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Sharma B, Angurana S, Bhat A, Verma S, Bakshi D, Bhat GR, Jamwal RS, Amin A, Qadri RA, Shah R, Kumar R. Genetic analysis of colorectal carcinoma using high throughput single nucleotide polymorphism genotyping technique within the population of Jammu and Kashmir. Mol Biol Rep 2021; 48:5889-5895. [PMID: 34319543 DOI: 10.1007/s11033-021-06583-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through MassARRAY™ is a cost-effective method to quantitatively analyse the variation of gene expression in multiple samples, making it a potential tool to identify the underlying causes of colorectal carcinogenesis. METHODS In the present study, SNP genotyping was carried out using Agena MassARRAY™, which is a cost-effective, robust, and sensitive method to analyse multiple SNPs simultaneously. We analysed 7 genes in 492 samples (100 cases and 392 controls) associated with CRC within the population of Jammu and Kashmir. These SNPs were selected based on their association with multiple cancers in literature. RESULTS This is the first study to explore these SNPs with colorectal cancer within the J&K population.7 SNPs with a call rate of 90% were selected for the study. Out of these, five SNPs rs2234593, rs1799966, rs2229080, rs8034191, rs1042522 were found to be significantly associated with the current study under the allelic model with an Odds Ratio OR = 2.981(1.731-5.136 at 95% CI); p value = 4.81E-05 for rs2234593,OR = 1.685(1.073-2.647 at 95% CI);; p value = 0.02292 for rs1799966, OR = 1.5 (1.1-2.3 at 95% CI), p value = 0.02 for rs2229080, OR = 1.699(1.035-2.791 at 95% CI); p value = 0.03521 for rs8034191, OR = 20.07 (11.26-35.75); p value = 1.84E-34 for rs1042522 respectively. CONCLUSION This is the first study to find the relation of Genetic variants with the colorectal cancer within the studied population using high throughput MassARRAY™ technology. It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.
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Affiliation(s)
- Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | | | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Sonali Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Ghulam Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Rajeshwer Singh Jamwal
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Asif Amin
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India
| | - Raies Ahmed Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India
| | - Ruchi Shah
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India.
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India.
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Malik MA, Malik SA, Haq MG, Bangri SA, Ahmad SZ, Shah OJ, Shah ZA. Genetic Susceptibility of DCC Gene in Gallbladder Cancer in Kashmir and Meta-Analysis. Nutr Cancer 2021; 74:947-955. [PMID: 34259111 DOI: 10.1080/01635581.2021.1949728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Deleted in colorectal carcinoma (DCC) A > G (rs714) is the most widely studied SNP of tumor suppressor DCC gene found to be associated with increased risk of various cancers. Therefore, the aim of present case control study was to investigate the role of DCC A > G (rs714) in gallbladder cancer (GBC) in Kashmir and to conduct a meta-analysis of DCC A > G (rs714) polymorphism to demonstrate the more accurate strength of these associations. Genotyping was done by PCR/RFLP and confirmed by sequencing in 100 GBC cases, and 150 controls. We also performed a comprehensive meta-analysis of 2223 subjects (1118 cases and 1105 controls) to evaluate the association between DCC A > G (rs714) polymorphisms and cancer. In present case control study DCC A > G (rs714) genotypes did not modulate the GBC cancer risk. Meta-analysis results showed that DCC A > G (rs714) is associated with increased overall cancer risk. DCC A > G (rs714) polymorphism conferred significant risk for cancer in dominant model but in recessive model P-value was at borderline. DCC A > G (rs714) genotype was associated with increased risk of cancer in Asians and Kashmiri population whereas no such association was observed in Europeans. The evidence in this meta-analysis supports a modest involvement of DCC A > G (rs714) tumoursupressor pathway genes in cancer susceptibility.
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Affiliation(s)
- Manzoor Ahmad Malik
- Cancer Diagnostic & Research Centre (CDRC), Department of Immunology & Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Subzar Ahmad Malik
- Department of Immunology & Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Malik Gowharul Haq
- Department of Immunology & Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Sadaf Ali Bangri
- Departments of Surgical Gastroenterology, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Sheikh Zahoor Ahmad
- Department of Surgical Oncology, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Omar Javed Shah
- Departments of Surgical Gastroenterology, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
| | - Zafar Amin Shah
- Cancer Diagnostic & Research Centre (CDRC), Department of Immunology & Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India.,Department of Immunology & Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Kashmir, India
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3
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Sindi IA, Babalghith AO, Tayeb MT, Mufti AH, Naffadi H, Ekram SN, Elhawary EN, Alenezi M, Elhawary NA. Risk of Colorectal Carcinoma May Predispose to the Genetic Variants of the GST, CYP450, and TP53 Genes Among Nonsmokers in the Saudi Community. Int J Gen Med 2021; 14:1311-1323. [PMID: 33883929 PMCID: PMC8055278 DOI: 10.2147/ijgm.s294802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Colorectal carcinoma (CRC) represents a considerable public health burden in Saudi Arabia. Several candidate genes and genetic variants have been associated with morbidity and mortality among patients with CRC. We explored whether allelic variants of the GSTM1, GSTT1, CYP450 (rs4646903 and rs1048943), and TP53 (rs1042522) genes predisposed nonsmoking Saudi individuals to increased risk for CRC. PATIENTS AND METHODS DNA from buccal cells of 158 participants (80 with CRC and 78 healthy controls) were analyzed for five SNPs using conventional PCR and TaqMan genotyping assays. The SNPStats software was utilized to choose the best interactive inheritance mode for selected SNPs (https://www.snpstats.net). RESULTS The mean age of diagnosis was 62.4±13.5 years (range, 40-83 years), with those aged 71-80 years and those aged 40-50 years accounting for the most diagnoses (35.7% and 28.6% of diagnosis, respectively). The GSTM1 and TP53 rs1042522 SNPs were associated with CRC (OR= 3.7; P< 0.0001, and OR= 1.6; P= 0.033, respectively). A plausible contribution to CRC was observed for the GSTM1 and TP53 rs1042522 SNPs (x 2 Yates= 14.7; P= 0.00013, and x 2 Yates= 11.2; P= 0.0008, respectively), while the GSTT1 null variant did not affect risk. Heterozygosity in the CYP450 (rs4646903 and rs1048943 SNPs) was associated with a significant risk for CRC. The GSTM1/GSTT1 and CYP450 rs4646903/rs1048943 SNP pairs were in linkage disequilibrium, and the associations were statistically significant (P= 0.01 and P= 4.6x10‒7, respectively). CONCLUSION The GSTM1 and TP53 rs1042522 variants can increase the development of CRC in Saudi nonsmokers. Even the presence of one copy of a variant allele in the CYP1A1 gene can predispose CRC risk. Additional studies should also examine other SNP combinations with lifestyle factors that may help prevent, rather than facilitate, colorectal tumorigenesis.
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Affiliation(s)
- Ikhlas A Sindi
- Department of Biotechnology, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Ikhlas A Sindi Department of Biotechnology, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia Email
| | - Ahmed O Babalghith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Mohammed T Tayeb
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Ahmad H Mufti
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Hind Naffadi
- Common Science, First Year Deanship, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Samar N Ekram
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
- Department of Medical Oncology, King Abdullah City Hospital, Mecca, Saudi Arabia
| | - Ezzeldin N Elhawary
- MS Genomic Medicine Program, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Faculty of Biotechnology, October Modern Sciences and Arts University, Giza, Egypt
| | - Munaifah Alenezi
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Nasser A Elhawary
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
- Department of Genetics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Correspondence: Nasser A Elhawary Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi ArabiaTel +966 55 369 2180 Email
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Song L, Yang C, He XF. Individual and combined effects of GSTM1 and GSTT1 polymorphisms on colorectal cancer risk: an updated meta-analysis. Biosci Rep 2020; 40:BSR20201927. [PMID: 32776111 PMCID: PMC7447855 DOI: 10.1042/bsr20201927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The presence or absence of glutathione S-transferase M1 gene (GSTM1) and glutathione S-transferase T1 gene (GSTT1) polymorphisms, and their combined effects have been suggested as a risk factor for colorectal cancer (CRC). However, the results are inconsistent. OBJECTIVES An updated meta-analysis was performed to solve the controversy. METHODS Meta-analyses of Observational Studies in Epidemiology (MOOSE) guidelines were used. RESULTS Overall, the GSTM1 null genotype was associated with an increased CRC risk in Caucasians (odds ratio (OR) = 1.14, 95% confidence interval (CI): 1.05-1.23), Asians (OR = 1.19, 95% CI: 1.08-1.32), high-quality studies (OR = 1.12, 95% CI: 1.06-1.18). Moreover, the GSTM1 null genotype was also associated with an increased colon cancer risk (OR = 1.32, 95% CI: 1.16-1.51). The GSTT1 null genotype was also associated with an increased CRC risk in Asians (OR = 1.08, 95% CI: 1.02-1.15) and Caucasians (OR = 1.24, 95% CI: 1.09-1.41). Moreover, The GSTT1 null genotype was associated with an increased rectal cancer risk (OR = 1.13, 95% CI: 1.01-1.27, I2 = 8.3%) in subgroup analysis by tumor location. Last, the GSTM1 null/GSTT1 null genotype was associated with an increased CRC risk in Asians. CONCLUSION This meta-analysis indicates that the GSTM1 and GSTT1 null genotypes are associated with increased CRC risk in Asians and Caucasians, and the GSTM1 null/GSTT1 null genotype was associated with increased CRC risk in Asians.
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Affiliation(s)
- Liang Song
- Endoscopy Room, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, 046000, People’s Republic of China
| | - Chen Yang
- Teaching Reform Class of 2016, First Clinical College, Changzhi Medical College, Shanxi, Changzhi, 046000, People’s Republic of China
| | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, 046000, People’s Republic of China
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5
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León-Mejía G, Quintana-Sosa M, de Moya Hernandez Y, Rodríguez IL, Trindade C, Romero MA, Luna-Carrascal J, Ortíz LO, Acosta-Hoyos A, Ruiz-Benitez M, Valencia KF, Rohr P, da Silva J, Henriques JAP. DNA repair and metabolic gene polymorphisms affect genetic damage due to diesel engine exhaust exposure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:20516-20526. [PMID: 32246425 DOI: 10.1007/s11356-020-08533-6] [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: 07/02/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Diesel engine exhaust (DEE) is a complex mixture of toxic gases, halogenated aromatic hydrocarbons, alkyl polycyclic aromatic hydrocarbons, polycyclic aromatic hydrocarbons, benzene derivatives, metals and diesel exhaust particles (DEPs) generated from the incomplete combustion of diesel fuel. Many of the compounds in this mixture can cause oxidative damage to DNA and are considered carcinogenic for humans. Further, chronic DEE exposure increases risks of cardiovascular and pulmonary diseases. Despite these pervasive health risks, there is limited and inconsistent information regarding genetic factors conferring susceptibility or resistance to DEE genotoxicity. The present study evaluated the effects of polymorphisms in two base excision repair (BER) genes (OGG1 Ser326Cys and XRCC1 Arg280His), one homologous recombination (HRR) gene (XRCC3 Thr241Met) and two xenobiotic metabolism genes (GSTM1 and GSTT1) on the genotoxicity profiles among 123 mechanics exposed to workplace DEE. Polymorphisms were determined by PCR-RFLP. In comet assay, individuals with the GSTT1 null genotype demonstrated significantly greater % tail DNA in lymphocytes than those with non-null genotype. In contrast, these null individuals exhibited significantly lower frequencies of binucleated (BN) cells and nuclear buds (NBUDs) in buccal cells than non-null individuals. Heterozygous hOGG1 326 individuals (hOGG1 326 Ser/Cys) exhibited higher buccal cell NBUD frequency than hOGG1 326 Ser/Ser individuals. Individuals carrying the XRCC3 241 Met/Met polymorphism also showed significantly higher buccal cell NBUD frequencies than those carrying the XRCC3 241 Thr/Thr polymorphism. We found a high flow of particulate matter with a diameter of < 2.5 μm (PM2.5) in the workplace. The most abundant metals in DEPs were iron, copper, silicon and manganese as detected by transmission electron microscopy-energy-dispersive X-ray spectroscopy (TEM-EDX). Scanning electron microscopy (SEM-EDS) revealed particles with diameters smaller than PM2.5, including nanoparticles forming aggregates and agglomerates. Our results demonstrate the genotoxic effects of DEE and the critical influence of genetic susceptibility conferred by DNA repair and metabolic gene polymorphisms that shed light into the understanding of underlying mechanisms.
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Affiliation(s)
- Grethel León-Mejía
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia.
| | - Milton Quintana-Sosa
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | | | - Ibeth Luna Rodríguez
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Cristiano Trindade
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Marco Anaya Romero
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Jaime Luna-Carrascal
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Ludis Oliveros Ortíz
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Antonio Acosta-Hoyos
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Martha Ruiz-Benitez
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Karen Franco Valencia
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Paula Rohr
- Laboratório de Genética, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Campus Carreiros, Av. Itália km 8, Rio Grande, RS, 96201-900, Brazil
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil
| | - João Antônio Pêgas Henriques
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Elshazli RM, Toraih EA, Elgaml A, Kandil E, Fawzy MS. Genetic polymorphisms of TP53 (rs1042522) and MDM2 (rs2279744) and colorectal cancer risk: An updated meta-analysis based on 59 case-control studies. Gene 2020; 734:144391. [PMID: 32001373 DOI: 10.1016/j.gene.2020.144391] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Several earlier reports implicated TP53 (rs1042522) and MDM2 (rs2279744) variants in outcome of colorectal cancer (CRC), but with inconclusive findings. This current meta-analysis designed to uncover the role of these variants in CRC risk. METHODOLOGY Two independent investigators extracted 59 eligible case-control studies from different electronic databases involving Scopus, Web of Science and PubMed prior to June 2019. Pooled odds ratios (ORs) and "95% confidence intervals (CIs)" were computed for different hereditary models. Stratification and heterogeneity analyses, and "Begg's funnel plots" were conducted. In silico data analyses of the functional and structural properties of the study variants were applied. RESULTS In general, 47 and 16 case-control reports for TP53 (11,589 patients and 13,622 controls) and MDM2 (6841 CRC patients and 8792 healthy controls), respectively were enrolled in this meta-analysis. A significant association of TP53 (rs1042522) variant with increased CRC risk in overall pooled subjects under recessive model [(CC vs. GC + GG, OR = 1.134, 95% CI = 1.006-1.278, P = 0.039)] was observed. Moreover, an evidence of MDM2 (rs2279744) association with increased CRC risk in overall pooled subjects under dominant and heterozygote models [(TG + GG vs. TT, OR = 1.120, 95% CI = 1.003-1.250, P = 0.044) and (TG vs. TT, OR = 1.189, 95% CI = 1.076-1.313, P = 0.001), respectively] was reported. Additionally, TP53 (rs1042522) and MDM2 (rs2279744) showed an association with CRC risk among Asians and Africans under a recessive model, and among Asians under different genetic models, respectively, by stratification analysis. CONCLUSION TP53 (rs1042522) and MDM2 (rs2279744) variants might represent candidate risk factors for CRC susceptibility.
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Affiliation(s)
- Rami M Elshazli
- Department of Biochemistry and Molecular Genetics, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt.
| | - Eman A Toraih
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA, USA; Genetics unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University - Egypt, New Damietta, Egypt
| | - Emad Kandil
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University School of Medicine, New Orleans, LA, USA
| | - Manal S Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt; Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
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Zhunussova G, Afonin G, Abdikerim S, Jumanov A, Perfilyeva A, Kaidarova D, Djansugurova L. Mutation Spectrum of Cancer-Associated Genes in Patients With Early Onset of Colorectal Cancer. Front Oncol 2019; 9:673. [PMID: 31428572 PMCID: PMC6688539 DOI: 10.3389/fonc.2019.00673] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/10/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Colorectal cancer (CRC) incidence is rising worldwide, as well as in the Republic of Kazakhstan, while its occurrence is also increasing in the younger population. Hereditary forms associated with the development of colon and rectal cancer and early-onset CRC have never been studied in the population of Kazakhstan. The aim of this research was to investigate the spectrum of CRC-related gene mutations to determine which mutations cause early onset of CRC in the Kazakhstan population. Methods: The study included 125 unrelated patients from Kazakhstan (range 17–50 years in age) with early onset CRC. Genomic DNA was obtained from peripheral blood of the patients. Next-generation sequencing was performed using the TruSightCancer Kit on the MiSeq platform. The Studio Variant was used to annotate and interpret genetic variants. Results: Bioinformatics analysis of Next-generation sequencing data revealed 11,152 variants from 85 genes, of them, 3,790 missense, 6,254 synonymous variants, 44 3′UTR variants, 10 frameshift variants, five stop-gain variants, four in-frame deletions, two splice donors, one splice acceptor variant, and 1,042 intron or non-coding variants. APC, BRCA2/1, ALK, BRIP1, EGFR, FANCA, FANCD2, FANCI, HNF1A, MEN1, NSD1, PMS2, RECQL4, RET, SLX4, WRN, and XPC genes mutated most often. According to the ACMG guidelines and LOVD/ClinVar databases, 24 variants were pathogenic (10 frameshifts, five missenses, five stop-gain, one in-frame deletion, and three splice-site mutations), and 289 were VUS with population frequency <1%, 131 of them were attributed as deleterious. In the study, 50% of all pathogenic mutations found in Kazakhstani patients with early CRC onset were identified in the subgroups with a family history of CRC and primary multiple tumors. In APC, pathogenic mutations were most often (21%). Conclusion: Pathogenic and likely pathogenic mutations were found in 20 (16%) out of 125 patients. Eight novel pathogenic mutations detected in FANCI, APC, BMPR1, ATM, and DICER1 genes have not been reported in previous literature. Given the high frequency and wide spectrum of mutations, NGS analysis must be carried out in families with a history of CRC/CRC-related cancers with the purpose to identify cause-effective mutations, clarify the clinical diagnosis, and prevent the development of the disease in other family members.
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Affiliation(s)
- Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of General Genetics and Cytology, Almaty, Kazakhstan.,Center of Thoracic and Abdominal Oncology, Kazakh Institute of Oncology and Radiology, Almaty, Kazakhstan.,Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Georgiy Afonin
- Center of Thoracic and Abdominal Oncology, Kazakh Institute of Oncology and Radiology, Almaty, Kazakhstan.,Department of Oncology, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Abai Jumanov
- Center of Thoracic and Abdominal Oncology, Kazakh Institute of Oncology and Radiology, Almaty, Kazakhstan.,Department of Oncology, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Dilyara Kaidarova
- Center of Thoracic and Abdominal Oncology, Kazakh Institute of Oncology and Radiology, Almaty, Kazakhstan.,Department of Oncology, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of General Genetics and Cytology, Almaty, Kazakhstan.,Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Anvarnia A, Mohaddes‐Gharamaleki F, Asadi M, Akbari M, Yousefi B, Shanehbandi D. Dysregulated microRNAs in colorectal carcinogenesis: New insight to cell survival and apoptosis regulation. J Cell Physiol 2019; 234:21683-21693. [DOI: 10.1002/jcp.28872] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alireza Anvarnia
- Department of Biochemistry and Clinical Laboratories Faculty of Medicine, Tabriz University of Medical Sciences Tabriz Iran
- Student Research Committee, Tabriz University of Medical Sciences Tabriz Iran
| | - Farzad Mohaddes‐Gharamaleki
- Department of Biochemistry and Clinical Laboratories Faculty of Medicine, Tabriz University of Medical Sciences Tabriz Iran
- Student Research Committee, Tabriz University of Medical Sciences Tabriz Iran
| | - Milad Asadi
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Bahman Yousefi
- Department of Biochemistry and Clinical Laboratories Faculty of Medicine, Tabriz University of Medical Sciences Tabriz Iran
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Dariush Shanehbandi
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
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9
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Zare M, Jafari-Nedooshan J, Jafari M, Neamatzadeh H, Abolbaghaei SM, Foroughi E, Nasiri R, Zare-Shehneh M. Relevance of hMLH1 -93G>A, 655A>G and 1151T>A polymorphisms with colorectal cancer susceptibility: a meta-analysis based on 38 case-control studies. ACTA ACUST UNITED AC 2019; 64:942-951. [PMID: 30517243 DOI: 10.1590/1806-9282.64.10.942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 01/02/2023]
Abstract
OBJECTIVE There has been increasing interest in the study of the association between human mutL homolog 1 (hMLH1) gene polymorphisms and risk of colorectal cancer (CRC). However, results from previous studies are inconclusive. Thus, a meta-analysis was conducted to derive a more precise estimation of the effects of this gene. METHODS A comprehensive search was conducted in the PubMed, EMBASE, Chinese Biomedical Literature databases until January 1, 2018. Odds ratio (OR) with 95% confidence interval (CI) was used to assess the strength of the association. RESULTS Finally, 38 case-control studies in 32 publications were identified met our inclusion criteria. There were 14 studies with 20668 cases and 19533 controls on hMLH1 -93G>A, 11 studies with 5,786 cases and 8,867 controls on 655A>G and 5 studies with 1409 cases and 1637 controls on 1151T>A polymorphism. The combined results showed that 655A>G and 1151T>A polymorphisms were significantly associated with CRC risk, whereas -93G>A polymorphism was not significantly associated with CRC risk. As for ethnicity, -93G>A and 655A>G polymorphisms were associated with increased risk of CRC among Asians, but not among Caucasians. More interestingly, subgroup analysis indicated that 655A>G might raise CRC risk in PCR-RFLP and HB subgroups. CONCLUSION Inconsistent with previous meta-analyses, this meta-analysis shows that the hMLH1 655A>G and 1151T>A polymorphisms might be risk factors for CRC. Moreover, the -93G>A polymorphism is associated with the susceptibility of CRC in Asian population.
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Affiliation(s)
- Mohammad Zare
- Department of General Surgery, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Jamal Jafari-Nedooshan
- Department of General Surgery, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammadali Jafari
- Department of Emergency Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Neamatzadeh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Elnaz Foroughi
- Department of Pediatric Dentistry, Arak university of Medical Sciences, Arak, Iran
| | - Rezvan Nasiri
- Department of Oral and Maxillofacial Surgery, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Zare-Shehneh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Zhu Y, Chen Z, Jiang H, Lu B. The genetic association between EGF A61G polymorphism (rs4444903) and risk of colorectal cancer: An update meta-analysis and trial sequential analysis. Medicine (Baltimore) 2019; 98:e14007. [PMID: 30633190 PMCID: PMC6336653 DOI: 10.1097/md.0000000000014007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Colorectal cancer was a complex disease with multiple causative factors including genetic and environmental factors, as well as the interaction of the 2 factors. Relationship between epidermal growth factor (EGF) A61G polymorphism and colorectal cancer risk has been widely investigated previously, whereas results derived from these studies were inconclusive and controversial. The aim of this study was to investigate the association between the EGF A61G polymorphism and colorectal cancer using a meta-analysis of existing literature. METHODS Literature search was conducted from PubMed, EMBASE, China National Knowledge Infrastructure, Wanfang, and Cochrane library databases before July 2017. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the strength of the association between EGF A61G and colorectal cancer. RESULTS A total of 9 studies that involved 1448 cases and 1928 healthy controls and found allelic (OR = 1.18, P = .04) and recessive models (OR = 1.36, P = .03) of EGF A61G were significantly associated with the risk of colorectal cancer. Stratification analyses by ethnicity indicated that the EGF 61G significantly increased the risk of colorectal cancer in the Caucasian subgroup (OR = 1.24, P = .02), but not in Asian subgroup (OR = 1.12, P = .08). And the frequency of GG genotype of EGF A61G significantly increased in cases than that in healthy controls in both Caucasian (OR = 1.40, P = .04) and Asian subgroups (OR = 1.27, P = .01). Furthermore, the sample sources and genotyping methods seem to have no influence on the correction of EGF A61G and colorectal cancer susceptibility (P > .05). CONCLUSION The results indicate that EGF A61G might increase the risk of colorectal cancers.
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Affiliation(s)
- Yi Zhu
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Jiaxing University
- Department of Gastroenterological Surgery, First Hospital of Jiaxing, Jiaxing, Zhejiang, China
| | - ZhiHeng Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Jiaxing University
| | - HongGang Jiang
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Jiaxing University
| | - BoHao Lu
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Jiaxing University
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11
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Dong Z, Zheng L, Liu W, Wang C. Association of mRNA expression of TP53 and the TP53 codon 72 Arg/Pro gene polymorphism with colorectal cancer risk in Asian population: a bioinformatics analysis and meta-analysis. Cancer Manag Res 2018; 10:1341-1349. [PMID: 29872345 PMCID: PMC5973318 DOI: 10.2147/cmar.s164892] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background The relationship between TP53 codon 72 Pro/Arg gene polymorphism and colorectal cancer risk in Asians is still controversial, and this bioinformatics analysis and meta-analysis was performed to assess the associations. Methods The association studies were identified from PubMed, and eligible reports were included. RevMan 5.3.1 software, Oncolnc, cBioPortal, and Oncomine online tools were used for statistical analysis. A random/fixed effects model was used in meta-analysis. The data were reported as risk ratios or mean differences with corresponding 95% CI. Results We confirmed that TP53 was associated with colorectal cancer, the alteration frequency of TP53 was 53% mutation and 7% deep deletion, and TP53 mRNA expression was different in different types of colorectal cancer based on The Cancer Genome Atlas database. Then, 18 studies were included that examine the association of TP53 codon 72 gene polymorphism with colorectal cancer risk in Asians. The meta-analysis indicated that TP53 Pro allele and Pro/Pro genotype were associated with colorectal cancer risk in Asian population, but Arg/Arg genotype was not (Pro allele: odds ratios [OR]=1.20, 95% CI: 1.06 to 1.35, P=0.003; Pro/Pro genotype: OR=1.39, 95% CI: 1.15 to 1.69, P=0.0007; Arg/Arg genotype: OR=0.86, 95% CI: 0.74 to 1.00, P=0.05). Interestingly, in the meta-analysis of the controls from the population-based studies, we found that TP53 codon 72 Pro/Arg gene polymorphism was associated with colorectal cancer risk (Pro allele: OR=1.33, 95% CI: 1.15 to 1.55, P=0.0002; Pro/Pro genotype: OR=1.61, 95% CI: 1.28 to 2.02, P<0.0001; Arg/Arg genotype: OR=0.77, 95% CI: 0.63 to 0.93, P=0.009). Conclusion TP53 was associated with colorectal cancer, but the different value levels of mRNA expression were not associated with survival rate of colon and rectal cancer. TP53 Pro allele and Pro/Pro genotype were associated with colorectal cancer risk in Asians.
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Affiliation(s)
- Zhiyong Dong
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Surgery, The Affiliated Hospital of Putian University, Putian, China
| | - Longzhi Zheng
- Department of Surgery, The Affiliated Hospital of Putian University, Putian, China
| | - Weimin Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Cunchuan Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Li S, Zheng Y, Tian T, Wang M, Liu X, Liu K, Zhai Y, Dai C, Deng Y, Li S, Dai Z, Lu J. Pooling-analysis on hMLH1 polymorphisms and cancer risk: evidence based on 31,484 cancer cases and 45,494 cancer-free controls. Oncotarget 2017; 8:93063-93078. [PMID: 29190978 PMCID: PMC5696244 DOI: 10.18632/oncotarget.21810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/08/2017] [Indexed: 01/18/2023] Open
Abstract
To elucidate the veritable relationship between three hMLH1 polymorphisms (rs1800734, rs1799977, rs63750447) and cancer risk, we performed this meta-analysis based on overall published data up to May 2017, from PubMed, Web of knowledge, VIP, WanFang and CNKI database, and the references of the original studies or review articles. 57 publications including 31,484 cancer cases and 45,494 cancer-free controls were obtained. The quality assessment of six articles obtained a summarized score less than 6 in terms of the Newcastle-Ottawa Scale (NOS). All statistical analyses were calculated with the software STATA (Version 14.0; Stata Corp, College Station, TX). We found all the three polymorphisms can enhance overall cancer risk, especially in Asians, under different genetic comparisons. In the subgroup analysis by cancer type, we found a moderate association between rs1800734 and the risk of gastric cancer (allele model: OR = 1.14, P = 0.017; homozygote model: OR = 1.33, P = 0.019; dominant model: OR = 1.27, P = 0.024) and lung cancer in recessive model (OR = 1.27, P = 0.024). The G allele of rs1799977 polymorphism was proved to connect with susceptibility of colorectal cancer (allele model: OR = 1.21, P = 0.023; dominate model: OR = 1.32, P <0.0001) and prostate cancer (dominate model: OR = 1.36, P <0.0001). Rs63750447 showed an increased risk of colorectal cancer, endometrial cancer and gastric cancer under all genetic models. These findings provide evidence that hMLH1 polymorphisms may associate with cancer risk, especially in Asians.
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Affiliation(s)
- Sha Li
- Clinical Research Center, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.,Department of Pharmacy, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Yi Zheng
- Clinical Research Center, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.,Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Tian Tian
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Meng Wang
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Xinghan Liu
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Kang Liu
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Yajing Zhai
- Clinical Research Center, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Cong Dai
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Yujiao Deng
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Shanli Li
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Zhijun Dai
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Jun Lu
- Clinical Research Center, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
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13
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An Association Study Between Genetic Polymorphisms in Functional Regions of Five Genes and the Risk of Schizophrenia. J Mol Neurosci 2016; 59:366-75. [PMID: 27055860 DOI: 10.1007/s12031-016-0751-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/28/2016] [Indexed: 02/08/2023]
Abstract
Schizophrenia is a severe mental disorder that is likely to be strongly determined by genetic factors. To identify markers of disks, large homolog 2 (DLG2), FAT atypical cadherin 3 (FAT3), kinectin1 (KTN1), deleted in colorectal carcinoma (DCC), and glycogen synthase kinase-3β (GSK3β) that contribute to the genetic susceptibility to schizophrenia, we systematically screened for polymorphisms in the functional regions of these genes. A total of 22 functional single-nucleotide polymorphisms (SNPs) in 940 Chinese subjects were genotyped using SNaPshot. The results first suggested that the allelic and genotypic frequencies of the DCC polymorphism rs2229080 were nominally associated with schizophrenia. The patients were significantly less likely to be CC homozygous (P = 0.005, odds ratio [OR] = 0.635, 95 % confidence interval [95 % CI] = 0.462-0.873), and the schizophrenia subjects exhibited lower frequency of the C allele (P = 0.024, OR = 0.811, 95 % CI = 0.676-0.972). Regarding GSK3β, there was a significant difference in genotype distribution of rs3755557 between schizophrenia and healthy control subjects (P = 0.009). The patients exhibited a significantly lower frequency of the T allele of rs3755557 (P = 0.002, OR = 0.654, 95 % CI = 0.498-0.860). Our results point to the polymorphisms of DCC and GSK3β as contributors to the genetic basis of individual differences in the susceptibility to schizophrenia.
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Chandra V, Kim JJ, Gupta U, Mittal B, Rai R. Impact of DCC (rs714) and PSCA (rs2294008 and rs2976392) Gene Polymorphism in Modulating Cancer Risk in Asian Population. Genes (Basel) 2016; 7:genes7020009. [PMID: 26891331 PMCID: PMC4773753 DOI: 10.3390/genes7020009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022] Open
Abstract
Multiple studies have investigated the association of gene variant of Deleted in colorectal carcinoma (DCC) and Prostate Stem cell antigen (PSCA) with various cancer susceptibility; however, the results are discrepant. Since SNPs are emerging as promising biomarker of cancer susceptibility, here, we aimed to execute a meta-analysis of DCC (rs714 A > G) and PSCA (rs2294008 C > T, rs2976392 G > A) polymorphism to demonstrate the more accurate strength of these associations. We followed a rigorous inclusion/exclusion criteria and calculated the pooled odds ratios (ORs) and 95% confidence intervals (CIs). Overall, the pooled analysis showed that the DCC rs714 conferred increased risk of cancer only in Asians (AA vs. GG: OR = 1.86, p ≤ 0.0001; AG vs. GG: OR = 1.43, p = 0.005; GA + AA vs. GG: OR = 1.66, p ≤ 0.0001; AA vs. GG + GA; OR = 1.52, p ≤ 0.004, A vs. G allele: OR = 1.41, p ≤ 0.0001). PSCA rs2294008 was associated with increased overall cancer risk (TT vs. CC: OR = 1.28, p = 0.002; CT vs. CC: OR = 1.21, p ≤ 0.0001; CT + TT vs. CC: OR = 1.24, p ≤ 0.0001; TT vs. CC + CT; OR = 1.17, p ≤ 0.005, T vs. C allele: OR = 1.16, p ≤ 0.0001); however, in stratified analysis this association was limited only to gastric and bladder cancer and the strength was more prominent in Asians. In contrast, the PSCA rs2976392 SNP did not modulate the cancer risk. Therefore, we concluded that rs714 and rs2294008 polymorphism may represent a potential genetic biomarker for cancer risk in Asians and gastric as well as bladder cancer, respectively. However, since our study is limited to Asians and cancer types, further larger studies involving other cancers and/or population, gene-environment interactions and the mechanism of DCC and PSCA gene deregulation are desired to define the role of genotype with overall cancer risk.
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Affiliation(s)
- Vishal Chandra
- Department of Biosciences, Integral University, Lucknow 226026 (Uttar Pradesh), India.
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea.
| | - Usha Gupta
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014 (Uttar Pradesh), India.
| | - Balraj Mittal
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014 (Uttar Pradesh), India.
| | - Rajani Rai
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea.
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Rai R, Kim JJ, Misra S, Kumar A, Mittal B. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations. Int J Mol Sci 2015; 16:28038-49. [PMID: 26602921 PMCID: PMC4691025 DOI: 10.3390/ijms161226077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 12/16/2022] Open
Abstract
Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR) and Classification and Regression Tree Analysis (CRT) to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634); FAS (rs2234767); FASL (rs763110); DCC (rs2229080, rs4078288, rs7504990, rs714); PSCA (rs2294008, rs2978974); ADRA2A (rs1801253); ADRB1 (rs1800544); ADRB3 (rs4994); CYP17 (rs2486758)) involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634), DCC (rs714, rs2229080, rs4078288) and ADRB3 (rs4994) polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994) to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10) or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10). Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.
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Affiliation(s)
- Rajani Rai
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea.
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow-226014, India.
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea.
| | - Sanjeev Misra
- Department of Surgical Oncology, King George's Medical University (KGMU), Lucknow-226003, India.
| | - Ashok Kumar
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow-226014, India.
| | - Balraj Mittal
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow-226014, India.
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Puerta-García E, Cañadas-Garre M, Calleja-Hernández MÁ. Molecular biomarkers in colorectal carcinoma. Pharmacogenomics 2015; 16:1189-222. [PMID: 26237292 DOI: 10.2217/pgs.15.63] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer is a tumor with increasing incidence which represents one of the first leading causes of death worldwide. Gene alterations described for colorectal cancer include genome instability (microsatellite and chromosomal instability), CpG islands methylator phenotype, microRNA, histone modification, protein biomarkers, gene mutations (RAS, BRAF, PI3K, TP53, PTEN) and polymorphisms (APC, CTNNB1, DCC). In this article, biomarkers with prognostic value commonly found in colorectal cancer will be reviewed.
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Affiliation(s)
- Elena Puerta-García
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Marisa Cañadas-Garre
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Miguel Ángel Calleja-Hernández
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
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Jiang HL, Liu X, Li Q. Application of transgenic animal models in colorectal cancer research. Shijie Huaren Xiaohua Zazhi 2015; 23:1603-1608. [DOI: 10.11569/wcjd.v23.i10.1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Due to the increasing incidence of colorectal cancer, the research in this area has been extensively carried out. So far, there have been about 30 kinds of transgenic animal models that are related to colorectal cancer. Compared to other animal models, transgenic animal models have showed more advantages in colorectal cancer research and have gradually become a hot spot in colorectal cancer research. This article will give an overview of conventional transgenic techniques and discuss the application of transgenic animal models in colorectal cancer research.
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