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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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Lee CT, Tsai WH, Chang CC, Chen PC, Fann CSJ, Chang HK, Liu SY, Wu MZ, Chiu PC, Hsu WM, Yang WS, Lai LP, Tsai WY, Yang SB, Chen PL. Genotype-phenotype correlation in Taiwanese children with diazoxide-unresponsive congenital hyperinsulinism. Front Endocrinol (Lausanne) 2023; 14:1283907. [PMID: 38033998 PMCID: PMC10687152 DOI: 10.3389/fendo.2023.1283907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Objective Congenital hyperinsulinism (CHI) is a group of clinically and genetically heterogeneous disorders characterized by dysregulated insulin secretion. The aim of the study was to elucidate genetic etiologies of Taiwanese children with the most severe diazoxide-unresponsive CHI and analyze their genotype-phenotype correlations. Methods We combined Sanger with whole exome sequencing (WES) to analyze CHI-related genes. The allele frequency of the most common variant was estimated by single-nucleotide polymorphism haplotype analysis. The functional effects of the ATP-sensitive potassium (KATP) channel variants were assessed using patch clamp recording and Western blot. Results Nine of 13 (69%) patients with ten different pathogenic variants (7 in ABCC8, 2 in KCNJ11 and 1 in GCK) were identified by the combined sequencing. The variant ABCC8 p.T1042QfsX75 identified in three probands was located in a specific haplotype. Functional study revealed the human SUR1 (hSUR1)-L366F KATP channels failed to respond to intracellular MgADP and diazoxide while hSUR1-R797Q and hSUR1-R1393C KATP channels were defective in trafficking. One patient had a de novo dominant mutation in the GCK gene (p.I211F), and WES revealed mosaicism of this variant from another patient. Conclusion Pathogenic variants in KATP channels are the most common underlying cause of diazoxide-unresponsive CHI in the Taiwanese cohort. The p.T1042QfsX75 variant in the ABCC8 gene is highly suggestive of a founder effect. The I211F mutation in the GCK gene and three rare SUR1 variants associated with defective gating (p.L366F) or traffic (p.R797Q and p.R1393C) KATP channels are also associated with the diazoxide-unresponsive phenotype.
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Affiliation(s)
- Cheng-Ting Lee
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Hao Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Pei-Chun Chen
- Department of Physiology, National Cheng-Kung University, Tainan, Taiwan
| | | | - Hsueh-Kai Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shih-Yao Liu
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mu-Zon Wu
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wen-Ming Hsu
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ling-Ping Lai
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Yu Tsai
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Lung Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
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Abbasi SF, Mahjabeen I, Parveen N, Qamar I, Haq MFU, Shafique R, Saeed N, Ashraf NS, Kayani MA. Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies. Mol Genet Genomics 2023; 298:1527-1543. [PMID: 37861816 DOI: 10.1007/s00438-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Hematologic malignancies (HMs) are a collection of malignant transformations, originating from the cells in the bone marrow and lymphoid organs. HMs comprise three main types; leukemia, lymphoma, and multiple myeloma. Globally, HMS accounts for approximately 10% of newly diagnosed cancer. DNA repair pathways defend the cells from recurrent DNA damage. Defective DNA repair mechanisms such as homologous recombination repair (HRR), nucleotide excision repair (NER), and base excision repair (BER) pathways may lead to genomic instability, which initiates HM progression and carcinogenesis. Expression deregulation of HRR, NER, and BER has been investigated in various malignancies. However, no studies have been reported to assess the differential expression of selected DNA repair genes combinedly in HMs. The present study was designed to assess the differential expression of HRR and BER pathway genes including RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 in blood cancer patients to highlight their significance as diagnostic/ prognostic marker in hematological malignancies. The study cohort comprised of 210 blood cancer patients along with an equal number of controls. For expression analysis, q-RT PCR was performed. DNA damage was measured in blood cancer patients and controls using the comet assay and LORD Q-assay. Data analysis showed significant downregulation of selected genes in blood cancer patients compared to healthy controls. To check the diagnostic value of selected genes, the Area under curve (AUC) was calculated and 0.879 AUC was observed for RAD51 (p < 0.0001) and 0.830 (p < 0.0001) for APEX1. Kaplan-Meier analysis showed that downregulation of RAD51 (p < 0.0001), XRCC3 (p < 0.02), and APEX1 (p < 0.0001) was found to be associated with a significant decrease in survival of blood cancer patients. Cox regression analysis showed that deregulation of RAD51 (p < 0.0001), XRCC2 (p < 0.02), XRCC3 (p < 0.003), and APEX1 (p < 0.00001) was found to be associated with the poor prognosis of blood cancer patients. Comet assay showed an increased number of comets in blood cancer patients compared to controls. These results are confirmed by performing the LORD q-assay and an increased frequency of lesions/Kb was observed in selected genes in cancer patients compared to controls. Our results showed significant downregulation of RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 genes with increased DNA damage in blood cancer patients. The findings of the current research suggested that deregulated expression of HRR and BER pathway genes can act as a diagnostic/prognostic marker in hematologic malignancies.
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Affiliation(s)
- Sumaira Fida Abbasi
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan.
| | - Neelam Parveen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Imama Qamar
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Maria Fazal Ul Haq
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Rabia Shafique
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nadia Saeed
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nida Sarosh Ashraf
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
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Das R, Kundu S, Laskar S, Choudhury Y, Ghosh SK. In silico assessment of DNA damage response gene variants associated with head and neck cancer. J Biomol Struct Dyn 2022; 41:2090-2107. [PMID: 35037836 DOI: 10.1080/07391102.2022.2027817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Head and neck cancer (HNC), the sixth most common cancer globally, stands first in India, especially Northeast India, where tobacco usage is predominant, which introduces various carcinogens leading to malignancies by accumulating DNA damages. Consequently, the present work aimed to predict the impact of significant germline variants in DNA repair and Tumour Suppressor genes on HNC development. WES in Ion ProtonTM platform on 'discovery set' (n = 15), followed by recurrence assessment of the observed variants on 'confirmation set' (n = 40) using Sanger Sequencing was performed on the HNC-prevalent NE Indian populations. Initially, 53 variants were identified, of which seven HNC-linked DNA damage response gene variants were frequent in the studied populations. Different tools ascertained the biological consequences of these variants, of which the non-coding variants viz. EXO1_rs4150018, RAD52_rs6413436, CHD5_rs2746066, HACE1_rs6918700 showed risk, while FLT3_rs2491227 and BMPR1A_rs7074064 conferred protection against HNC by affecting transcriptional regulation and splicing mechanism. Molecular Dynamics Simulation of the full-length p53 model predicted that the observed coding TP53_rs1042522 variant conferred HNC-risk by altering the structural dynamics of the protein, which displayed difficulty in the transition between active and inactive conformations due to high-energy barrier. Subsequent pathway and gene ontology analysis revealed that EXO1, RAD52 and TP53 variants affected the Double-Strand Break Repair pathway, whereas CHD5 and HACE1 variants inactivated DNA repair cascade, facilitating uncontrolled cell proliferation, impaired apoptosis and malignant transformation. Conversely, FLT3 and BMPR1A variants protected against HNC by controlling tumorigenesis, which requires experimental validation. These findings may serve as prognostic markers for developing preventive measures against HNC.
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Affiliation(s)
- Raima Das
- Department of Biotechnology, Assam University, Silchar, India
| | - Sharbadeb Kundu
- Genome Science, School of Interdisciplinary Studies, University of Kalyani, Nadia, West India
| | - Shaheen Laskar
- Department of Biotechnology, Assam University, Silchar, India
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Fan Y, Gao Z, Li X, Wei S, Yuan K. Gene expression and prognosis of x-ray repair cross-complementing family members in non-small cell lung cancer. Bioengineered 2021; 12:6210-6228. [PMID: 34486486 PMCID: PMC8806547 DOI: 10.1080/21655979.2021.1964193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The X-ray repair cross-complementing gene (XRCC) family participates in DNA damage repair and its dysregulation is associated with the development and progression of a variety of cancers. However, XRCCs have not been systematically studied in non-small cell lung cancer (NSCLC). Using The Cancer Genome Atlas (TCGA) and Oncomine databases, we compared the expression levels of XRCCs between NSCLC and normal tissues and performed survival analysis using the data from TCGA. The correlations of XRCCs with the clinical parameters were then analyzed using UCSC Xena. Genetic alterations in XRCCs in NSCLC and their effects on the prognosis of patients were presented using cBioPortal. SurvivalMeth was used to explore the differentially methylated sites associated with NSCLC and their effect on prognosis. Next, the immunological correlations of XRCCs expression level were analyzed using TIMER 2.0. Finally, GeneMANIA was used to visualize and analyze the functionally relevant genes, while Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional and pathway enrichment analyses of prognostic genes. Our results revealed that XRCCs were overexpressed in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Univariate and multivariate Cox analyses showed that XRCC4/5/6 were independent risk factors for LUAD. Additionally, genetic alterations, methylation, and immune cell infiltration demonstrated an association between XRCC4/5/6 and poor prognosis in LUAD. Finally, the KEGG-enriched and non-homologous end-joining (NHEJ) pathways were shown to be associated with XRCC4/5/6. In conclusion, our study demonstrated that XRCC4/5/6 could be used as diagnostic and prognostic biomarkers for LUAD.
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Affiliation(s)
- Yongfei Fan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China
| | - Zhaojia Gao
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China.,Heart and Lung Disease Laboratory, the Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China
| | - Xinwei Li
- Department of Gastroenterology, Affiliated Cancer Hospital of Bengbu Medical College, Bengbu China
| | - Shuzhang Wei
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China
| | - Kai Yuan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China.,Heart and Lung Disease Laboratory, the Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou China
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Mozaffari HR, Rostamnia M, Sharifi R, Safaei M, Zavattaro E, Tadakamadla SK, Imani MM, Sadeghi M, Golshah A, Moradpoor H, Rezaei F, Omidpanah N, Hatami M. A PRISMA-compliant meta-analysis on association between X-ray repair cross complementing (XRCC1, XRCC2, and XRCC3) polymorphisms and oral cancer susceptibility. Gene 2021; 781:145524. [PMID: 33631241 DOI: 10.1016/j.gene.2021.145524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/09/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Oral Cancer (OC) is one of the leading causes of death and the disease mainly occurs over 50 years of age. Herein, a meta-analysis aimed to assess the association between X-ray repair cross complementing (XRCC) polymorphisms and OC risk. METHODS Four databases were searched extensively until June 5, 2020. Subgroup analysis, meta-regression, and funnel plots, as well as the quality assessment were estimated. RESULTS Fifteen studies were entered to the analysis. With regards to allele, homozygote, heterozygote, recessive, and dominant models, the pooled ORs for XRCC1 rs1799782 polymorphism were 1.51 (P = 0.01), 1.45 (P = 0.11), 1.45 (P = 0.0003), 1.44 (P = 0.0002), and 1.29 (P = 0.26); for XRCC1 rs1799782 polymorphism were 1.65 (P = 0.11), 1.50 (P = 0.33), 1.06 (P = 0.83), 1.57 (P = 0.12), and 1.32 (P = 0.45); for XRCC1 rs25489 polymorphism were 0.01 (P = 0.19), 1.44 (P = 0.48), 1.21 (P = 0.72), 1.17 (P = 0.19), and 1.38 (P = 0.54); for XRCC2 rs2040639 polymorphism were 0.68 (P = 0.0002), 0.63 (P = 0.02), 0.95 (P = 0.92), 0.79 (P = 0.49), and 0.61 (P = 0.005); and for XRCC3 rs861539 polymorphism were 1.24 (P = 0.20), 1.28 (P = 0.48), 0.99 (P = 0.95), 1.15 (P = 0.46), and 1.52 (P = 0.15), respectively. CONCLUSIONS The T allele and CT genotype of XRCC1 rs1799782 polymorphism had an elevated risk, whereas the G allele and GG genotype of XRCC2 rs2040639 polymorphism had a protective role in OC.
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Affiliation(s)
- Hamid Reza Mozaffari
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Maryam Rostamnia
- Students Research Committee, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran
| | - Roohollah Sharifi
- Department of Endodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Mohsen Safaei
- Advanced Dental Sciences Research Center, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Elisa Zavattaro
- Dermatology Unit, Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy
| | - Santosh Kumar Tadakamadla
- School of Dentistry and Oral Health, Menzies Health Institute Queensland, Griffith University, Gold Coast 4214, Australia
| | - Mohammad Moslem Imani
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Masoud Sadeghi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran.
| | - Amin Golshah
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Hedaiat Moradpoor
- Department of Prosthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Farzad Rezaei
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Neda Omidpanah
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
| | - Masoud Hatami
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah 6713954658, Iran
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Ahmad S, Arif B, Akram Z, Ahmed MW, Khan AU, Hussain MZ, Rahman F, Kayani MA, Mahjabeen I. Association of intronic polymorphisms (rs1549339, rs13402242) and mRNA expression variations in PSMD1 gene in arsenic-exposed workers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11425-11437. [PMID: 31965495 DOI: 10.1007/s11356-019-07422-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Ubiquitin-proteasome system (UPS) gene, PSMD1, is an important gene for neutralization of damaged and misfolded protein(s). The current study was designed to study the genetic and expression variations of PSMD1 gene as a consequence of arsenic exposure and its potential implications in arsenic induced diseases. In the present study, 250 blood samples of exposed industrial workers along with 250 controls were used. Initially, tetra amplification refractory mutation system-PCR was used to determine the role of PSMD1 gene polymorphisms (rs1549339, rs13402242) in industrial workers and controls. Frequency of homozygous mutant genotype of rs1549339 (OR: 2.23, 95% CI: 1.51-3.32, p = 0.0001) and rs13402242 (OR: 2.96, 95% CI: 1.52-5.75, p = 0.001) was observed significantly higher in exposed individuals vs controls. Secondly, qPCR was performed for expression analysis of PSMD1 gene. Significant down-regulated expression of PSMD1 gene (p < 0.0001) was observed vs controls, and this down-regulation was observed more pronounced in smokers (p < 0.0001) with maximum exposure duration (p < 0.0008). This down-regulated expression was observed significantly more pronounced in welding (p < 0.004) and brick kiln industries (p < 0.04) compared to other selected industries. The obtained results suggest that the exposure to arsenic may have an increased risk of developing disease(s) because of arsenic-induced PSMD1 variations.
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Affiliation(s)
- Saqiba Ahmad
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Bushra Arif
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Zertashia Akram
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Asad Ullah Khan
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | | | - Faisal Rahman
- Federal Govt Education Institution, Rawalpindi, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan.
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Evaluation of X-Ray Repair Cross-Complementing Family Members as Potential Biomarkers for Predicting Progression and Prognosis in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5751939. [PMID: 32258128 PMCID: PMC7103035 DOI: 10.1155/2020/5751939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022]
Abstract
The X-ray repair cross-complementing (XRCC) gene family has been revealed to participate in the carcinogenesis and development of numerous cancers. However, the expression profiles and prognostic values of XRCCs (XRCC1-6) in hepatocellular carcinoma (HCC) have not been explored up to now. The transcriptional levels of XRCCs in primary HCC tissues were analyzed by UALCAN and GEPIA. The relationship between XRCCs expression and HCC clinical characteristics was evaluated using UALCAN. Moreover, the prognostic values of XRCCs expression and mutations in HCC patients were investigated via the GEPIA and cBioPortal, respectively. Last but not least, the functions and pathways of XRCCs in HCC were also predicted by cBioPortal and DVAID. The transcriptional levels of all XRCCs in HCC tissues were notably elevated compared with normal liver tissues. Meanwhile, upregulated XRCCs expression was positively associated with clinical stages and tumor grades of HCC patients. Survival analysis using the GEPIA database revealed that high transcription levels of XRCC2/3/4/5/6 were associated with lower overall survival (OS) and high transcription levels of XRCC1/2/3/6 were correlated with poor disease-free survival (DFS) in HCC patients. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated the possible mechanisms of XRCCs and their associated genes participating in the oncogenesis of HCC. Our findings systematically elucidate the expression profiles and distinct prognostic values of XRCCs in HCC, which might provide promising therapeutic targets and novel prognostic biomarkers for HCC patients.
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Ahmed MW, Mahjabeen I, Gul S, Khursheed A, Mehmood A, Kayani MA. Relationship of single nucleotide polymorphisms and haplotype interaction of mitochondrial unfolded protein response pathway genes with head and neck cancer. Future Oncol 2019; 15:3819-3829. [PMID: 31651195 DOI: 10.2217/fon-2019-0365] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: In this study, we evaluated the effect of selected polymorphisms of mitochondrial unfolded protein response (UPRmt) pathway in 500 head and neck cancer (HNC) patients and 500 healthy controls from Pakistan. Materials & methods: The experiments were conducted using tetra-ARMS PCR followed by DNA sequencing. Results: Multivariate analysis showed that AA genotype of rs3782116 showed fivefold, GG genotype of rs6598072 approximately twofold and CC genotype of rs4946936 and TT genotype of rs12212067 showed twofold increased risk of HNC. Furthermore, haplotype analysis showed that certain haplotypes of UPRmt pathway single nucleotide polymorphisms have significant association with increased HNC risk. Conclusion: These results show that genetic aberrations in UPRmt pathway genes have association with increased HNC risk and can be an indicator of advance clinical outcome especially invasion and metastasis.
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Affiliation(s)
- Malik Waqar Ahmed
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
| | - Shazma Gul
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
| | - Anum Khursheed
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
| | - Azhar Mehmood
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan
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Assessment of DNA repair susceptibility genes identified by whole exome sequencing in head and neck cancer. DNA Repair (Amst) 2018; 66-67:50-63. [PMID: 29747023 DOI: 10.1016/j.dnarep.2018.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC), the sixth most common cancer globally, stands second in India. In Northeast (NE) India, it is the sixth most common cause of death in males and seventh in females. Prolonged tobacco and alcohol consumption constitute the major etiological factors for HNC development, which induce DNA damage. Therefore, DNA repair pathway is a crucial system in maintaining genomic integrity and preventing carcinogenesis. The present work was aimed to predict the consequence of significant germline variants of the DNA repair genes in disease predisposition. Whole exome sequencing was performed in Ion Proton™ platform on 15 case-control samples from the HNC-prevalent states of Manipur, Mizoram, and Nagaland. Variant annotation was done in Ion Reporter™ as well as wANNOVAR. Subsequent statistical and bioinformatics analysis identified significant exonic and intronic variants associated with HNC. Amongst our observed variants, 78.6% occurred in ExAC, 94% reported in dbSNP and 5.8% & 9.3% variants were present in ClinVar and HGMD, respectively. The total variants were dispersed among 199 genes with DSBR and FA pathway being the most mutated pathways. The allelic association test suggested that the intronic variants in HLTF and RAD52 gene significantly associated (P < 0.05) with the risk (OR > 5), while intronic variants in PARP4, RECQL5, EXO1 and PER1 genes and exonic variant in TDP2 gene showed protection (OR < 1) for HNC. MDR analysis proposed the exonic variants in MSH6, BRCA2, PALB2 and TP53 genes and intronic variant in RECQL5 genetic region working together during certain phase of DNA repair mechanism for HNC causation. In addition, other intronic and 3'UTR variations caused modifications in the transcription factor binding sites and miRNA target sites associated with HNC. Large-scale validation in NE Indian population, in-depth structure prediction and subsequent simulation of our recognized polymorphisms is necessary to identify true causal variants related to HNC.
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