1
|
Li J, Zhou L, Ouyang X, He P. Transcription Factor-7-Like-2 (TCF7L2) in Atherosclerosis: A Potential Biomarker and Therapeutic Target. Front Cardiovasc Med 2021; 8:701279. [PMID: 34568447 PMCID: PMC8459927 DOI: 10.3389/fcvm.2021.701279] [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: 04/27/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Transcription factor-7-like-2 (TCF7L2), a vital member of the T-cell factor/lymphoid enhancer factor (TCF/LEF) family, plays an important role in normal human physiological and pathological processes. TCF7L2 exhibits multiple anti-atherosclerotic effects through the activation of specific molecular mechanisms, including regulation of metabolic homeostasis, macrophage polarization, and neointimal hyperplasia. A single-nucleotide substitution of TCF7L2, rs7903146, is a genetic high-risk factor for type 2 diabetes and indicates susceptibility to cardiovascular disease as a link between metabolic disorders and atherosclerosis. In this review, we summarize the anti-atherosclerosis effect and novel mechanisms underlying the function of TCF7L2 to elucidate its potential as an anti-atherosclerosis biomarker and provide a novel therapeutic target for cardiovascular diseases.
Collapse
Affiliation(s)
- Junyi Li
- School of Nursing, Hengyang Medical College, University of South China, Hengyang, China
| | - Li Zhou
- Department of Pathology, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing, China
| | - Xinping Ouyang
- Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Department of Physiology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, The Neuroscience Institute, University of South China, Hengyang, China
| | - Pingping He
- School of Nursing, Hengyang Medical College, University of South China, Hengyang, China
| |
Collapse
|
2
|
Zicola J, Liu L, Tänzler P, Turck F. Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana. NATURE PLANTS 2019; 5:300-307. [PMID: 30833712 DOI: 10.1038/s41477-019-0375-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
Abstract
FLOWERING LOCUS T (FT) plays a major role in regulating the floral transition in response to an inductive long day photoperiod in Arabidopsis thaliana. Expression of FT in leaves is dependent on the distal transcriptional enhancer Block C, located 5-kilobases (kb) upstream of the transcriptional start site (TSS). We expressed an inverted repeat of Block C to induce local DNA methylation and heterochromatin formation, which lead to FT downregulation in an inductive photoperiod. Using targeted DNA methylation as a tool to uncover further regulatory regions at the FT locus, we identified Block E, located 1 kb downstream of the gene, as a novel enhancer of FT. As Block C, Block E is conserved across Brassicaceae and located in accessible chromatin. Block C and E act as additive transcriptional enhancers that, in combination with the proximal FT promoter, control expression of FT in response to photoperiod in the leaf phloem.
Collapse
Affiliation(s)
- Johan Zicola
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Liangyu Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Petra Tänzler
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| |
Collapse
|
3
|
Admixture mapping and fine-mapping of type 2 diabetes susceptibility loci in African American women. J Hum Genet 2018; 63:1109-1117. [PMID: 30135545 PMCID: PMC6202164 DOI: 10.1038/s10038-018-0503-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
Abstract
African American women are disproportionately affected by type 2 diabetes. Genetic factors may explain part of the excess risk. More than 100 genetic variants have been associated with risk of type 2 diabetes, but most studies have been conducted in white populations. Two genome-wide association studies (GWAS) in African Americans have identified three novel genetic variants only. We conducted admixture mapping using 2,918 ancestral informative markers in 2,632 cases of type 2 diabetes and 2,596 controls nested in the ongoing Black Women’s Health Study cohort, with the goal of identifying genomic loci with local African ancestry associated with type 2 diabetes. In addition, we performed replication analysis of 71 previously identified index SNPs, and fine-mapped those genetic loci to identify better or new genetic variants associated with type 2 diabetes in African Americans. We found that individual African ancestry was associated with higher risk of type 2 diabetes. In addition, we identified two genomic regions, 3q26 and 12q23, with excess of African ancestry associated with higher risk of type 2 diabetes. Lastly, we replicated 8 out of 71 index SNPs from previous GWAS, including, for the first time in African Americans, the X-linked rs5945326 SNP near the DUSP9 gene. In addition, our fine-mapping efforts suggest independent signals at five loci. Our detailed analysis identified two genomic regions associated with risk of type 2 diabetes, and showed that many genetic risk variants are shared across ancestries.
Collapse
|
4
|
Moorthy SD, Davidson S, Shchuka VM, Singh G, Malek-Gilani N, Langroudi L, Martchenko A, So V, Macpherson NN, Mitchell JA. Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. Genome Res 2016; 27:246-258. [PMID: 27895109 PMCID: PMC5287230 DOI: 10.1101/gr.210930.116] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/18/2016] [Indexed: 12/31/2022]
Abstract
Transcriptional enhancers are critical for maintaining cell-type-specific gene expression and driving cell fate changes during development. Highly transcribed genes are often associated with a cluster of individual enhancers such as those found in locus control regions. Recently, these have been termed stretch enhancers or super-enhancers, which have been predicted to regulate critical cell identity genes. We employed a CRISPR/Cas9-mediated deletion approach to study the function of several enhancer clusters (ECs) and isolated enhancers in mouse embryonic stem (ES) cells. Our results reveal that the effect of deleting ECs, also classified as ES cell super-enhancers, is highly variable, resulting in target gene expression reductions ranging from 12% to as much as 92%. Partial deletions of these ECs which removed only one enhancer or a subcluster of enhancers revealed partially redundant control of the regulated gene by multiple enhancers within the larger cluster. Many highly transcribed genes in ES cells are not associated with a super-enhancer; furthermore, super-enhancer predictions ignore 81% of the potentially active regulatory elements predicted by cobinding of five or more pluripotency-associated transcription factors. Deletion of these additional enhancer regions revealed their robust regulatory role in gene transcription. In addition, select super-enhancers and enhancers were identified that regulated clusters of paralogous genes. We conclude that, whereas robust transcriptional output can be achieved by an isolated enhancer, clusters of enhancers acting on a common target gene act in a partially redundant manner to fine tune transcriptional output of their target genes.
Collapse
Affiliation(s)
- Sakthi D Moorthy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Scott Davidson
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Virlana M Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Gurdeep Singh
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Nakisa Malek-Gilani
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Lida Langroudi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Alexandre Martchenko
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Vincent So
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Neil N Macpherson
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| |
Collapse
|
5
|
Salinas YD, Wang L, DeWan AT. Multiethnic genome-wide association study identifies ethnic-specific associations with body mass index in Hispanics and African Americans. BMC Genet 2016; 17:78. [PMID: 27296613 PMCID: PMC4907283 DOI: 10.1186/s12863-016-0387-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/01/2016] [Indexed: 01/03/2023] Open
Abstract
Background Genome-wide association studies of obesity have typically assumed fixed genetic effects across ethnicities, rarely attempting to thoroughly compare and contrast findings across various ethnic groups. Therefore, our study aimed to identify novel genetic associations with body mass index (BMI), a common measure of obesity, and explore their cross-ethnic generalizability in a multiethnic population. To that end, we conducted ethnic-specific genome-wide association analyses among 1235 Hispanic, 706 Asian, 1549 African American, and 2395 European American subjects from the Multi-ethnic Study of Atherosclerosis (MESA). We compared findings across ethnicities and investigated single-nucleotide polymorphisms (SNPs) with suggestive BMI-association p-values among 3379 Hispanic and 6871 African American subjects from the Women’s Health Initiative (WHI). Results We identified a genome-wide significant association in MESA Hispanics—rs12253976 in KLF6 (beta = 5.792 kg/m2 per-allele, 95 % confidence interval (CI): 3.885, 7.698; p = 3.43 × 10−9)—and suggestive SNPs with p < 5 × 10−6 in MESA Hispanics, European Americans and African Americans that display ethnic-specific effects on BMI. Of these suggestive SNPs, Hispanic SNP rs12255372 and African American SNP rs6435678 had the most evidence of replication in WHI. rs12255372 (in TCF7L2) was associated with lower BMI in both MESA (beta = −1.111 kg/m2, 95 % CI: −1.578, −0.645; p = 3.33 × 10−6) and WHI Hispanics (beta = −0.304 kg/m2, 95 % CI: −0.613, 0.006; p = 0.054). This TCF7L2 intronic region contains several SNPs (rs7901695, rs4506565, rs4132670, and rs12243326) with low p-values (p < 10−3) in MESA and betas of similar magnitude and direction in MESA and WHI, but only rs12243326 is in strong linkage disequilibrium with rs12255372 in our Hispanic populations, suggesting independent signals in this region. rs6435678 (in ERBB4) was associated with greater BMI in both MESA (beta = 1.104 kg/m2, 95 % CI: 0.643, 1.564; p = 2.85 × 10−6) and WHI African Americans (beta = 0.219 kg/m2, 95 % CI: −0.021, 0.460; p = 0.074). Conclusions Two BMI-association signals are present in the TCF7L2 intronic region of Hispanics, one of which is tagged by rs12255372. ERBB4 rs6435678 is a novel BMI-association signal in African Americans. Overall, our data suggest that ethnic-specific associations are involved in the genetic determination of BMI. Ethnic-specificity has potential implications for the development of gene-based therapies for obesity. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0387-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yasmmyn D Salinas
- Department of Chronic Disease Epidemiology, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Leyao Wang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
| |
Collapse
|
6
|
Acosta JL, Hernández-Mondragón AC, Correa-Acosta LC, Cazañas-Padilla SN, Chávez-Florencio B, Ramírez-Vega EY, Monge-Cázares T, Aguilar-Salinas CA, Tusié-Luna T, Del Bosque-Plata L. Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico. BMC Genet 2016; 17:68. [PMID: 27230431 PMCID: PMC4880969 DOI: 10.1186/s12863-016-0372-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 04/22/2016] [Indexed: 12/17/2022] Open
Abstract
Background Genetic variations of the TCF7L2 gene are associated with the development of Type 2 diabetes (T2D). The associated mutations have demonstrated an adaptive role in some human populations, but no studies have determined the impact of evolutionary forces on genetic diversity in indigenous populations from Mexico. Here, we sequenced and analyzed the variation of the TCF7L2 gene in three Amerindian populations and compared the results with whole-exon-sequencing of Mestizo populations from Sigma and the 1000 Genomes Project to assess the roles of selection and recombination in diversity. Results The diversity in the indigenous populations was biased to intronic regions. Most of the variation was low frequency. Only mutations rs77961654 and rs61724286 were located on exon 15. We did not observe variation in intronic region 4–6 in any of the three indigenous populations. In addition, we identified peaks of selective sweeps in the mestizo samples from the Sigma Project within this region. By replicating the analysis of association with T2D between case-controls from the Sigma Project, we determined that T2D was most highly associated with the rs7903146 risk allele and to a lesser extent with the other six variants. All associated markers were located in intronic region 4–6, and their r2 values of linkage disequilibrium were significantly higher in the Mexican population than in Africans from the 1000 Genomes Project. We observed reticulations in both the haplotypes network analysis from seven marker associates and the neighborNet tree based on 6061 markers in the TCF7L2 gene identified from all samples of the 1000 Genomes Project. Finally, we identified two recombination hotspots in the upstream region and 3’ end of the TCF7L2 gene. Conclusions The lack of diversity in intronic region 4–6 in Indigenous populations could be an effect of selective sweeps generated by the selection of neighboring rare variants at T2D-associated mutations. The survivors’ variants make the intronic region 4–6 the area of the greatest population differentiation within the TCF7L2 gene. The abundance of selective peak sweeps in the downstream region of the TCF7L2 gene suggests that the TCF7L2 gene is part of a region that is in constant recombination between populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0372-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jose Luis Acosta
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada No. 950, Puerta 7, Edificio O, Planta Baja, Col. Independencia, 44340 Guadalajara, Jalisco, Mexico.,Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)-Unidad, Blvd, Juan de Dios Bátiz Paredes #250, 81101 Sinaloa, Mexico
| | - Alma Cristal Hernández-Mondragón
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Laura Carolina Correa-Acosta
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Sandra Nathaly Cazañas-Padilla
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Berenice Chávez-Florencio
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Elvia Yamilet Ramírez-Vega
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Tulia Monge-Cázares
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición, Vasco de Quiroga 15, 14000 Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto de Investigaciones Biomédicas, UNAM, Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ, 04510 Mexico City, Mexico
| | - Laura Del Bosque-Plata
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, 14610 Mexico City, Mexico.
| |
Collapse
|