1
|
Kaur S, Vashistt J, Sharma A, Parkash J, Kumar A, Duseja A, Changotra H. Mutagenic primer-based novel multiplex PCR-RFLP technique to genotype BECN1 SNPs rs10512488 and rs11552192. Mol Biol Rep 2024; 51:384. [PMID: 38438793 DOI: 10.1007/s11033-024-09277-z] [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: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Single Nucleotide Polymorphisms (SNPs) in candidate autophagy gene BECN1 could influence its functions thereby autophagy process. BECN1 noncoding SNPs were found to be significantly associated with neurodegenerative disease and type 2 diabetes mellitus. This study aimed to develop a simultaneous genotyping technique for two BECN1 SNPs (rs10512488 and rs11552192). METHODS A mutagenic primer-based approach was used to introduce a NdeI restriction site to genotype rs10512488 by Artificial-Restriction Fragment Length Polymorphism (A-RFLP) along with rs11552192 by Polymerase Chain Reaction (PCR)-RFLP. Multiplexing PCR and restriction digestion reactions were set up for simultaneous genotyping of both SNPs in 100 healthy individuals. Genotypic and allele frequencies were manually calculated, and the Hardy-Weinberg Equilibrium was assessed using the chi-square test. RESULTS We successfully developed PCR and RFLP conditions for the amplification and restriction digestion of both SNPs within the same tube for genotyping. The results of genotyping by newly developed multiplexing PCR-RFLP technique were concordant with the genotypes obtained by Sanger sequencing of samples. Allelic frequencies of rs10512488 obtained were 0.15 (A) and 0.85 (G), whereas allelic frequencies of rs11552192 were 0.16 (T) and 0.84 (A). CONCLUSION The newly developed technique is rapid, cost-effective and time-saving for large-scale applications compared to sequencing methods and would play an important role in low-income settings. For the first time, allelic frequencies of rs10512488 and rs11552192 were reported among the North Indian population.
Collapse
Affiliation(s)
- Sargeet Kaur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Himachal Pradesh, Waknaghat, Solan, 173 234, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Himachal Pradesh, Waknaghat, Solan, 173 234, India
| | - Arti Sharma
- Department of Computational Biology, School of Biological Sciences, Central University of Punjab, Bathinda 151 401, Punjab, India
| | - Jyoti Parkash
- Department of Zoology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151 001, India
| | - Ajay Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India
| | - Ajay Duseja
- Department of Hepatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Harish Changotra
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, 143 005, Punjab, India.
| |
Collapse
|
2
|
Kaur S, Vashistt J, Changotra H. Autophagy Gene BECN1 Intronic Variant rs9890617 Predisposes Individuals to Hepatitis B Virus Infection. Biochem Genet 2023:10.1007/s10528-023-10608-1. [PMID: 38103127 DOI: 10.1007/s10528-023-10608-1] [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: 06/07/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Beclin 1 protein encoded by the BECN1 gene plays a critical role in the autophagy pathway which is utilized by the Hepatitis B virus (HBV) for its replication. HBV is known for the subversion of the host's autophagy process for its multiplication. The aim of this study was to determine the role of BECN1 intronic variants in HBV susceptibility. Intronic region variant rs9890617 was analyzed using Human splicing finder v3.1 and was found to alter splicing signals. A total of 712 individuals (494 HBV infected and 218 healthy controls) were recruited in the study and genotyped by applying Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Statistical analysis revealed that the mutant allele T of rs9890617 was significantly associated with the overall disease risk in the allelic model (OR 1.41; 95%CI 1.00-1.99, p = 0.04). On stratifying the data based on the different stages of HBV infection, the mutant genotype showed a significant association with the chronic group in allelic (OR 1.62; 95%CI 1.11-2.39, p = 0.01), dominant (OR 1.64; 95%CI 1.07-2.52, p = 0.02), and co-dominant (OR 1.55; 95%CI 1.00-2.40, p = 0.04) models. Overall, this is the first study regarding beclin 1 variant rs9890617 and we found a significant association of the mutant T allele with the genetic predisposition to HBV infection.
Collapse
Affiliation(s)
- Sargeet Kaur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India
| | - Harish Changotra
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India.
| |
Collapse
|
3
|
Interactions between exposure to polycyclic aromatic hydrocarbons and xenobiotic metabolism genes, and risk of breast cancer. Breast Cancer 2021; 29:38-49. [PMID: 34351578 DOI: 10.1007/s12282-021-01279-0] [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: 08/13/2020] [Accepted: 07/25/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental pollutants associated with multiple cancers, including female breast cancer. Several xenobiotic metabolism genes (XMGs), including the CYP450 family, play an important role in activating and detoxifying PAHs, and variations in the activity of the enzymes they encode can impact this process. This study aims to examine the association between XMGs and breast cancer, and to assess whether these variants modify the effects of PAH exposure on breast cancer risk. METHODS In a case-control study in Vancouver, British Columbia, and Kingston, Ontario, 1037 breast cancer cases and 1046 controls had DNA extracted from blood or saliva and genotyped for 138 single nucleotide polymorphisms (SNPs) and tagSNPs in 27 candidate XMGs. Occupational PAH exposure was assessed using a measurement-based job-exposure matrix. RESULTS An association between genetic variants and breast cancer was observed among six XMGs, including increased risk among the minor allele carriers of AKR1C3 variant rs12387 (OR 2.71, 95% CI 1.42-5.19) and AKR1C4 variant rs381267 (OR 2.50, 95% CI 1.23-5.07). Heterogeneous effects of occupational PAH exposure were observed among carriers of AKR1C3/4 variants, as well as the PTGS2 variant rs5275. CONCLUSION Our findings support an association between SNPs of XMGs and female breast cancer, including novel genetic variants that modify the toxicity of PAH exposure. These results highlight the interplay between genetic and environmental factors, which can be helpful in understanding the modifiable risks of breast cancer and its complex etiology.
Collapse
|
4
|
Hamadou WS, Mani R, Bouali N, Besbes S, Bourdon V, El Abed R, Ben Youssef Y, Mari V, Gesta P, Dreyfus H, Bonadona V, Dugast C, Zattara H, Faivre L, Noguchi T, Khélif A, Sobol H, Soua Z. Mutational analysis of apoptotic genes in familial aggregation of hematological malignancies. Bull Cancer 2021; 108:798-805. [PMID: 34140154 DOI: 10.1016/j.bulcan.2021.04.009] [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: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Apoptosis deregulation have been associated to tumorigenesis process and was highlighted as a prominent hallmark of cancer. Several mutations have been reported in several forms of Blood cancer. However, it has never been investigated in familial aggregations of hematological malignancies. METHODS In this study, we performed a mutational analysis by sequencing the entire coding regions in four key apoptotic genes FAS, FASLG, CASP8 and CASP10 in 92 independent families belonging to French and Tunisian populations and diagnosed with several forms of familial hematological malignancies. RESULTS We report 15 genetic variations among which 7 were previously reported in several form of cancers and have a potential effect on gene expression. Particularly, the CASP8 variants p.Asp302His and p.Lys337Lys were detected in 15% and 10% of our group of patients respectively and were previously reported in association to breast cancer and to breast cancer susceptibility. DISCUSSION In this study, we do not report the underlining deleterious mutations in familial hematological malignancies, but we describe some variants with potential risk of developing blood cancer. To gain further insights on the association between apoptosis pathway deregulation and familial hematological malignancies, more apoptotic genes should be investigated.
Collapse
Affiliation(s)
- Walid Sabri Hamadou
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; Hail university, biology department, Hail, Saudi Arabia.
| | - Rahma Mani
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Nouha Bouali
- Hail university, biology department, Hail, Saudi Arabia
| | - Sawsen Besbes
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Violaine Bourdon
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Rym El Abed
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Yosra Ben Youssef
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Véronique Mari
- Centre de lutte contre le cancer, centre Antoine-Lacassagne, service d'oncologie génétique, Nice, France
| | - Paul Gesta
- Centre hospitalier, service d'oncologie génétique, Niort, France
| | | | - Valérie Bonadona
- Centre Léon-Bérard, unité de génétique épidémiologique, Lyon, France
| | | | - Hélène Zattara
- Hôpital de la Timone, département de génétique, Marseille, France
| | | | - Tetsuro Noguchi
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Abderrahim Khélif
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Hagay Sobol
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Zohra Soua
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| |
Collapse
|
5
|
The Association of ATG16L1 Variations with Clinical Phenotypes of Adult-Onset Still's Disease. Genes (Basel) 2021; 12:genes12060904. [PMID: 34208077 PMCID: PMC8230810 DOI: 10.3390/genes12060904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 01/07/2023] Open
Abstract
Adult-onset Still’s disease (AOSD) is a rare autoinflammatory disease, which has elevated autophagosome levels regulated by autophagy-related gene (ATG) expression. We investigated the associations of ATG polymorphisms with AOSD susceptibility, clinical manifestations, and disease course. The six-candidate single-nucleotide polymorphisms (SNPs) involved in autophagy were genotyped using direct sequencing on samples from 129 AOSD patients and 129 healthy participants. The differentially expressed gene products were quantified using PCR and ELISA. Significant linkage disequilibrium was noted in three SNPs of autophagy-related 16-like 1 (ATG16L1) gene (rs10210302, rs2241880, and rs1045100). Although the AA/CC/TT haplotype of ATG16L1 was not associated with the susceptibility of our AOSD patients compared with other haplotypes, those carrying this haplotype had lower mRNA expression levels of LC3-II, reflecting by autophagosome formation (p = 0.026). Patients carrying AA/CC/TT haplotype also have a significantly higher proportion of skin rash and a lower proportion of arthritis compared with other haplotypes. The AA/CC/TT haplotype was significantly associated with systemic pattern (odds ratio, 3.25; 95% confidence interval, 1.15–9.14; p = 0.026). In summary, the AA/CC/TT haplotype encoded lower levels of autophagosome formation and was associated with a higher proportion of skin rash and systemic pattern of AOSD compared with other haplotypes.
Collapse
|
6
|
Zayed SA, Zahran NM, Khorshied MM, Abdel-Aziz AO, Mahmoud O, Morsy SA, Shousha HI, Elbaz TM, Nabeel MM, Harb ARK. Genetic variations in death receptor domain 4 gene and the susceptibility to hepatitis C related hepatocellular carcinoma. J Med Virol 2019; 91:1537-1544. [PMID: 30945308 DOI: 10.1002/jmv.25476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality worldwide, particularly in Egypt. The role of apoptosis in tumorigenesis has been well-documented and resistance to apoptosis is a hallmark of cancer. Several studies discussed the association between death receptor 4 (DR4) genetic variants and HCC risk. AIM To study the possible link between DR4 gene polymorphisms and the susceptibility to HCC. METHODS Genotyping of DR4-C626G, -A683C, and DR4-A1322G single nucleotide polymorphisms (SNP) was determined by polymerase chain reaction assay for 100 de novo HCV-related HCC patients, 100 chronic hepatitis C-related liver cirrhosis patients, and 150 healthy controls. RESULTS DR4-A1322G polymorphic genotypes (AG and GG) were significantly higher in HCC and cirrhotic patients than controls. The AG genotype conferred two-fold increased risk of HCC (odds ratio [OR], 2.34; 95% confidence interval [CI], 1.56-3.51) and the risk increased to three-fold for the GG genotype (OR, 3.51; 95%CI, 2.33-5.28). The frequency of DR4-C626G and -A683C SNPs in HCC and cirrhotic patients were not significantly different from the controls. Combined genotype analysis showed that coinheritance of the polymorphic genotypes of DR4-C626G and -A1322G conferred nine-fold increased risk of HCC (OR, 9.34; 95%CI, 3.76-23.12). The risk increased to be 12-fold when DR4-A683C and -A1322G variants were coinherited (OR, 11.9; 95%CI, 4.82-29.39). Coexistence of the variant genotypes of the three SNPs conferred almost 10-fold increased risk of HCC (OR, 9.75; 95%CI, 1.86-51.19). CONCLUSIONS The G allele of DR4 -A1322G could be considered as a novel independent molecular predictor for HCV-related HCC in the Egyptian population.
Collapse
Affiliation(s)
- Shahira Amin Zayed
- Department of Clinical & Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nariman M Zahran
- Department of Clinical & Chemical Pathology, Hematology Laboratory, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Mervat Mamdooh Khorshied
- Department of Clinical & Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ashraf Omar Abdel-Aziz
- Department of Endemic medicine and Hepato-gastroenterology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ola Mahmoud
- Department of Clinical & Chemical Pathology, Hematology Laboratory, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Shereif Ahmed Morsy
- Department Tropical and Internal Medicine, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Hend Ibrahim Shousha
- Department of Endemic Medicine and Hepato-gastroenterology, Faculty of medicine, Cairo University, Cairo, Egypt
| | - Tamer Mahmoud Elbaz
- Department of Endemic Medicine and Hepato-gastroenterology, Cairo University, Cairo, Egypt
| | | | | |
Collapse
|
7
|
Bashash M, Connors JM, Gascoyne RD, Meissner B, Schuetz JM, Leach S, Slack GW, Berry BR, Hu H, Sehn LH, Brooks-Wilson AR, Spinelli JJ. Genetic polymorphism at BCL2 as a predictor for rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone efficacy in patients with diffuse large B-cell lymphoma. Haematologica 2017; 102:e199-e202. [PMID: 28154089 DOI: 10.3324/haematol.2016.159087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Morteza Bashash
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada.,Dalla Lana School of Public Health, University of Toronto, ON, Canada
| | - Joseph M Connors
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Randy D Gascoyne
- Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Barbara Meissner
- Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Johanna M Schuetz
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Stephen Leach
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Graham W Slack
- Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Brian R Berry
- Department of Pathology, Royal Jubilee Hospital, Victoria, BC, Canada
| | - Howard Hu
- Dalla Lana School of Public Health, University of Toronto, ON, Canada
| | - Laurie H Sehn
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology, Royal Jubilee Hospital, Victoria, BC, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - John J Spinelli
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada .,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
8
|
Bradshaw G, Sutherland HG, Haupt LM, Griffiths LR. Dysregulated MicroRNA Expression Profiles and Potential Cellular, Circulating and Polymorphic Biomarkers in Non-Hodgkin Lymphoma. Genes (Basel) 2016; 7:genes7120130. [PMID: 27999330 PMCID: PMC5192506 DOI: 10.3390/genes7120130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023] Open
Abstract
A large number of studies have focused on identifying molecular biomarkers, including microRNAs (miRNAs) to aid in the diagnosis and prognosis of the most common subtypes of non-Hodgkin lymphoma (NHL), Diffuse Large B-cell Lymphoma and Follicular Lymphoma. NHL is difficult to diagnose and treat with many cases becoming resistant to chemotherapy, hence the need to identify improved biomarkers to aid in both diagnosis and treatment modalities. This review summarises more recent research on the dysregulated miRNA expression profiles found in NHL, as well as the regulatory role and biomarker potential of cellular and circulating miRNAs found in tissue and serum, respectively. In addition, the emerging field of research focusing on miRNA single nucleotide polymorphisms (miRSNPs) in genes of the miRNA biogenesis pathway, in miRNA genes themselves, and in their target sites may provide new insights on gene expression changes in these genes. These miRSNPs may impact miRNA networks and have been shown to play a role in a host of different cancer types including haematological malignancies. With respect to NHL, a number of SNPs in miRNA-binding sites in target genes have been shown to be associated with overall survival.
Collapse
Affiliation(s)
- Gabrielle Bradshaw
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| |
Collapse
|
9
|
Du L, Liu Y, Xue P, Song C, Shen J, He Q, Peng Y, Tong X, Tang L, Zhang Y. The Arg399Gln polymorphism in the XRCC1 gene is associated with increased risk of hematological malignancies. Tumour Biol 2015; 36:4545-54. [DOI: 10.1007/s13277-015-3099-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/03/2014] [Indexed: 12/11/2022] Open
|
10
|
Dzikiewicz-Krawczyk A. MicroRNA polymorphisms as markers of risk, prognosis and treatment response in hematological malignancies. Crit Rev Oncol Hematol 2014; 93:1-17. [PMID: 25217091 DOI: 10.1016/j.critrevonc.2014.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 12/26/2022] Open
Abstract
MicroRNA dysregulation is a common event in hematological malignancies. Apart from genomic and epigenetic alterations, miRNA networks may be disturbed by polymorphisms in the miRNA regulatory pathway (miRSNPs). In this review we provide an overview of three categories of miRSNPs: (1) SNPs in genes involved in miRNA biogenesis and processing; (2) SNPs in miRNA genes; and (3) SNPs in miRNA binding sites in target genes and discuss their potential role as markers of disease risk, prognosis and treatment response in hematological cancers. Although so far only the tip of the iceberg has been touched, studies of polymorphisms in the miRNA regulatory pathways have already provided some clues for the mechanisms of miRNA dysregulation in cancer and open new perspectives in the management of hematological malignancies.
Collapse
|
11
|
Toll-like receptor 2 and 9 genetic polymorphisms and the susceptibility to B cell Non-Hodgkin Lymphoma in Egypt. Ann Hematol 2014; 93:1859-65. [PMID: 24912772 DOI: 10.1007/s00277-014-2131-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
Non-Hodgkin lymphomas (NHL) entail considerable heterogeneity regarding their morphology, clinical course, etiological factors, or response to therapy. Increased incidence of NHL in immunocompromised individuals and after autoimmune diseases suggests that infections and immune dysregulation could play a role in the susceptibility to NHL. Accordingly, genetic variation in Toll-like receptor (TLR) genes might be considered as molecular risk factors for NHL. The aim of the current study was to investigate the possible association between genetic polymorphism of the TLRs genes and B cell NHL (B-NHL) risk in Egypt. The present study included 100 B-NHL patients and 100 healthy controls. Genotyping of TLR2-1350 T/C and TLR9-1237 T/C were done by polymerase chain reaction restricted fragment length polymorphism (PCR-RFLP) technique. The frequency of TLR2-1350 T/C polymorphic genotypes in B-NHL patients was 18 % for the heteromutant genotype (TC) and 1 % for the homomutant (CC). There was no statistical difference in the distribution of TLR2-1350 T/C genotypes between B-NHL patients and controls. As for TLR9-1237 T/C, the frequency of the heteromutant genotype (TC) was 58 % and the homomutant genotype (CC) was 1 % in B-NHL patients. Calculated risk estimation revealed that TLR9-1237 (TC) heterotype conferred almost fourfold increased risk of B-NHL (odds ratio (OR) = 3.93, 95 % confidence interval (CI) = 2.16-7.14), and the risk was higher in patients with indolent subtypes (OR = 6.64, 95 %CI = 2.31-9.08). In conclusion, the study revealed that TLR9-1237 T/C polymorphism can be considered as molecular risk factor for B-NHL among Egyptians.
Collapse
|
12
|
Sieni E, Cetica V, Hackmann Y, Coniglio ML, Da Ros M, Ciambotti B, Pende D, Griffiths G, Aricò M. Familial hemophagocytic lymphohistiocytosis: when rare diseases shed light on immune system functioning. Front Immunol 2014; 5:167. [PMID: 24795715 PMCID: PMC3997030 DOI: 10.3389/fimmu.2014.00167] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/29/2014] [Indexed: 12/03/2022] Open
Abstract
The human immune system depends on the activity of cytotoxic T lymphocytes (CTL), natural killer (NK) cells, and NKT cells in order to fight off a viral infection. Understanding the molecular mechanisms during this process and the role of individual proteins was greatly improved by the study of familial hemophagocytic lymphohistiocytosis (FHL). Since 1999, genetic sequencing is the gold standard to classify patients into different subgroups of FHL. The diagnosis, once based on a clinical constellation of abnormalities, is now strongly supported by the results of a functional flow-cytometry screening, which directs the genetic study. A few additional congenital immune deficiencies can also cause a resembling or even identical clinical picture to FHL. As in many other rare human disorders, the collection and analysis of a relatively large number of cases in registries is crucial to draw a complete picture of the disease. The conduction of prospective therapeutic trials allows investigators to increase the awareness of the disease and to speed up the diagnostic process, but also provides important functional and genetic confirmations. Children with confirmed diagnosis may undergo hematopoietic stem cell transplantation, which is the only cure known to date. Moreover, detailed characterization of these rare patients helped to understand the function of individual proteins within the exocytic machinery of CTL, NK, and NKT cells. Moreover, identification of these genotypes also provides valuable information on variant phenotypes, other than FHL, associated with biallelic and monoallelic mutations in the FHL-related genes. In this review, we describe how detailed characterization of patients with genetic hemophagocytic lymphohistiocytosis has resulted in improvement in knowledge regarding contribution of individual proteins to the functional machinery of cytotoxic T- and NK-cells. The review also details how identification of these genotypes has provided valuable information on variant phenotypes.
Collapse
Affiliation(s)
- Elena Sieni
- Department Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria Meyer Children Hospital , Florence , Italy
| | - Valentina Cetica
- Department Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria Meyer Children Hospital , Florence , Italy ; Pediatric Hematology Oncology Network, Istituto Toscano Tumori (I.T.T.) , Florence , Italy
| | - Yvonne Hackmann
- Cambridge Institute for Medical Research, University of Cambridge Biomedical Campus , Cambridge , UK
| | - Maria Luisa Coniglio
- Department Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria Meyer Children Hospital , Florence , Italy
| | - Martina Da Ros
- Department Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria Meyer Children Hospital , Florence , Italy
| | - Benedetta Ciambotti
- Department Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria Meyer Children Hospital , Florence , Italy
| | - Daniela Pende
- Istituto di Ricovero e Cura a Carattere Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Nazionale per la Ricerca sul Cancro , Genoa , Italy
| | - Gillian Griffiths
- Cambridge Institute for Medical Research, University of Cambridge Biomedical Campus , Cambridge , UK
| | - Maurizio Aricò
- Pediatric Hematology Oncology Network, Istituto Toscano Tumori (I.T.T.) , Florence , Italy
| |
Collapse
|
13
|
Xie Y, Diao L, Zhang L, Liu C, Xu Z, Liu S. A miR-SNP of the KRT81 gene is associated with the prognosis of non-Hodgkin's lymphoma. Gene 2014; 539:198-202. [PMID: 24530479 DOI: 10.1016/j.gene.2014.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022]
Abstract
MicroRNA (miRNA), which plays an important role in tumorigenesis, can regulate post-transcriptional gene expression by binding to the 3' untranslated regions (3'-UTRs) of messenger RNAs and repressing its translation. Several single nucleotide polymorphisms (SNPs) are considered to have significant impacts on susceptibility of the role these genetic polymorphisms in development of carcinogenesis through that mechanism. But few of them focus their impact on non-Hodgkin's lymphoma (NHL). Therefore, we conducted this study to investigate the associations between the genetic variants and cancer risk or cancer outcome. MiRNA-related single nucleotide polymorphism (miR-SNP) sites rs3660 of KRT81, rs1044129 of RYR3, rs4901706 of f101, and rs1053667 of KIAA0423 were selected and analyzed in 210 patients in NHL to evaluate their association with cancer risk and prognosis. The results indicated that none of them is associated with the cancer risk in NHL. Otherwise KRT81 rs3660 GG type is associated with a shorter survival time (p=0.012), after being assessed by multivariate Cox analyses, its effect on prognosis was verified (p=0.003). It suggests that KRT81 rs3660 GG type is an independent prognostic marker in NHL.
Collapse
Affiliation(s)
- Ying Xie
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Lanping Diao
- Department of Hematology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Li Zhang
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Chao Liu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Zengnian Xu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Shufeng Liu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China.
| |
Collapse
|
14
|
Schuetz JM, Daley D, Leach S, Conde L, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Bracci PM, Skibola CF, Spinelli JJ, Brooks-Wilson AR. Non-Hodgkin lymphoma risk and variants in genes controlling lymphocyte development. PLoS One 2013; 8:e75170. [PMID: 24098683 PMCID: PMC3787098 DOI: 10.1371/journal.pone.0075170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
Non-Hodgkin lymphomas (NHL) are a heterogeneous group of solid tumours of lymphoid cell origin. Three important aspects of lymphocyte development include immunity and inflammation, DNA repair, and programmed cell death. We have used a previously established case-control study of NHL to ask whether genetic variation in genes involved in these three important processes influences risk of this cancer. 118 genes in these three categories were tagged with single nucleotide polymorphisms (SNPs), which were tested for association with NHL and its subtypes. The main analysis used logistic regression (additive model) to estimate odds ratios in European-ancestry cases and controls. 599 SNPs and 1116 samples (569 cases and 547 controls) passed quality control measures and were included in analyses. Following multiple-testing correction, one SNP in MSH3, a mismatch repair gene, showed an association with diffuse large B-cell lymphoma (OR: 1.91; 95% CI: 1.41–2.59; uncorrected p = 0.00003; corrected p = 0.010). This association was not replicated in an independent European-ancestry sample set of 251 diffuse large B-cell lymphoma cases and 737 controls, indicating this result was likely a false positive. It is likely that moderate sample size, inter-subtype and other genetic heterogeneity, and small true effect sizes account for the lack of replicable findings.
Collapse
Affiliation(s)
- Johanna M. Schuetz
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Denise Daley
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen Leach
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Lucia Conde
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brian R. Berry
- Department of Pathology, Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | | | - Joseph M. Connors
- Division of Medical Oncology and Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Randy D. Gascoyne
- Department of Pathology and Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Christine F. Skibola
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John J. Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela R Brooks-Wilson
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
| |
Collapse
|
15
|
Bretherick KL, Schuetz JM, Morton LM, Purdue MP, Conde L, Gallagher RP, Connors JM, Gascoyne RD, Berry BR, Armstrong B, Kricker A, Vajdic CM, Grulich A, Hjalgrim H, Smedby KE, Skibola CF, Rothman N, Spinelli JJ, Brooks-Wilson AR. Sex- and subtype-specific analysis of H2AFX polymorphisms in non-Hodgkin lymphoma. PLoS One 2013; 8:e74619. [PMID: 24069324 PMCID: PMC3775730 DOI: 10.1371/journal.pone.0074619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/03/2013] [Indexed: 11/21/2022] Open
Abstract
H2AFX encodes a histone variant involved in signaling sites of DNA damage and recruiting repair factors. Genetic variants in H2AFX may influence risk of non-Hodgkin lymphoma (NHL), a heterogeneous group of lymphoid tumors that are characterized by chromosomal translocations. We previously reported that rs2509049, a common variant in the promoter of H2AFX, was associated with risk for NHL in the British Columbia population. Here we report results for 13 single nucleotide polymorphisms (SNPs) in 100 Kb surrounding H2AFX in an expanded collection of 568 NHL cases and 547 controls. After correction for multiple testing, significant associations were present for mantle cell lymphoma (p=0.007 for rs604714) and all B-cell lymphomas (p=0.046 for rs2509049). Strong linkage disequilibrium in the 5 Kb upstream of H2AFX limited the ability to determine which specific SNP (rs2509049, rs7759, rs8551, rs643788, rs604714, or rs603826), if any, was responsible. There was a significant interaction between sex and rs2509049 in the all B-cell lymphomas group (p=0.002); a sex-stratified analysis revealed that the association was confined to females (p=0.001). Neither the overall nor the female-specific association with rs2509049 was replicated in any of four independent NHL sample sets. Meta-analysis of all five study populations (3,882 B-cell NHL cases and 3,718 controls) supported a weak association with B-cell lymphoma (OR=0.92, 95% CI=0.86-0.99, p=0.034), although this association was not significant after exclusion of the British Columbia data. Further research into the potential sex-specificity of the H2AFX-NHL association may identify a subset of NHL cases that are influenced by genotype at this locus.
Collapse
Affiliation(s)
- Karla L. Bretherick
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Johanna M. Schuetz
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Lucia Conde
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California, United States of America
| | | | - Joseph M. Connors
- Division of Medical Oncology and Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Randy D. Gascoyne
- Department of Pathology and Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Brian R. Berry
- Department of Pathology, Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Bruce Armstrong
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Claire M. Vajdic
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, Faculty of Medicine at the University of New South Wales, Sydney, Australia
| | - Andrew Grulich
- The Kirby Institute for infection and immunity in society, University of New South Wales, New South Wales, Australia
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Karin E. Smedby
- Unit of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden
| | - Christine F. Skibola
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California, United States of America
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - John J. Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela R. Brooks-Wilson
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
| |
Collapse
|
16
|
Wu XJ, Mi YY, Yang H, Hu AK, Li C, Li XD, Zhang QG. Association of the hsa-mir-499 (rs3746444) polymorphisms with gastric cancer risk in the Chinese population. ACTA ACUST UNITED AC 2013; 36:573-6. [PMID: 24107911 DOI: 10.1159/000355518] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) in microRNAs (miRNA) have been shown to be related with susceptibility to several human cancers. We evaluated the associations of rs3746444 in pre-miRNA hsa-mir-499 with the risk of gastric cancer (GC) in the Chinese population. PATIENTS AND METHODS The rs3746444 (A>G) SNPs were genotyped in 201 GC and 213 non-cancer subjects in a case-control study by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. RESULTS There was no significant overall difference in the genotype distributions of rs3746444 (A>G) SNPs between cases and controls. In the logistic regression analyses, no significantly increased risk of GC was found to be associated with variant genotypes. CONCLUSION The rs3746444 (A>G) SNP is not associated with susceptibility to GC in the Chinese population.
Collapse
Affiliation(s)
- Xiao-Jin Wu
- Department of Radiation Oncology, The First People's Hospital of Xuzhou, China
| | | | | | | | | | | | | |
Collapse
|
17
|
Kuan YC, Wu YJ, Hung CL, Sheu F. Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model. PLoS One 2013; 8:e72422. [PMID: 24019869 PMCID: PMC3760908 DOI: 10.1371/journal.pone.0072422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 07/10/2013] [Indexed: 12/31/2022] Open
Abstract
Background Trametes versicolor (Yun-Zhi) is a medicinal fungus used as a chemotherapy co-treatment to enhance anti-tumor immunity. Although the efficacies of T. versicolor extracts have been documented, the active ingredients and mechanisms underlying the actions of these extracts remain uncharacterized. Results We purified a new protein, YZP, from the fruiting bodies of T. versicolor and identified the gene encoding YZP using RNA-seq and de novo assembly technologies. YZP is a 12-kDa non-glycosylated protein comprising 139 amino acids, including an 18-amino acids signal peptide. YZP induced a greater than 60-fold increase in IL-10 secretion in mice B lymphocytes; moreover, YZP specifically triggered the differentiation of CD1d+ B cells into IL-10-producing regulatory B cells (Bregs) and enhanced the expression of CD1d. YZP-induced B cells suppressed approximately 40% of the LPS-activated macrophage production of inflammatory cytokines in a mixed leukocyte reaction and significantly alleviated the disease activity and colonic inflammation in a DSS-induced acute colitis murine model. Furthermore, YZP activated Breg function via interaction with TLR2 and TLR4 and up-regulation of the TLR-mediated signaling pathway. Conclusions We purified a novel Breg-stimulating protein, YZP, from T. versicolor and developed an advanced approach combining RNA-seq and de novo assembly technologies.to clone its gene. We demonstrated that YZP activated CD1d+ Breg differentiation through TLR2/4-mediated signaling pathway, and the YZP-stimulated B cells exhibited anti-inflammatory efficacies in vitro and in murine acute colitis models.
Collapse
Affiliation(s)
- Yen-Chou Kuan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Horticulture, National Taiwan University, Taipei, Taiwan
| | - Ying-Jou Wu
- Department of Horticulture, National Taiwan University, Taipei, Taiwan
| | - Chih-Liang Hung
- Department of Horticulture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Horticulture, National Taiwan University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
18
|
Grundy A, Schuetz JM, Lai AS, Janoo-Gilani R, Leach S, Burstyn I, Richardson H, Brooks-Wilson A, Spinelli JJ, Aronson KJ. Shift work, circadian gene variants and risk of breast cancer. Cancer Epidemiol 2013; 37:606-12. [PMID: 23725643 DOI: 10.1016/j.canep.2013.04.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/26/2022]
Abstract
Circadian (clock) genes have been linked with several functions relevant to cancer, and epidemiologic research has suggested relationships with breast cancer risk for variants in NPAS2, CLOCK, CRY2 and TIMELESS. Increased breast cancer risk has also been observed among shift workers, suggesting potential interactions in relationships of circadian genes with breast cancer. Relationships with breast cancer of 100 SNPs in 14 clock-related genes, as well as potential interactions with shift work history, were investigated in a case-control study (1042 cases, 1051 controls). Odds ratios in an additive genetic model for European-ancestry participants (645 cases, 806 controls) were calculated, using a two-step correction for multiple testing: within each gene through permutation testing (10,000 permutations), and correcting for the false discovery rate across genes. Interactions of genotypes with ethnicity and shift work (<2 years vs ≥2 years) were evaluated individually. Following permutation analysis, two SNPs (rs3816360 in ARNTL and rs11113179 in CRY1) displayed significant associations with breast cancer and one SNP (rs3027188 in PER1) was marginally significant; however, none were significant following adjustment for the false discovery rate. No significant interaction with shift work history was detected. If shift work causes circadian disruption, this was not reflected in associations between clock gene variants and breast cancer risk in this study. Larger studies are needed to assess interactions with longer durations (>30 years) of shift work that have been associated with breast cancer.
Collapse
Affiliation(s)
- Anne Grundy
- Department of Community Health and Epidemiology and Queen's Cancer Research Institute, Queen's University, 10 Stuart Street, Kingston, Ontario, Canada K7L 3N6
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Nembot-Simo A, Graham J, McNeney B. CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals. SOURCE CODE FOR BIOLOGY AND MEDICINE 2013; 8:5. [PMID: 23384435 PMCID: PMC3764977 DOI: 10.1186/1751-0473-8-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022]
Abstract
Background In population association studies, standard methods of statistical inference
assume that study subjects are independent samples. In genetic association
studies, it is therefore of interest to diagnose undocumented close relationships
in nominally unrelated study samples. Results We describe the R package CrypticIBDcheck to identify pairs of
closely-related subjects based on genetic marker data from single-nucleotide
polymorphisms (SNPs). The package is able to accommodate SNPs in linkage
disequibrium (LD), without the need to thin the markers so that they are
approximately independent in the population. Sample pairs are identified by
superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD
coefficients for pairs of simulated subjects from one of several common close
relationships. Conclusions The methods implemented in CrypticIBDcheck are particularly relevant to
candidate-gene association studies, in which dependent SNPs cluster in a
relatively small number of genes spread throughout the genome. The accommodation
of LD allows the use of all available genetic data, a desirable property when
working with a modest number of dependent SNPs within candidate genes.
CrypticIBDcheck is available from the Comprehensive R Archive Network
(CRAN).
Collapse
Affiliation(s)
- Annick Nembot-Simo
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, Canada.
| | | | | |
Collapse
|
20
|
Srivastava K, Srivastava A. Comprehensive review of genetic association studies and meta-analyses on miRNA polymorphisms and cancer risk. PLoS One 2012; 7:e50966. [PMID: 23226435 PMCID: PMC3511416 DOI: 10.1371/journal.pone.0050966] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 10/29/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small RNA molecules that regulate the expression of corresponding messenger RNAs (mRNAs). Variations in the level of expression of distinct miRNAs have been observed in the genesis, progression and prognosis of multiple human malignancies. The present study was aimed to investigate the association between four highly studied miRNA polymorphisms (mir-146a rs2910164, mir-196a2 rs11614913, mir-149 rs2292832 and mir-499 rs3746444) and cancer risk by using a two-sided meta-analytic approach. METHODS An updated meta-analysis based on 53 independent case-control studies consisting of 27573 cancer cases and 34791 controls was performed. Odds ratio (OR) and 95% confidence interval (95% CI) were used to investigate the strength of the association. RESULTS Overall, the pooled analysis showed that mir-196a2 rs11614913 was associated with a decreased cancer risk (OR = 0.846, P = 0.004, TT vs. CC) while other miRNA SNPs showed no association with overall cancer risk. Subgroup analyses based on type of cancer and ethnicity were also performed, and results indicated that there was a strong association between miR-146a rs2910164 and overall cancer risk in Caucasian population under recessive model (OR = 1.274, 95%CI = 1.096-1.481, P = 0.002). Stratified analysis by cancer type also associated mir-196a2 rs11614913 with lung and colorectal cancer at allelic and genotypic level. CONCLUSIONS The present meta-analysis suggests an important role of mir-196a2 rs11614913 polymorphism with overall cancer risk especially in Asian population. Further studies with large sample size are needed to evaluate and confirm this association.
Collapse
Affiliation(s)
- Kshitij Srivastava
- Medical Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA.
| | | |
Collapse
|