta
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
| | - John D Mikhail
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
| | - Michael J Levitt
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
| | - Mohammad A Hossain
- Internal Medicine Residency Program, Department of Medicine, Jersey Shore University Medical Center, Hackensack Meridian Health, Neptune, NJ, 07753, USA
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44
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Macedo GS, Alemar B, Ashton-Prolla P. Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era. Genet Mol Biol 2019; 42:215-231. [PMID: 31067289 PMCID: PMC6687356 DOI: 10.1590/1678-4685-gmb-2018-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA) genes confer high risk of developing cancer, especially breast and ovarian tumors. Since the cloning of these tumor suppressor genes over two decades ago, a significant amount of research has been done. Most recently, monoallelic loss-of-function mutations in PALB2 have also been shown to increase the risk of breast cancer. The identification of BRCA1, BRCA2 and PALB2 as proteins involved in DNA double-strand break repair by homologous recombination and of the impact of complete loss of BRCA1 or BRCA2 within tumors have allowed the development of novel therapeutic approaches for patients with germline or somatic mutations in said genes. Despite the advances, especially in the clinical use of PARP inhibitors, key gaps remain. Now, new roles for BRCA1 and BRCA2 are emerging and old concepts, such as the classical two-hit hypothesis for tumor suppression, have been questioned, at least for some BRCA functions. Here aspects regarding cancer predisposition, cellular functions, histological and genomic findings in BRCA and PALB2-related tumors will be presented, in addition to an up-to-date review of the evolution and challenges in the development and clinical use of PARP inhibitors.
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Affiliation(s)
- Gabriel S Macedo
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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45
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Analysis of Outcomes in Patients With BRCA1/2 Breast Cancer Mutations Treated With Accelerated Partial Breast Irradiation (APBI). Am J Clin Oncol 2019; 42:446-453. [PMID: 30973374 DOI: 10.1097/coc.0000000000000542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To analyze outcomes and survival for BRCA1/2+ patients treated with accelerated partial breast irradiation (APBI). MATERIALS AND METHODS Retrospective review was performed on 341 women treated with intracavitary APBI (Mammosite or Contura) postlumpectomy from 2002 to 2013. Patients were treated to 34.0 Gy in 10 BID fractions. Of 341 treated patients, 11 (3.2%) had BRCA1/2 mutations, 5 of whom had an oophorectomy. Ipsilateral breast tumor recurrence (IBTR), contralateral breast tumor recurrence (CBTR), and breast tumor recurrence progression-free survival were analyzed using SPSS-17. BRCA1/2+ patient outcomes were compared with a general population treated cohort. RESULTS Median age at diagnosis was 66 years, for BRCA1/2+ women it was 61 years. Median follow-up was 8.4 years and for BRCA1/2+ patients it was 8.8 years. IBTR for the entire cohort was 3.5%, while CBTR was 1.2%. Both IBTR and CBTR for the BRCA1/2+ group were 0%. The 5-year IBTR-free survival was 97.3% (95% confidence interval [CI]=94.9%, 98.6%), and the CBTR-free survival was 99.4% (95% CI=97.6%, 99.9%). The 5-year breast tumor recurrence-free survival was 96.7% (95% CI=94.1%, 98.2%). As no patients with BRCA1/2+ mutation died of metastatic breast cancer or recurrence during follow-up and review, overall survival could not be evaluated. CONCLUSIONS To date, BRCA1/2+ patients treated with APBI sustained no recurrences, or second cancers. Most patients had an ER+ status and underwent oophorectomy, which may be a protective mechanism for recurrence. This is the first outcomes report in the literature of BRCA1/2 mutations treated with APBI technique.
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46
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Jiao J, Sagnelli M, Shi B, Fang Y, Shen Z, Tang T, Dong B, Li D, Wang X. Genetic and epigenetic characteristics in ovarian tissues from polycystic ovary syndrome patients with irregular menstruation resemble those of ovarian cancer. BMC Endocr Disord 2019; 19:30. [PMID: 30866919 PMCID: PMC6416936 DOI: 10.1186/s12902-019-0356-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/03/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Irregular menstruation is clinically associated with an increased risk for ovarian cancer and disease-related mortality. This relationship remains poorly understood, and a mechanism explaining it has yet to be described. METHODS Ovarian tissues from women with polycystic ovary syndrome (PCOS) and regular menstruation (n = 10) or irregular menstruation (n = 10) were subjected to DNA methylation sequencing, real-time PCR array, whole-exome sequencing, and bioinformatics analysis. RESULTS We demonstrated that ovarian tissue from PCOS patients with irregular menstruation displayed global DNA hypomethylation, as well as hypomethylation at several functionally and oncologically significant regions. Furthermore, we showed that several cancer-related genes were aberrantly expressed in ovarian tissue from patients with irregular menstruation, and that their mRNA and microRNA profiles shared appreciable levels of coincidence with those from ovarian cancer tissue. We identified multiple point mutations in both the BRCA1 and MLH1 genes in patients with irregular menstruation, and predicted the potential pathogenicity of these mutations using bioinformatics analyses. CONCLUSIONS Due to the nature of ovarian cancer, it is important to broaden our understanding of the pathogenesis and risk factors of the disease. Herein, we provide the first description of a genetic and epigenetic basis for the clinical relationship between irregular menstruation and an increased risk for ovarian cancer.
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Affiliation(s)
- Jiao Jiao
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Matthew Sagnelli
- University of Connecticut School of Medicine, Farmington, CT 06030 USA
| | - Bei Shi
- Department of Physiology, College of Life Science, China Medical University, Shenyang, 110122 China
- Functional Laboratory Center, College of Basic Medical Science, China Medical University, Shenyang, 110122 China
| | - Yuanyuan Fang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Ziqi Shen
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Tianyu Tang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Bingying Dong
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Xiuxia Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
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47
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Li J, Wen WX, Eklund M, Kvist A, Eriksson M, Christensen HN, Torstensson A, Bajalica‐Lagercrantz S, Dunning AM, Decker B, Allen J, Luccarini C, Pooley K, Simard J, Dorling L, Easton DF, Teo S, Hall P, Borg Å, Grönberg H, Czene K. Prevalence of BRCA1 and BRCA2 pathogenic variants in a large, unselected breast cancer cohort. Int J Cancer 2019; 144:1195-1204. [PMID: 30175445 PMCID: PMC6320715 DOI: 10.1002/ijc.31841] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/30/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
Breast cancer patients with BRCA1/2-driven tumors may benefit from targeted therapy. It is not clear whether current BRCA screening guidelines are effective at identifying these patients. The purpose of our study was to evaluate the prevalence of inherited BRCA1/2 pathogenic variants in a large, clinically representative breast cancer cohort and to estimate the proportion of BRCA1/2 carriers not detected by selectively screening individuals with the highest probability of being carriers according to current clinical guidelines. The study included 5,122 unselected Swedish breast cancer patients diagnosed from 2001 to 2008. Target sequence enrichment (48.48 Fluidigm Access Arrays) and sequencing were performed (Illumina Hi-Seq 2,500 instrument, v4 chemistry). Differences in patient and tumor characteristics of BRCA1/2 carriers who were already identified as part of clinical BRCA1/2 testing routines and additional BRCA1/2 carriers found by sequencing the entire study population were compared using logistic regression models. Ninety-two of 5,099 patients with valid variant calls were identified as BRCA1/2 carriers by screening all study participants (1.8%). Only 416 study participants (8.2%) were screened as part of clinical practice, but this identified 35 out of 92 carriers (38.0%). Clinically identified carriers were younger, less likely postmenopausal and more likely to be associated with familiar ovarian cancer compared to the additional carriers identified by screening all patients. More BRCA2 (34/42, 81.0%) than BRCA1 carriers (23/50, 46%) were missed by clinical screening. In conclusion, BRCA1/2 mutation prevalence in unselected breast cancer patients was 1.8%. Six in ten BRCA carriers were not detected by selective clinical screening of individuals.
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Affiliation(s)
- Jingmei Li
- Human GeneticsGenome Institute of SingaporeSingaporeSingapore
- Department of SurgeryYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Wei Xiong Wen
- Cancer Research Malaysia, Sime Darby Medical CentreSubang JayaSelangorMalaysia
| | - Martin Eklund
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical SciencesLund UniversityLundSweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | | | | | | | - Alison M. Dunning
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Brennan Decker
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of HealthBethesdaMD
- Department of PathologyBrigham and Women's HospitalBostonMA
| | - Jamie Allen
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Craig Luccarini
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Karen Pooley
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec‐Université Laval Research CenterCanada Research Chair in Oncogenetics, Université LavalQuebec CityCanada
| | - Leila Dorling
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic EpidemiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Soo‐Hwang Teo
- Cancer Research Malaysia, Sime Darby Medical CentreSubang JayaSelangorMalaysia
| | - Per Hall
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical SciencesLund UniversityLundSweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Kamila Czene
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
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48
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Mori M, Hira A, Yoshida K, Muramatsu H, Okuno Y, Shiraishi Y, Anmae M, Yasuda J, Tadaka S, Kinoshita K, Osumi T, Noguchi Y, Adachi S, Kobayashi R, Kawabata H, Imai K, Morio T, Tamura K, Takaori-Kondo A, Yamamoto M, Miyano S, Kojima S, Ito E, Ogawa S, Matsuo K, Yabe H, Yabe M, Takata M. Pathogenic mutations identified by a multimodality approach in 117 Japanese Fanconi anemia patients. Haematologica 2019; 104:1962-1973. [PMID: 30792206 PMCID: PMC6886416 DOI: 10.3324/haematol.2018.207241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Fanconi anemia is a rare recessive disease characterized by multiple congenital abnormalities, progressive bone marrow failure, and a predisposition to malignancies. It results from mutations in one of the 22 known FANC genes. The number of Japanese Fanconi anemia patients with a defined genetic diagnosis was relatively limited. In this study, we reveal the genetic subtyping and the characteristics of mutated FANC genes in Japan and clarify the genotype-phenotype correlations. We studied 117 Japanese patients and successfully subtyped 97% of the cases. FANCA and FANCG pathogenic variants accounted for the disease in 58% and 25% of Fanconi anemia patients, respectively. We identified one FANCA and two FANCG hot spot mutations, which are found at low percentages (0.04-0.1%) in the whole-genome reference panel of 3,554 Japanese individuals (Tohoku Medical Megabank). FANCB was the third most common complementation group and only one FANCC case was identified in our series. Based on the data from the Tohoku Medical Megabank, we estimate that approximately 2.6% of Japanese are carriers of disease-causing FANC gene variants, excluding missense mutations. This is the largest series of subtyped Japanese Fanconi anemia patients to date and the results will be useful for future clinical management.
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Affiliation(s)
- Minako Mori
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Asuka Hira
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Michiko Anmae
- Medical Genetics Laboratory, Graduate School of Science and Engineering, Kindai University, Osaka, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Tomoo Osumi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Souichi Adachi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics and Adolescence, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Hiroshi Kawabata
- Department of Hematology and Immunology, Kanazawa Medical University, Uchinada-machi, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuo Tamura
- Medical Genetics Laboratory, Graduate School of Science and Engineering, Kindai University, Osaka, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiromasa Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Miharu Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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49
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Single gold-bridged nanoprobes for identification of single point DNA mutations. Nat Commun 2019; 10:836. [PMID: 30783107 PMCID: PMC6381086 DOI: 10.1038/s41467-019-08769-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
Consensus ranking of protein affinity to identify point mutations has not been established. Therefore, analytical techniques that can detect subtle variations without interfering with native biomolecular interactions are required. Here we report a rapid method to identify point mutations by a single nanoparticle sensing system. DNA-directed gold crystallization forms rod-like nanoparticles with bridges based on structural design. The nanoparticles enhance Rayleigh light scattering, achieving high refractive-index sensitivity, and enable the system to monitor even a small number of protein-DNA binding events without interference. Analysis of the binding affinity can compile an atlas to distinguish the potential of various point mutations recognized by MutS protein. We use the atlas to analyze the presence and type of single point mutations in BRCA1 from samples of human breast and ovarian cancer cell lines. The strategy of synthesis-by-design of plasmonic nanoparticles for sensors enables direct identification of subtle biomolecular binding distortions and genetic alterations.
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50
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Fernández-Lopez JC, Romero-Córdoba S, Rebollar-Vega R, Alfaro-Ruiz LA, Jiménez-Morales S, Beltrán-Anaya F, Arellano-Llamas R, Cedro-Tanda A, Rios-Romero M, Ramirez-Florencio M, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Hidalgo-Miranda A. Population and breast cancer patients' analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population. Hum Genomics 2019; 13:3. [PMID: 30630528 PMCID: PMC6327376 DOI: 10.1186/s40246-018-0188-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/18/2018] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in clinically relevant genes. Public availability of data obtained from high-throughput genotyping and/or exome massive parallel sequencing (MPS)-based projects from several thousands of outbred samples might become useful tools to evaluate the pathogenicity of a VUS, based on its frequency in different populations. In the case of the Mexican and other Latino populations, several thousands of samples have been genotyped or sequenced during the last few years as part of different efforts to identify common variants associated to common diseases. In this report, we analyzed Mexican population data from a sample of 3985 outbred individuals, and additional 66 hereditary breast cancer patients were analyzed in order to better define the spectrum of common genomic variation of the BRCA1 and BRCA2 genes. Our analyses identified the most common genetic variants in these clinically relevant genes as well as the presence and frequency of specific pathogenic mutations present in the Mexican population. Analysis of the 3985 population samples by MPS identified three pathogenic mutations in BRCA1, only one population sample showed a BRCA1 exon 16-17 deletion by MLPA. This resulted in a basal prevalence of deleterious mutations of 0.10% (1:996) for BRCA1 and 11 pathogenic mutations in BRCA2, resulting in a basal prevalence of deleterious mutations of 0.276% (1:362) for BRCA2, combined of 0.376% (1:265). Separate analysis of the breast cancer patients identified the presence of pathogenic mutations in 18% (12 pathogenic mutations in 66 patients) of the samples by MPS and 13 additional alterations by MLPA. These results will support a better interpretation of clinical studies focused on the detection of BRCA mutations in Mexican and Latino populations and will help to define the general prevalence of deleterious mutations within these populations.
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Affiliation(s)
- J C Fernández-Lopez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Romero-Córdoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Rebollar-Vega
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - L A Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - S Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - F Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - R Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - M Ramirez-Florencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico
| | - V Bautista-Piña
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - C Dominguez-Reyes
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - F Villegas-Carlos
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Tenorio-Torres
- Instituto de Enfermedades la Mama FUCAM, Avenida El Bordo 100, Santa Ursula Coapa, 04980, Mexico City, CP, Mexico
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Perfiérico Sur, 4809, Arenal Tepepan, 14610, Mexico City, CP, Mexico.
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