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Gao J, Wu Y, Yu J, Qiu Y, Yi T, Luo C, Zhang J, Lu G, Li X, Xiong F, Wu X, Pan X. Impact of genomic and epigenomic alterations of multigene on a multicancer pedigree. Cancer Med 2024; 13:e7394. [PMID: 38970307 PMCID: PMC11226725 DOI: 10.1002/cam4.7394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/14/2024] [Accepted: 06/05/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Germline mutations have been identified in a small number of hereditary cancers, but the genetic predisposition for many familial cancers remains to be elucidated. METHODS This study identified a Chinese pedigree that presented different cancers (breast cancer, BRCA; adenocarcinoma of the esophagogastric junction, AEG; and B-cell acute lymphoblastic leukemia, B-ALL) in each of the three generations. Whole-genome sequencing and whole-exome sequencing were performed on peripheral blood or bone marrow and cancer biopsy samples. Whole-genome bisulfite sequencing was conducted on the monozygotic twin brothers, one of whom developed B-ALL. RESULTS According to the ACMG guidelines, bioinformatic analysis of the genome sequencing revealed 20 germline mutations, particularly mutations in the DNAH11 (c.9463G > A) and CFH (c.2314G > A) genes that were documented in the COSMIC database and validated by Sanger sequencing. Forty-one common somatic mutated genes were identified in the cancer samples, displaying the same type of single nucleotide substitution Signature 5. Meanwhile, hypomethylation of PLEK2, MRAS, and RXRA as well as hypermethylation of CpG island associated with WT1 was shown in the twin with B-ALL. CONCLUSIONS These findings reveal genomic alterations in a pedigree with multiple cancers. Mutations found in the DNAH11, CFH genes, and other genes predispose to malignancies in this family. Dysregulated methylation of WT1, PLEK2, MRAS, and RXRA in the twin with B-ALL increases cancer susceptibility. The similarity of the somatic genetic changes among the three cancers indicates a hereditary impact on the pedigree. These familial cancers with germline and somatic mutations, as well as epigenomic alterations, represent a common molecular basis for many multiple cancer pedigrees.
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Affiliation(s)
- Jinyu Gao
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Yongzhang Wu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Department of Biochemistry and Molecular BiologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Jieming Yu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical UniversityShenzhenChina
| | - Yinbin Qiu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Tiantian Yi
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Chaochao Luo
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Junxiao Zhang
- SequMed Institute of Biomedical SciencesGuangzhouChina
| | - Gary Lu
- Department of Fetal Medicine and Prenatal DiagnosisZhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Xu Li
- Kaiser Permanente Regional Genetics Laboratory, San Jose Medical CenterSan JoseCaliforniaUSA
| | - Fu Xiong
- Department of Medical GeneticsSchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Xuedong Wu
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Xinghua Pan
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Department of Biochemistry and Molecular BiologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Precision Regenerative Medicine Research Centre, Division of Medical SciencesMacau University of Science and TechnologyMacaoChina
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Zhang X, Yang F, Zhu T, Zhao X, Zhang J, Wen J, Zhang Y, Wang G, Ren X, Chen A, Wang X, Wang L, Lv X, Yang W, Qu C, Wang H, Ning Z, Qu L. Whole genome resequencing reveals genomic regions related to red plumage in ducks. Poult Sci 2024; 103:103694. [PMID: 38663207 PMCID: PMC11068611 DOI: 10.1016/j.psj.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Plumage color is a characteristic trait of ducks that originates as a result of natural and artificial selection. As a conspicuous phenotypic feature, it is a breed characteristic. Previous studies have identified some genes associated with the formation of black and white plumage in ducks. However, studies on the genetic basis underlying the red plumage phenotype in ducks are limited. Here, genome-wide association analysis (GWAS) and selection signal detection (Fst, θπ ratio, and cross-population composite likelihood ratio [XP-CLR]) were conducted to identify candidate regions and genes underlying duck plumage color phenotype. Selection signal detection revealed 29 overlapping genes (including ENPP1 and ULK1) significantly associated with red plumage color in Ji'an Red ducks. ENSAPLG00000012679, ESRRG, and SPATA5 were identified as candidate genes associated with red plumage using GWAS. Selection signal detection revealed that 19 overlapping genes (including GMDS, PDIA6, and ODC1) significantly correlated with light brown plumage in Brown Tsaiya ducks. GWAS to narrow down the significant regions further revealed nine candidate genes (AKT1, ATP6V1C2, GMDS, LRP4, MAML3, PDIA6, PLD5, TMEM63B, and TSPAN8). Notably, in Brown Tsaiya ducks, GMDS, ODC1, and PDIA6 exhibit significantly differentiated allele frequencies among other feather-colored ducks, while in Ji'an Red ducks, ENSAPLG00000012679 has different allele frequency distributions compared with that in other feather-colored ducks. This study offers new insights into the variation and selection of the red plumage phenotype using GWAS and selective signals.
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Affiliation(s)
- Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fangxi Yang
- Beijing Nankou Duck Breeding Technology Co., Ltd., Beijing, China
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinxin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Anqi Chen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Daxing District, Beijing, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Huie Wang
- College of Animal Science, Tarim University, Xinjiang, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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3
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Sharma M, Verma S, Angurana SL, Tufail Z, Bhagat V, Nagyal S, Jamwal RS, Sharma B, Shah R, Bhat A, Chander G, Kumar R. Exome sequencing identifies ADGRG4 G-protein-coupled receptors gene as a novel cancer biomarker in ovarian cancer patients from North India. J Biochem Mol Toxicol 2024; 38:e23672. [PMID: 38462741 DOI: 10.1002/jbt.23672] [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: 09/12/2023] [Revised: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 03/12/2024]
Abstract
Adhesion G protein-coupled receptor G4 (ADGRG4) is a G protein-coupled receptor (GPCR) that belongs to the adhesion family. Participation of ADGRG4 in cell adhesion and migration, signaling pathway activation, influence on angiogenesis, and modulation of immune responses are some of the possible ways through which it may contribute to oncogenesis. Conducting extensive omics studies poses budgetary challenges to small labs in peripheral areas, primarily due to restricted research funding and resource limitations. Here we propose a low-budget model for biomarker screening. A total of 11 ovarian cancer samples were sent for exome sequencing. Among various genes, ADGRG4 variants were present in all 11 samples and thus were chosen as a potential biomarker in the present population. However, the precise role of ADGRG4 in cancer is not fully understood. The present study aims to look at the association between the ADGRG4 gene variants and their risk of ovarian cancer in the North Indian region of Jammu and Kashmir, India. Overall, 235 individuals (115 cases and 120 healthy controls) were genotyped for the selected biomarker using Sanger sequencing. Logistic regression was used to assess the relationship between the variant and ovarian cancer. A statistically significant association was identified between the ADGRG4 variant rs5930932 polymorphism and the incidence of ovarian cancer among the study population. When corrected for age and BMI, the dominating OR of variant rs5930932 was 1.035 (1.003-1.069) under HWE patients (0.95) and controls (0.18), with a p-value of (0.03). According to the findings of the current investigation, the ADGRG4 gene variant rs5930932 increases the chance of developing ovarian cancer in the studied population.
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Affiliation(s)
- Minerva Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Sonali Verma
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, India
| | | | - Ziya Tufail
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vanshika Bhagat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Sonia Nagyal
- Department of Histopathology, Shri Mata Vaishno Devi Narayana Multispeciality Clinic, Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | | | - Bhawani Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ruchi Shah
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India, Jammu & Kashmir, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu & Kashmir, India
| | - Gresh Chander
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, India
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Gonzalez-Bosquet J, McDonald ME, Bender DP, Smith BJ, Leslie KK, Goodheart MJ, Devor EJ. Microbial Communities in Gynecological Cancers and Their Association with Tumor Somatic Variation. Cancers (Basel) 2023; 15:3316. [PMID: 37444425 DOI: 10.3390/cancers15133316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
There are strong correlations between the microbiome and human disease, including cancer. However, very little is known about potential mechanisms associated with malignant transformation in microbiome-associated gynecological cancer, except for HPV-induced cervical cancer. Our hypothesis is that differences in bacterial communities in upper genital tract epithelium may lead to selection of specific genomic variation at the cellular level of these tissues that may predispose to their malignant transformation. We first assessed differences in the taxonomic composition of microbial communities and genomic variation between gynecologic cancers and normal samples. Then, we performed a correlation analysis to assess whether differences in microbial communities selected for specific single nucleotide variation (SNV) between normal and gynecological cancers. We validated these results in independent datasets. This is a retrospective nested case-control study that used clinical and genomic information to perform all analyses. Our present study confirms a changing landscape in microbial communities as we progress into the upper genital tract, with more diversity in lower levels of the tract. Some of the different genomic variations between cancer and controls strongly correlated with the changing microbial communities. Pathway analyses including these correlated genes may help understand the basis for how changing bacterial landscapes may lead to these cancers. However, one of the most important implications of our findings is the possibility of cancer prevention in women at risk by detecting altered bacterial communities in the upper genital tract epithelium.
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Affiliation(s)
- Jesus Gonzalez-Bosquet
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Megan E McDonald
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - David P Bender
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Brian J Smith
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Kimberly K Leslie
- Division of Molecular Medicine, Department of Internal Medicine and Obstetrics and Gynecology, The University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Michael J Goodheart
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Eric J Devor
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
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5
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Fan B, Zhou J, Zhao Y, Zhu X, Zhu M, Peng Q, Li J, Chang X, Shi D, Yin J, Guo R, Li Y, He K, Fan H, Li B. Identification of Cell Types and Transcriptome Landscapes of Porcine Epidemic Diarrhea Virus-Infected Porcine Small Intestine Using Single-Cell RNA Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:271-282. [PMID: 36548460 DOI: 10.4049/jimmunol.2101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Swine coronavirus-porcine epidemic diarrhea virus (PEDV) with specific susceptibility to pigs has existed for decades, and recurrent epidemics caused by mutant strains have swept the world again since 2010. In this study, single-cell RNA sequencing was used to perform for the first time, to our knowledge, a systematic analysis of pig jejunum infected with PEDV. Pig intestinal cell types were identified by representative markers and identified a new tuft cell marker, DNAH11. Excepting enterocyte cells, the goblet and tuft cells confirmed susceptibility to PEDV. Enrichment analyses showed that PEDV infection resulted in upregulation of cell apoptosis, junctions, and the MAPK signaling pathway and downregulation of oxidative phosphorylation in intestinal epithelial cell types. The T cell differentiation and IgA production were decreased in T and B cells, respectively. Cytokine gene analyses revealed that PEDV infection downregulated CXCL8, CXCL16, and IL34 in tuft cells and upregulated IL22 in Th17 cells. Further studies found that infection of goblet cells with PEDV decreased the expression of MUC2, as well as other mucin components. Moreover, the antimicrobial peptide REG3G was obviously upregulated through the IL33-STAT3 signaling pathway in enterocyte cells in the PEDV-infected group, and REG3G inhibited the PEDV replication. Finally, enterocyte cells expressed almost all coronavirus entry factors, and PEDV infection caused significant upregulation of the coronavirus receptor ACE2 in enterocyte cells. In summary, this study systematically investigated the responses of different cell types in the jejunum of piglets after PEDV infection, which deepened the understanding of viral pathogenesis.
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Affiliation(s)
- Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China.,School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Yongxiang Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Xuejiao Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Mingjun Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Qi Peng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Xinjian Chang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Danyi Shi
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Jie Yin
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Yunchuan Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Kongwang He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Huiying Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; and
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China.,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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A Novel Four Mitochondrial Respiration-Related Signature for Predicting Biochemical Recurrence of Prostate Cancer. J Clin Med 2023; 12:jcm12020654. [PMID: 36675580 PMCID: PMC9866444 DOI: 10.3390/jcm12020654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The biochemical recurrence (BCR) of patients with prostate cancer (PCa) after radical prostatectomy is high, and mitochondrial respiration is reported to be associated with the metabolism in PCa development. This study aimed to establish a mitochondrial respiratory gene-based risk model to predict the BCR of PCa. RNA sequencing data of PCa were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and mitochondrial respiratory-related genes (MRGs) were sourced via GeneCards. The differentially expressed mitochondrial respiratory and BCR-related genes (DE-MR-BCRGs) were acquired through overlapping BCR-related differentially expressed genes (BCR-DEGs) and differentially expressed MRGs (DE-MRGs) between PCa samples and controls. Further, univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analyses were performed to construct a DE-MRGs-based risk model. Then, a nomogram was established by analyzing the independent prognostic factor of five clinical features and risk scores. Moreover, Gene Set Enrichment Analysis (GSEA), tumor microenvironment, and drug susceptibility analyses were employed between high- and low-risk groups of PCa patients with BCR. Finally, qRT-PCR was utilized to validate the expression of prognostic genes. We identified 11 DE-MR-BCRGs by overlapping 132 DE-MRGs and 13 BCR-DEGs and constructed a risk model consisting of 4 genes (APOE, DNAH8, EME2, and KIF5A). Furthermore, we established an accurate nomogram, including a risk score and a Gleason score, for the BCR prediction of PCa patients. The GSEA result suggested the risk model was related to the PPAR signaling pathway, the cholesterol catabolic process, the organic hydroxy compound biosynthetic process, the small molecule catabolic process, and the steroid catabolic process. Simultaneously, we found six immune cell types relevant to the risk model: resting memory CD4+ T cells, monocytes, resting mast cells, activated memory CD4+ T cells, regulatory T cells (Tregs), and macrophages M2. Moreover, the risk model could affect the IC50 of 12 cancer drugs, including Lapatinib, Bicalutamide, and Embelin. Finally, qRT-PCR showed that APOE, EME2, and DNAH8 were highly expressed in PCa, while KIF5A was downregulated in PCa. Collectively, a mitochondrial respiratory gene-based nomogram including four genes and one clinical feature was established for BCR prediction in patients with PCa, which could provide novel strategies for further studies.
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7
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Verma S, Bakshi D, Bhat GR, Bhat A, Shah R, Sharma B, Wakhloo A, Heer V, Chander G, Kumar R. Genetic analysis of polymorphism rs10937405 of TP63 gene in breast and ovarian cancer patients of North Indian Cohort. J Cancer Res Ther 2023; 19:214-217. [PMID: 37006060 DOI: 10.4103/jcrt.jcrt_1517_20] [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] [Indexed: 04/04/2023]
Abstract
INTRODUCTION Ovarian and breast cancers are highly prevalent in the population of Jammu and Kashmir (J&K). However, case-control association studies on breast and ovarian cancers are lacking in this population. Moreover, no case-control study is available on variant rs10937405 of TP63 in breast and ovarian cancers. Thus, we designed to replicate the cancer susceptible variant rs10937405 of TP63 in ovarian and breast cancers in the population of J&K because the TP63 gene act as a tumor suppressor gene and was previously associated with various cancers. MATERIALS AND METHODS This case-control association study conducted at the Shri Mata Vaishno Devi University, includes 150 breast, 150 ovarian cancer cases, and 210 healthy controls (age and sex-matched). Variant rs10937405 of the TP63 gene was determined by the TaqMan assay. Hardy-Weinberg equilibrium for the variant was assessed using the Chi-square test. The allele and genotype-specific risks were estimated by odds ratios (ORs) with 95% confidence intervals (CI). RESULTS In this study, variant rs10937405 of TP63 gene did not show any risk with ovarian and breast cancer with (P-value = 0.70) having OR 0.94, (0.69-1.28 at 95% CI) and (P-value = 0.16) having OR 0.80, (0.59-1.10). DISCUSSION Our results indicate that the variant rs10937405 of the TP63 gene did not impart any risk of breast and ovarian cancer in the population of J&K. Our results indicate that a larger sample size is needed for further statistical validation. As the study was for a particular variant, it warrants the analysis of other variants of this gene.
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Affiliation(s)
- Sonali Verma
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
| | - Divya Bakshi
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Amrita Bhat
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ruchi Shah
- Department of Biotechnology, Kashmir University, Jammu and Kashmir, India
| | - Bhanu Sharma
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ajay Wakhloo
- Department of Obstetrics and Gynaecology, Government Medical College Jammu, Jammu and Kashmir, India
| | - Vikas Heer
- Department of Surgical Oncology, Shri Mata Vaishno Devi Super Specialty Narayana Hospital, Katra, Jammu and Kashmir, India
| | - Gresh Chander
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
| | - Rakesh Kumar
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
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Jiang A, Luo P, Chen M, Fang Y, Liu B, Wu Z, Qu L, Wang A, Wang L, Cai C. A new thinking: deciphering the aberrance and clinical implication of copper-death signatures in clear cell renal cell carcinoma. Cell Biosci 2022; 12:209. [PMID: 36581992 PMCID: PMC9801655 DOI: 10.1186/s13578-022-00948-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
RATIONALE Recent research has indicated that cuprotosis, or copper induced cell death, is a novel type of cell death that could be utilized as a new weapon for cancer management. However, the characteristics and implications of such signatures in cancers, especially in clear cell renal cell cancer (ccRCC), remain elusive. METHODS Expression, methylation, mutation, clinical information, copy number variation, functional implication, and drug sensitivity data at the pan-cancer level were collected from The Cancer Genome Atlas. An unsupervised clustering algorithm was applied to decipher ccRCC heterogeneity. Immune microenvironment construction, immune therapy response, metabolic pattern, and cancer progression signature between subgroups were also investigated. RESULTS Cuprotosis related genes were specifically downregulated in various cancer tissues compared with normal tissues and were correlated with hypermethylation and copy number variation. Cuprotosis scores were also dysregulated in tumor tissues, and we found that such a signature could positively regulate oxidative phosphorylation and Myc and negatively regulate epithelial mesenchymal translation and myogenesis pathways. CPCS1 (cuprotosis scores high) and CPCS2 (cuprotosis scores low) in ccRCC displayed distinctive clinical profiles and biological characteristics; the CPCS2 subtype had a higher clinical stage and a worse prognosis and might positively regulate cornification and epidermal cell differentiation to fuel cancer progression. CPCS2 also displayed a higher tumor mutation burden and low tumor stemness index, while it led to a low ICI therapy response and dysfunctional tumor immunity state. The genome-copy numbers of CPCS2, including arm- gain and arm- loss, were higher than those of CPCS1. The prognostic model constructed based on subgroup biomarkers exerted satisfactory performance in both the training and validation cohorts. In addition, overexpression of the copper death activator DLAT suppressed the malignant ability, including cell migration and proliferation, of renal cell lines in vitro and in vivo. Finally, activation of cuprotosis in tumors could enhance antitumor immunity through dsDNA-cGAS-STING signaling in ccRCC. CONCLUSION The activation of cuprotosis might function as a promising approach among multiple cancers. The cuprotosis related signatures could reshape tumor immunity in the ccRCC microenvironment via cGAS-STING signal, thus activating tumor antigen-presenting process. Upregulation of DLAT expression in ccRCC cell lines could reactivate the copper death pattern and be treated as a suitable target for ccRCC.
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Affiliation(s)
- Aimin Jiang
- grid.73113.370000 0004 0369 1660Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200433 China
| | - Peng Luo
- grid.284723.80000 0000 8877 7471Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280 China
| | - Ming Chen
- grid.73113.370000 0004 0369 1660Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003 China
| | - Yu Fang
- grid.73113.370000 0004 0369 1660Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200433 China
| | - Bing Liu
- grid.73113.370000 0004 0369 1660Department of Urology, The Third Affiliated Hospital, Naval Medical University (Second Military Medical University), Shanghai, 201805 China
| | - Zhenjie Wu
- grid.73113.370000 0004 0369 1660Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200433 China
| | - Le Qu
- grid.41156.370000 0001 2314 964XDepartment of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210046 China
| | - Anbang Wang
- grid.73113.370000 0004 0369 1660Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003 China
| | - Linhui Wang
- grid.73113.370000 0004 0369 1660Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200433 China
| | - Chen Cai
- grid.73113.370000 0004 0369 1660Department of Special Clinic, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200433 China
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9
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Zhou Y, Xu L, Wang J, Ge B, Wang Q, Wang T, Liu C, Wei B, Wang Q, Gao Y. LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway. Cancer Sci 2022; 113:3566-3578. [PMID: 35879265 PMCID: PMC9530863 DOI: 10.1111/cas.15510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
As a neuronal transmembrane protein, leucine-rich repeat and fibronectin type-III domain-containing protein 2 (LRFN2) can recruit and combine with N-methyl-D-aspartic acid receptors (NMDARs) to promote nerve growth. Genetic studies suggest that mutations in LRFN2 are associated with various cancers. However, the role and mechanism of LRFN2 in the progression of esophageal squamous cell carcinoma (ESCC) have not been elucidated. In this study, we demonstrated that LRFN2 was significantly downregulated in ESCC tissues by qRT-PCR and immunohistochemistry. Low LRFN2 expression was an adverse prognostic factor in patients with ESCC. Overexpression of LRFN2 effectively suppressed the proliferation, migration, invasion and epithelial-to-mesenchymal transition in vitro and tumor growth in vivo. Bioinformatics analysis indicated that Wnt/β-catenin signaling regulation was one of the most potential mechanisms and studies confirmed that overexpression of LFRN2 obviously downregulated the expression of β-catenin, c-Myc and cyclin D1 in ESCC cells and tumor tissues. Further studies revealed that LRFN2 plays anti-ESCC role by binding with NMDAR-GRIN2B and this effect can be weakened by NR2B-selective NMDA antagonist-NMDA-IN-1. Moreover, the bioinformatics analysis showed that the interaction of GRIN2B and GSK3β affects the NF-κB pathway, which was demonstrated by western blot experiments. Collectively, our results indicate that LRFN2 binding to NMDARs inhibits the progression of ESCC by regulating the Wnt/β-catenin and NF-κB pathway, which provides a new therapeutic target for improving the prognosis of patients with ESCC.
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Affiliation(s)
- Yu Zhou
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Lijuan Xu
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Jiru Wang
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Beibei Ge
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Qiuzi Wang
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Tao Wang
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Chang Liu
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Bin Wei
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
| | - Qilong Wang
- Department of Central Laboratory, Cancer Center, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, China
| | - Yong Gao
- Department of Medical Oncology, Cancer Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, China
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10
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Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. Cancers (Basel) 2022; 14:cancers14143363. [PMID: 35884425 PMCID: PMC9317824 DOI: 10.3390/cancers14143363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/27/2023] Open
Abstract
Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.
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Affiliation(s)
- Martine Dumont
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Charles Joly-Beauparlant
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Arnaud Droit
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Stéphane Dubois
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Annie-Claude Collin-Deschesnes
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Penny Soucy
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Maxime Vallée
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Frédéric Fournier
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Audrey Lemaçon
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Muriel A. Adank
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, 24105 Kiel, Germany;
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, 3584 Utrecht, The Netherlands;
| | - Riccardo Berutti
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shelley Bull
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Michael R. Dufault
- Precision Medicine and Computational Biology, Sanofi Genzyme, Cambridge, MA 02142, USA;
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany;
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University of Würzburg, 97074 Würzburg, Germany;
| | | | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Jessica Green
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Julia Hentschel
- Institute of Human Genetics, University Leipzig, 04103 Leipzig, Germany;
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Judit Horváth
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany;
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 Rotterdam, The Netherlands;
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Da Kuang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), Department of Neurodegenerative Diseases and Geriatric Psychiatry, Medical Faculty, University Hospital Bonn, 53127 Bonn, Germany;
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 13353 Berlin, Germany;
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Department of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Alfredo Ramirez
- Division for Neurogenetics and Molecular Psychiatry, Medical Faculty, University of Cologne, 50937 Cologne, Germany;
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany;
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Antje Stäbler
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany;
| | - Tim M. Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
| | - Lizet van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Rob B. van der Luijt
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
- Department of Medical Genetics, University Medical Center, 3584 Utrecht, The Netherlands
| | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany;
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University of Ulm, 89081 Ulm, Germany;
| | - Bernhard H. F. Weber
- Institute of Human Genetics, Regensburg University, 93053 Regensburg, Germany;
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | | | - Peter Devilee
- Department of Pathology, Department of Human Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands;
| | - Sean Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gary D. Bader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - David E. Goldgar
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Jacques Simard
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +418-654-2264
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Sharma B, Angurana S, Shah R, Verma S, Bhat A, Bhat GR, Bakshi D, Jamwal RS, Tanwar M, Singh S, Bhat A, Vaishnavi S, Kumar R. Genetic association of ARID5B with the risk of colorectal cancer within Jammu and Kashmir, India. Genes Genet Syst 2021; 96:187-191. [PMID: 34803080 DOI: 10.1266/ggs.21-00010] [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] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer (CRC), which includes the development of cancer from the colon or rectum, is one of the highly prevalent cancers in the populations of Jammu and Kashmir (J&K) in India. However, case-control genetic association studies on CRC are lacking in this population. Various genome-wide association studies have previously shown that single-nucleotide polymorphisms (SNPs) of the AT-rich interaction domain 5B (ARID5B) gene located on chromosome 10q21.2 contribute substantially to the development of colorectal cancer. The association between ARID5B and CRC risk in north Indian population groups is still unknown. To understand the role of ARID5B SNPs in CRC in the population of J&K, we designed a case-control study to investigate the association of the cancer susceptibility variant rs10740055 of ARID5B with CRC in the population of J&K. The study included 180 cases and 390 healthy controls. Genotyping of the rs10740055 variant was performed by RT-PCR using the TaqMan assay technique. Hardy-Weinberg equilibrium of the variant was assessed using the chi-squared test. The allele- and genotype-specific risks were estimated by odds ratios (ORs) with 95% confidence intervals (CIs). The rs10740055 variant showed a higher risk for colorectal cancer with an OR of 3.35 (1.99-5.65 at 95% CI) and P = 0.000005 corrected for age, gender, ethnicity, BMI, alcohol intake and smoking. Our results indicate that the A allele of rs10740055 imparts risk to the population and also that a larger sample size is needed for further statistical validation. The association of other variants in other ARID family genes should also be tested as their role cannot be ruled out.
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Affiliation(s)
- Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University
| | | | - Ruchi Shah
- Department of Biotechnology, University of Kashmir
| | - Sonali Verma
- Indian Council of Medical Research-Centre for Advanced Research, School of Biotechnology Shri Mata Vaishno Devi University
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University
| | - G R Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University
| | | | - Mukesh Tanwar
- Department of Genetics, Maharshi Dayanand University
| | | | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu
| | | | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University.,Indian Council of Medical Research-Centre for Advanced Research, School of Biotechnology Shri Mata Vaishno Devi University
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12
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Jamwal RS, Mahajan N, Bhat GR, Bhat A, Shah R, Verma S, Sharma M, Sharma B, Qadri RA, Kumar R, Bhat A. REV3L single nucleotide variants lead to increased susceptibility towards non-small cell lung cancer in the population of Jammu and Kashmir. Cancer Epidemiol 2021; 75:102047. [PMID: 34655923 DOI: 10.1016/j.canep.2021.102047] [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: 06/17/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the most common lung cancer, accounting for 80-85% of all lung cancer cases. Various genetic studies have associated REV3L (Protein reversion less 3-like) gene mutations, which encodes the catalytic subunit of error prone translesion synthesis polymerase zeta with cancer, including lung cancer; however, no such data is available from any North Indian population. In this study we attempted to screen the North Indian population of Jammu and Kashmir (J&K) for the potential role of REV3L gene polymorphisms in NSCLC. METHODS A total of four REV3L single nucleotide variants were selected for genotyping based on the available literature. The genotyping was carried out by using the TaqMan allele discrimination assay in 500 subjects (200 NSCLC patients and 300 age and sex matched healthy controls). The association of variants with NSCLC was evaluated by logistic regression. RESULTS Out of the four REV3L variants genotyped; rs1002481, rs462779, and rs465646 were found significantly associated with NSCLC risk under the recessive model, with an Odds Ratio (OR) of 3.52(2.14-5.8 at 95% CI, p-value = 0.00000062), 3.7 (1.8-7.6 at 95% CI, p-value = 0.00031), and 2.2 (1.47-3.37 at 95% CI, p-value = 0.0003), respectively. DISCUSSION Our data supports a strong association between variants rs1002481, rs462779, rs465646 and NSCLC, indicating a potential role of these REV3L variants in increasing the risk for the development of NSCLC in the studied population. Although a first report from any Indian population, these variants have been previously reported to be associated with lung and colorectal cancers in different world populations. Our data along with the existing data supports the notation that these variants can be used as potential genetic predisposition markers. AVAILABILITY OF DATA AND MATERIALS Data generated and analysed during study is not available publicly but can be made available from the corresponding author upon reasonable request.
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Affiliation(s)
| | - Nikita Mahajan
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Ruchi Shah
- Department of Biotechnology, University of Kashmir, Jammu & Kashmir, India.
| | - Sonali Verma
- Indian Council of Medical Research-Centre for Advanced Research, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India.
| | - Minerva Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Bhawani Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Raies A Qadri
- Department of Biotechnology, University of Kashmir, Jammu & Kashmir, India.
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India; Indian Council of Medical Research-Centre for Advanced Research, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India.
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu & Kashmir, India.
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Huang J, Yang H, Wang M, Zhao X, Shao S, Zhang F, Que R, Hu Q, Liang T. Gallbladder Adenosquamous Cancer with Situs Inversus Totalis: A Case Report and Literature Review. Onco Targets Ther 2021; 14:4299-4304. [PMID: 34349522 PMCID: PMC8327361 DOI: 10.2147/ott.s319030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Background Situs inversus totalis (SIT) is a rare genetic congenital disease, characterized with complete right-to-left inversion of all the internal organs. We herein describe a meaningful case which was diagnosed as gallbladder adenosquamous carcinoma, a rare histology type of gallbladder cancer, with SIT. Case Presentation A 59-year-old Chinese woman was admitted for persistent epigastric distention and intermittent abdominal pain. The abdominal CT scan revealed a huge mass at the gallbladder bottom, involving the adjacent transverse colon and liver. En-bloc radical resection of the gallbladder cancer, including partial colectomy and hepatectomy with regional node dissection, followed by colocolostomy and Roux-en-Y choledochojejunostomy, was successfully performed. Pathology analysis indicated an adenosquamous carcinoma with positive adenocarcinoma markers (CK7, CK19) and squamous carcinoma markers (CK5/6, P63). Conclusion The SIT anomaly might increase the risk of malignancies by sharing genome mutations, suggesting the importance of surveillance in the SIT settings.
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Affiliation(s)
- Junming Huang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Hanjin Yang
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Meng Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Xinyu Zhao
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Shiyi Shao
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Fu Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Risheng Que
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Qida Hu
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
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14
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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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15
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Bhat A. Meet Our Editorial Board Member. Curr Pharm Biotechnol 2021. [DOI: 10.2174/138920102208210507102808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir,India
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16
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Verma S, Sharma I, Sharma V, Bhat A, Shah R, Bhat GR, Sharma B, Bakshi D, Nagpal A, Wakhloo A, Bhat A, Kumar R. MassArray analysis of genomic susceptibility variants in ovarian cancer. Sci Rep 2020; 10:21101. [PMID: 33273524 PMCID: PMC7713113 DOI: 10.1038/s41598-020-76491-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/28/2020] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer (OC), a multifaceted and genetically heterogeneous malignancy is one of the most common cancers among women. The aim of the study is to unravel the genetic factors associated with OC and the extent of genetic heterogeneity in the populations of Jammu and Kashmir (J&K).Using the high throughput Agena MassARRAY platform, present case control study was designed which comprises 200 histopathological confirmed OC patients and 400 age and ethnicity matched healthy controls to ascertain the association of previously reported eleven single nucleotide polymorphisms (SNPs) spread over ten genes (DNMT3A, PIK3CA, FGFR2, GSTP1, ERCC5, AKT1, CASC16, CYP19A1, BCL2 and ERCC1) within the OC population of Jammu and Kashmir, India. The association of each variant was estimated using logistic regression analyses. Out of the 11 SNPs the odds ratio observed for three SNPs; rs2699887 was (1.72 at 95% CI: 1.19-2.48, p = 0.004), rs1695 was (1.87 at 95% CI: 1.28-2.71, p = 0.001), and rs2298881 was (0.66 at 95% CI: 0.46-0.96, p = 0.03) were found significantly associated with the OC after correction with confounding factors i.e. age & BMI. Furthermore, the estimation of interactive analyses was performed and odds ratio observed was 2.44 (1.72-3.47), p value < 0. 001 suggests that there was a strong existence of interplay between the selected genetic variants in OC, which demonstrate that interactive analysis highlights the role of gene-gene interaction that provides an insight among multiple little effects of various polymorphisms in OC.
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Affiliation(s)
- Sonali Verma
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Indu Sharma
- Ancient DNA Laboratory, Birbal Shani Institute of Paleo Sciences, Lucknow, Uttar Pradesh, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Shani Institute of Paleo Sciences, Lucknow, Uttar Pradesh, India
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ruchi Shah
- Department of Biotechnology, Kashmir University, Srinagar, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ashna Nagpal
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ajay Wakhloo
- Department of Obstetrics and Gynecology, Government Medical College, Jammu, Jammu and Kashmir, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Rakesh Kumar
- Indian Council of Medical Research-Centre for Advance Research, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
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Ben Kridis-Rejeb W, Ben Ayed-Guerfali D, Ammous-Boukhris N, Ayadi W, Kifagi C, Charfi S, Saguem I, Sellami-Boudawara T, Daoud J, Khanfir A, Mokdad-Gargouri R. Identification of novel candidate genes by exome sequencing in Tunisian familial male breast cancer patients. Mol Biol Rep 2020; 47:6507-6516. [PMID: 32901360 DOI: 10.1007/s11033-020-05703-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
Abstract
Male Breast Cancer (MBC) is a rare and aggressive disease that is associated with genetic factors. Mutations in BRCA1 and BRCA2 account for 10% of all MBC cases suggesting that other genetic factors are involved. The aim of the present study is to screen whole BRCA1 and BRCA2 exons using the Ampliseq BRCA panel in Tunisian MBC patients with family history. Furthermore, we performed exome sequencing using the TruSight One sequencing panel on an early onset BRCA negative patient. We showed that among the 6 MBC patients, only one (MBC-F1) harbored a novel frameshift mutation in exon 2 of the BRCA2 gene (c.17-20delAAGA, p.Lys6Xfs) resulting in a short BRCA2 protein of only 6 amino-acids. We selected 9 rare variants after applying several filter steps on the exome sequencing data. Among these variants, and based on their role in breast carcinogenesis, we retained 6 candidate genes (MSH5, DCC, ERBB3, NOTCH3, DIAPH1, and DNAH11). Further studies are needed to confirm the association of the selected genes with family MBC.
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Affiliation(s)
| | - Dorra Ben Ayed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Chamseddine Kifagi
- Division of Immunology & Vaccinology, DTU Nanotech, Department of Micro-and Nanotechnology, Kemitorvet, Buildings 202 and 204, Lyngby Campus, 2800, Kgs. Lyngby, Denmark
| | - Slim Charfi
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Ines Saguem
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Tahia Sellami-Boudawara
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Afef Khanfir
- Department of Oncology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia.
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Bhat GR, Verma S, Bhat A, Shah R, Sethi I, Dar KA, Abrol D, Bhat A, Raina R, Kumar R. Genetic variant rs2494938 of LRFN2 gene is associated with non-small cell lung cancer risk in North-Indian population. 3 Biotech 2020; 10:410. [PMID: 32904533 DOI: 10.1007/s13205-020-02403-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/19/2020] [Indexed: 11/25/2022] Open
Abstract
Various Genome-wide association studies (GWAS) have reported the association of variant rs2494938 with lung cancer. However, genetic association of LRFN2 genetic variation with non-small cell lung cancer (NSCLC) in North Indian population remained unexplored. We conducted a case-control association study using TaqMan-based chemistry in which a total of 619 individuals, 189 NSCLC cases and 430 controls, were genotyped to explore the association of rs2494938 genetic variant of the LRFN2 gene with NSCLC patients from North India. The allele 'G' (risk allele) of the genetic variant rs2494938 was significantly associated with the NSCLC [OR = 1.51 (1.18-1.93 at 95% CI); p value = 0.0009]. Genetic association was also explored by applying different genetic models (Dominant, Additive). These results suggest that rs2494938 polymorphism of the LRFN2 gene is a risk factor in the North Indian populations to develop NSCLC. The LD (Linkage Disequilibrium) plot demonstrates the variant and its LD SNPs (r 2 > 0.8) and the variant has direct regulatory effect, which could affect the overall physiology of the gene. These findings could be used as diagnostic and prognostic markers in clinical studies of lung cancer patients in North Indian population groups. The present study also provides an important evidence on the genetic etiology of NSCLC in North Indian populations and further expounds GWAS findings on the role of LRFN2 in lung cancer risk. This study provides the holistic view about the non-small cell lung cancer in Jammu and Kashmir, North Indian population and it can be a hallmark of cancer if verified on a very large sample size (cohort).
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Affiliation(s)
- Gh Rasool Bhat
- Cancer Genetics Research Group, ICMR, Centre for Advanced Research, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
| | - Sonali Verma
- Cancer Genetics Research Group, ICMR, Centre for Advanced Research, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
| | - Amrita Bhat
- Cancer Genetics Research Group, ICMR, Centre for Advanced Research, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
| | - Ruchi Shah
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
| | - Itty Sethi
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
| | - Khursheed A Dar
- Chest Disease Hospital, Government Medical College, Srinagar, J&K UT India
| | - Deepak Abrol
- Department of Radiotherapy, Govt. Medical College Kathua, Jammu, J&K UT India
| | - Audesh Bhat
- Central University of Jammu, Jammu, J&K UT India
| | - Rakesh Raina
- Siddhi Vinayak Dental and Health Care Centre, Roop Nagar Jammu, Jammu, J&K UT India
| | - Rakesh Kumar
- Cancer Genetics Research Group, ICMR, Centre for Advanced Research, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT India
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