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Khan MA, Varma AK. In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2. J Biomol Struct Dyn 2023; 41:9879-9889. [PMID: 36404616 DOI: 10.1080/07391102.2022.2148127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as 'Variants of Uncertain Significance' (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mudassar Ali Khan
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Ashok K Varma
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
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2
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Khan MA, Siddiqui MQ, Kuligina E, Varma AK. Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. Int J Biol Macromol 2022; 209:716-724. [PMID: 35413318 DOI: 10.1016/j.ijbiomac.2022.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair mechanism of DNA double-strand breaks and interstrand cross-links by Homologous recombination. Germline mutations identified in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer. Missense mutations are identified all over the gene, including the DNA binding region of BRCA2 that interacts with FANCD2. However, the majority of these missense mutations are classified as 'Variants of Uncertain Significance' due to a lack of structural, functional and clinical correlations. Therefore, multi-disciplinary in-silico, in-vitro and biophysical approaches have been explored to characterize an unclassified missense mutation, BRCA2 Arg2502Cys, identified from a case-control study. Circular-dichroism and Fluorescence spectroscopy show that the Arg2502Cys mutation in hBRCA2 (residues 2350-2545) decreases the α-helical/β-sheet propensity of the wild-type protein and perturb the tertiary structure conformation. Molecular dynamics simulations revealed alteration in the intramolecular H-bonds, overall compactness and stability of the hydrophobic core were observed in the mutant protein. Principle component analysis indicated that Arg2502Cys mutant exhibited comparatively large conformational transitions and periodic fluctuation. Therefore, to our conclusion, BRCA2 Arg2502Cys mutant perturbed the structural integrity and conformational dynamics of BRCA2.
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Affiliation(s)
- Mudassar Ali Khan
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Present address: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Ekaterina Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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de Meric de Bellefon M, Lemanski C, Ducteil A, Fenoglietto P, Azria D, Bourgier C. Management of the Axilla in the Era of Breast Cancer Heterogeneity. Front Oncol 2018; 8:84. [PMID: 29670853 PMCID: PMC5893721 DOI: 10.3389/fonc.2018.00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/12/2018] [Indexed: 01/07/2023] Open
Abstract
Systemic cancer therapies take into account breast cancer (BC) heterogeneity by targeting pathways specifically involved in some BC subtypes. On the other hand, BC intrinsic radiosensitivity is poorly understood and studied. Hence, radiotherapy personalization in BC is still “work in progress”. In this review, we will summarize the existing data on the management of axillary lymph nodes in BC, the impact of BC radiotherapy on axillary management, the indications for axillary radiotherapy, and biomarkers to predict patients’ outcome (tumor control and late toxicities) after axillary irradiation.
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Affiliation(s)
| | - Claire Lemanski
- Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Angélique Ducteil
- Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | | | - David Azria
- Institut Régional du Cancer de Montpellier (ICM), Montpellier, France.,Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Celine Bourgier
- Institut Régional du Cancer de Montpellier (ICM), Montpellier, France.,Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France
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Ma H, Ursin G, Xu X, Lee E, Togawa K, Malone KE, Marchbanks PA, McDonald JA, Simon MS, Folger SG, Lu Y, Sullivan-Halley J, Deapen DM, Press MF, Bernstein L. Body mass index at age 18 years and recent body mass index in relation to risk of breast cancer overall and ER/PR/HER2-defined subtypes in white women and African-American women: a pooled analysis. Breast Cancer Res 2018; 20:5. [PMID: 29357906 PMCID: PMC5778748 DOI: 10.1186/s13058-017-0931-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/28/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Although it has been well-documented that obesity is associated with decreased risk of premenopausal breast cancer and increased risk of postmenopausal breast cancer, it is unclear whether these associations differ among breast cancer subtypes defined by the tumor protein expression status of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). METHODS We evaluated the associations of body mass index (BMI) at age 18 years and recent BMI in relation to risk of breast cancer overall and ER/PR/HER2-defined subtypes, in 6320 women (3934 case-patient participants, 2386 control participants) aged 35-64 years, who participated in one of three population-based case-control studies. We estimated multivariable-adjusted odd ratios (ORs) and corresponding 95% confidence intervals (CIs) using polychotomous unconditional logistic regression methods for case-control comparisons in premenopausal women and postmenopausal women. RESULTS BMI at age 18 years was inversely associated with risk of breast cancer, particularly among premenopausal women (≥ 25 vs. < 20 kg/m2, OR = 0.72, 95% CI = 0.53-0.96; per 5 kg/m2 increase, OR = 0.83, 95% CI = 0.73-0.95). This inverse association did not differ across ER/PR/HER2-defined subtypes or by race (white women, African-American women). Recent BMI was not associated with risk of premenopausal breast cancer after adjustment for BMI at age 18 years; nevertheless, the analysis for the joint effects of BMI at age 18 years and recent BMI showed that premenopausal women in the highest categories of the two BMI measures (≥ 25 kg/m2 at age 18 years and ≥ 30 kg/m2 for recent BMI) had 46% lower risk of breast cancer than premenopausal women in the lowest categories of the two BMI measures (< 20 kg/m2 at age 18 years and < 25 kg/m2 for recent BMI; OR = 0.54, 95% CI = 0.38-0.78). Neither measure of BMI was statistically significantly associated with risk of postmenopausal breast cancer. CONCLUSION Our findings indicate that high BMI near the end of adolescence decreases risk of all ER/PR/HER2-defined subtypes of premenopausal breast cancer and also suggest that this benefit could be maximized among premenopausal women who consistently have high BMI during their premenopausal years.
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Affiliation(s)
- Huiyan Ma
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
| | - Giske Ursin
- Cancer Registry of Norway, Oslo, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Xinxin Xu
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Kayo Togawa
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Kathleen E. Malone
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Polly A. Marchbanks
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Jill A. McDonald
- College of Health and Social Services, New Mexico State University, Las Cruces, NM 88003 USA
| | - Michael S. Simon
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI 48201 USA
| | - Suzanne G. Folger
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Yani Lu
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
| | - Jane Sullivan-Halley
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
| | - Dennis M. Deapen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Michael F. Press
- Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA 91010 USA
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Zaidi S, Hussain S, Verma S, Veqar Z, Khan A, Nazir SU, Singh N, Moiz JA, Tanwar P, Srivastava A, Rath GK, Mehrotra R. Efficacy of Complementary Therapies in the Quality of Life of Breast Cancer Survivors. Front Oncol 2018; 7:326. [PMID: 29376027 PMCID: PMC5768617 DOI: 10.3389/fonc.2017.00326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) is the most common cancer diagnosed in women and the second most common cancer overall, ranking as the fifth cause of death from cancer. The chronicity of the disease produces long-term physiological and psychological manifestations, which adversely affect the quality of life of the individual. The primary treatment while managing cancer presents with various debilitating side effects. With the recent advances in treatment techniques that have improved the survival rate, patients suffer from continuing posttreatment complications. Patients seem to cope well with the stress of treatment of BC and sustain a normal life; however, the deterioration in physical well-being makes the patient functionally inefficient. Exercise has been proven to be an effective, safe, and feasible tool in combating the adverse effects of treatment, prevents complications and decreases the risk of BC-specific mortality. This review briefly presents an overview of the burden of the disease and its management strategies. Owing to the heterogeneity of the population and the multitude of therapies they receive, the response of each patient to treatment is different and so is the magnitude of adverse effects. The review discusses the late sequelae following treatment and evidence supporting the role of physical activity in their management. In conclusion, there is a need for personalized physical activity plans to be developed to suit the individual and their circumstances.
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Affiliation(s)
- Sahar Zaidi
- Centre for Physiotherapy and Rehabilitation Sciences, Jamia Millia Islamia (Central University), New Delhi, India
| | - Showket Hussain
- National Institute of Cancer Prevention and Research, Indian Council of Medical Research (NICPR-ICMR), New Delhi, India
| | - Shalini Verma
- Centre for Physiotherapy and Rehabilitation Sciences, Jamia Millia Islamia (Central University), New Delhi, India
| | - Zubia Veqar
- Centre for Physiotherapy and Rehabilitation Sciences, Jamia Millia Islamia (Central University), New Delhi, India
| | - Asiya Khan
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sheeraz Un Nazir
- National Institute of Cancer Prevention and Research, Indian Council of Medical Research (NICPR-ICMR), New Delhi, India
| | - Neha Singh
- Institute of Clinical Sciences, Sahlgrenska University Hospital, Gothenberg University, Gothenberg, Sweden
| | - Jamal Ali Moiz
- Centre for Physiotherapy and Rehabilitation Sciences, Jamia Millia Islamia (Central University), New Delhi, India
| | - Pranay Tanwar
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | | | - G K Rath
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ravi Mehrotra
- National Institute of Cancer Prevention and Research, Indian Council of Medical Research (NICPR-ICMR), New Delhi, India
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6
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Lai KN, Ho WK, Kang IN, Kang PCE, Phuah SY, Mariapun S, Yip CH, Mohd Taib NA, Teo SH. Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study. BMC Cancer 2017; 17:149. [PMID: 28222693 PMCID: PMC5320733 DOI: 10.1186/s12885-017-3099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Background Genetic testing for BRCA1 and BRCA2 has led to the accurate identification of individuals at higher risk of cancer and the development of new therapies. Approximately 10-20% of the genetic testing for BRCA1 and BRCA2 leads to the identification of variants of uncertain significance (VUS), with higher proportions in Asians. We investigated the functional significance of 7 BRCA1 and 25 BRCA2 variants in a multi-ethnic Asian cohort using a case-control approach. Methods The MassARRAY genotyping was conducted in 1,394 Chinese, 406 Malay and 310 Indian breast cancer cases and 1,071 Chinese, 167 Malay and 255 Indian healthy controls. The association of individual variant with breast cancer risk was analyzed using logistic regression model adjusted for ethnicity, age and family history. Results Our study confirmed BRCA2 p.Ile3412Val is presented in >2% of unaffected women and is likely benign, and BRCA2 p.Ala1996Thr which is predicted to be likely pathogenic by in-silico models is presented in 2% of healthy Indian women suggesting that it may not be associated with breast cancer risk. Single-variant analysis suggests that BRCA1 p.Arg762Ser may be associated with breast cancer risk (OR = 7.4; 95% CI, 0.9–62.3; p = 0.06). Conclusions Our study shows that BRCA2 p.Ile3412Val and p.Ala1996Thr are likely benign and highlights the need for population-specific studies to determine the likely functional significance of population-specific variants. Our study also suggests that BRCA1 p.Arg762Ser may be associated with increased risk of breast cancer but other methods or larger studies are required to determine a more precise estimate of breast cancer risk. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3099-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kah Nyin Lai
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Weang Kee Ho
- Department of Applied Mathematics, Faculty of Engineering, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
| | - In Nee Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Peter Choon Eng Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Sze Yee Phuah
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Shivaani Mariapun
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Cheng-Har Yip
- Subang Jaya Medical Centre, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia. .,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia.
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Ma H, Ursin G, Xu X, Lee E, Togawa K, Duan L, Lu Y, Malone KE, Marchbanks PA, McDonald JA, Simon MS, Folger SG, Sullivan-Halley J, Deapen DM, Press MF, Bernstein L. Reproductive factors and the risk of triple-negative breast cancer in white women and African-American women: a pooled analysis. Breast Cancer Res 2017; 19:6. [PMID: 28086982 PMCID: PMC5237290 DOI: 10.1186/s13058-016-0799-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/22/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Early age at menarche, nulliparity, late age at first completed pregnancy, and never having breastfed, are established breast cancer risk factors. However, among breast cancer subtypes, it remains unclear whether all of these are risk factors for triple-negative breast cancer (TNBC). METHODS We evaluated the associations of these reproductive factors with TNBC, in 2658 patients with breast cancer (including 554 with TNBC) and 2448 controls aged 20-64 years, who participated in one of the three population-based case-control studies: the Women's Contraceptive and Reproductive Experiences Study, the Women's Breast Carcinoma in situ Study, or the Women's Learning the Influence of Family and Environment Study. We used multivariable polychotomous unconditional logistic regression methods to conduct case-control comparisons among breast cancer subtypes defined by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2 expression status. RESULTS TNBC risk decreased with increasing duration of breastfeeding (P trend = 0.006), but age at menarche, age at first completed pregnancy, and nulliparity were not associated with risk of TNBC. Parous women who breastfed for at least one year had a 31% lower risk of TNBC than parous women who had never breastfed (odds ratio, OR = 0.69; 95% confidence interval, CI = 0.50-0.96). The association between breastfeeding and risk of TNBC was modified by age and race. Parous African-American women aged 20-44 years who breastfed for 6 months or longer had an 82% lower risk of TNBC than their counterparts who had never breastfed (OR = 0.18, 95% CI = 0.07-0.46). CONCLUSIONS Our data indicate that breastfeeding decreases the risk of TNBC, especially for younger African-American women.
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Affiliation(s)
- Huiyan Ma
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
| | - Giske Ursin
- Cancer Registry of Norway, Oslo, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Xinxin Xu
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Kayo Togawa
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Lei Duan
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
- School of Social Work, University of Southern California, Los Angeles, CA 90033 USA
| | - Yani Lu
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
| | - Kathleen E. Malone
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Polly A. Marchbanks
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Jill A. McDonald
- College of Health and Social Services, New Mexico State University, Las Cruces, NM 88003 USA
| | - Michael S. Simon
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI 48201 USA
| | - Suzanne G. Folger
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Jane Sullivan-Halley
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
| | - Dennis M. Deapen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Michael F. Press
- Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute, 1500 East Duarte Rd. Duarte, City of Hope, CA 91010 USA
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Prendergast D, Woad KJ, Chamley LW, Holland OJ, Shelling AN. SPACA3gene variants in a New Zealand cohort of infertile and fertile couples. HUM FERTIL 2014; 17:106-13. [DOI: 10.3109/14647273.2014.907506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Dowty JG, Lee E, McKean-Cowdin R, Henderson BE, Bernstein L, Ursin G, Hopper JL. Estimating risks for variants of unknown significance according to their predicted pathogenicity classes with application to BRCA1. Breast Cancer Res Treat 2014; 144:171-7. [PMID: 24481681 DOI: 10.1007/s10549-014-2845-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/17/2014] [Indexed: 11/29/2022]
Abstract
Sequence-based testing of disease-susceptibility genes has identified many variants of unknown significance (VUSs) whose pathogenicity is unknown at the time of their measurement. Female breast cancer cases aged 20-49 years at diagnosis and who have VUSs in BRCA1 and no mutations in BRCA2 have previously been identified through the population-based Los Angeles County Cancer Surveillance Program. These nominal BRCA1 VUSs have been classified as "low," "medium," and "high" risk by four classification methods: Align-GVGD, Polyphen, Grantham matrix scores, and sequence conservation in mammalian species. Average hazard ratios (HRs) for classes of variants, i.e., the age-specific incidences of cancer for carriers of such variants divided by the population incidences, were estimated from the cancer family histories of first- and second-degree relatives of the index cases using modified segregation analysis. The study sample comprised 270 index cases and 4,543 of their relatives. There was weak evidence that the risk of breast cancer increases with the degree of sequence conservation (P = 0.03) and that missense variants at highly conserved sites are associated with a 5.6-fold (95 % confidence interval 1.4-22.2; P = 0.05) increased incidence of breast cancer. An upper bound of 2.3 is given for the average breast cancer HRs corresponding to variants classified as "low risk" by any of the four VUS classification methods. In summary, we have given a method to estimate cancer risks for groups of VUSs by combining existing classification methods with traditional penetrance analyses. This analysis suggests that classification methods for BRCA1 variants based on sequence conservation might be useful in a clinical setting. We have shown in principle that our method can be used to classify VUSs into clinically useful risk categories, but our specific findings should not be put into clinical practice unless confirmed by larger studies.
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Affiliation(s)
- J G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Level 3/207 Bouverie St., Carlton, VIC, 3053, Australia
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Vietri MT, Molinari AM, Laura De Paola M, Cantile F, Fasano M, Cioffi M. Identification of a novel in-frame deletion in BRCA2 and analysis of variants of BRCA1/2 in Italian patients affected with hereditary breast and ovarian cancer. Clin Chem Lab Med 2013; 50:2171-80. [PMID: 23096105 DOI: 10.1515/cclm-2012-0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022]
Abstract
BACKGROUND An estimated 5 % – 10 % of all breast cancers are due to an inherited predisposition and, out of these, about 30 % are caused by germline mutations of the BRCA1 and BRCA2 genes. The prevalence of germline mutations in theBRCA1 and BRCA2 genes varies among ethnic groups. The aims of this study are to evaluate deleterious mutations and genomic rearrangements in BRCA1/2 genes and the CHEK21100delC mutation in a cohort of Italian women affected with hereditary breast and/or ovarian cancer. In addition we clarify the effect of the novel variants identified in BRCA2 gene bymRNA analysis and prediction software. METHODS We enrolled 103 consecutive Italian patients affected with hereditary breast and/or ovarian cancer, aged23 – 69 years. RESULTS We found BRCA1/2 mutations in 15/103 probands(14.6 % ). Among these, a BRCA2 gene mutation has not been described previously. In addition, we identified five novel BRCA2 variants (S1341, IVS1-59t > c, IVS11-74insA, IVS12 + 74c > g and I1167V). No genomic BRCA1/2re arrangements or CHEK2 1100delC mutation was found in our patients. The novel BRCA2 mutation NS1742del(p.N1742_S1743del) was an in-frame 6 bp deletion that results in loss of two amino acids. CONCLUSIONS In silico analysis conducted for S1341, IVS1-59t > c, IVS11-74insA and IVS12 + 74c > g of BRCA2 predicted the variants as neutral and benign, whereas the results for I1167V was inconclusive. mRNA analysis for the novel BRCA2 intronic variant IVS11-74insA and the already published BRCA1 variant C197 shows that they have no effect on the splicing. These results are in agreement with in silico analysis.
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Affiliation(s)
- Maria Teresa Vietri
- Dipartimento di Patologia Generale , Facoltà di Medicina e Chirurgia Seconda Università degli studi, Naples , Italy
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Caputo S, Benboudjema L, Sinilnikova O, Rouleau E, Béroud C, Lidereau R. Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases. Nucleic Acids Res 2011; 40:D992-1002. [PMID: 22144684 PMCID: PMC3245050 DOI: 10.1093/nar/gkr1160] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BRCA1 and BRCA2 are the two main genes responsible for predisposition to breast and ovarian cancers, as a result of protein-inactivating monoallelic mutations. It remains to be established whether many of the variants identified in these two genes, so-called unclassified/unknown variants (UVs), contribute to the disease phenotype or are simply neutral variants (or polymorphisms). Given the clinical importance of establishing their status, a nationwide effort to annotate these UVs was launched by laboratories belonging to the French GGC consortium (Groupe Génétique et Cancer), leading to the creation of the UMD-BRCA1/BRCA2 databases (http://www.umd.be/BRCA1/ and http://www.umd.be/BRCA2/). These databases have been endorsed by the French National Cancer Institute (INCa) and are designed to collect all variants detected in France, whether causal, neutral or UV. They differ from other BRCA databases in that they contain co-occurrence data for all variants. Using these data, the GGC French consortium has been able to classify certain UVs also contained in other databases. In this article, we report some novel UVs not contained in the BIC database and explore their impact in cancer predisposition based on a structural approach.
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Affiliation(s)
- Sandrine Caputo
- Institut Curie-Hôpital René Huguenin, Service d'Oncogénétique, U735 INSERM-Saint-Cloud, France.
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Lee E, McKean-Cowdin R, Ma H, Spicer DV, Van Den Berg D, Bernstein L, Ursin G. Characteristics of triple-negative breast cancer in patients with a BRCA1 mutation: results from a population-based study of young women. J Clin Oncol 2011; 29:4373-80. [PMID: 22010008 DOI: 10.1200/jco.2010.33.6446] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Triple-negative breast cancers (TNBCs) are tumors with low or no expression of estrogen receptor, progesterone receptor, or human epidermal growth factor receptor 2. These tumors have a poor prognosis, remain a clinical challenge, and are more common among women with BRCA1 mutations. We tested whether there are distinguishing features of TNBC after BRCA1 mutation status has been taken into account. PATIENTS AND METHODS We sequenced BRCA1 and BRCA2 genes in a population-based sample of 1,469 patients with incident breast cancer age 20 to 49 years from Los Angeles County (California). Information on tumor receptor status was available for 1,167 women. Clinical, pathologic, and hormone-related lifestyle characteristics were compared across patient subgroups defined by BRCA1 mutation status and triple-negative receptor status. RESULTS Forty-eight percent of BRCA1 mutation carriers had TNBC compared with only 12% of noncarriers. Within BRCA1 mutation carriers, as well as within noncarriers, triple-negative receptor status was associated with younger age at diagnosis and higher tumor grade. Among women without a BRCA1 mutation, we observed that women with TNBC had higher premenopausal body mass index and earlier age at first full-term pregnancy than those with non-TNBC. Age at menarche and other reproductive factors were not associated with triple-negative status regardless of BRCA1 mutation status. Within BRCA1 mutation carriers, Ashkenazi Jewish women were about five times more likely to have TNBC than non-Ashkenazi Jewish women. CONCLUSION Our results suggest that among BRCA1 mutation carriers, as among noncarriers, there are unique characteristics associated with the triple-negative subtype. The findings in Ashkenazi Jewish BRCA1 mutation carriers should be confirmed.
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Affiliation(s)
- Eunjung Lee
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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Cote S, Arcand SL, Royer R, Nolet S, Mes-Masson AM, Ghadirian P, Foulkes WD, Tischkowitz M, Narod SA, Provencher D, Tonin PN. The BRCA2 c.9004G>A (E2003K) variant is likely pathogenic and recurs in breast and/or ovarian cancer families of French Canadian descent. Breast Cancer Res Treat 2011; 131:333-40. [DOI: 10.1007/s10549-011-1796-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 09/16/2011] [Indexed: 12/14/2022]
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van der Groep P, van der Wall E, van Diest PJ. Pathology of hereditary breast cancer. Cell Oncol (Dordr) 2011; 34:71-88. [PMID: 21336636 PMCID: PMC3063560 DOI: 10.1007/s13402-011-0010-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2010] [Indexed: 12/11/2022] Open
Abstract
Background Hereditary breast cancer runs in families where several members in different generations are affected. Most of these breast cancers are caused by mutations in the high penetrance genes BRCA1 and BRCA2 accounting for about 5% of all breast cancers. Other genes that include CHEK2, PTEN, TP53, ATM, STK11/LKB1, CDH1, NBS1, RAD50, BRIP1 and PALB2 have been described to be high or moderate penetrance breast cancer susceptibility genes, all contributing to the hereditary breast cancer spectrum. However, in still a part of familial hereditary breast cancers no relationship to any of these breast cancer susceptibility genes can be found. Research on new susceptibility genes is therefore ongoing. Design In this review we will describe the function of the today known high or moderate penetrance breast cancer susceptibility genes and the consequences of their mutated status. Furthermore, we will focus on the histology, the immunophenotype and genotype of breast cancers caused by mutations in BRCA1 and BRCA2 genes and the other high or moderate penetrance breast cancer susceptibility genes. Finally, an overview of the clinical implications of hereditary breast cancer patients will be provided. Conclusion This information leads to a better understanding of the morphological, immunohistochemical and molecular characteristics of different types of hereditary breast cancers. Further, these characteristics offer clues for diagnosis and new therapeutic approaches.
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Affiliation(s)
- Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
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Comprehensive BRCA1 and BRCA2 mutation analyses and review of French Canadian families with at least three cases of breast cancer. Fam Cancer 2010; 9:507-17. [DOI: 10.1007/s10689-010-9372-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Clinical relevance of rare germline sequence variants in cancer genes: evolution and application of classification models. Curr Opin Genet Dev 2010; 20:315-23. [PMID: 20456937 DOI: 10.1016/j.gde.2010.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 12/11/2022]
Abstract
Multifactorial models developed for BRCA1/2 variant classification have proved very useful for delineating BRCA1/2 variants associated with very high risk of cancer, or with little clinical significance. Recent linkage of this quantitative assessment of risk to clinical management guidelines has provided a basis to standardize variant reporting, variant classification and management of families with such variants, and can theoretically be applied to any disease gene. As proof of principle, the multifactorial approach already shows great promise for application to the evaluation of mismatch repair gene variants identified in families with suspected Lynch syndrome. However there is need to be cautious of the noted limitations and caveats of the current model, some of which may be exacerbated by differences in ascertainment and biological pathways to disease for different cancer syndromes.
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High-throughput resequencing in the diagnosis of BRCA1/2 mutations using oligonucleotide resequencing microarrays. Breast Cancer Res Treat 2009; 122:287-97. [PMID: 19941162 DOI: 10.1007/s10549-009-0639-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Breast cancer is the most frequent form of carcinoma in European females (incidence 65 per 100,000). In about 10% of all cases, pedigree analysis predicts a hereditary breast-ovarian cancer syndrome (HBOC) to be causative for the disease. Frequently, mutations in two genes, BRCA1 (Chr. 17q21) and BRCA2 (Chr. 13q12), are associated with HBOC. In females, mutations in these genes result in a lifetime risk of 80-85% for breast cancer and 54% (BRCA1) or 23% (BRCA2) for ovarian cancer. Current genetic diagnostic tools for BRCA1 and BRCA2 remain laborious and expensive. Here, we present the first oligonucleotide resequencing microarray covering the complete coding sequence of both genes. In total, 36 previously characterized DNAs were resequenced; all 11 patients with single-nucleotide mutations and, due to a special mutational design, eight patients with heterozygous deletions were detected correctly. In total, 47 different single-nucleotide variants (SNVs) were found. A newly developed software, SeqC, reduced the number of ambiguous calls with the help of a statistical module comparing the acquired data to an online-database. SeqC improved the average call rate to 99% (GSeq: 97%) and reduced time and efforts for manual analysis. SeqC confirmed the results obtained by GSeq and found an additional 33 sequences changes representing 14 SNVs. In total, 945 kb were screened and the overall turnaround time for each patient took approximately 3 days, including analysis.
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Haffty BG, Choi DH, Goyal S, Silber A, Ranieri K, Matloff E, Lee MH, Nissenblatt M, Toppmeyer D, Moran MS. Breast cancer in young women (YBC): prevalence of BRCA1/2 mutations and risk of secondary malignancies across diverse racial groups. Ann Oncol 2009; 20:1653-9. [PMID: 19491284 DOI: 10.1093/annonc/mdp051] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Despite significant differences in age of onset and incidence of breast cancer between Caucasian (CA), African-American (AA) and Korean (KO) women, little is known about differences in BRCA1/2 mutations in these populations. The purpose of this study is to evaluate the prevalence of BRCA1/2 mutations and the association between BRCA1/2 mutation status and secondary malignancies among young women with breast cancer in these three racially diverse groups. METHODS Patients presenting to our breast cancer follow-up clinics selected solely on having a known breast cancer diagnosis at a young age (YBC defined as age <45 years at diagnosis) were invited to participate in this study. A total of 333 eligible women, 166 CA, 66 AA and 101 KO underwent complete sequencing of BRCA1/2 genes. Family history (FH) was classified as negative, moderate or strong. BRCA1/2 status was classified as wild type (WT), variant of uncertain significance (VUS) or deleterious (DEL). RESULTS DEL across these three racially diverse populations of YBC were nearly identical: CA 17%, AA 14% and KO 14%. The type of DEL differed with AA having more frequent mutations in BRCA2, compared with CA and KO. VUS were predominantly in BRCA2 and AA had markedly higher frequency of VUS (38%) compared with CA (10%) and KO (12%). At 10-year follow-up from the time of initial diagnosis of breast cancer, the risk of secondary malignancies was similar among WT (14%) and VUS (16%), but markedly higher among DEL (39%). CONCLUSIONS In these YBC, the frequency of DEL in BRCA1/2 is remarkably similar among the racially diverse groups at 14%-17%. VUS is more common in AA, but aligns closely with WT in risk of second cancers, age of onset and FH.
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Affiliation(s)
- B G Haffty
- Department of Radiation Oncology, UMDNJ-RWJMS and Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA.
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Lee E, Ma H, McKean-Cowdin R, Van Den Berg D, Bernstein L, Henderson BE, Ursin G. Effect of reproductive factors and oral contraceptives on breast cancer risk in BRCA1/2 mutation carriers and noncarriers: results from a population-based study. Cancer Epidemiol Biomarkers Prev 2009; 17:3170-8. [PMID: 18990759 DOI: 10.1158/1055-9965.epi-08-0396] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Multiparity and breast-feeding reduce breast cancer risk, whereas oral contraceptive use may slightly increase breast cancer risk in the general population. However, the effects of these factors in BRCA1 and BRCA2 mutation carriers are less clear. METHODS Case patients were 1,469 women from Los Angeles County ages 20 to 49 years with newly diagnosed breast cancer. Control subjects were 444 women without breast cancer, individually matched to a subset of cases on race, age, and neighborhood. BRCA1/2 genes were sequenced in the cases, and odds ratios of breast cancer associated with various reproductive and hormonal factors in BRCA1/2 mutation carriers and noncarriers were estimated using multivariable logistic regression. RESULTS Ninety-four women had a deleterious BRCA1 or BRCA2 mutation. Number of full-term pregnancies was inversely associated with breast cancer risk regardless of BRCA1/2 mutation status. Longer breast-feeding duration was protective among noncarriers but not among mutation carriers; however, this apparent effect modification was not statistically significant (P = 0.23). Neither oral contraceptive use overall nor the use of low-dose oral contraceptives was associated with an increased risk of breast cancer in any subgroup. CONCLUSIONS Our results suggest that parity protects against breast cancer in BRCA1/2 mutation carriers, whereas breast-feeding does not. Our data suggest no association between oral contraceptive use and breast cancer risk in BRCA1/2 mutation carriers. Further confirmation that currently available low-dose oral contraceptives do not increase breast cancer risk in carriers is important from a public health perspective given the high prevalence of oral contraceptive use in the United States.
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Affiliation(s)
- Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Room 4407, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
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