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Ahmad H, Ali A, Khalil AT, Ali R, Khan I, Khan MM, Ahmed I, Basharat Z, Alorini M, Mehmood A. Clinico-genomic findings, molecular docking, and mutational spectrum in an understudied population with breast cancer patients from KP, Pakistan. Front Genet 2024; 15:1383284. [PMID: 38784039 PMCID: PMC11111998 DOI: 10.3389/fgene.2024.1383284] [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: 02/07/2024] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we report the mutational profiles, pathogenicity, and their association with different clinicopathologic and sociogenetic factors in patients with Pashtun ethnicity for the first time. A total of 19 FFPE blocks of invasive ductal carcinoma (IDC) from the Breast Cancer (BC) tissue and 6 normal FFPE blocks were analyzed by whole-exome sequencing (WES). Various somatic and germline mutations were identified in cancer-related genes, i.e., ATM, CHEK2, PALB2, and XRCC2. Among a total of 18 mutations, 14 mutations were somatic and 4 were germline. The ATM gene exhibited the maximum number of mutations (11/18), followed by CHEK2 (3/18), PALB2 (3/18), and XRCC2 (1/18). Except one frameshift deletion, all other 17 mutations were nonsynonymous single-nucleotide variants (SNVs). SIFT prediction revealed 7/18 (38.8%) mutations as deleterious. PolyPhen-2 and MutationTaster identified 5/18 (27.7%) mutations as probably damaging and 10/18 (55.5%) mutations as disease-causing, respectively. Mutations like PALB2 p.Q559R (6/19; 31.5%), XRCC2 p.R188H (5/19; 26.31%), and ATM p.D1853N (4/19; 21.05%) were recurrent mutations and proposed to have a biomarker potential. The protein network prediction was performed using GeneMANIA and STRING. ISPRED-SEQ indicated three interaction site mutations which were further used for molecular dynamic simulation. An average increase in the radius of gyration was observed in all three mutated proteins revealing their perturbed folding behavior. Obtained SNVs were further correlated with various parameters related to the clinicopathological status of the tumors. Three mutation positions (ATM p. D1853N, CHEK2 p.M314I, and PALB2 p.T1029S) were found to be highly conserved. Finally, the wild- and mutant-type proteins were screened for two drugs: elagolix (DrugBank ID: DB11979) and LTS0102038 (a triterpenoid, isolated from the anticancer medicinal plant Fagonia indica). Comparatively, a higher number of interactions were noted for normal ATM with both compounds, as compared to mutants.
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Affiliation(s)
- Hilal Ahmad
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Asif Ali
- Institute of Pathology and Diagnostic Medicine (IPDM), Khyber Medical University, Peshawar, Pakistan
- College of Medicine, Gulf Medical University, Ajman, United Arab Emirates
- School of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Ali Talha Khalil
- Department of Pathology, Lady Reading Hospital Medical Teaching Institution, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Ishaq Khan
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Mah Muneer Khan
- Department of Surgery, Khyber Teaching Hospital, Medical Teaching Institution, Peshawar, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics (Private) Limited, Islamabad, Pakistan
- Microbiological Analysis Team, Group for Biometrology, The Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | | | - Mohammed Alorini
- Department of Pathology, College of Medicine, Qassim University, Unaizah, Saudi Arabia
| | - Amna Mehmood
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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Luo Y, Pan R, Rao H, Chen X, Yang H. Association Between Germline BRCA1/2 Gene Variants and Clinicopathological Features of Ovarian Cancer. Int J Gen Med 2024; 17:75-84. [PMID: 38226182 PMCID: PMC10789571 DOI: 10.2147/ijgm.s445660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024] Open
Abstract
Objective To investigate the relationship between BRCA1/2 gene mutation and clinicopathological features in ovarian cancer patients, so as to develop precise individualized treatment plan for patients. Methods Patients diagnosed with ovarian cancer between January 2018 and July 2023 who underwent BRCA1/2 genetic testing were retrospectively analyzed. The clinicopathological characteristics (age, body mass index (BMI), family history of ovarian cancer, pregnancy history, menopause status, tumor size, histopathology, Federation of Gynecology and Obstetrics (FIGO) staging, and ascites) of non-carriers and BRCA1/2 variant carriers were compared. Logistic regression analysis was used to explore the relationship between BRCA1/2 variants and clinicopathological characteristics of ovarian cancer. Results A total of 284 ovarian cancer patients were collected, and the subjects were divided into two groups, 197 non-carriers and 87 BRCA1/2 variants carriers. The proportion of serous ovarian carcinoma in BRCA1/2 variant carriers is higher than that in non-BRCA variant carriers (78.2% vs 60.9%, p=0.015). There were 51 patients with BRCA pathogenic or likely pathogenic variant, 22 patients with BRCA likely benign variant, and 14 patients with BRCA variants of uncertain significance (VUS). The proportion of serous ovarian carcinoma in patients with BRCA pathogenic/likely pathogenic variant is higher than that in patients with BRCA likely benign variant and BRCA VUS (94.1% vs 50.0% and 64.3%. p<0.001). There were no statistically significant differences in BMI, family history of ovarian cancer, pregnancy history, menopause status, maximum diameter of the tumor lesion, FIGO stage, and ascites among patients with different grades of variants. Multivariate logistic regression analysis showed that serous ovarian carcinoma was related to BRCA mutation (Serous carcinoma vs non-serous carcinoma: OR 2.145, 95% CI: 1.044-4.407) (p=0.038). Conclusion Patients with BRCA1 variant develop ovarian cancer at a younger age than those with the BRCA2 variant. The proportion of FIGO stage III-IV in patients with BRCA pathogenic + likely pathogenic variant was significantly higher than those in patients with other variants. Germline BRCA1/2 variants were most frequently identified in serous ovarian carcinoma patients.
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Affiliation(s)
- Yu Luo
- Department of Gynaecology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People’s Hospital, Meizhou, People’s Republic of China
| | - Ru Pan
- Department of Gynaecology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People’s Hospital, Meizhou, People’s Republic of China
| | - Hui Rao
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People’s Hospital, Meizhou, People’s Republic of China
- Department of Laboratory Medicine, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Xing Chen
- Data Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Haikun Yang
- Department of Gynaecology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People’s Hospital, Meizhou, People’s Republic of China
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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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Jiang C, Lu Y, Liu H, Cai G, Peng Z, Feng W, Lin L. Clinical characterization and genomic landscape of gynecological cancers among patients attending a Chinese hospital. Front Oncol 2023; 13:1143876. [PMID: 37064128 PMCID: PMC10101327 DOI: 10.3389/fonc.2023.1143876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundGynecological cancers are the most lethal malignancies among females, most of which are associated with gene mutations. Few studies have compared the differences in the genomic landscape among various types of gynecological cancers. In this study, we evaluated the diversity of mutations in different gynecological cancers.MethodsA total of 184 patients with gynecological cancer, including ovarian, cervical, fallopian tube, and endometrial cancer, were included. Next-generation sequencing was performed to detect the mutations and tumor mutational burden (TMB). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were also conducted.ResultsWe found that 94.57% of patients had at least one mutation, among which single nucleotide variants, insertions and InDels were in the majority. TP53, PIK3CA, PTEN, KRAS, BRCA1, BRCA2, ARID1A, KMT2C, FGFR2, and FGFR3 were the top 10 most frequently mutated genes. Patients with ovarian cancer tended to have higher frequencies of BRCA1 and BRCA2 mutations, and the frequency of germline BRCA1 mutations (18/24, 75.00%) was higher than that of BRCA2 (11/19, 57.89%). A new mutation hotspot in BRCA2 (I770) was firstly discovered among Chinese patients with gynecological cancer. Patients with TP53, PIK3CA, PTEN, and FGFR3 mutations had significantly higher TMB values than those with wild-type genes. A significant cross was discovered between the enriched KEGG pathways of gynecological and breast cancers. GO enrichment revealed that the mutated genes were crucial for the cell cycle, neuronal apoptosis, and DNA repair.ConclusionVarious gynecological cancer types share similarities and differences both in clinical characterization and genomic mutations. Taken together with the results of TMB and enriched pathways, this study provided useful information on the molecular mechanism underlying gynecological cancers and the development of targeted drugs and precision medicine.
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Affiliation(s)
- Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiyi Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hua Liu
- Department of Obstetrics & Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gang Cai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhao Peng
- Genecast Biotechnology Co., Ltd., Wuxi, China
| | - Weiwei Feng
- Department of Obstetrics & Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Weiwei Feng, ; Lin Lin,
| | - Lin Lin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Weiwei Feng, ; Lin Lin,
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D’Elia G, Caliendo G, Passariello L, Albanese L, Makker J, Molinari AM, Vietri MT. Hereditary Cancer Syndrome in a Family with Double Mutation in BRIP1 and MUTYH Genes. Genes (Basel) 2023; 14:428. [PMID: 36833355 PMCID: PMC9957058 DOI: 10.3390/genes14020428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Hereditary cancer syndromes predispose to several types of cancer due to inherited pathogenic variants in susceptibility genes. We describe the case of a 57-year-old woman, diagnosed with breast cancer, and her family. The proband belongs to a family with a suspected tumor syndrome, due to other cancer cases in her family from the paternal and maternal sides. After oncogenetic counseling, she was subjected to mutational analysis with an NGS panel analyzing 27 genes. The genetic analysis showed two monoallelic mutations in low penetrance genes, c.1187G>A (p.G396D) in MUTYH and c.55dup (p.Tyr19Leufs*2) in BRIP1. One of the mutations was inherited from the maternal side and the other from the paternal side, suggesting two different cancer syndrome types in the family. MUTYH mutation was related to the onset of cancers on the paternal side, as confirmed by the occurrence of the same mutation in the proband's cousin. BRIP1 mutation was found in the proband's mother, indicating that it was related to the cancer cases observed on the maternal side, including breast cancer and sarcoma. Advances in NGS technologies have allowed the identification of mutations in families with hereditary cancers in genes other than those related to a specific suspected syndrome. A complete oncogenetic counseling, together with molecular tests that enable a simultaneous analysis of multiple genes, is essential for the identification of a correct tumor syndrome and for clinical decision-making in a patient and his/her family. The detection of mutations in multiple susceptibility genes allows the initiation of early risk-reducing measures for identified mutation carriers among family members and to include them in a proper surveillance program for specific syndromes. Moreover, it may enable an adapted treatment for the affected patient, permitting personalized therapeutic options.
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Affiliation(s)
- Giovanna D’Elia
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Gemma Caliendo
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Luana Passariello
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Luisa Albanese
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Jasmine Makker
- Department of GKT, School of Medical Education, King’s College London, London WC2R 2LS, UK
| | - Anna Maria Molinari
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Maria Teresa Vietri
- Unity of Clinical and Molecular Pathology, AOU University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
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Corso G, Magnoni F, Veronesi P. Points to Consider Regarding De-Escalation Surgery in High-Risk Breast Cancer. Ann Surg Oncol 2022; 29:8084-8089. [DOI: 10.1245/s10434-022-12542-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/31/2022] [Indexed: 12/23/2022]
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