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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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Sukpan P, Sangkhathat S, Sriplung H, Laochareonsuk W, Choochuen P, Auseng N, Khoonjan W, Salaeh R, Thangnaphadol K, Wanawanakorn K, Kanokwiroon K. Exome Sequencing Reveals Novel Germline Variants in Breast Cancer Patients in the Southernmost Region of Thailand. J Pers Med 2023; 13:1587. [PMID: 38003901 PMCID: PMC10672121 DOI: 10.3390/jpm13111587] [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: 09/29/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Germline carriers of pathogenic variants in cancer susceptibility genes are at an increased risk of breast cancer (BC). We characterized germline variants in a cohort of 151 patients diagnosed with epithelial BC in the southernmost region of Thailand, where the predominant ethnicity differs from that of the rest of the country. Whole exome sequencing was used to identify and subsequently filter variants present in 26 genes known to be associated with cancer predisposition. Of the 151 individuals assessed, 23, corresponding to 15.2% of the sample, exhibited the presence of one or more pathogenic or likely pathogenic variants associated with BC susceptibility. We identified novel germline truncating variants in BRIP1, CHEK2, MSH6, PALB2, and PTEN and annotated variants of uncertain significance (VUSs), both novel and previously documented. Therefore, it is advisable to use genetic testing as an additional risk screening method for BC in this area.
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Affiliation(s)
- Panupong Sukpan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.S.); (S.S.); (W.L.); (P.C.)
- Medical Education Center, Naradhiwas Rajanagarindra Hospital, Narathiwat 96000, Thailand; (N.A.); (W.K.)
| | - Surasak Sangkhathat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.S.); (S.S.); (W.L.); (P.C.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Hutcha Sriplung
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Wison Laochareonsuk
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.S.); (S.S.); (W.L.); (P.C.)
| | - Pongsakorn Choochuen
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.S.); (S.S.); (W.L.); (P.C.)
| | - Nasuha Auseng
- Medical Education Center, Naradhiwas Rajanagarindra Hospital, Narathiwat 96000, Thailand; (N.A.); (W.K.)
| | - Weerawan Khoonjan
- Medical Education Center, Naradhiwas Rajanagarindra Hospital, Narathiwat 96000, Thailand; (N.A.); (W.K.)
| | - Rusta Salaeh
- Department of Surgery, Pattani Hospital, Pattani 94000, Thailand;
| | | | | | - Kanyanatt Kanokwiroon
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (P.S.); (S.S.); (W.L.); (P.C.)
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Kotnik U, Maver A, Peterlin B, Lovrecic L. Assessment of pathogenic variation in gynecologic cancer genes in a national cohort. Sci Rep 2023; 13:5307. [PMID: 37002323 PMCID: PMC10066348 DOI: 10.1038/s41598-023-32397-8] [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: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Population-based estimates of pathogenic variation burden in gynecologic cancer predisposition genes are a prerequisite for the development of effective precision public health strategies. This study aims to reveal the burden of pathogenic variants in a comprehensive set of clinically relevant breast, ovarian, and endometrial cancer genes in a large population-based study. We performed a rigorous manual classification procedure to identify pathogenic variants in a panel of 17 gynecologic cancer predisposition genes in a cohort of 7091 individuals, representing 0.35% of the general population. The population burden of pathogenic variants in hereditary gynecologic cancer-related genes in our study was 2.14%. Pathogenic variants in genes ATM, BRCA1, and CDH1 are significantly enriched and the burden of pathogenic variants in CHEK2 is decreased in our population compared to the control population. We have identified a high burden of pathogenic variants in several gynecologic cancer-related genes in the Slovenian population, most importantly in the BRCA1 gene.
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Affiliation(s)
- Urška Kotnik
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Ansari N, Shahrabi S, Khosravi A, Shirzad R, Rezaeean H. Prognostic Significance of CHEK2 Mutation in Progression of Breast Cancer. Lab Med 2019; 50:e36-e41. [PMID: 31220302 DOI: 10.1093/labmed/lmz009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers among women; genetic mutations reflect the development of this disease. Mutations in cell signaling factors can be the main cause of BC development. In this study, we focused on mutations in checkpoint kinase 2 (CHEK2) and their impact as a prognostic factor in the pathogenesis of BC. CHEK2 is controlled in cell signaling pathways through the influence of upstream genes. Also, several downstream genes are regulated by CHEK2. In addition, mutations in CHEK2 lead to resistance of BC cells to chemotherapy and metastasis of cancer cells to other parts of the body. Finally, detection of mutations in CHEK2 can be used as a prognostic factor for patient response to treatment and for targeting downstream molecules of CHEK2 that are involved in the proliferation of breast tumor cells. Mutations such as c.1100delC and I157T can distinguish which patients are susceptible to metastasis.
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Affiliation(s)
- Narges Ansari
- Isfahan Bone Metabolic Disorders Research Center, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saeid Shahrabi
- Department of Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Abbas Khosravi
- Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Reza Shirzad
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hadi Rezaeean
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Abstract
RATIONALE Neurofibromatosis, including type 1 and type 2, is inherited dominant disease that causes serious consequences. The genetic mechanism of these diseases has been described, but germline mutation of checkpoint 2 kinase gene, together with other DNA repair related genes, has not been fully elucidated in the context of neurofibromatosis. PATIENT CONCERNS In this article, we reported identical germline mutation of CHEK2 gene (p.R180C) in a 7-year-old Tibetan boy with NF1, and in a 12-year-old Chinese girl with NF2. DIAGNOSES Neurofibromatosis 1 and 2 with CHECK2 gene germline mutation. INTERVENTIONS Both patients underwent operation to obtain tumor tissue, and peripheral blood of their family was tested. OUTCOMES Identical germline mutation of CHEK2 gene (p.R180C) was detected in both patients, and germline mutations of POLE, MUTYH and ATR were also detected. LESSONS This is the first article to describe CHEK2 mutation in both NF1 and NF2. This article highlights a possible role of CHEK2, in association with other germline genetic mutations, in tumorigenesis of NF1 and NF2.
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Affiliation(s)
- Qiang Li
- Department of Neurosurgery, West China Hospital of Sichuan University, Sichuan Province
| | - Feilong Zhao
- Medical Science Liaison, Genetron Health Inc, Beijing, China
| | - Yan Ju
- Department of Neurosurgery, West China Hospital of Sichuan University, Sichuan Province
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Fan Z, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Xu Y, Xie Y. Identification and analysis of CHEK2 germline mutations in Chinese BRCA1/2-negative breast cancer patients. Breast Cancer Res Treat 2018; 169:59-67. [PMID: 29356917 DOI: 10.1007/s10549-018-4673-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/13/2018] [Indexed: 11/25/2022]
Abstract
PURPOSE Cell-cycle-checkpoint kinase 2 (CHEK2) is an important moderate-penetrance breast cancer predisposition gene; however, recurrent CHEK2 mutations found in Caucasian women are very rare in Chinese population. We investigated the mutation spectrum and clinical relevance of CHEK2 germline mutations in Chinese breast cancer patients. METHODS The entire coding regions and splicing sites of CHEK2 were screened in 7657 Chinese BRCA1/2-negative breast cancer patients, using 62-gene panel-based sequencing. RESULTS Out of 7657 BRCA1/2-negative breast cancer patients, 26 (0.34%) carried CHEK2 pathogenic germline mutations. Most of these mutations (92.3%, 24/26) were nonsense or frameshift mutations; 84.6% (22/26) of them were in forkhead-associated (FHA) or kinase domains. Of the 18 types of CHEK2 mutations we found, 61.1% (11/18) of were novel mutations and two recurrent mutations (Y139X and R137X) were found in this cohort. Patients with CHEK2 mutations were significantly more likely to have family histories of breast and/or ovarian cancer (23.1% vs. 8.6%, p = 0.022) and family histories of any cancer (50.0% vs. 31.6%, p = 0.044); and were significantly more likely to have lymph node-positive (53.8% vs. 27.3%, p = 0.002) and progesterone receptor (PR)-positive (88.5% vs. 64.5%, p = 0.011) breast cancers. CONCLUSIONS Among Chinese breast cancer patients, the CHEK2 germline mutation rate is approximately 0.34% and two specific mutations (Y139X and R137X) are recurrent. Patients with CHEK2 mutations are significantly more likely to have family histories of cancer, and to develop lymph node-positive and/or PR-positive breast cancers.
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Affiliation(s)
- Zhenhua Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tao Ouyang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Jinfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tianfeng Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Zhaoqing Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tie Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Benyao Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Ye Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.
| | - Yuntao Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.
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Sisawo EJ, Ouédraogo SYYA, Huang SL. Workplace violence against nurses in the Gambia: mixed methods design. BMC Health Serv Res 2017; 17:311. [PMID: 28454539 PMCID: PMC5410097 DOI: 10.1186/s12913-017-2258-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/21/2017] [Indexed: 11/27/2022] Open
Abstract
Background The aim of this study was to assess the prevalence, perpetrators and factors associated with workplace violence against nurses in public secondary health care facilities from two health regions in the Gambia. Methods Data was collected from 219 nurses using self-administered questionnaire and 35 face-to-face interviews. The data collection was conducted between July and September 2014 in 14 public secondary health care facilities. Results A sizable majority of respondents (62.1%) reported exposure to violence in the 12 months prior to the survey; exposure to verbal abuse, physical violence, and sexual harassment was 59.8%, 17.2%, and 10% respectively. The perpetrators were mostly patients’ escorts/relatives followed by patients themselves. Perceived reasons of workplace violence were mainly attributed to nurse-client disagreement, understaffing, shortage of drugs and supplies, security vacuum, and lack of management attention to workplace violence. Conclusions Nurses in the Gambia are at a relatively high risk of violent incidents at work. Policies and strategies that are sensitive to local circumstances and needs should be developed for the prevention of workplace violence. Electronic supplementary material The online version of this article (doi:10.1186/s12913-017-2258-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ebrima J Sisawo
- The University of the Gambia, Brikama, The Gambia.,International Health Program, National Yang-Ming University, Taipei, Taiwan
| | | | - Song-Lih Huang
- Institute of Public Health, National Yang-Ming University, No.155, Sec.2, Li-Nong Street, Taipei, 112, Taiwan, Republic of China.
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