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Garg P, Jadhav B, Lee W, Rodriguez OL, Martin-Trujillo A, Sharp AJ. A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits. Am J Hum Genet 2022; 109:1065-1076. [PMID: 35609568 PMCID: PMC9247821 DOI: 10.1016/j.ajhg.2022.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/28/2022] [Indexed: 01/04/2023] Open
Abstract
The human genome contains tens of thousands of large tandem repeats and hundreds of genes that show common and highly variable copy-number changes. Due to their large size and repetitive nature, these variable number tandem repeats (VNTRs) and multicopy genes are generally recalcitrant to standard genotyping approaches and, as a result, this class of variation is poorly characterized. However, several recent studies have demonstrated that copy-number variation of VNTRs can modify local gene expression, epigenetics, and human traits, indicating that many have a functional role. Here, using read depth from whole-genome sequencing to profile copy number, we report results of a phenome-wide association study (PheWAS) of VNTRs and multicopy genes in a discovery cohort of ∼35,000 samples, identifying 32 traits associated with copy number of 38 VNTRs and multicopy genes at 1% FDR. We replicated many of these signals in an independent cohort and observed that VNTRs showing trait associations were significantly enriched for expression QTLs with nearby genes, providing strong support for our results. Fine-mapping studies indicated that in the majority (∼90%) of cases, the VNTRs and multicopy genes we identified represent the causal variants underlying the observed associations. Furthermore, several lie in regions where prior SNV-based GWASs have failed to identify any significant associations with these traits. Our study indicates that copy number of VNTRs and multicopy genes contributes to diverse human traits and suggests that complex structural variants potentially explain some of the so-called "missing heritability" of SNV-based GWASs.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - William Lee
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA.
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Tekcan A, Yigit S, Nursal AF, Tumer MK, Yerliyurt K, Kuruca N. Analysis of Interleukin-1 Receptor Antagonist Variable Number Tandem Repeat Variant in Recurrent Aphthous Stomatitis. Endocr Metab Immune Disord Drug Targets 2021; 21:139-144. [PMID: 32282310 DOI: 10.2174/1871530320666200413092239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND/AIMS Recurrent aphthous stomatitis (RAS) is one of the common oral inflammatory diseases. As immunological and genetic factors have been held responsible for the pathogenesis of RAS, the objective of this study was to determine whether the interleukin-1 receptor antagonist (IL-1Ra) gene variable number tandem repeat (VNTR) variant is a risk factor for the development of RAS in Turkish patients and to define its contribution to the increased risk. METHODS The IL-1Ra VNTR variant was evaluated in 169 RAS patients and 171 healthy controls by the polymerase chain reaction (PCR) method. RESULTS No statistically significant difference was found in the genotype distributions and allele frequencies of IL-1Ra VNTR variant between RAS patients and healthy controls. CONCLUSION Lack of association between IL-1Ra VNTR variant and RAS could indicate that IL-1Ra has no significant role in the pathophysiology of RAS. However, it still appears to be very worthwhile to continue to search for cytokine gene variants in order to predict the development of such disease.
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Affiliation(s)
- Akin Tekcan
- Department of Medical Biology, Faculty of Medicine, Amasya University, Amasya, Turkey
| | - Serbulent Yigit
- Gaziosmanpasa University, Faculty of Medicine, Department of Medical Biology, Tokat, Turkey
| | - Ayse F Nursal
- Hitit University, Faculty of Medicine, Department of Medical Genetics, Corum, Turkey
| | - Mehmet K Tumer
- Gaziosmanpasa University, Faculty of Dentistry, Department of Maxillofacial Surgery, Tokat, Turkey
| | - Kaan Yerliyurt
- Gaziosmanpasa University, Faculty of Dentistry, Department of Prosthodontics, Tokat, Turkey
| | - Nilufer Kuruca
- Ondokuz Mayıs University, Faculty of Veterinary Medicine, Department of Pathology, Samsun, Turkey
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Magee M, Sletten TL, Murray JM, Gordon CJ, Lovato N, Bartlett DJ, Kennaway DJ, Lockley SW, Lack LC, Grunstein RR, Archer SN, Rajaratnam SMW. A PERIOD3 variable number tandem repeat polymorphism modulates melatonin treatment response in delayed sleep-wake phase disorder. J Pineal Res 2020; 69:e12684. [PMID: 32682347 DOI: 10.1111/jpi.12684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022]
Abstract
We examined whether a polymorphism of the PERIOD3 gene (PER3; rs57875989) modulated the sleep-promoting effects of melatonin in Delayed Sleep-Wake Phase Disorder (DSWPD). One hundred and four individuals (53 males; 29.4 ±10.0 years) with DSWPD and a delayed dim light melatonin onset (DLMO) collected buccal swabs for genotyping (PER34/4 n = 43; PER3 5 allele [heterozygous and homozygous] n = 60). Participants were randomised to placebo or 0.5 mg melatonin taken 1 hour before desired bedtime (or ~1.45 hours before DLMO), with sleep attempted at desired bedtime (4 weeks; 5-7 nights/week). We assessed sleep (diary and actigraphy), Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), Patient-Reported Outcomes Measurement Information System (PROMIS: Sleep Disturbance, Sleep-Related Impairment), Sheehan Disability Scale (SDS) and Patient- and Clinician-Global Improvement (PGI-C, CGI-C). Melatonin treatment response on actigraphic sleep onset time did not differ between genotypes. For PER34/4 carriers, self-reported sleep onset time was advanced by a larger amount and sleep onset latency (SOL) was shorter in melatonin-treated patients compared to those receiving placebo (P = .008), while actigraphic sleep efficiency in the first third of the sleep episode (SE T1) did not differ. For PER3 5 carriers, actigraphic SOL and SE T1 showed a larger improvement with melatonin (P < .001). Melatonin improved ISI (P = .005), PROMIS sleep disturbance (P < .001) and sleep-related impairment (P = .017), SDS (P = .019), PGI-C (P = .028) and CGI-C (P = .016) in PER34/4 individuals only. Melatonin did not advance circadian phase. Overall, PER34/4 DSWPD patients have a greater response to melatonin treatment. PER3 genotyping may therefore improve DSWPD patient outcomes.
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Affiliation(s)
- Michelle Magee
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Centre for Neuroscience of Speech, Department of Audiology and Speech Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Tracey L Sletten
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
| | - Jade M Murray
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
| | - Christopher J Gordon
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
- Sydney Nursing School, The University of Sydney, Sydney, NSW, Australia
| | - Nicole Lovato
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Adelaide Institute for Sleep Health: A Flinders Centre of Research Excellence, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Delwyn J Bartlett
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - David J Kennaway
- Robinson Research Institute, Adelaide School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Steven W Lockley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Leon C Lack
- Adelaide Institute for Sleep Health: A Flinders Centre of Research Excellence, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Ronald R Grunstein
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Simon N Archer
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Shantha M W Rajaratnam
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
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Lee HE, Park SJ, Huh JW, Imai H, Kim HS. Enhancer Function of MicroRNA-3681 Derived from Long Terminal Repeats Represses the Activity of Variable Number Tandem Repeats in the 3' UTR of SHISA7. Mol Cells 2020; 43:607-618. [PMID: 32655015 PMCID: PMC7398795 DOI: 10.14348/molcells.2020.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023] Open
Abstract
microRNAs (miRNAs) are non-coding RNA molecules involved in the regulation of gene expression. miRNAs inhibit gene expression by binding to the 3' untranslated region (UTR) of their target gene. miRNAs can originate from transposable elements (TEs), which comprise approximately half of the eukaryotic genome and one type of TE, called the long terminal repeat (LTR) is found in class of retrotransposons. Amongst the miRNAs derived from LTR, hsa-miR-3681 was chosen and analyzed using bioinformatics tools and experimental analysis. Studies on hsa-miR-3681 have been scarce and this study provides the relative expression analysis of hsa-miR-3681-5p from humans, chimpanzees, crab-eating monkeys, and mice. Luciferase assay for hsa-miR-3681-5p and its target gene SHISA7 supports our hypothesis that the number of miRNA binding sites affects target gene expression. Especially, the variable number tandem repeat (VNTR) and hsa-miR-3681-5p share the binding sites in the 3' UTR of SHISA7, which leads the enhancer function of hsa-miR-3681-5p to inhibit the activity of VNTR. In conclusion, hsa-miR-3681-5p acts as a super-enhancer and the enhancer function of hsa-miR-3681-5p acts as a repressor of VNTR activity in the 3' UTR of SHISA7.
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Affiliation(s)
- Hee-Eun Lee
- Department of Integrated Biological Science, Pusan National University, Busan 4624, Korea
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon 3113, Korea
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama 484-806, Japan
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 4241, Korea
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ANLIAÇIK SÖ, TOKGÖZ S, ZAMANİ AG, YILDIRIM MS, İYİSOY MS. Investigation of the relationship between ischemic stroke and endothelial nitric oxide synthase gene polymorphisms [G894T, intron 4 VNTR and T786C]. Turk J Med Sci 2019; 49:589-594. [PMID: 30997974 PMCID: PMC7018372 DOI: 10.3906/sag-1808-57] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background/aim We aimed to investigate the associations between endothelial nitric oxide synthase (eNOS) gene polymorphisms [G894T (rs1799983)], intron 4 (27-bpTR) variable number tandem repeat (VNTR) and T786C (rs2070744), and ischemic stroke in the Anatolian population. Materials and methods This case-control study included 112 patients with “stroke of undetermined etiology” and 160 controls. Real-time polymerase chain reaction (RT-PCR) analysis was used to analyze these polymorphisms. Between-group frequencies of alleles and genotypes were compared using binary logistic regression analysis. Results No significant difference was observed between the two groups in terms of the genotype and allele distributions of the eNOS G894T (rs1799983) polymorphism (P > 0.05). The a alleles and the 4b/a and 4a/a genotypes of the intron 4 (27-bpTR) VNTR polymorphism had significantly higher frequencies in the patient group than in the control group (OR: 2.715, P < 0.001; OR: 3.396, P < 0.001; OR: 10.631, P = 0.016, respectively). On the contrary, the TC genotype and C alleles of the T786C (rs2070744) polymorphism had a significantly lower frequency in the patient group than in the control group (OR: 0.244, P < 0.001, OR: 0.605, P = 0.006, respectively). Conclusion Our findings indicate that the eNOS G894T and T786C [rs2070744] polymorphisms are not associated with the risk of ischemic stroke, whereas the intron 4 [27-bpTR] VNTR may be a risk factor in the Anatolian population.
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Affiliation(s)
- Süleyman Ömer ANLIAÇIK
- Department of Neurology, Meram Medical Faculty, Necmettin Erbakan University, KonyaTurkey
| | - Serhat TOKGÖZ
- Department of Neurology, Meram Medical Faculty, Necmettin Erbakan University, KonyaTurkey
- * To whom correspondence should be addressed. E-mail:
| | - Ayşe Gül ZAMANİ
- Department of Molecular Biology and Genetics, Meram Medical Faculty, Necmettin Erbakan University, KonyaTurkey
| | - Mahmut Selman YILDIRIM
- Department of Molecular Biology and Genetics, Meram Medical Faculty, Necmettin Erbakan University, KonyaTurkey
| | - Mehmet Sinan İYİSOY
- Department of Medical Education and Informatics, Meram Medical Faculty, Necmettin Erbakan University, KonyaTurkey
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Abstract
OBJECTIVE The results of published studies which examined the association between variable number tandem repeat (VNTR) polymorphism of interleukin-1 receptor antagonist (IL-1RN) and ischemic stroke (IS) are conflicting. Thus, we performed a meta-analysis to examine the potential association between IL-1RN VNTR polymorphism and IS risk. METHODS A systematic literature search of PubMed, Embase, Medline, Web of Science, Cochrane Library, Chinese Biomedical Literature Database, Chinese National Knowledge Infrastructure, CQVIP, and WANFANG Database identified 10 studies with 2331 cases and 3335 controls. The pooled odds ratio (OR) with 95% confidence interval (95% CI) was calculated to evaluate the strength of the association. Subgroup analysis and meta-regression analysis were used to investigate the potential sources of heterogeneity. Begg funnel plots were used to explore the publication bias. RESULTS In this study, no enough proof was found to prove the association between IL-1RN 86-bp VNTR polymorphism and IS risk with random-effects model in the homozygous model (1/1 vs 2/2, OR = 0.97, 95% CI = 0.50-1.87, Pheterogeneity = .00), the heterozygous model (1/2 vs 2/2, OR = 0.64, 95% CI = 0.41-1.01, Pheterogeneity = .10), the dominant model (1/1 + 1/2 vs 2/2, OR = 0.85, 95% CI = 0.51-1.42, Pheterogeneity = .02), the recessive model (1/1 vs 1/2 + 2/2, OR = 0.69, 95% CI = 0.46-1.03, Pheterogeneity = .00), and allelic model (1 vs 2, OR = 1.24, 95% CI = 0.89-1.74, Pheterogeneity = .00). A marginally significant negative association was observed between IL-1RN 86-bp VNTR polymorphism and IS risk in the heterozygous model in the fixed-effects model (1/2 vs 2/2, OR = 0.71, 95% CI = 0.53-0.95, Pheterogeneity = .10). In subgroup analyses, similar association was found in the group whose control size was lower than 300. CONCLUSION In conclusion, our results suggested that there was no sufficient evidence to support the association between IL-1RN 86-bp VNTR polymorphism and IS. Further large epidemiologic studies need to be done to confirm these findings.
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Affiliation(s)
| | - Wenhui Wu
- Department of Hemodialysis, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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Dursun G, Nursal AF, Demir HD, Karakuş N, Demir O, Yiğit S. Investigation of the role of interleukin-1 receptor antagonist VNTR variant on the Behçet's disease. Eur J Rheumatol 2018; 5:27-31. [PMID: 29657871 DOI: 10.5152/eurjrheum.2017.16102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/22/2022] Open
Abstract
Objective Behçet's disease (BD), a chronic multisystem inflammatory disorder, is mainly characterized by relapsing periods of a wide range of clinical symptoms. Several cytokine genes may play important roles in the pathogenesis of BD. Therefore, interleukin-1 receptor antagonist (IL-1Ra) gene 86bp variable number tandem repeat (VNTR) variant was investigated in patients with BD in a Turkish population. Methods One hundred nine patients (60 females, 49 males; the mean age±standard deviation [SD] was 36.56±9.571 years) with BD and one hundred healthy individuals (54 females, 46 males; the mean age±SD was 36.64±2.294 years) were examined in the study. For genotyping, polymerase chain reaction-restriction fragment length polymorphism analysis was employed. Data were analyzed using Statistical Package for Social Sciences (SPSS) 22.0 (IBM Corp.; Armonk, NY, USA) (p<0.05). Results The genotype distribution and allele frequencies of the IL-1Ra VNTR variant did not differ significantly between the patients and the controls (p>0.05). The frequency of the a1/a1, a1/a2 genotypes and a1, a2 alleles were the most common both in patients and healthy controls (p=0.37, p=0.26, and p=0.53, respectively). Also, no statistically significant difference was found between the IL-1Ra VNTR variant genotypes and clinical characteristics (p>0.05). Conclusion The results of this study do not support an association between the IL-1Ra VNTR variant and the risk of BD in a Turkish population. However, further studies of this variant with larger sample sizes and different ethnicities are required for confirmation.
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Affiliation(s)
- Gül Dursun
- Department of Medical Biology, Gaziosmanpaşa University School of Medicine, Tokat, Turkey
| | - Ayşe Feyda Nursal
- Department of Medical Genetics, Hitit University School of Medicine, Çorum, Turkey
| | - Helin Deniz Demir
- Department of Opthalmology, Gaziosmanpaşa University School of Medicine, Tokat, Turkey
| | - Nevin Karakuş
- Department of Medical Biology, Gaziosmanpaşa University School of Medicine, Tokat, Turkey
| | - Osman Demir
- Department of Biostatistics, Gaziosmanpaşa University School of Medicine, Tokat, Turkey
| | - Serbülent Yiğit
- Department of Medical Biology, Gaziosmanpaşa University School of Medicine, Tokat, Turkey
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Li H, Anderson SK. Association of TNFRSF1B Promoter Polymorphisms with Human Disease: Further Studies Examining T-Regulatory Cells Are Required. Front Immunol 2018; 9:443. [PMID: 29559979 PMCID: PMC5845690 DOI: 10.3389/fimmu.2018.00443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/19/2018] [Indexed: 11/13/2022] Open
Abstract
The TNFR2 receptor is expressed by highly active regulatory T cells, and thus constitutes an important therapeutic target for the treatment of autoimmune disease and cancer. Disease susceptibility as well as the potential response to therapies directed at TNFR2 could be significantly impacted by genetic variation in the promoter of the TNFRSF1B gene that codes for the TNFR2 protein. To date, only a few studies have examined the association of TNFRSF1B promoter variation with disease, and the potential impact on T-regulatory cell (Treg) number and function has not been examined. We propose that copy number variation of a key transcription factor binding site has a significant effect on TNFRSF1B promoter activity, and should be considered in studies of disease susceptibility and especially with regard to variation in the level of TNFR2 expression on Tregs.
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Affiliation(s)
- Hongchuan Li
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen K Anderson
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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Abstract
MIR137 has been identified as a candidate gene for schizophrenia from genome-wide association studies via association with an intronic single nucleotide polymorphism (SNP), rs1625579. The location of the SNP suggests one mechanism in which transcriptional or posttranscriptional regulation of miR-137 expression could underlie schizophrenia. We identified and validated a novel promoter of the MIR137 gene adjacent to miR-137 itself which can direct the expression of distinct mRNA isoforms encoding miR-137. Analysis of both endogenous gene expression and reporter gene assays determined that this internal promoter is regulated by repressor element-1 silencing transcription factor (REST), which has previously been associated with pathways linked to schizophrenia. Distinct isoforms of REST mediate differential expression at this locus, suggesting the relative levels of these isoforms are important for miR-137 expression profiles. The internal promoter contains a variable number tandem repeat (VNTR) domain adjacent to the pre-miR-137 sequence. The reporter gene activity directed by this promoter was modified by the genotype of the VNTR. Differential expression was also observed in response to cocaine, which is known to regulate the REST pathway in SH-SY5Y cells. Our data support the hypothesis that a "gene × environment" interaction could modify the level of miR-137 expression via this internal promoter and that the genotype of the VNTR could modulate transcriptional responses. We demonstrate that this promoter region is not in disequilibrium with rs1625579 and therefore would supply a distinct pathway to potentially alter miR-137 levels in response to environmental cues.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - Gerome Breen
- King’s College London, MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, London, UK; ,National Institute for Health Research (NIHR), Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King’s College London SE5 8DF, UK;
| | - Dan Rujescu
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK; ,*To whom correspondence should be addressed; Department of Molecular and Clinical Pharmacology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK; tel: +44-151-794-5498, fax: +44-151-794-5517, e-mail:
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ALEXANDER MELANNIE, BURCH JAMESB, STECK SUSANE, CHEN CHINFU, HURLEY THOMASG, CAVICCHIA PHILIP, RAY MEREDITH, SHIVAPPA NITIN, GUESS JACLYN, ZHANG HONGMEI, YOUNGSTEDT SHAWND, CREEK KIME, LLOYD STEPHEN, YANG XIAOMING, HÉBERT JAMESR. Case-control study of the PERIOD3 clock gene length polymorphism and colorectal adenoma formation. Oncol Rep 2015; 33:935-41. [PMID: 25501848 PMCID: PMC4306271 DOI: 10.3892/or.2014.3667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 09/18/2014] [Indexed: 01/02/2023] Open
Abstract
Clock genes are expressed in a self-perpetuating, circadian pattern in virtually every tissue including the human gastrointestinal tract. They coordinate cellular processes critical for tumor development, including cell proliferation, DNA damage response and apoptosis. Circadian rhythm disturbances have been associated with an increased risk for colon cancer and other cancers. This mechanism has not been elucidated, yet may involve dysregulation of the 'period' (PER) clock genes, which have tumor suppressor properties. A variable number tandem repeat (VNTR) in the PERIOD3 (PER3) gene has been associated with sleep disorders, differences in diurnal hormone secretion, and increased premenopausal breast cancer risk. Susceptibility related to PER3 has not been examined in conjunction with adenomatous polyps. This exploratory case-control study was the first to test the hypothesis that the 5-repeat PER3 VNTR sequence is associated with increased odds of adenoma formation. Information on demographics, medical history, occupation and lifestyle was collected prior to colonoscopy. Cases (n=49) were individuals with at least one histopathologically confirmed adenoma. Controls (n=97) included patients with normal findings or hyperplastic polyps not requiring enhanced surveillance. Unconditional multiple logistic regression was used to calculate odds ratios (ORs) with 95% confidence intervals (CIs), after adjusting for potential confounding. Adenomas were detected in 34% of participants. Cases were more likely to possess the 5-repeat PER3 genotype relative to controls (4/5 OR, 2.1; 95% CI, 0.9-4.8; 5/5 OR, 5.1; 95% CI, 1.4-18.1; 4/5+5/5 OR, 2.5; 95% CI, 1.7-5.4). Examination of the Oncomine microarray database indicated lower PERIOD gene expression in adenomas relative to adjacent normal tissue. Results suggest a need for follow-up in a larger sample.
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Affiliation(s)
- MELANNIE ALEXANDER
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - JAMES B. BURCH
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA
| | - SUSAN E. STECK
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - CHIN-FU CHEN
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - THOMAS G. HURLEY
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
| | - PHILIP CAVICCHIA
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - MEREDITH RAY
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - NITIN SHIVAPPA
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - JACLYN GUESS
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - HONGMEI ZHANG
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - SHAWN D. YOUNGSTEDT
- College of Nursing and Health Innovation, and College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - KIM E. CREEK
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - STEPHEN LLOYD
- South Carolina Medical Endoscopy Center, and Department of Family Medicine, University of South Carolina School of Medicine, Columbia, SC, USA
| | - XIAOMING YANG
- Medical Chronobiology Laboratory, Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA
| | - JAMES R. HÉBERT
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Family and Preventive Medicine, School of Medicine, University of South Carolina, Columbia, SC, USA
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Delaney MA, Colegrove KM, Spraker TR, Zuerner RL, Galloway RL, Gulland FM. Isolation of Leptospira from a phocid: acute renal failure and mortality from Leptospirosis in rehabilitated northern elephant seals (Mirounga angustirostris), California, USA. J Wildl Dis 2014; 50:621-7. [PMID: 24807176 DOI: 10.7589/2013-08-195] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During rehabilitation, acute renal failure due to leptospirosis occurred in eight male northern elephant seals (Mirounga angustirostris) that stranded along the central California coast in 2011. Characteristic histologic lesions including renal tubular degeneration, necrosis, and mineralization, and mild lymphoplasmacytic interstitial nephritis were noted in the six animals examined. Immunohistochemistry, bacterial culture, and PCR were positive in 2/3, 2/3, and 3/4 seals, respectively, and 6/8 had high serum antibody titers to Leptospira interrogans serovar pomona. Pulsed-field gel electrophoresis confirmed one isolate as serovar pomona. Variable number tandem repeat (VNTR) analysis showed both elephant seal isolates were identical to each other but distinct from those isolated from California sea lions (Zalophus californianus). The time from stranding to onset of azotemia was 1 to 38 (median=24) days, suggesting some seals were infected at the rehabilitation facility. Based on temporal and spatial incidence of infection, transmission among elephant seals likely occurred during rehabilitation. Molecular (VNTR) analysis of the two isolates indicates there is a unique L. interrogans serovar pomona genotype in elephant seals, and sea lions were not the source of infection prior to or during rehabilitation. This study confirms the susceptibility of northern elephant seals to leptospirosis, indicates intraspecies transmission during rehabilitation, and reports the first isolation and preliminary characterization of leptospires from elephant seals.
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Yigit S, Inanir A, Tekcan A, Tural E, Ozturk GT, Kismali G, Karakus N. Significant association of interleukin-4 gene intron 3 VNTR polymorphism with susceptibility to knee osteoarthritis. Gene 2014; 537:6-9. [PMID: 24406619 DOI: 10.1016/j.gene.2013.12.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/07/2013] [Accepted: 12/27/2013] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Interleukin-4 (IL-4) is a strong chondroprotective cytokine and polymorphisms within this gene may be a risk factor for osteoarthritis (OA). We aimed to investigate genotype and allele frequencies of IL-4 gene intron 3 variable number of tandem repeats (VNTR) polymorphism in patients with knee OA in a Turkish population. METHODS The study included 202 patients with knee OA and 180 healthy controls. Genomic DNA was isolated and IL-4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers followed by restriction fragment length polymorphism (RFLP) analysis. RESULTS Our result show that there was statistically significant difference between knee OA patients and control group with respect to IL-4 genotype distribution and allele frequencies (p=0.000, OR: 0.20, 95% CI: 0.10-0.41, OR: 0.22, 95% CI: 0.12-0.42, respectively). CONCLUSIONS Our findings suggest that there is an association of IL-4 gene intron 3 VNTR polymorphism with susceptibility of a person for development of knee OA. As a result, IL-4 gene intron 3 VNTR polymorphism could be a genetic marker in OA in a Turkish study population. This is the first association study that evaluates the associations between IL-4 gene VNTR polymorphism and knee OA.
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O'Brien TC, Mustanski BS, Skol A, Cook EH, Wakschlag LS. Do dopamine gene variants and prenatal smoking interactively predict youth externalizing behavior? Neurotoxicol Teratol 2013; 40:67-73. [PMID: 24064458 DOI: 10.1016/j.ntt.2013.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/16/2022]
Abstract
Externalizing behaviors (encompassing antisocial, impulsive, and substance use behaviors) are pervasive and impairing across a multitude of settings and developmental contexts. These behaviors, though often investigated separately, are highly comorbid. Prenatal tobacco exposure in interaction with various genetic influences has predicted later externalizing behavior, and recent evidence supports investigating sex differences in these patterns. In the current study, we extend this work by (a) examining two functional genetic markers in the dopamine system: the transporter gene (DAT1) and the dopamine receptor D4 gene (DRD4) in interaction with prenatal tobacco exposure to predict a latent composite of externalizing behavior and (b) testing whether these patterns differ by sex of youth in a community sample of adolescents (n=176). The relatively small sample is partially offset by high quality, multi-method prospective measurement. We assessed prenatal tobacco exposure using prospective repeated cotinine-corrected reports and externalizing behaviors were assessed utilizing multiple measures across three waves. The interaction between DAT1 (but not DRD4) and prenatal tobacco exposure was statistically significant in boys, and patterns appeared to differ by sex. Risk for externalizing behaviors for exposed boys increased linearly as a function of the 10r DAT1 allele. For exposed girls, there was a trend such that DAT1 heterozygotes had a marginally higher risk than homozygotes. This pattern was not explained by passive gene-environment correlation. Elucidating sex-specific pathways through which early adverse exposures and genetic susceptibilities contribute to externalizing behavior can inform early targeted prevention efforts for those children at highest risk.
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Affiliation(s)
- T Caitlin O'Brien
- Department of Medical Social Sciences, Northwestern University, 633 N. St. Clair, 19th Floor, Chicago, IL 60611, USA.
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Cabrera CM, Cobo F, Nieto A, Cortés JL, Montes RM, Catalina P, Concha A. Identity tests: determination of cell line cross-contamination. Cytotechnology 2006; 51:45-50. [PMID: 19002894 PMCID: PMC3449683 DOI: 10.1007/s10616-006-9013-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 06/15/2006] [Indexed: 10/24/2022] Open
Abstract
Cell line cross-contamination is a phenomenon that arises as a result of the continuous cell line culture. It has been estimated that around 20% of the cell lines are misidentified, therefore it is necessary to carry out quality control tests for the detection of this issue. Since cell line cross-contamination discovery, different methods have been applied, such as isoenzyme analysis for inter-species cross-contamination; HLA typing, and DNA fingerprinting using short tandem repeat and a variable number of tandem repeat for intra-species cross-contamination. The cell banks in this sense represent the organizations responsible for guaranteeing the authenticity of cell lines for future research and clinical uses.
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Affiliation(s)
- C M Cabrera
- Stem Cell Bank of Andalucia (Spanish Central Node), Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas No. 2, 18014, Granada, Spain,
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