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Zhao CH. The association between the single-nucleotide polymorphism of site rs1333040 in region 9p21 and the risk of coronary heart disease in Chinese population. Acta Cardiol 2024:1-10. [PMID: 39145594 DOI: 10.1080/00015385.2024.2391132] [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: 07/03/2023] [Revised: 02/26/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Rs1333040 is the single-nucleotide polymorphisms (SNP) related with coronary heart disease (CHD). The aim of the present study is to examine the association between rs1333040 polymorphism genotypes and CHD and to further explore the molecular mechanism in Chinese population. METHODS A case-control study was used in this study, including 500 CHD patients and 500 control subjects. CHD patients and controls were distinguished by coronary angiography. Genotypes of rs1333040 were determined on the Agena MassARRAY system. Statistical analysis was conducted by SPSS (Ver 16.0) and plink (Ver. 1.07, Shaun Purcell). RESULTS Fisher's exact test by plink indicated a significant difference in the allele distribution between cases and controls, the allele T may be associated with a higher risk of CHD (p = 0.012, odds ratio (OR) = 1.258). The serum levels of low-density lipoprotein cholesterol (LDL-C) (p = 0.029) and Gensini score (p = 0.008) distributed differently in patients with various alleles. In the recessive model, the levels of high-density lipoprotein (HDL) and apolipoprotein A (ApoA) were higher in the TC + CC genotype than in the TT genotype. The TC + TT genotype was found to be risk factors against CHD in a dominant model (OR = 1.278, p = 0.014). The TC + TT genotype along with multiple risk factors significantly positively correlated with the risk of CHD. CONCLUSIONS The present study investigates the association between the rs1333040 polymorphism genotypes and CHD. The T allele of rs1333040 is the susceptibility site of CHD. The interaction between SNP and various risk factors plays an important role in the development of CHD.
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Affiliation(s)
- Chen-Hui Zhao
- Department of Cardiovascular Medicine, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China
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2
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Shi W, Song J, Weiner JM, Chopra A, Dommisch H, Beule D, Schaefer AS. lncRNA CDKN2B-AS1 regulates collagen expression. Hum Genet 2024; 143:907-919. [PMID: 38833008 PMCID: PMC11294485 DOI: 10.1007/s00439-024-02674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/27/2024] [Indexed: 06/06/2024]
Abstract
The long noncoding RNA CDKN2B-AS1 harbors a major coronary artery disease risk haplotype, which is also associated with progressive forms of the oral inflammatory disease periodontitis as well as myocardial infarction (MI). Despite extensive research, there is currently no broad consensus on the function of CDKN2B-AS1 that would explain a common molecular role of this lncRNA in these diseases. Our aim was to investigate the role of CDKN2B-AS1 in gingival cells to better understand the molecular mechanisms underlying the increased risk of progressive periodontitis. We downregulated CDKN2B-AS1 transcript levels in primary gingival fibroblasts with LNA GapmeRs. Following RNA-sequencing, we performed differential expression, gene set enrichment analyses and Western Blotting. Putative causal alleles were searched by analyzing associated DNA sequence variants for changes of predicted transcription factor binding sites. We functionally characterized putative functional alleles using luciferase-reporter and antibody electrophoretic mobility shift assays in gingival fibroblasts and HeLa cells. Of all gene sets analysed, collagen biosynthesis was most significantly upregulated (Padj=9.7 × 10- 5 (AUC > 0.65) with the CAD and MI risk gene COL4A1 showing strongest upregulation of the enriched gene sets (Fold change = 12.13, Padj = 4.9 × 10- 25). The inflammatory "TNFA signaling via NFKB" gene set was downregulated the most (Padj=1 × 10- 5 (AUC = 0.60). On the single gene level, CAPNS2, involved in extracellular matrix organization, was the top upregulated protein coding gene (Fold change = 48.5, P < 9 × 10- 24). The risk variant rs10757278 altered a binding site of the pathogen responsive transcription factor STAT1 (P = 5.8 × 10- 6). rs10757278-G allele reduced STAT1 binding 14.4% and rs10757278-A decreased luciferase activity in gingival fibroblasts 41.2% (P = 0.0056), corresponding with GTEx data. CDKN2B-AS1 represses collagen gene expression in gingival fibroblasts. Dysregulated collagen biosynthesis through allele-specific CDKN2B-AS1 expression in response to inflammatory factors may affect collagen synthesis, and in consequence tissue barrier and atherosclerotic plaque stability.
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Affiliation(s)
- Weiwei Shi
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Jiahui Song
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - January Mikolaj Weiner
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Avneesh Chopra
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Henrik Dommisch
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany
| | - Arne S Schaefer
- Dept. of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany.
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3
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Wu R, Wu T, Wang Q, Shi Y, Dong Q, Rong X, Chen M, He Z, Fu Y, Liu L, Shao S, Guan X, Zhang C. The ischemia-enhanced myocardial infarction protection-related lncRNA protects against acute myocardial infarction. MedComm (Beijing) 2024; 5:e632. [PMID: 38988491 PMCID: PMC11234438 DOI: 10.1002/mco2.632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 07/12/2024] Open
Abstract
Long non-coding RNA RP11-64B16.4 (myocardial infarction protection-related lncRNA [MIPRL]) is among the most abundant and the most upregulated lncRNAs in ischemic human hearts. However, its role in ischemic heart disease is unknown. We found MIPRL was conserved between human and mouse and its expression was increased in mouse hearts after acute myocardial infarction (AMI) and in cultured human and mouse cardiomyocytes after hypoxia. The infarcted size, cardiac cell apoptosis, cardiac dysfunction, and cardiac fibrosis were aggravated in MIPRL knockout mice after AMI. The above adverse results could be reversed by re-expression of MIPRL via adenovirus expressing MIPRL. Both in vitro and in vivo, we identified that heat shock protein beta-8 (HSPB8) was a target gene of MIPRL, which was involved in MIPRL-mediated anti-apoptotic effects on cardiomyocytes. We further discovered that MIPRL could combine with the messenger RNA (mRNA) of HSPB8 and increase its expression in cardiomyocytes by enhancing the stability of HSPB8 mRNA. In summary, we have found for the first time that the ischemia-enhanced lncRNA MIPRL protects against AMI via its target gene HSPB8. MIPRL might be a novel promising therapeutic target for ischemic heart diseases such as AMI.
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Affiliation(s)
- Rongzhou Wu
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Tingting Wu
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Qiaoyu Wang
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Youyang Shi
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Qianqian Dong
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Xing Rong
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Meiting Chen
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Zhiyu He
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Yu Fu
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Lei Liu
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Shuai Shao
- Department of CardiologyKey Laboratory of Medical ElectrophysiologyMinistry of EducationInstitute of Cardiovascular ResearchInstitute of Metabolic Diseasesthe Affiliated Hospital of Southwest Medical UniversitySouthwest Medical UniversityLuzhouChina
| | - Xueqiang Guan
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
| | - Chunxiang Zhang
- Children's Heart CenterThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityInstitute of Cardiovascular Development and Translational MedicineThe Second School of MedicineWenzhou Medical UniversityWenzhouChina
- Department of CardiologyKey Laboratory of Medical ElectrophysiologyMinistry of EducationInstitute of Cardiovascular ResearchInstitute of Metabolic Diseasesthe Affiliated Hospital of Southwest Medical UniversitySouthwest Medical UniversityLuzhouChina
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4
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Riccio C, Jansen ML, Guo L, Ziegler A. Variant effect predictors: a systematic review and practical guide. Hum Genet 2024; 143:625-634. [PMID: 38573379 PMCID: PMC11098935 DOI: 10.1007/s00439-024-02670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Large-scale association analyses using whole-genome sequence data have become feasible, but understanding the functional impacts of these associations remains challenging. Although many tools are available to predict the functional impacts of genetic variants, it is unclear which tool should be used in practice. This work provides a practical guide to assist in selecting appropriate tools for variant annotation. We conducted a MEDLINE search up to November 10, 2023, and included tools that are applicable to a broad range of phenotypes, can be used locally, and have been recently updated. Tools were categorized based on the types of variants they accept and the functional impacts they predict. Sequence Ontology terms were used for standardization. We identified 118 databases and software packages, encompassing 36 variant types and 161 functional impacts. Combining only three tools, namely SnpEff, FAVOR, and SparkINFERNO, allows predicting 99 (61%) distinct functional impacts. Thirty-seven tools predict 89 functional impacts that are not supported by any other tool, while 75 tools predict pathogenicity and can be used within the ACMG/AMP guidelines in a clinical context. We launched a website allowing researchers to select tools based on desired variants and impacts. In summary, more than 100 tools are already available to predict approximately 160 functional impacts. About 60% of the functional impacts can be predicted by the combination of three tools. Unexpectedly, recent tools do not predict more impacts than older ones. Future research should allow predicting the functionality of so far unsupported variant types, such as gene fusions.URL: https://cardio-care.shinyapps.io/VEP_Finder/ .Registration: OSF Registries on November 10, 2023, https://osf.io/s2gct .
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Affiliation(s)
- Cristian Riccio
- Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 1, Davos Wolfgang, 7265, Davos, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Max L Jansen
- Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 1, Davos Wolfgang, 7265, Davos, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Linlin Guo
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- University Center of Cardiovascular Science & Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Ziegler
- Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 1, Davos Wolfgang, 7265, Davos, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- University Center of Cardiovascular Science & Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
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Becker S, L'Ecuyer Z, Jones BW, Zouache MA, McDonnell FS, Vinberg F. Modeling complex age-related eye disease. Prog Retin Eye Res 2024; 100:101247. [PMID: 38365085 PMCID: PMC11268458 DOI: 10.1016/j.preteyeres.2024.101247] [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: 08/15/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Modeling complex eye diseases like age-related macular degeneration (AMD) and glaucoma poses significant challenges, since these conditions depend highly on age-related changes that occur over several decades, with many contributing factors remaining unknown. Although both diseases exhibit a relatively high heritability of >50%, a large proportion of individuals carrying AMD- or glaucoma-associated genetic risk variants will never develop these diseases. Furthermore, several environmental and lifestyle factors contribute to and modulate the pathogenesis and progression of AMD and glaucoma. Several strategies replicate the impact of genetic risk variants, pathobiological pathways and environmental and lifestyle factors in AMD and glaucoma in mice and other species. In this review we will primarily discuss the most commonly available mouse models, which have and will likely continue to improve our understanding of the pathobiology of age-related eye diseases. Uncertainties persist whether small animal models can truly recapitulate disease progression and vision loss in patients, raising doubts regarding their usefulness when testing novel gene or drug therapies. We will elaborate on concerns that relate to shorter lifespan, body size and allometries, lack of macula and a true lamina cribrosa, as well as absence and sequence disparities of certain genes and differences in their chromosomal location in mice. Since biological, rather than chronological, age likely predisposes an organism for both glaucoma and AMD, more rapidly aging organisms like small rodents may open up possibilities that will make research of these diseases more timely and financially feasible. On the other hand, due to the above-mentioned anatomical and physiological features, as well as pharmacokinetic and -dynamic differences small animal models are not ideal to study the natural progression of vision loss or the efficacy and safety of novel therapies. In this context, we will also discuss the advantages and pitfalls of alternative models that include larger species, such as non-human primates and rabbits, patient-derived retinal organoids, and human organ donor eyes.
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Affiliation(s)
- Silke Becker
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Zia L'Ecuyer
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Bryan W Jones
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Moussa A Zouache
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Fiona S McDonnell
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA; Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Frans Vinberg
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA; Biomedical Engineering, University of Utah, Salt Lake City, UT, USA.
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6
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Xie F, Wang D, Cheng M. CDKN2B-AS1 may act as miR-92a-3p sponge in coronary artery disease. Minerva Cardiol Angiol 2024; 72:125-133. [PMID: 38231078 DOI: 10.23736/s2724-5683.23.06441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
BACKGROUND LncRNAs, miRNAs, and the sponge effect between them exert diverse biological influences on the pathogenesis and progression of coronary artery disease (CAD), thus necessitating an exploration of the lncRNA-miRNA-gene regulatory network in CAD. METHODS Expression profile GSE98583 was obtained from NCBI, containing the data of 12 CAD patients and 6 controls. Limma package was utilized to determine the differentially expressed genes (DEGs). Functional enrichment analysis was performed by DAVID. The CAD-related miRNA-DEG associations were retrieved via HMDD and miRTarBase, and the CAD-related lncRNA-miRNA associations were retrieved via LncRNADisease and starBase. The CAD-related lncRNA-miRNA-DEG regulatory network was constructed by combining these associations. The dual luciferase test was carried out to validate the connections among lncRNA, miRNA, and gene. RESULTS Overall, 534 DEGs were identified between CAD samples and controls, including 243 up-regulated and 291 down-regulated, and were enriched in various gene ontology biological processes and KEGG pathways. The CAD-related miRNAs targeting DEGs included hsa-miR-206, has-miR-320b, has-miR-4513, has-miR-765, and has-miR-92a-3p, and hsa-miR-92a-3p regulated the most DEGs. In the lncRNA-miRNA associations, only CDKN2B-AS1 regulated the CAD-related miRNA, hsa-miR-92a-3p, which was validated using the dual luciferase test. CONCLUSIONS CDKN2B-AS1 may act as an hsa-miR-92a-3p sponge to regulate the downstream DEGs in CAD. CDKN2B-AS1/ hsa-miR-92a-3p/GATA2 might be a novel mechanism for CAD.
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Affiliation(s)
- Fei Xie
- Department of Cardiac Surgery, The Second Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China
| | - Dan Wang
- Department of Cardiac Surgery, The Second Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming Cheng
- Department of Cardiac Surgery, The Second Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China -
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Shou F, Li G, Morshedi M. Long Non-coding RNA ANRIL and Its Role in the Development of Age-Related Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04074-y. [PMID: 38443729 DOI: 10.1007/s12035-024-04074-y] [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: 10/16/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
ANRIL is known as a lncRNA that has many linear and circular isoforms and its polymorphisms are observed to be associated with the pathogenesis of many diseases including age-related diseases. Age-related diseases including atherosclerosis, ischemic heart disease, and Alzheimer's and Parkinson's disease are the most common cause of mortality in both developed and undeveloped countries and that is why a better understanding of their pathogenesis and underlying mechanisms is necessary for controlling their healthcare burden.In this review, we aim to gather the data of researches which have investigated the role of ANRIL in aging and its related diseases. The conclusions of this paper might give a new insight for decreasing the mortality rate of these diseases.
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Affiliation(s)
- Feiyan Shou
- Shaoxing People's Hospital, Shaoxing, 312000, Zhejiang, China
| | - Gang Li
- Shaoxing People's Hospital, Shaoxing, 312000, Zhejiang, China.
| | - Mohammadamin Morshedi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Akan G, Nyawawa E, Nyangasa B, Turkcan MK, Mbugi E, Janabi M, Atalar F. Severity of coronary artery disease is associated with diminished circANRIL expression: A possible blood based transcriptional biomarker in East Africa. J Cell Mol Med 2024; 28:e18093. [PMID: 38149798 PMCID: PMC10844708 DOI: 10.1111/jcmm.18093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 12/28/2023] Open
Abstract
Antisense Noncoding RNA in the INK4 Locus (ANRIL) is the prime candidate gene at Chr9p21, the well-defined genetic risk locus associated with coronary artery disease (CAD). ANRIL and its transcript variants were investigated for the susceptibility to CAD in adipose tissues (AT) and peripheral blood mononuclear cells (PBMCs) of the study group and the impact of 9p21.3 locus mutations was further analysed. Expressions of ANRIL, circANRIL (hsa_circ_0008574), NR003529, EU741058 and DQ485454 were detected in epicardial AT (EAT) mediastinal AT (MAT), subcutaneous AT (SAT) and PBMCs of CAD patients undergoing coronary artery bypass grafting and non-CAD patients undergoing heart valve surgery. ANRIL expression was significantly upregulated, while the expression of circANRIL was significantly downregulated in CAD patients. Decreased circANRIL levels were significantly associated with the severity of CAD and correlated with aggressive clinical characteristics. rs10757278 and rs10811656 were significantly associated with ANRIL and circANRIL expressions in AT and PBMCs. The ROC-curve analysis suggested that circANRIL has high diagnostic accuracy (AUC: 0.9808, cut-off: 0.33, sensitivity: 1.0, specificity: 0.88). circANRIL has high diagnostic accuracy (AUC: 0.9808, cut-off: 0.33, sensitivity: 1.0, specificity: 0.88). We report the first data demonstrating the presence of ANRIL and its transcript variants expressions in the AT and PBMCs of CAD patients. circANRIL having a synergetic effect with ANRIL plays a protective role in CAD pathogenesis. Therefore, altered circANRIL expression may become a potential diagnostic transcriptional biomarker for early CAD diagnosis.
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Affiliation(s)
- Gokce Akan
- Biochemistry Department, MUHAS Genetics Laboratory, School of MedicineMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
- Near East UniversityDESAM Research InstituteMersinNorth CyprusTurkey
| | | | | | | | - Erasto Mbugi
- Biochemistry Department, MUHAS Genetics Laboratory, School of MedicineMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
| | | | - Fatmahan Atalar
- Biochemistry Department, MUHAS Genetics Laboratory, School of MedicineMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
- Department of Rare DiseasesIstanbul University, Child Health InstituteIstanbulTurkey
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Dowaidar M. Gene-environment interactions that influence CVD, lipid traits, obesity, diabetes, and hypertension appear to be able to influence gene therapy. Mol Aspects Med 2023; 94:101213. [PMID: 37703607 DOI: 10.1016/j.mam.2023.101213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Most mind boggling diseases are accepted to be impacted by both genetic and environmental elements. As of late, there has been a flood in the improvement of different methodologies, concentrate on plans, and measurable and logical techniques to examine gene-environment cooperations (G × Es) in enormous scope studies including human populaces. The many-sided exchange between genetic elements and environmental openings has long charmed the consideration of clinicians and researchers looking to grasp the complicated starting points of diseases. While single variables can add to disease, the blend of genetic variations and environmental openings frequently decides disease risk. The fundamental point of this paper is to talk about the Gene-Environment Associations That Impact CVD, Lipid Characteristics, Obesity, Diabetes, and Hypertension Have all the earmarks of being Ready to Impact Gene Therapy. This survey paper investigates the meaning of gene-environment collaborations (G × E) in disease advancement. The intricacy of genetic and environmental communications in disease causation is explained, underlining the multifactorial idea of many circumstances. The job of gene-environment cooperations in cardiovascular disease, lipid digestion, diabetes, obesity, and hypertension is investigated. This audit fixates on Gene by Environment (G × E) collaborations, investigating their importance in disease etiology.
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Affiliation(s)
- Moataz Dowaidar
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia; Interdisciplinary Research Center for Hydrogen and Energy Storage (IRC-HES), King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia; Interdisciplinary Research Center for Health & Biosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia.
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Zheng L, Chopra A, Weiner J, Beule D, Dommisch H, Schaefer AS. miRNAs from Inflamed Gingiva Link Gene Signaling to Increased MET Expression. J Dent Res 2023; 102:1488-1497. [PMID: 37822091 PMCID: PMC10683346 DOI: 10.1177/00220345231197984] [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] [Indexed: 10/13/2023] Open
Abstract
Several array-based microRNA (miRNA) expression studies independently showed increased expression of miRNAs hsa-miR-130a-3p, -142-3p, -144-3p, -144-5p, -223-3p, -17-5p, and -30e-5p in gingiva affected by periodontal inflammation. We aimed to determine direct target genes and signaling pathways regulated by these miRNAs to identify processes relevant to gingival inflammatory responses and tissue homeostasis. We transfected miRNA mimics (mirVana) for each of the 7 miRNAs separately into human primary gingival fibroblasts cultured from 3 different donors. Following RNA sequencing, differential gene expression and second-generation gene set enrichment analyses were performed. miRNA inhibition and upregulation was validated at the transcript and protein levels using quantitative reverse transcriptase polymerase chain reaction, Western blotting, and reporter gene assays. All 7 miRNAs significantly increased expression of the gene MET proto-oncogene, receptor tyrosine kinase (MET). Expression of known periodontitis risk genes CPEB1, ABCA1, and ATP6V1C1 was significantly repressed by hsa-miR-130a-3p, -144-3p, and -144-5p, respectively. The genes WASL, ENPP5, ARL6IP1, and IDH1 showed the most significant and strongest downregulation after hsa-miR-142-3p, -17-5p, -223-3p, and -30e-5p transfection, respectively. The most significantly regulated gene set of each miRNA related to cell cycle (hsa-miRNA-144-3p and -5p [Padj = 4 × 10-40 and Padj = 4 × 10-6], -miR-17-5p [Padj = 9.5 × 10-23], -miR-30e-5p [Padj = 8.2 × 10-18], -miR-130a-3p [Padj = 5 × 10-15]), integrin cell surface interaction (-miR-223-3p [Padj = 2.4 × 10-7]), and interferon signaling (-miR-142-3p [Padj = 5 × 10-11]). At the end of acute inflammation, gingival miRNAs bring together complex regulatory networks that lead to increased expression of the gene MET. This underscores the importance of mesenchymal cell migration and invasion during gingival tissue remodeling and proliferation in restoring periodontal tissue homeostasis after active inflammation. MET, a receptor of the mitogenic hepatocyte growth factor fibroblast secreted, is a core gene of this process.
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Affiliation(s)
- L. Zheng
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - A. Chopra
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - J. Weiner
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - D. Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - H. Dommisch
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - A. S. Schaefer
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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11
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Zhu Y, Rosenfeld MG, Suh Y. Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture. Proc Natl Acad Sci U S A 2023; 120:e2313285120. [PMID: 37922325 PMCID: PMC10636305 DOI: 10.1073/pnas.2313285120] [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: 08/02/2023] [Accepted: 09/27/2023] [Indexed: 11/05/2023] Open
Abstract
The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here, we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize multirestriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantitatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gauge regulatory interaction networks, identifying >20-fold more enhancer:promoter (E:P) loops than in situ Hi-C. In addition to vastly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically associating domain boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high-resolution interactome maps required for characterizing fine-gauge regulatory chromatin interactions in analysis of development, homeostasis, and disease.
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Affiliation(s)
- Yizhou Zhu
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032
| | - Michael G. Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA92093
- Department of Genetics and Development, Columbia University, New York, NY10032
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032
- Department of Genetics and Development, Columbia University, New York, NY10032
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12
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Yari A, Karam ZM, Meybodi SME, Sargazi ML, Saeidi K. CDKN2B-AS (rs2891168), SOD2 (rs4880), and PON1 (rs662) polymorphisms and susceptibility to coronary artery disease and type 2 diabetes mellitus in Iranian patients: A case-control study. Health Sci Rep 2023; 6:e1717. [PMID: 38028681 PMCID: PMC10665643 DOI: 10.1002/hsr2.1717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/28/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background and Aims Coronary artery disease (CAD) is a devastating illness and primary cause of death worldwide that arises from a combination of genetic and environmental factors. Several large-scale studies found that 9p21.3, superoxide dismutase 2 (SOD2), and paraoxonase 1 (PON1) polymorphisms increase type 2 diabetes mellitus (T2DM) and/or coronary artery disease (CAD) risk. Our research aimed to investigate whether the SNPs of the 9p21.3 locus (rs28911698), SOD2 (rs4880), and PON1 (rs662) genes were associated with the risk of T2DM and/or CAD in the Iranian population. Methods In this case-control study four group subjects including patients with CAD non-T2DM, with CAD and T2DM, non-CAD with T2DM, and non-CAD non-T2DM were recruited to the study from 2019 to 2020. Molecular analysis was carried out by allele specific-polymerase chain reaction (AS-PCR) technique for rs4880, Taqman genotyping assay for rs2891168, and PCR followed by restriction fragment length polymorphism (PCR-RFLP) technique for rs662. Results The rs2891168 polymorphism presented an elevated risk of CAD in non-T2DM with CAD and with T2DM CAD groups compared to the non-T2DM non-CAD group with GG genotype and dominant model after adjustment (p < 0.05). G-allele in PON1 rs662 polymorphism associated with increased risk of T2DM in T2DM non-CAD, and T2DM CAD groups compared to non-T2DM non-CAD group with dominant model, GG and AG genotypes (p < 0.05). However, SOD2 rs4880 polymorphism presented no significant association with the development of diabetes or CAD. Conclusion These results provide a prime witness that rs2891168 and rs662 gene variants might have a possible increased risk of CAD and T2DM occurrence, respectively. To obtain more definitive and accurate results in this area, further research is required.
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Affiliation(s)
- Abolfazl Yari
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
- Department of Medical Genetics, Afzalipour Faculty of MedicineKerman University of Medical SciencesKermanIran
| | - Zahra M. Karam
- Department of Medical Genetics, Afzalipour Faculty of MedicineKerman University of Medical SciencesKermanIran
- Physiology Research Center, Institute of NeuropharmacologyKerman University of Medical SciencesKermanIran
| | - Seyed M. E. Meybodi
- Yazd Cardiovascular Research Center, Non‐communicable Disease Research InstituteShahid Sadoughi University of Medical SciencesYazdIran
| | - Marzieh L. Sargazi
- Physiology Research Center, Institute of NeuropharmacologyKerman University of Medical SciencesKermanIran
| | - Kolsoum Saeidi
- Physiology Research Center, Institute of NeuropharmacologyKerman University of Medical SciencesKermanIran
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13
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Zhu Y, Ryu S, Tare A, Barzilai N, Atzmon G, Suh Y. Targeted sequencing of the 9p21.3 region reveals association with reduced disease risks in Ashkenazi Jewish centenarians. Aging Cell 2023; 22:e13962. [PMID: 37605876 PMCID: PMC10577543 DOI: 10.1111/acel.13962] [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: 05/05/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
Genome-wide association studies (GWAS) have pinpointed the chromosomal locus 9p21.3 as a genetic hotspot for various age-related disorders. Common genetic variants in this locus are linked to multiple traits, including coronary artery diseases, cancers, and diabetes. Centenarians are known for their reduced risk and delayed onset of these conditions. To investigate whether this evasion of disease risks involves diminished genetic risks in the 9p21.3 locus, we sequenced this region in an Ashkenazi Jewish centenarian cohort (centenarians: n = 450, healthy controls: n = 500). Risk alleles associated with cancers, glaucoma, CAD, and T2D showed a significant depletion in centenarians. Furthermore, the risk and non-risk genotypes are linked to two distinct low-frequency variant profiles, enriched in controls and centenarians, respectively. Our findings provide evidence that the extreme longevity cohort is associated with collectively lower risks of multiple age-related diseases in the 9p21.3 locus.
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Affiliation(s)
- Yizhou Zhu
- Department of Obstetrics and GynecologyColumbia UniversityNew York CityNew YorkUSA
| | - Seungjin Ryu
- Department of Pharmacology, College of MedicineHallym UniversityChuncheonGangwonKorea
| | - Archana Tare
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Nir Barzilai
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
- Institute for Aging ResearchAlbert Einstein College of MedicineBronxNew YorkUSA
- Department of MedicineAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Gil Atzmon
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
- Department of MedicineAlbert Einstein College of MedicineBronxNew YorkUSA
- Department of Human Biology, Faculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Yousin Suh
- Department of Obstetrics and GynecologyColumbia UniversityNew York CityNew YorkUSA
- Department of Genetics and DevelopmentColumbia UniversityNew York CityNew YorkUSA
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14
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Quaye LNK, Dalzell CE, Deloukas P, Smith AJP. The Genetics of Coronary Artery Disease: A Vascular Perspective. Cells 2023; 12:2232. [PMID: 37759455 PMCID: PMC10527262 DOI: 10.3390/cells12182232] [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: 07/03/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified a large number of genetic loci for coronary artery disease (CAD), with many located close to genes associated with traditional CAD risk pathways, such as lipid metabolism and inflammation. It is becoming evident with recent CAD GWAS meta-analyses that vascular pathways are also highly enriched and present an opportunity for novel therapeutics. This review examines GWAS-enriched vascular gene loci, the pathways involved and their potential role in CAD pathogenesis. The functionality of variants is explored from expression quantitative trait loci, massively parallel reporter assays and CRISPR-based gene-editing tools. We discuss how this research may lead to novel therapeutic tools to treat cardiovascular disorders.
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Affiliation(s)
| | | | - Panos Deloukas
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; (L.N.K.Q.); (C.E.D.); (A.J.P.S.)
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15
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Borghini A, Mercuri A, Campolo J, Parolini M, Ndreu R, Turchi S, Andreassi MG. Influence of Chromosome 9p21.3 rs1333049 Variant on Telomere Length and Their Interactive Impact on the Prognosis of Coronary Artery Disease. J Cardiovasc Dev Dis 2023; 10:387. [PMID: 37754816 PMCID: PMC10531536 DOI: 10.3390/jcdd10090387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Both telomere shortening and the chromosome 9p21.3 (Chr9p21) rs1333049 (G/C) variant are involved in coronary artery disease (CAD) risk, likely affecting mechanisms related to cell cycle arrest and vascular senescence. The aim of the study was to examine the link between Chr9p21 rs1333049 variant and leucocyte telomere length (LTL), as well as their interactive effect on the risk of major adverse cardiovascular events (MACEs). METHODS A cohort of 472 patients with angiographically proven and clinically stable CAD were included in the study. At baseline, the LTL, biochemical parameters, and genotype analysis of Chr9p21 rs1333049 variant were measured in all patients. The primary endpoint of this study was the occurrence of MACE defined as a composite of coronary-related death, nonfatal MI, and coronary revascularization. RESULTS On multivariable linear regression analysis, age (p = 0.02) and Chr9p21 rs1333049 variant (p = 0.002) were the only independent predictors of LTL levels. Carriers of the CC genotype of this SNP had shorter telomeres than GC carriers (p = 0.02) and GG carriers (p = 0.0005). After a follow-up with a mean period of 62 ± 19 months, 90 patients (19.1%) had MACE. Short LTL was an independent prognostic factor of MACE incidence (HR:2.2; 95% CI: 1.3-3.7; p = 0.005) after adjustment for potential confounders. There was a significant interaction (p = 0.01) between the LTL and rs1333049 variant, with patients with risk-allele C and short LTL having a higher risk (HR:5.8; 95% CI: 1.8-19.2; p = 0.004). CONCLUSION A strong relationship between LTL and Chr9p21 rs1333049 variant was identified, and they interactively affect the risk of poor prognosis in CAD patients.
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Affiliation(s)
- Andrea Borghini
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (A.M.); (R.N.); (S.T.); (M.G.A.)
| | - Antonella Mercuri
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (A.M.); (R.N.); (S.T.); (M.G.A.)
| | - Jonica Campolo
- CNR Institute of Clinical Physiology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (J.C.); (M.P.)
| | - Marina Parolini
- CNR Institute of Clinical Physiology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (J.C.); (M.P.)
| | - Rudina Ndreu
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (A.M.); (R.N.); (S.T.); (M.G.A.)
| | - Stefano Turchi
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (A.M.); (R.N.); (S.T.); (M.G.A.)
| | - Maria Grazia Andreassi
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (A.M.); (R.N.); (S.T.); (M.G.A.)
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16
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Zhu Y, Tazearslan C, Rosenfeld MG, Fiser A, Suh Y. Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16 INK4a. Aging Cell 2023; 22:e13908. [PMID: 37345431 PMCID: PMC10497822 DOI: 10.1111/acel.13908] [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: 12/11/2017] [Revised: 05/05/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications. The chromosome 9p21.3 locus is among the most replicated glaucoma risk loci discovered by GWAS. Nonetheless, the absence of protein-coding genes in the locus makes interpreting the disease association challenging, leaving the causal variant and molecular mechanism elusive. In this study, we report the identification of a functional glaucoma risk variant, rs6475604. By employing computational and experimental methods, we demonstrated that rs6475604 resides in a repressive regulatory element. Risk allele of rs6475604 disrupts the binding of YY1, a transcription factor known to repress the expression of a neighboring gene in 9p21.3, p16INK4A, which plays a crucial role in cellular senescence and aging. These findings suggest that the glaucoma disease variant contributes to accelerated senescence, providing a molecular link between glaucoma risk and an essential cellular mechanism for human aging.
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Affiliation(s)
- Yizhou Zhu
- Department of Obstetrics and GynecologyColumbia UniversityNew YorkNew YorkUSA
| | - Cagdas Tazearslan
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Michael G. Rosenfeld
- Department of MedicineSchool of MedicineUniversity of CaliforniaLa JollaCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Andras Fiser
- Department of Systems & Computational BiologyAlbert Einstein College of MedicineNew YorkNew YorkUSA
- Department of BiochemistryAlbert Einstein College of MedicineNew YorkNew YorkUSA
| | - Yousin Suh
- Department of Obstetrics and GynecologyColumbia UniversityNew YorkNew YorkUSA
- Department of Genetics and DevelopmentColumbia UniversityNew YorkNew YorkUSA
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17
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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18
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Zhu Y, Tazearslan C, Rosenfeld MG, Fiser A, Suh Y. Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16 INK4a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541339. [PMID: 37292862 PMCID: PMC10245730 DOI: 10.1101/2023.05.18.541339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications. The chromosome 9p21.3 locus is among the most replicated glaucoma risk loci discovered by GWAS. Nonetheless, the absence of protein-coding genes in the locus makes interpreting the disease association challenging, leaving the causal variant and molecular mechanism elusive. In this study, we report the identification of a functional glaucoma risk variant, rs6475604. By employing computational and experimental methods, we demonstrated that rs6475604 resides in a repressive regulatory element. Risk allele of rs6475604 disrupts the binding of YY1, a transcription factor known to repress the expression of a neighboring gene in 9p21.3, p16INK4A, which plays a crucial role in cellular senescence and aging. These findings suggest that the glaucoma disease variant contributes to accelerated senescence, providing a molecular link between glaucoma risk and an essential cellular mechanism for human aging.
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Affiliation(s)
- Yizhou Zhu
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032, USA
| | - Cagdas Tazearslan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY10461, USA
| | - Michael G. Rosenfeld
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Andras Fiser
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032, USA
- Department of Genetics and Development, Columbia University, New York, NY10032, USA
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19
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Severino P, D'Amato A, Prosperi S, Myftari V, Colombo L, Tomarelli E, Piccialuti A, Di Pietro G, Birtolo LI, Maestrini V, Badagliacca R, Sardella G, Fedele F, Vizza CD, Mancone M. Myocardial Infarction with Non-Obstructive Coronary Arteries (MINOCA): Focus on Coronary Microvascular Dysfunction and Genetic Susceptibility. J Clin Med 2023; 12:jcm12103586. [PMID: 37240691 DOI: 10.3390/jcm12103586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Among the most common causes of death worldwide, ischemic heart disease (IHD) is recognized to rank first. Even if atherosclerotic disease of the epicardial arteries is known as the leading cause of IHD, the presence of myocardial infarction with non-obstructive coronary artery disease (MINOCA) is increasingly recognized. Notwithstanding the increasing interest, MINOCA remains a puzzling clinical entity that can be classified by distinguishing different underlying mechanisms, which can be divided into atherosclerotic and non-atherosclerotic. In particular, coronary microvascular dysfunction (CMD), classifiable in non-atherosclerotic mechanisms, is a leading factor for the pathophysiology and prognosis of patients with MINOCA. Genetic susceptibility may have a role in primum movens in CMD. However, few results have been obtained for understanding the genetic mechanisms underlying CMD. Future studies are essential in order to find a deeper understanding of the role of multiple genetic variants in the genesis of microcirculation dysfunction. Progress in research would allow early identification of high-risk patients and the development of pharmacological, patient-tailored strategies. The aim of this review is to revise the pathophysiology and underlying mechanisms of MINOCA, focusing on CMD and actual knowledge about genetic predisposition to it.
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Affiliation(s)
- Paolo Severino
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Andrea D'Amato
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Silvia Prosperi
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Vincenzo Myftari
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Lorenzo Colombo
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Elisa Tomarelli
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Alice Piccialuti
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Gianluca Di Pietro
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Lucia Ilaria Birtolo
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Viviana Maestrini
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Roberto Badagliacca
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Gennaro Sardella
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Francesco Fedele
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Carmine Dario Vizza
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Massimo Mancone
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
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20
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Khan SU, Saeed S, Alsuhaibani AM, Fatima S, Ur Rehman K, Zaman U, Ullah M, Refati MS, Lu K. Advances and Challenges for GWAS Analysis in Cardiac Diseases: A Focus on Coronary Artery Disease (CAD). Curr Probl Cardiol 2023:101821. [PMID: 37211304 DOI: 10.1016/j.cpcardiol.2023.101821] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
The achievement of genome-wide association studies (GWAS) has rapidly progressed our understanding of the etiology of coronary artery disease (CAD). It unlocks new strategies to strengthen the stalling of CAD drug development. In this review, we highlighted the recent drawbacks, mainly pointing out those involved in identifying causal genes and interpreting the connections between disease pathology and risk variants. We also benchmark the novel insights into the biological mechanism behind the disease primarily based on outcomes of GWAS. Furthermore, we also shed light on the successful discovery of novel treatment targets by introducing various layers of "omics" data and applying systems genetics strategies. Lastly, we discuss in-depth the significance of precision medicine that is helpful to improve through GWAS analysis in cardiovascular research.
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Affiliation(s)
- Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, Pakistan
| | - Sumbul Saeed
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia
| | - Amnah Mohammed Alsuhaibani
- Department of Physical Sport Science, College of Education, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Sumaya Fatima
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Khalil Ur Rehman
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Umber Zaman
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Muneeb Ullah
- Department of Pharmacy, Kohat University of Science and Technology, 26000, KPK, Pakistan
| | - Moamen S Refati
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China.
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21
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Shen Y, Huang Z, Yang R, Chen Y, Wang Q, Gao L. Insights into Enhancer RNAs: Biogenesis and Emerging Role in Brain Diseases. Neuroscientist 2023; 29:166-176. [PMID: 34612730 DOI: 10.1177/10738584211046889] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enhancers are cis-acting elements that control the transcription of target genes and are transcribed into a class of noncoding RNAs (ncRNAs) termed enhancer RNAs (eRNAs). eRNAs have shorter half-lives than mRNAs and long noncoding RNAs; however, the frequency of transcription of eRNAs is close to that of mRNAs. eRNA expression is associated with a high level of histone mark H3K27ac and a low level of H3K27me3. Although eRNAs only account for a small proportion of ncRNAs, their functions are important. eRNAs can not only increase enhancer activity by promoting the formation of enhancer-promoter loops but also regulate transcriptional activation. Increasing numbers of studies have found that eRNAs play an important role in the occurrence and development of brain diseases; however, further research into eRNAs is required. This review discusses the concept, characteristics, classification, function, and potential roles of eRNAs in brain diseases.
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Affiliation(s)
- Yuxin Shen
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Zhengyi Huang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ruiqing Yang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yunlong Chen
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Qiang Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Linbo Gao
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
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22
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Buki G, Szalai R, Pinter A, Hadzsiev K, Melegh B, Rauch T, Bene J. Correlation between large FBN1 deletions and severe cardiovascular phenotype in Marfan syndrome: Analysis of two novel cases and analytical review of the literature. Mol Genet Genomic Med 2023:e2166. [PMID: 36945115 DOI: 10.1002/mgg3.2166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/26/2023] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Marfan syndrome (MFS) is a clinically heterogeneous hereditary connective tissue disorder. Severe cardiovascular manifestations (i.e., aortic aneurysm and dissection) are the most life-threatening complications. Most of the cases are caused by mutations, a minor group of which are copy number variations (CNV), in the FBN1 gene. METHODS Multiplex ligation-dependent probe amplification test was performed to detect CNVs in 41 MFS patients not carrying disease-causing mutations in FBN1 gene. Moreover, the association was analyzed between the localization of CNVs, the affected regulatory elements and the cardiovascular phenotypes among all cases known from the literature. RESULTS A large two-exon deletion (exon 46 and 47) was identified in two related patients, which was associated with a mild form of cardiovascular phenotype. Severe cardiovascular symptoms were found significantly more frequent in patients with FBN1 large deletion compared to our patients with intragenic small scale FBN1 mutation. Bioinformatic data analyses of regulatory elements located within the FBN1 gene revealed an association between the deletion of STAT3 transcription factor-binding site and cardiovascular symptoms in five out of 25 patients. CONCLUSION Our study demonstrated that large CNVs are often associated with severe cardiovascular manifestations in MFS and the localization of these CNVs affect the phenotype severity.
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Affiliation(s)
- Gergely Buki
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Renata Szalai
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Adrienn Pinter
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Bela Melegh
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Tibor Rauch
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
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23
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Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194906. [PMID: 36690178 PMCID: PMC10013089 DOI: 10.1016/j.bbagrm.2023.194906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Genome-wide association studies (GWAS) have mapped over 90 % of disease- or trait-associated variants within the non-coding genome, like cis-regulatory elements (CREs). Non-coding single nucleotide polymorphisms (SNPs) are genomic variants that can change how DNA-binding regulatory proteins, like transcription factors (TFs), interact with the genome and regulate gene expression. NKX2-5 is a TF essential for proper heart development, and mutations affecting its function have been associated with congenital heart diseases (CHDs). However, establishing a causal mechanism between non-coding genomic variants and human disease remains challenging. To address this challenge, we identified 8475 SNPs predicted to alter NKX2-5 DNA-binding using a position weight matrix (PWM)-based predictive model. Five variants were prioritized for in vitro validation; four of them are associated with traits and diseases that impact cardiovascular health. The impact of these variants on NKX2-5 binding was evaluated with electrophoretic mobility shift assay (EMSA) using purified recombinant NKX2-5 homeodomain. Binding curves were constructed to determine changes in binding between variant and reference alleles. Variants rs7350789, rs7719885, rs747334, and rs3892630 increased binding affinity, whereas rs61216514 decreased binding by NKX2-5 when compared to the reference genome. Our findings suggest that differential TF-DNA binding affinity can be key in establishing a causal mechanism of pathogenic variants.
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24
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Liu Y, Zhu ZX, Zboinski EK, Qiu W, Lian J, Liu S, Van Dyke TE, Johansson HE, Tu Q, Luo E, Chen JJ. Long non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues. RNA Biol 2023; 20:836-846. [PMID: 37953645 PMCID: PMC10653663 DOI: 10.1080/15476286.2023.2268489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 11/14/2023] Open
Abstract
The long noncoding RNA (lncR) ANRIL in the human genome is an established genetic risk factor for atherosclerosis, periodontitis, diabetes, and cancer. However, the regulatory role of lncR-ANRIL in bone and adipose tissue metabolism remains unclear. To elucidate the function of lncRNA ANRIL in a mouse model, we investigated its ortholog, AK148321 (referred to as lncR-APDC), located on chr4 of the mouse genome, which is hypothesized to have similar biological functions to ANRIL. We initially revealed that lncR-APDC in mouse bone marrow cells (BMSCs) and lncR-ANRIL in human osteoblasts (hFOBs) are both increased during early osteogenesis. Subsequently, we examined the osteogenesis, adipogenesis, osteoclastogenesis function with lncR-APDC deletion/overexpression cell models. In vivo, we compared the phenotypic differences in bone and adipose tissue between APDC-KO and wild-type mice. Our findings demonstrated that lncR-APDC deficiency impaired osteogenesis while promoting adipogenesis and osteoclastogenesis. Conversely, the overexpression of lncR-APDC stimulated osteogenesis, but impaired adipogenesis and osteoclastogenesis. Furthermore, KDM6B was downregulated with lncR-APDC deficiency and upregulated with overexpression. Through binding-site analysis, we identified miR-99a as a potential target of lncR-APDC. The results suggest that lncR-APDC exerts its osteogenic function via miR-99a/KDM6B/Hox pathways. Additionally, osteoclasto-osteogenic imbalance was mediated by lncR-APDC through MAPK/p38 and TLR4/MyD88 activation. These findings highlight the pivotal role of lncR-APDC as a key regulator in bone and fat tissue metabolism. It shows potential therapeutic for addressing imbalances in osteogenesis, adipogenesis, and osteoclastogenesis.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Zoe Xiaofang Zhu
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Elissa K. Zboinski
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Wei Qiu
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junxiang Lian
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
- Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shibo Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Thomas E. Van Dyke
- Center for Clinical and Translational Research, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection, and Immunity, Faculty of Medicine, Harvard University, Boston, MA, USA
| | - Hans E. Johansson
- Research and Development, LGC Biosearch Technologies, Petaluma, CA, USA
| | - Qisheng Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - En Luo
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
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25
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Islam Z, Saravanan B, Walavalkar K, Farooq U, Singh AK, Radhakrishnan S, Thakur J, Pandit A, Henikoff S, Notani D. Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries. Genome Res 2023; 33:1-17. [PMID: 36650052 PMCID: PMC9977152 DOI: 10.1101/gr.276643.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/10/2022] [Indexed: 01/19/2023]
Abstract
Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF and MYC TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.
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Affiliation(s)
- Zubairul Islam
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India;,Sastra Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Bharath Saravanan
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India;,Sastra Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Kaivalya Walavalkar
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India
| | - Umer Farooq
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India;,The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, Karnataka 560064, India
| | - Anurag Kumar Singh
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India
| | - Sabarinathan Radhakrishnan
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India
| | - Jitendra Thakur
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Awadhesh Pandit
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Dimple Notani
- National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India
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26
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Falahi S, Feizolahi P, Monshizadeh A, Mahmoudi Z, Mahdavi J, Salari F, Karaji AG, Rezaiemanesh A. Association of ANRIL Gene Single-Nucleotide Polymorphisms With Allergic Rhinitis in Kurdish Population From Kermanshah, Iran. THERAPEUTIC ADVANCES IN ALLERGY AND RHINOLOGY 2023; 14:27534030231170874. [PMID: 37200985 PMCID: PMC10185863 DOI: 10.1177/27534030231170874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/04/2023] [Indexed: 05/20/2023]
Abstract
Background Allergic rhinitis (AR) is the most common inflammatory disorder of the upper airway caused by aberrant immune responses to allergens in genetically predisposed individuals. Recently, the long noncoding RNA (lncRNA) antisense noncoding RNA in the INK4 locus (ANRIL) has been identified as a novel genetic factor associated with increased AR risk. Objectives This study aimed to evaluate the potential correlation of ANRIL gene single nucleotide polymorphisms (SNPs) with AR risk in the Kurdish population of Kermanshah, Iran. Methods In this case-control study, 130 AR patients and 130 healthy controls were recruited to genotype for two SNPs of the ANRIL gene (rs1333048 and rs10757278) using the Tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) method. Results Our results showed no significant difference for the alleles and genotypes frequency distribution of lncRNA ANRIL SNPs (rs1333048 and rs10757278) between AR patients and healthy controls (p > 0.05). Additionally, the dominant, additive and recessive genetic models of both SNPs were not associated with altered susceptibility to AR risk (p > 0.05). Conclusion The results demonstrated that the ANRIL gene rs1333048 and rs10757278 polymorphisms might not be associated with susceptibility to AR in the Kurdish population of Kermanshah, Iran.
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Affiliation(s)
- Sara Falahi
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parisa Feizolahi
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Monshizadeh
- Department of Pathology, Legal Medicine Organization, Kermanshah, Iran
| | - Zahra Mahmoudi
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Jila Mahdavi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Farhad Salari
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Gorgin Karaji
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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27
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Hu X, Guo L, Liu G, Dai Z, Wang L, Zhang J, Wang J. Novel cellular senescence-related risk model identified as the prognostic biomarkers for lung squamous cell carcinoma. Front Oncol 2022; 12:997702. [DOI: 10.3389/fonc.2022.997702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
BackgroundLung cancer is one of the top causes of cancer-related death worldwide. Cellular senescence is a characteristic of cell cycle arrest that plays a role in carcinogenesis and immune microenvironment modulation. Despite this, the clinical and immune cell infiltration features of senescence in lung squamous cell carcinoma (LUSC) are unknown.MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to get RNA-seq data and clinical information for LUSC. The least absolute shrinkage and selection operator (LASSO)-Cox regression, receiver operating characteristic (ROC), and Kaplan-Meier analysis were used to evaluate a risk model for predicting overall survival based on six differentially expressed genes. The tumor microenvironment (TME) and immunotherapy response were also studied.ResultsTo discriminate LUSC into high- and low-risk subgroups, a risk model comprised of six cellular senescence-related genes (CDKN1A, CEBPB, MDH1, SIX1, SNAI1, and SOX5) was developed. The model could stratify patients into high-risk and low-risk groups, according to ROC and Kaplan-Meier analysis. In the TCGA-LUSC and GSE73403 cohorts, the high-risk group had a worse prognosis (P<0.05), and was associated with immune cell inactivation and being insensitive to immunotherapy in IMvigor210.ConclusionsWe discovered a new LUSC classification based on six cellular senescence-related genes, which will aid in identifying patients who will benefit from anti-PD-1 treatment. Targeting senescence-related genes appears to be another option for improving clinical therapy for LUSC.
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Mahdavi S, Jenkins DJ, El-Sohemy A. Genetic variation in 9p21, dietary patterns, and insulin sensitivity. Front Genet 2022; 13:988873. [PMID: 36313440 PMCID: PMC9616109 DOI: 10.3389/fgene.2022.988873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Single nucleotide polymorphisms in the 9p21 region have been associated with cardiovascular disease and to a lesser extent insulin sensitivity. Previous studies have focused on older populations, and few have examined the impact of gene-diet interactions. The objective of this study was to determine the interaction between dietary patterns and 9p21 genotypes on insulin sensitivity in young adults from different ethnic groups. Methods: Subjects were 1,333 participants aged 20–29 years from the Toronto Nutrigenomics and Health Study (405 men and 928 women; 776 Caucasians and 557 East Asians). Fasting blood was collected to measure glucose, insulin, c-reactive protein and serum lipids, as well as to isolate DNA for genotyping subjects for five SNPs in 9p21 (rs10757274, rs10757278, rs1333049, rs2383206, and rs4977574). Insulin resistance (HOMA-IR) and beta-cell dysfunction (HOMA-Beta) were calculated from fasting insulin and glucose concentrations. The Toronto-modified Harvard 196-item semi-quantitative food frequency questionnaire was used to measure dietary intake over 1 month and principal components analysis was used to identify three dietary patterns (Prudent, Western and Eastern). ANOVA and ANCOVA were used to examine gene-diet interactions on markers of insulin sensitivity. Results: Significant gene-diet interactions on insulin sensitivity using HOMA-IR were observed with all five SNPs, which remained significant after adjusting for covariates (p < 0.05). Among those who were homozygous for the 9p21 risk allele (rs1333049), fasting insulin was 40% higher in those who were consuming a low-prudent diet compared to those consuming a high-prudent diet (p < 0.05). No differences were observed between those following a low versus high-prudent diet among those who did not carry a 9p21 risk allele. Similar findings were observed with HOMA-Beta, however, the association was only significant for rs10757274 (p = 0.04). Conclusion: Our findings suggest that a prudent dietary pattern may protect against the effects of 9p21 risk genotypes on insulin sensitivity.
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Affiliation(s)
- Sara Mahdavi
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, Risk Factor Modification Centre and Division of Endocrinology and Metabolism, St. Michael’s Hospital, St. Michael’s Health Centre, Toronto, ON, Canada
| | - David J.A. Jenkins
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, Risk Factor Modification Centre and Division of Endocrinology and Metabolism, St. Michael’s Hospital, St. Michael’s Health Centre, Toronto, ON, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- *Correspondence: Ahmed El-Sohemy,
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29
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Farooq U, Notani D. Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms. Front Cell Dev Biol 2022; 10:948351. [PMID: 36158211 PMCID: PMC9500187 DOI: 10.3389/fcell.2022.948351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 12/12/2022] Open
Abstract
9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16INK4a, p15INK4b, and p14ARF proteins, and it also harbors a long gene desert adjacent to these genes. The polymorphisms that are associated with several diseases and cancers are present in these genes and the gene desert region. These proteins are critical cell cycle regulators whose transcriptional dysregulation is strongly linked with cellular regeneration, stemness, aging, and cancers. Given the importance of this locus, intense scientific efforts on understanding the regulation of these genes via promoter-driven mechanisms and recently, via the distal regulatory mechanism have provided major insights. In this review, we describe these mechanisms and propose the ways by which this locus can be targeted in pathologies and aging.
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Affiliation(s)
- Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
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30
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Wei B, Liu Y, Li H, Peng Y, Luo Z. Effect of 9p21.3 (lncRNA and CDKN2A/2B) variant on lipid profile. Front Cardiovasc Med 2022; 9:946289. [PMID: 36158791 PMCID: PMC9489913 DOI: 10.3389/fcvm.2022.946289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background Several 9p21.3 variants, such as rs1333049, rs4977574, rs10757274, rs10757278, and rs10811661, identified from recent genome-wide association studies (GWASs) are reported to be associated with coronary artery disease (CAD) susceptibility but independent of dyslipidemia. This study investigated whether these 9p21.3 variants influenced lipid profiles. Methods and results By searching the PubMed and Cochrane databases, 101,099 individuals were included in the analysis. The consistent finding for the rs1333049 C allele on lipid profiles increased the triglyceride (TG) levels. Moreover, the rs4977574 G allele and the rs10757274 G allele, respectively, increased low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C) levels. However, the rs10811661 C allele largely reduced LDL-C levels. Subgroup analyses indicated that the effects of the rs1333049 C allele, rs4977574 G allele, and rs10757274 G allele on lipid profiles were stronger in Whites compared with Asians. In contrast, the effect of the rs10811661 C allele on lipid profiles was stronger in Asians compared with Whites. Conclusion The rs1333049 C allele, rs4977574 G allele, and rs10757274 G allele of lncRNA, and the rs10811661 G allele of CDKN2A/2B had a significant influence on lipid levels, which may help the understanding of the underlying mechanisms between 9p21.3 variants and CAD.
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Affiliation(s)
- Baozhu Wei
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
- *Correspondence: Baozhu Wei,
| | - Yang Liu
- Department of Endocrinology, China Resources and WISCO General Hospital, Wuhan, China
| | - Hang Li
- Department of Gerontology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yuanyuan Peng
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Zhi Luo
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Zhi Luo,
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31
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Sandhu RK, Dron JS, Liu Y, Moorthy MV, Chatterjee NA, Ellinor PT, Chasman DI, Cook NR, Khera AV, Albert CM. Polygenic Risk Score Predicts Sudden Death in Patients With Coronary Disease and Preserved Systolic Function. J Am Coll Cardiol 2022; 80:873-883. [PMID: 36007985 PMCID: PMC10460525 DOI: 10.1016/j.jacc.2022.05.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND A familial predisposition to sudden and/or arrhythmic death (SAD) in the setting of coronary artery disease (CAD) exists; however, the genetic basis is poorly understood. OBJECTIVES The purpose of this study was to determine whether a genome-wide polygenic score for coronary artery disease (GPSCAD) might have utility in SAD risk stratification in CAD patients without severe systolic dysfunction. METHODS A previously validated GPSCAD was generated utilizing genome-wide genotyping in 4,698 PRE-DETERMINE participants of European ancestry with CAD and left ventricular ejection fraction >30%-35%. The population was dichotomized according to top GPSCAD decile as defined by the general population, and absolute, proportional, and relative risks for SAD and non-SAD were estimated using competing risk analyses. RESULTS Over a median follow-up of 8.0 years, participants in the top GPSCAD decile were at elevated absolute SAD risk (8.0%; 95% CI: 5.1%-12.4% vs 4.8%; 95% CI: 3.3%-7.0%; P = 0.005) and proportional SAD risk (29% vs 16%; P = 0.0003) compared with the remainder. After controlling for left ventricular ejection fraction, clinical factors, and electrocardiogram parameters, the top GPSCAD decile was associated with SAD (subdistribution HR: 1.77; 95% CI: 1.23-2.54; P = 0.002) but not non-SAD (subdistribution HR: 1.00; 95% CI: 0.80-1.25; P = 0.98) (P for Δ = 0.003). The addition of the top GPSCAD decile to the multivariable model significantly improved net reclassification indexes (NRIs) (continuous NRI: 14.0%; P = 0.024; and categorical NRI: 6.6%; P = 0.005) but not the C-index (difference in C-index: 0.007; P = 0.143). CONCLUSIONS Among CAD patients without severe systolic dysfunction, high GPSCAD specifically predicted SAD and enriched for both absolute and proportional SAD risk, identifying a population who might benefit from defibrillator therapy.
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Affiliation(s)
- Roopinder K Sandhu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA; Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada
| | - Jacqueline S Dron
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yunxian Liu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - M Vinayaga Moorthy
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Neal A Chatterjee
- Division of Cardiology, University of Washington, Seattle, Washington, USA
| | - Patrick T Ellinor
- Division of Cardiology and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Nancy R Cook
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Amit V Khera
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Division of Cardiology and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Christine M Albert
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
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Bencivenga D, Stampone E, Vastante A, Barahmeh M, Della Ragione F, Borriello A. An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs. Cells 2022; 11:cells11081346. [PMID: 35456025 PMCID: PMC9028986 DOI: 10.3390/cells11081346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.
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Spiliopoulou P, Yang SC, Bruce JP, Wang BX, Berman HK, Pugh TJ, Siu LL. All is not lost: learning from 9p21 loss in cancer. Trends Immunol 2022; 43:379-390. [DOI: 10.1016/j.it.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
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Harley IT, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
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Affiliation(s)
- Isaac T.W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA,Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA,Rocky Mountain Regional Veteran’s Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA,Corresponding author at: Isaac TW Harley, MD, PhD, MS, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Barbara Davis Center, Mail Stop B115, 1775 Aurora Court, Aurora, CO 80045, USA, (I.T.W. Harley)
| | - Amr H. Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Corresponding author at: Amr H. Sawalha, MD, University of Pittsburgh, 7123 Rangos Research Center, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, (A.H. Sawalha)
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Miller EC, Wilczek A, Bello NA, Tom S, Wapner R, Suh Y. Pregnancy, preeclampsia and maternal aging: From epidemiology to functional genomics. Ageing Res Rev 2022; 73:101535. [PMID: 34871806 PMCID: PMC8827396 DOI: 10.1016/j.arr.2021.101535] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/15/2021] [Accepted: 12/01/2021] [Indexed: 01/03/2023]
Abstract
Women live longer than men but experience greater disability and a longer period of illness as they age. Despite clear sex differences in aging, the impact of pregnancy and its complications, such as preeclampsia, on aging is an underexplored area of geroscience. This review summarizes our current knowledge about the complex links between pregnancy and age-related diseases, including evidence from epidemiology, clinical research, and genetics. We discuss the relationship between normal and pathological pregnancy and maternal aging, using preeclampsia as a primary example. We review the results of human genetics studies of preeclampsia, including genome wide association studies (GWAS), and attempted to catalog genes involved in preeclampsia as a gateway to mechanisms underlying an increased risk of later life cardio- and neuro- vascular events. Lastly, we discuss challenges in interpreting the GWAS of preeclampsia and provide a functional genomics framework for future research needed to fully realize the promise of GWAS in identifying targets for geroprotective prevention and therapeutics against preeclampsia.
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Affiliation(s)
- Eliza C. Miller
- Department of Neurology, Division of Stroke and Cerebrovascular Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Ashley Wilczek
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie A. Bello
- Department of Medicine, Division of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah Tom
- Department of Neurology, Division of Neurology Clinical Outcomes Research and Population Science and the Department of Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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Mo L, Ma C, Wang Z, Li J, He W, Niu W, Chen Z, Zhou C, Liu Y. Integrated Bioinformatic Analysis of the Shared Molecular Mechanisms Between Osteoporosis and Atherosclerosis. Front Endocrinol (Lausanne) 2022; 13:950030. [PMID: 35937806 PMCID: PMC9353191 DOI: 10.3389/fendo.2022.950030] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Osteoporosis and atherosclerosis are common in the elderly population, conferring a heavy worldwide burden. Evidence links osteoporosis and atherosclerosis but the exact underlying common mechanism of its occurrence is unclear. The purpose of this study is to further explore the molecular mechanism between osteoporosis and atherosclerosis through integrated bioinformatic analysis. METHODS The microarray data of osteoporosis and atherosclerosis in the Gene Expression Omnibus (GEO) database were downloaded. The Weighted Gene Co-Expression Network Analysis (WGCNA) and differentially expressed genes (DEGs) analysis were used to identify the co-expression genes related to osteoporosis and atherosclerosis. In addition, the common gene targets of osteoporosis and atherosclerosis were analyzed and screened through three public databases (CTD, DISEASES, and GeneCards). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by Metascape. Then, the common microRNAs (miRNAs) in osteoporosis and atherosclerosis were screened out from the Human microRNA Disease Database (HMDD) and the target genes of whom were predicted through the miRTarbase. Finally, the common miRNAs-genes network was constructed by Cytoscape software. RESULTS The results of common genes analysis showed that immune and inflammatory response may be a common feature in the pathophysiology of osteoporosis and atherosclerosis. Six hub genes (namely, COL1A1, IBSP, CTSD, RAC2, MAF, and THBS1) were obtained via taking interaction of different analysis results. The miRNAs-genes network showed that has-let-7g might play an important role in the common mechanisms between osteoporosis and atherosclerosis. CONCLUSION This study provides new sights into shared molecular mechanisms between osteoporosis and atherosclerosis. These common pathways and hub genes may offer promising clues for further experimental studies.
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Affiliation(s)
- Liang Mo
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chao Ma
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhangzheng Wang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianxiong Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei He
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Research Institute for Orthopedics and Traumatology of Chinese Medicine, Guangzhou, China
| | - Wei Niu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhengqiu Chen
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Yuhao Liu, ; Chi Zhou, ; Zhengqiu Chen,
| | - Chi Zhou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Yuhao Liu, ; Chi Zhou, ; Zhengqiu Chen,
| | - Yuhao Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Yuhao Liu, ; Chi Zhou, ; Zhengqiu Chen,
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Sun Q, Chong F, Jiang X, Wang Y, Xu K, Zou Y, Song C. Association study of SNPs in LncRNA CDKN2B-AS1 with breast cancer susceptibility in Chinese Han population. Int J Biochem Cell Biol 2021; 143:106139. [PMID: 34954153 DOI: 10.1016/j.biocel.2021.106139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/12/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND The study aimed to analysis the genetic variation of the lncRNA CDKN2B-AS1 SNPs, and explored the regulation of SNPs on the invasion and metastasis of Breast cancer (BC). METHODS The SNPs (Single Nucleotide Polymorphisms) was screened for genotyping among 504 Chinese Han patients and 505 controls, which were frequency-matched for age ( ± 2 years). Logistic analysis was to explore the relationship between SNPs and the BC risk. Interactions between SNPs and reproductive factors was explored using the multifactor dimensionality reduction (MDR) method. qRT-PCR was conducted to detect the CDKN2B-AS1 expression in plasma of different rs10965215 and rs2518723 genotypes. The effect of rs10965215 A>G mutation on the binding ability of CDKN2B-AS1 and miR-4440 was verified by dual luciferase experiment. CCK-8, scratch and Transwell experiment were performed to explore the effect of miR-4440 over-expression on BC cell proliferation, migration and invasion. RESULTS A total of 13 SNP was screened. The individuals with SNPs rs2518723C>T, rs10965215 A>G, rs77792598C>G, rs4977753 T > C, rs75917766C>T and rs78545330C>G mutations might increase the BC risk. MDR results revealed that individuals with rs10965215 G genotype who age at menarche≥ 13 and regardless of the number of abortion< 2 or ≥ 2 had a higher risk of BC. The relative expression of CDKN2B-AS1 in rs10965215 homozygous wild AA genotype (8.88 ± 3.43) was lower than heterozygous GA (11.08 ± 2.90) and homozygous mutant GG genotype (11.31 ± 2.90). When rs10965215 wild A genotype was carried, there was an interaction between CDKN2B-AS1 and miR-4440. The CCK-8, Transwell, and scratch experiment were all found that miR-4440 over-expression might enhance the proliferation, invasion and migration of BC cells. - CONCLUSION CDKN2B-AS1 gene polymorphism might be related to the susceptibility of BC, CDKN2B-AS1 rs10965215 A/G genotype probably affect the proliferation, invasion and migration of BC cells by modulating the interactions with of miR-4440.
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Affiliation(s)
- Qiuyu Sun
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Feifei Chong
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Xiaoru Jiang
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Yanli Wang
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Kedi Xu
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Yuanlin Zou
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| | - Chunhua Song
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan Province, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, Henan Province, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province 450052, China.
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Davari DR, Orlow I, Kanetsky PA, Luo L, Edmiston SN, Conway K, Parrish EA, Hao H, Busam KJ, Sharma A, Kricker A, Cust AE, Anton-Culver H, Gruber SB, Gallagher RP, Zanetti R, Rosso S, Sacchetto L, Dwyer T, Ollila DW, Begg CB, Berwick M, Thomas NE. Disease-Associated Risk Variants in ANRIL Are Associated with Tumor-Infiltrating Lymphocyte Presence in Primary Melanomas in the Population-Based GEM Study. Cancer Epidemiol Biomarkers Prev 2021; 30:2309-2316. [PMID: 34607836 PMCID: PMC8643342 DOI: 10.1158/1055-9965.epi-21-0686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/19/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies have reported that genetic variation at ANRIL (CDKN2B-AS1) is associated with risk of several chronic diseases including coronary artery disease, coronary artery calcification, myocardial infarction, and type 2 diabetes mellitus. ANRIL is located at the CDKN2A/B locus, which encodes multiple melanoma tumor suppressors. We investigated the association of these variants with melanoma prognostic characteristics. METHODS The Genes, Environment, and Melanoma Study enrolled 3,285 European origin participants with incident invasive primary melanoma. For each of ten disease-associated SNPs at or near ANRIL, we used linear and logistic regression modeling to estimate, respectively, the per allele mean changes in log of Breslow thickness and ORs for presence of ulceration and tumor-infiltrating lymphocytes (TIL). We also assessed effect modification by tumor NRAS/BRAF mutational status. RESULTS Rs518394, rs10965215, and rs564398 passed false discovery and were each associated (P ≤ 0.005) with TILs, although only rs564398 was independently associated (P = 0.0005) with TILs. Stratified by NRAS/BRAF mutational status, rs564398*A was significantly positively associated with TILs among NRAS/BRAF mutant, but not wild-type, cases. We did not find SNP associations with Breslow thickness or ulceration. CONCLUSIONS ANRIL rs564398 was associated with TIL presence in primary melanomas, and this association may be limited to NRAS/BRAF-mutant cases. IMPACT Pathways related to ANRIL variants warrant exploration in relationship to TILs in melanoma, especially given the impact of TILs on immunotherapy and survival.
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Affiliation(s)
- Danielle R. Davari
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter A. Kanetsky
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Li Luo
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Sharon N. Edmiston
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathleen Conway
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eloise A. Parrish
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Honglin Hao
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Klaus J. Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ajay Sharma
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Anne E. Cust
- Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California, Irvine, Irvine, California
| | | | - Richard P. Gallagher
- BC Cancer and Department of Dermatology and Skin Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roberto Zanetti
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Stefano Rosso
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Lidia Sacchetto
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Terence Dwyer
- Murdoch Children's Research Institute, Melbourne, Australia
- The Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Oxford Martin School, University of Oxford, Oxford, United Kingdom
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Colin B. Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Nancy E. Thomas
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Liu S, Chen S, Niu T. Genetic association between CDKN2B-AS1 polymorphisms and the susceptibility of primary open-angle glaucoma (POAG): a meta-analysis from 21,775 subjects. Ir J Med Sci 2021; 191:2385-2392. [PMID: 34648117 PMCID: PMC9492586 DOI: 10.1007/s11845-021-02794-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Background Primary open-angle glaucoma (POAG) is affected by both genetics and environmental factors. CDKN2B-AS1 polymorphisms have been reported to be involved in the pathogenesis of POAG. However, the results of the genetic associations between the CDKN2B-AS1 polymorphisms and POAG risk were inconclusive. Aims This study aimed to evaluate the correlation of CDKN2B-AS1 polymorphisms and POAG susceptibility using a meta-analysis. Methods Meta-analysis was performed by searching PubMed, Web of science, the Cochrane database of system reviews, CNKI, and Embase databases. The relationship of CDKN2B-AS1 rs4977756, rs10120688, rs2157719, and rs7049105 polymorphisms and POAG risk was evaluated by the odds ratios (ORs) and 95% confidence intervals (CIs). Results Eleven studies with 8290 cases and 13,485 controls were included in the present meta-analysis. The alleles of rs4977756 and rs10120688 significantly increased the risk of POAG (rs4977756: OR = 1.20, 95%CI = 1.03–1.39, p = 0.02; rs10120688: OR = 1.36, 95%CI = 1.29–1.44, p < 0.00001). As for ethnicity, rs4977756 polymorphism significantly increased POAG risk in Caucasians (OR = 1.33, 95%CI = 1.12–1.57, p = 0.0009), but not in Asians. In addition, the rs2157719 allele was significantly associated with POAG risk in Asians (OR = 0.66, 95%CI = 0.55–0.80, p < 0.0001), but not in Caucasians (p > 0.05). Conclusions The CDKN2B-AS1 rs4977756 might increase the POAG risk in Caucasian population, and rs2157719 might decrease the POAG risk in Asian population, while rs10120688 might increase the risk of POAG.
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Affiliation(s)
- Shanshan Liu
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China
| | - Siwen Chen
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China
| | - Tongtong Niu
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China.
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Xu B, Xu Z, Chen Y, Lu N, Shu Z, Tan X. Genetic and epigenetic associations of ANRIL with coronary artery disease and risk factors. BMC Med Genomics 2021; 14:240. [PMID: 34615528 PMCID: PMC8496081 DOI: 10.1186/s12920-021-01094-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Both DNA genotype and methylation of antisense non-coding RNA in the INK4 locus (ANRIL) have been robustly associated with coronary artery disease (CAD), but the interdependent mechanisms of genotype and methylation remain unclear. METHODS Eighteen tag single nucleotide polymorphisms (SNPs) of ANRIL were genotyped in a matched case-control study (cases 503 and controls 503). DNA methylation of ANRIL and the INK4/ARF locus (p14ARF, p15INK4b and p16INK4a) was measured using pyrosequencing in the same set of samples (cases 100 and controls 100). RESULTS Polymorphisms of ANRIL (rs1004638, rs1333048 and rs1333050) were significantly associated with CAD (p < 0.05). The incidence of CAD, multi-vessel disease, and modified Gensini scores demonstrated a strong, direct association with ANRIL gene dosage (p < 0.05). There was no significant association between ANRIL polymorphisms and myocardial infarction/acute coronary syndrome (MI/ACS) (p > 0.05). Methylation levels of ANRIL were similar between the two studied groups (p > 0.05), but were different in the rs1004638 genotype, with AA and AT genotype having a higher level of ANRIL methylation (pos4, p = 0.006; pos8, p = 0.019). Further Spearman analyses indicated that methylation levels of ANRIL were positively associated with systolic blood pressure (pos6, r = 0.248, p = 0.013), diastolic blood pressure (pos3, r = 0.213, p = 0.034; pos6, r = 0.220, p = 0.028), and triglyceride (pos4, r = 0.253, p = 0.013), and negatively associated with high-density lipoprotein cholesterol (pos2, r = - 0.243, p = 0.017). Additionally, we identified 12 transcription factor binding sites (TFBS) within the methylated ANRIL region, and functional annotation indicated these TFBS were associated with basal transcription. Methylation at the INK4/ARF locus was not associated with ANRIL genotype. CONCLUSIONS These results indicate that ANRIL genotype (tag SNPs rs1004638, rs1333048 and rs1333050) mainly affects coronary atherosclerosis, but not MI/ACS. There may be allele-related DNA methylation and allele-related binding of transcription factors within the ANRIL promoter.
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Affiliation(s)
- Bayi Xu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Zhixia Xu
- Department of Medical Service, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yequn Chen
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Nan Lu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Zhouwu Shu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xuerui Tan
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China.
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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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Yang Z, Wang C, Erjavec S, Petukhova L, Christiano A, Ionita-Laza I. A semi-supervised model to predict regulatory effects of genetic variants at single nucleotide resolution using massively parallel reporter assays. Bioinformatics 2021; 37:1953–1962. [PMID: 33515242 PMCID: PMC8337004 DOI: 10.1093/bioinformatics/btab040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION Predicting regulatory effects of genetic variants is a challenging but important problem in functional genomics. Given the relatively low sensitivity of functional assays, and the pervasiveness of class imbalance in functional genomic data, popular statistical prediction models can sharply underestimate the probability of a regulatory effect. We describe here the presence-only model (PO-EN), a type of semi-supervised model, to predict regulatory effects of genetic variants at sequence-level resolution in a context of interest by integrating a large number of epigenetic features and massively parallel reporter assays (MPRAs). RESULTS Using experimental data from a variety of MPRAs we show that the presence-only model produces better calibrated predicted probabilities and has increased accuracy relative to state-of-the-art prediction models. Furthermore, we show that the predictions based on pre-trained PO-EN models are useful for prioritizing functional variants among candidate eQTLs and significant SNPs at GWAS loci. In particular, for the costimulatory locus, associated with multiple autoimmune diseases, we show evidence of a regulatory variant residing in an enhancer 24.4 kb downstream of CTLA4, with evidence from capture Hi-C of interaction with CTLA4. Furthermore, the risk allele of the regulatory variant is on the same risk increasing haplotype as a functional coding variant in exon 1 of CTLA4, suggesting that the regulatory variant acts jointly with the coding variant leading to increased risk to disease. AVAILABILITY The presence-only model is implemented in the R package 'PO.EN', freely available on CRAN. A vignette describing a detailed demonstration of using the proposed PO-EN model can be found on github at https://github.com/Iuliana-Ionita-Laza/PO.EN/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zikun Yang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Stephanie Erjavec
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Lynn Petukhova
- Department of Epidemiology, Columbia University, New York, NY 10032, USA
- Department of Dermatology, Columbia University, New York, NY 10032, USA
| | - Angela Christiano
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
- Department of Dermatology, Columbia University, New York, NY 10032, USA
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Chang KW, Hung WW, Chou CH, Tu HF, Chang SR, Liu YC, Liu CJ, Lin SC. LncRNA MIR31HG Drives Oncogenicity by Inhibiting the Limb-Bud and Heart Development Gene ( LBH) during Oral Carcinoma. Int J Mol Sci 2021; 22:ijms22168383. [PMID: 34445087 PMCID: PMC8395036 DOI: 10.3390/ijms22168383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
The miR-31 host gene (MIR31HG) encodes a long non-coding RNA (LncRNA) that harbors miR-31 in its intron 2; miR-31 promotes malignant neoplastic progression. Overexpression of MIR31HG and of miR-31 occurs during oral squamous cell carcinoma (OSCC). However, the downstream effectors modulated by MIR31HG during OSCC pathogenesis remain unclear. The present study identifies up-regulation of MIR31HG expression during the potentially premalignant disorder stage of oral carcinogenesis. The potential of MIR31HG to enhance oncogenicity and to activate Wnt and FAK was identified when there was exogenous MIR31HG expression in OSCC cells. Furthermore, OSCC cell subclones with MIR31HG deleted were established using a Crispr/Cas9 strategy. RNA sequencing data obtained from cells expressing MIR31HG, cells with MIR31HG deleted and cells with miR-31 deleted identified 17 candidate genes that seem to be modulated by MIR31HG in OSCC cells. A TCGA database algorithm pinpointed MMP1, BMP2 and Limb-Bud and Heart development (LBH) as effector genes controlled by MIR31HG during OSCC. Exogenous LBH expression decreases tumor cell invasiveness, while knockdown of LBH reverses the oncogenic suppression present in MIR31HG deletion subclones. The study provides novel insights demonstrating the contribution of the MIR31HG-LBH cascade to oral carcinogenesis.
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Affiliation(s)
- Kuo-Wei Chang
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (K.-W.C.); (H.-F.T.); (C.-J.L.)
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wan-Wen Hung
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
| | - Chung-Hsien Chou
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
| | - Hsi-Feng Tu
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (K.-W.C.); (H.-F.T.); (C.-J.L.)
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
- Department of Dentistry, National Yang Ming Chiao Tung Hospital, Yilan 260, Taiwan
| | - Shi-Rou Chang
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
| | - Ying-Chieh Liu
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
| | - Chung-Ji Liu
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (K.-W.C.); (H.-F.T.); (C.-J.L.)
- Department of Dentistry, Taipei MacKay Memorial Hospital, Taipei 104, Taiwan
| | - Shu-Chun Lin
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (K.-W.C.); (H.-F.T.); (C.-J.L.)
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-W.H.); (C.-H.C.); (S.-R.C.); (Y.-C.L.)
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Correspondence: ; Fax: +886-2-2826-4053
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Mushimiyimana I, Niskanen H, Beter M, Laakkonen JP, Kaikkonen MU, Ylä-Herttuala S, Laham-Karam N. Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis. Nucleic Acids Res 2021; 49:8078-8096. [PMID: 34320216 PMCID: PMC8373076 DOI: 10.1093/nar/gkab633] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/28/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
Super-enhancers are clusters of enhancers associated with cell lineage. They can be powerful gene-regulators and may be useful in cell-type specific viral-vector development. Here, we have screened for endothelial super-enhancers and identified an enhancer from within a cluster that conferred 5–70-fold increase in transgene expression. Importantly, CRISPR/Cas9 deletion of enhancers demonstrated regulation of ADAMTS18, corresponding to evidence of chromatin contacts between these genomic regions. Cell division-related pathways were primarily affected by the enhancer deletions, which correlated with significant reduction in cell proliferation. Furthermore, we observed changes in angiogenesis-related genes consistent with the endothelial specificity of this SE. Indeed, deletion of the enhancers affected tube formation, resulting in reduced or shortened sprouts. The super-enhancer angiogenic role is at least partly due to its regulation of ADAMTS18, as siRNA knockdown of ADAMTS18 resulted in significantly shortened endothelial sprouts. Hence, functional characterization of a novel endothelial super-enhancer has revealed substantial downstream effects from single enhancer deletions and led to the discovery of the cis-target gene ADAMTS18 and its role in endothelial function.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Mustafa Beter
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Johanna P Laakkonen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland.,Heart Center and Gene Therapy Unit; Kuopio University Hospital; Kuopio 70029, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio 70211, Finland
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45
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Teng EL, Masutani EM, Yeoman B, Fung J, Lian R, Ngo B, Kumar A, Placone JK, Lo Sardo V, Engler AJ. High shear stress enhances endothelial permeability in the presence of the risk haplotype at 9p21.3. APL Bioeng 2021; 5:036102. [PMID: 34327295 PMCID: PMC8315817 DOI: 10.1063/5.0054639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are exceedingly common in non-coding loci, and while they are significantly associated with a myriad of diseases, their specific impact on cellular dysfunction remains unclear. Here, we show that when exposed to external stressors, the presence of risk SNPs in the 9p21.3 coronary artery disease (CAD) risk locus increases endothelial monolayer and microvessel dysfunction. Endothelial cells (ECs) derived from induced pluripotent stem cells of patients carrying the risk haplotype (R/R WT) differentiated similarly to their non-risk and isogenic knockout (R/R KO) counterparts. Monolayers exhibited greater permeability and reactive oxygen species signaling when the risk haplotype was present. Addition of the inflammatory cytokine TNFα further enhanced EC monolayer permeability but independent of risk haplotype; TNFα also did not substantially alter haplotype transcriptomes. Conversely, when wall shear stress was applied to ECs in a microfluidic vessel, R/R WT vessels were more permeable at lower shear stresses than R/R KO vessels. Transcriptomes of sheared cells clustered more by risk haplotype than by patient or clone, resulting in significant differential regulation of EC adhesion and extracellular matrix genes vs static conditions. A subset of previously identified CAD risk genes invert expression patterns in the presence of high shear concomitant with altered cell adhesion genes, vessel permeability, and endothelial erosion in the presence of the risk haplotype, suggesting that shear stress could be a regulator of non-coding loci with a key impact on CAD.
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Affiliation(s)
- Evan L Teng
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Evan M Masutani
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Benjamin Yeoman
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Jessica Fung
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Rachel Lian
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Brenda Ngo
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Jesse K Placone
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Valentina Lo Sardo
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, USA
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46
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Yu H, Guo Y, Yang Z, Zhang Q, Xu J, Yang Q, Qu Y, Tan R, Li L, He Y, Li C, Zhang S, Luo B, Gao Y. Regulatory variation within 3’UTR of STAT5A correlates with sudden cardiac death in Chinese populations. Forensic Sci Res 2021; 7:726-735. [PMID: 37101540 PMCID: PMC9976584 DOI: 10.1080/20961790.2021.1895410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Definitive diagnosis to sudden cardiac death (SCD) is often challenging since the postmortem examination on SCD victims could hardly demonstrate an adequate cause of death. It is therefore important to uncover the inherited risk component to SCD. Signal transducer and activators of transcription 5 A (STAT5A) is a member of the STAT family and a transcription factor that is activated by many cell ligands and associated with various cardiovascular processes. In this study, we performed a systematic variant screening on the STAT5A to filter potential functional genetic variations. Based on the screening results, an insertion/deletion polymorphism (rs3833144) in 3'UTR of STAT5A was selected as the candidate variant. A total of 159 SCD cases and 668 SCD matched healthy controls was enrolled to perform a case-control study and evaluate the association between rs3833144 and SCD susceptibility in Chinese populations. Logistic regression analysis showed that the deletion allele of rs3833144 had significantly increased the SCD risk (odds ratio (OR) = 1.54; 95% confidence interval (CI) = 1.18-2.01; P = 0.000955). Further genotype-expression eQTL analysis showed that samples with deletion allele appeared to lower expression of STAT5A, and in silico prediction suggested the local 3 D structure changes of STAT5A mRNA caused by the variant. On the other hand, the bioinformatic analysis presented that promoters of RARA and PTGES3L-AARSD1 could interact with rs3833144, and eQTL analysis showed the higher expression of both genes in samples with deletion allele. Dual-luciferase activity assays also suggested the significant regulatory role of rs3833144 in gene transcription. Our current data thus suggested a possible involvement of rs3833144 to SCD predisposition in Chinese populations and rs3833144 with potential function roles may become a candidate marker for SCD diagnosis and prevention.
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Affiliation(s)
- Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Jiabin Xu
- Public Security Bureau of Taixing, Taizhou, China
| | - Qi Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yiling Qu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Rui Tan
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Bin Luo
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
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47
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López-Díez R, Egaña-Gorroño L, Senatus L, Shekhtman A, Ramasamy R, Schmidt AM. Diabetes and Cardiovascular Complications: The Epidemics Continue. Curr Cardiol Rep 2021; 23:74. [PMID: 34081211 PMCID: PMC8173334 DOI: 10.1007/s11886-021-01504-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW The cardiovascular complications of type 1 and 2 diabetes are major causes of morbidity and mortality. Extensive efforts have been made to maximize glycemic control; this strategy reduces certain manifestations of cardiovascular complications. There are drawbacks, however, as intensive glycemic control does not impart perennial protective benefits, and these efforts are not without potential adverse sequelae, such as hypoglycemic events. RECENT FINDINGS Here, the authors have focused on updates into key areas under study for mechanisms driving these cardiovascular disorders in diabetes, including roles for epigenetics and gene expression, interferon networks, and mitochondrial dysfunction. Updates on the cardioprotective roles of the new classes of hyperglycemia-targeting therapies, the sodium glucose transport protein 2 inhibitors and the agonists of the glucagon-like peptide 1 receptor system, are reviewed. In summary, insights from ongoing research and the cardioprotective benefits of the newer type 2 diabetes therapies are providing novel areas for therapeutic opportunities in diabetes and CVD.
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Affiliation(s)
- Raquel López-Díez
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Lander Egaña-Gorroño
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Laura Senatus
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Alexander Shekhtman
- Department of Chemistry, The State University of New York at Albany, Albany, NY USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
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48
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Phneh KY, Chong ETJ, Lee PC. Role of single nucleotide polymorphisms in susceptibility of stroke: A systemic review. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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49
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Zhang Q, Yu H, Yang Z, Li L, He Y, Zhu S, Li C, Zhang S, Luo B, Gao Y. A Functional Indel Polymorphism Within MIR155HG Is Associated With Sudden Cardiac Death Risk in a Chinese Population. Front Cardiovasc Med 2021; 8:671168. [PMID: 34136547 PMCID: PMC8200405 DOI: 10.3389/fcvm.2021.671168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
Sudden cardiac death (SCD) is a devastating complication of multiple disease processes and has gradually became a major public health issue. miR-155 is one of the best characterized miRNAs and plays a critical role in several physiological and pathological process, including cardiovascular diseases. In this study, we systematically screened the whole region of miR-155 host gene (MIR155HG) and identified a 4-bp insertion/deletion variant (rs72014506) residing in the intron region of MIR155HG as the candidate polymorphism. The association of rs72014506 with SCD susceptibility was evaluated using 166 SCD cases and 830 healthy controls in a Chinese population. Logistic regression analysis suggested that the homozygote del/del genotype significantly decreased the risk of SCD [odds ratio (OR) = 0.29; 95% confidence interval (CI) = 0.12–0.74; Ptrend = 0.0004]. Further genotype–expression association study using human myocardium tissue samples suggested that the deletion allele was intimately linked to lower the expression of both MIR155HG and mature miR155. Luciferase activity assay also revealed that the deletion allele of rs72014506 inhibited gene transcriptional activity. Finally, we performed electrophoretic mobility shift assay and verified the preferential binding affinity of the deletion allele with POU2F1 (POU domain class 2 transcription factor 1). Collectively, we have successfully identified a SCD risk conferring polymorphism in the MIR155HG gene and a likely biological mechanism for the decreased risk of SCD associated with the deletion allele. This novel variant may thus serve as a potential genetic marker for SCD diagnosis and prevention in natural populations, if validated by further studies with a larger sample size.
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Affiliation(s)
- Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China
| | - Shaohua Zhu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Bin Luo
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
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50
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Farooq U, Saravanan B, Islam Z, Walavalkar K, Singh AK, Jayani RS, Meel S, Swaminathan S, Notani D. An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus. Cell Rep 2021; 34:108898. [PMID: 33761351 PMCID: PMC7611173 DOI: 10.1016/j.celrep.2021.108898] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/13/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
The INK4a/ARF locus encodes important cell-cycle regulators p14ARF, p15INK4b, and p16INK4a. The neighboring gene desert to this locus is the most reproducible GWAS hotspot that harbors one of the densest enhancer clusters in the genome. However, how multiple enhancers that overlap with GWAS variants regulate the INK4a/ARF locus is unknown, which is an important step in linking genetic variation with associated diseases. Here, we show that INK4a/ARF promoters interact with a subset of enhancers in the cluster, independent of their H3K27ac and eRNA levels. Interacting enhancers transcriptionally control each other and INK4a/ARF promoters over long distances as an interdependent single unit. The deletion of even a single interacting enhancer results in an unexpected collapse of the entire enhancer cluster and leads to EZH2 enrichment on promoters in an ANRIL-independent manner. Dysregulated genes genome-wide mimic 9p21-associated diseases under these scenarios. Our results highlight intricate dependencies of promoter-interacting enhancers on each other.
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Affiliation(s)
- Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India; The University of Trans-Disciplinary Health Sciences and Technology, IVRI Road, Bangalore 560064, India
| | - Bharath Saravanan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India; Sastra Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Zubairul Islam
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India; Sastra Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Kaivalya Walavalkar
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Anurag Kumar Singh
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Ranveer Singh Jayani
- School of Medicine, Howard Hughes Medical Centre, University of California, La Jolla, La Jolla, CA 92093, USA
| | - Sweety Meel
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Sudha Swaminathan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India.
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