Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan
Gene mutations are a source of genetic instability which fuels the progression of cancer. Mutations in BRCA1 and BRCA2 are considered as major drivers in the progression of breast cancer and their detection indispensable for devising therapeutic and management approaches. The current study aims to i...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-05-01
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| Series: | Neoplasia: An International Journal for Oncology Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1476558624000265 |
| _version_ | 1797208814713307136 |
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| author | Hilal Ahmad Asif Ali Roshan Ali Ali Talha Khalil Ishaq Khan Mah Muneer Khan Mohammed Alorini |
| author_facet | Hilal Ahmad Asif Ali Roshan Ali Ali Talha Khalil Ishaq Khan Mah Muneer Khan Mohammed Alorini |
| author_sort | Hilal Ahmad |
| collection | DOAJ |
| description | Gene mutations are a source of genetic instability which fuels the progression of cancer. Mutations in BRCA1 and BRCA2 are considered as major drivers in the progression of breast cancer and their detection indispensable for devising therapeutic and management approaches. The current study aims to identify novel pathogenic and recurrent mutations in BRCA1 and BRCA2 in Pakhtun population from the Khyber Pakhtunkhwa. To determine the BRCA1 and BRCA2 pathogenic mutation prevalence in Pakhtun population from KP, whole exome sequencing of 19 patients along with 6 normal FFPE embedded blocks were performed. The pathogenicity of the mutations were determined and they were further correlated with different hormonal, sociogenetic and clinicopathological features. We obtained a total of 10 mutations (5 somatic and 5 germline) in BRCA1 while 27 mutations (24 somatic and 3 germline) for BRCA2. Five and seventeen pathogenic or deleterious mutations were identified in BRCA1 and BRCA2 respectively by examining the mutational spectrum through SIFT, PolyPhen-2 and Mutation Taster. Among the SNVs, BRCA1 p.P824L, BRCA2 p. P153Q, p.I180F, p.D559Y, p.G1529R, p.L1576F, p.E2229K were identified as mutations of the interaction sites as predicted by the deep algorithm based ISPRED-SEQ prediction tool. SAAFEQ-SEQ web-based algorithm was used to calculate the changes in free energy and effect of SNVs on protein stability. All SNVs were found to have a destabilizing effect on the protein. ConSurf database was used to determine the evolutionary conservation scores and nature of the mutated residues. Gromacs 4.5 was used for the molecular simulations. Ramachandran plots were generated using procheck server. STRING and GeneMania was used for prediction of the gene interactions. The highest number of mutations (BRCA1 7/10, 70 %) were on exon 9 and (BRCA2, 11/27; 40 %) were on exon 11. 40 % and 60 % of the BRCA2 mutations were associated Grade 2 and Grade 3 tumors respectively. The present study reveals unique BRCA1 and BRCA2 mutations in Pakhtun population. We further suggest sequencing of the large cohorts for further characterizing the pathogenic mutations. |
| first_indexed | 2024-04-24T09:44:47Z |
| format | Article |
| id | doaj.art-cb057f86b6e04b518936e505b98f21bd |
| institution | Directory Open Access Journal |
| issn | 1476-5586 |
| language | English |
| last_indexed | 2024-04-24T09:44:47Z |
| publishDate | 2024-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Neoplasia: An International Journal for Oncology Research |
| spelling | doaj.art-cb057f86b6e04b518936e505b98f21bd2024-04-15T04:05:36ZengElsevierNeoplasia: An International Journal for Oncology Research1476-55862024-05-0151100989Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), PakistanHilal Ahmad0Asif Ali1Roshan Ali2Ali Talha Khalil3Ishaq Khan4Mah Muneer Khan5Mohammed Alorini6Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, PakistanInstitute of Pathology and Diagnostic Medicine (IPDM), Khyber Medical University, Peshawar, KP, Pakistan; College of Medicine, Gulf Medical University, Ajman, United Arab Emirates; School of Medicine, University of Glasgow, UK; Corresponding author at: Institute of Pathology and Diagnostic Medicine (IPDM), Khyber Medical University, Peshawar, KP, Pakistan.Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, PakistanDepartment of Pathology, Lady Reading Hospital Medical Teaching Institution, Peshawar, KP, Pakistan; Corresponding author at: Department of Pathology, Lady Reading Hospital Medical Teaching Institution, Peshawar, KP, Pakistan.Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, PakistanDepartment of Surgery, Khyber Teaching Hospital, Medical Teaching Institution, Peshawar, KP, PakistanDepartment of Basic Medical Sciences, Unaizah College of Medicine and Medical Sciences, Qassim University, Unaizah, Saudi ArabiaGene mutations are a source of genetic instability which fuels the progression of cancer. Mutations in BRCA1 and BRCA2 are considered as major drivers in the progression of breast cancer and their detection indispensable for devising therapeutic and management approaches. The current study aims to identify novel pathogenic and recurrent mutations in BRCA1 and BRCA2 in Pakhtun population from the Khyber Pakhtunkhwa. To determine the BRCA1 and BRCA2 pathogenic mutation prevalence in Pakhtun population from KP, whole exome sequencing of 19 patients along with 6 normal FFPE embedded blocks were performed. The pathogenicity of the mutations were determined and they were further correlated with different hormonal, sociogenetic and clinicopathological features. We obtained a total of 10 mutations (5 somatic and 5 germline) in BRCA1 while 27 mutations (24 somatic and 3 germline) for BRCA2. Five and seventeen pathogenic or deleterious mutations were identified in BRCA1 and BRCA2 respectively by examining the mutational spectrum through SIFT, PolyPhen-2 and Mutation Taster. Among the SNVs, BRCA1 p.P824L, BRCA2 p. P153Q, p.I180F, p.D559Y, p.G1529R, p.L1576F, p.E2229K were identified as mutations of the interaction sites as predicted by the deep algorithm based ISPRED-SEQ prediction tool. SAAFEQ-SEQ web-based algorithm was used to calculate the changes in free energy and effect of SNVs on protein stability. All SNVs were found to have a destabilizing effect on the protein. ConSurf database was used to determine the evolutionary conservation scores and nature of the mutated residues. Gromacs 4.5 was used for the molecular simulations. Ramachandran plots were generated using procheck server. STRING and GeneMania was used for prediction of the gene interactions. The highest number of mutations (BRCA1 7/10, 70 %) were on exon 9 and (BRCA2, 11/27; 40 %) were on exon 11. 40 % and 60 % of the BRCA2 mutations were associated Grade 2 and Grade 3 tumors respectively. The present study reveals unique BRCA1 and BRCA2 mutations in Pakhtun population. We further suggest sequencing of the large cohorts for further characterizing the pathogenic mutations.http://www.sciencedirect.com/science/article/pii/S1476558624000265Breast cancerBRCA1BRCA2NovelMutationsMolecular simulations |
| spellingShingle | Hilal Ahmad Asif Ali Roshan Ali Ali Talha Khalil Ishaq Khan Mah Muneer Khan Mohammed Alorini Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan Neoplasia: An International Journal for Oncology Research Breast cancer BRCA1 BRCA2 Novel Mutations Molecular simulations |
| title | Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan |
| title_full | Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan |
| title_fullStr | Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan |
| title_full_unstemmed | Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan |
| title_short | Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan |
| title_sort | preliminary insights on the mutational spectrum of brca1 and brca2 genes in pakhtun ethnicity breast cancer patients from khyber pakhtunkhwa kp pakistan |
| topic | Breast cancer BRCA1 BRCA2 Novel Mutations Molecular simulations |
| url | http://www.sciencedirect.com/science/article/pii/S1476558624000265 |
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