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Hridoy HM, Haidar MN, Khatun C, Sarker A, Hossain MP, Aziz MA, Hossain MT. In silico based analysis to explore genetic linkage between atherosclerosis and its potential risk factors. Biochem Biophys Rep 2023; 36:101574. [PMID: 38024867 PMCID: PMC10652116 DOI: 10.1016/j.bbrep.2023.101574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Atherosclerosis (ATH) is a chronic cardiovascular disease characterized by plaque formation in arteries, and it is a major cause of illness and death. Although therapeutic advances have significantly improved the prognosis of ATH, missing therapeutic targets pose a significant residual threat. This research used a systems biology approach to identify the molecular biomarkers involved in the onset and progression of ATH, analysing microarray gene expression datasets from ATH and tissues impacted by risk factors such as high cholesterol, adipose tissue, smoking, obesity, sedentary lifestyle, stress, alcohol consumption, hypertension, hyperlipidaemia, high fat, diabetes to find the differentially expressed genes (DEGs). Bioinformatic analyses of Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on differentially expressed genes, revealing metabolic and signaling pathways (the chemokine signaling pathway, cytokine-cytokine receptor interaction, the cytosolic DNA-sensing pathway, the peroxisome proliferator-activated receptors signaling pathway, and the nuclear factor-kappa B signaling pathway), ten hubs proteins (CCL5, CCR1, TLR1, CCR2, FCGR2A, IL1B, CD163, AIF1, CXCL-1 and TNF), five transcription factors (YY1, FOXL1, FOXC1, SRF, and GATA2), and five miRNAs (mir-27a-3p, mir-124-3p, mir-16-5p, mir-129-2-3p, mir-1-3p). These findings identify potential biomarkers that may increase knowledge of the mechanisms underlying ATH and their connection to risk factors, aiding in the development of new therapies.
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Affiliation(s)
- Hossain Mohammad Hridoy
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nasim Haidar
- Department of Electrical and Electronic Engineering, Rangpur Engineering College, Rangpur, Bangladesh
| | - Chadni Khatun
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Arnob Sarker
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Pervez Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Abdul Aziz
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Tofazzal Hossain
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
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Genome-wide enrichment of m6A-associated single-nucleotide polymorphisms in the lipid loci. THE PHARMACOGENOMICS JOURNAL 2018; 19:347-357. [DOI: 10.1038/s41397-018-0055-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/07/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
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3
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Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non- BRCA1/2 high risk breast cancer families. Oncotarget 2017; 8:78691-78712. [PMID: 29108258 PMCID: PMC5667991 DOI: 10.18632/oncotarget.20219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Approximately 25% of hereditary breast cancer cases are associated with a strong familial history which can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome was undertaken to potentially reveal transcripts implicated in breast cancer susceptibility and development. RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals. We found 67 transcripts, which could discriminate BRCAX from BRCA1/BRCA2 individuals while 28 transcripts discriminate affected from unaffected BRCAX individuals. To our knowledge, this represents the first study identifying transcripts differentially expressed in lymphoblastoid cell lines from major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.
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Purwada A, Singh A. Immuno-engineered organoids for regulating the kinetics of B-cell development and antibody production. Nat Protoc 2016; 12:168-182. [PMID: 28005068 DOI: 10.1038/nprot.2016.157] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Induction of B-cell immunity against infection depends on the initiation of the germinal center (GC) reaction in secondary lymphoid organs. Ex vivo recapitulation of the GC reaction in 2D cultures results in transient cell growth, with poor yield and short-term survival. Furthermore, no reported 2D ex vivo system can modulate the kinetics of a GC-like phenotype or the rate of antibody class switching. This protocol describes a methodology for developing immune organoids that partially mimic the B-cell zone of a lymphoid tissue, for efficient and rapid generation of B cells with a GC-like phenotype from naive murine B cells. The organoid is composed of a bioadhesive protein, gelatin, that is transformed into an ionically cross-linked hydrated network using biocompatible silicate nanoparticles (SiNPs). We explain how to establish the immune organoid culture to sustain immune cell proliferation and transformation into a GC-like phenotype. Starting with cell encapsulation in digested lymphoid tissues, clusters of proliferating B cells with a GC-like phenotype can be generated in the organoids at controlled rates, within ∼1 week. The culture methodology described here is currently the only one that allows the accelerated induction of a GC-like phenotype in B cells and supports a controllable immunoglobulin class-switching reaction. This method can be easily implemented in a typical tissue culture room by personnel with standard mammalian cell culture expertise.
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Affiliation(s)
- Alberto Purwada
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Ankur Singh
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
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Fu R, Zhang Y, Guo Y, Zhang Y, Xu Y, Chen F. Digital gene expression analysis of the pathogenesis and therapeutic mechanisms of ligustrazine and puerarin in rat atherosclerosis. Gene 2014; 552:75-80. [DOI: 10.1016/j.gene.2014.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/18/2014] [Accepted: 09/08/2014] [Indexed: 01/30/2023]
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6
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Medina MW, Bauzon F, Naidoo D, Theusch E, Stevens K, Schilde J, Schubert C, Mangravite LM, Rudel LL, Temel RE, Runz H, Krauss RM. Transmembrane protein 55B is a novel regulator of cellular cholesterol metabolism. Arterioscler Thromb Vasc Biol 2014; 34:1917-23. [PMID: 25035345 DOI: 10.1161/atvbaha.113.302806] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Interindividual variation in pathways affecting cellular cholesterol metabolism can influence levels of plasma cholesterol, a well-established risk factor for cardiovascular disease. Inherent variation among immortalized lymphoblastoid cell lines from different donors can be leveraged to discover novel genes that modulate cellular cholesterol metabolism. The objective of this study was to identify novel genes that regulate cholesterol metabolism by testing for evidence of correlated gene expression with cellular levels of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) mRNA, a marker for cellular cholesterol homeostasis, in a large panel of lymphoblastoid cell lines. APPROACH AND RESULTS Expression array profiling was performed on 480 lymphoblastoid cell lines established from participants of the Cholesterol and Pharmacogenetics (CAP) statin clinical trial, and transcripts were tested for evidence of correlated expression with HMGCR as a marker of intracellular cholesterol homeostasis. Of these, transmembrane protein 55b (TMEM55B) showed the strongest correlation (r=0.29; P=4.0E-08) of all genes not previously implicated in cholesterol metabolism and was found to be sterol regulated. TMEM55B knockdown in human hepatoma cell lines promoted the decay rate of the low-density lipoprotein receptor, reduced cell surface low-density lipoprotein receptor protein, impaired low-density lipoprotein uptake, and reduced intracellular cholesterol. CONCLUSIONS Here, we report identification of TMEM55B as a novel regulator of cellular cholesterol metabolism through the combination of gene expression profiling and functional studies. The findings highlight the value of an integrated genomic approach for identifying genes that influence cholesterol homeostasis.
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Affiliation(s)
- Marisa W Medina
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.).
| | - Frederick Bauzon
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Devesh Naidoo
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Elizabeth Theusch
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Kristen Stevens
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Jessica Schilde
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Christian Schubert
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Lara M Mangravite
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Lawrence L Rudel
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Ryan E Temel
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Heiko Runz
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
| | - Ronald M Krauss
- From the Children's Hospital Oakland Research Institute, CA (M.W.M., F.B., D.N., E.T., K.S., R.M.K.); Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany (J.S., H.R.); Sage Bionetworks, Seattle, WA (L.M.M.); Section on Lipid Sciences, Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC (L.L.R., R.E.T.); and Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany (C.S., H.R.)
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Laguna JC, Alegret M. Regulation of gene expression in atherosclerosis: insights from microarray studies in monocytes/macrophages. Pharmacogenomics 2012; 13:477-95. [PMID: 22380002 DOI: 10.2217/pgs.12.9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atherosclerosis is a pathological phenomenon in which the walls of large arteries thicken and lose elasticity as a result of the growth of atheromatous lesions. It is a complex, multifactorial disease that involves several cell types and various pathobiological processes. Its genetic basis has not yet been deciphered, but it is related to complex multigene patterns influenced by environmental interactions. In this review, we focus specifically on the application of microarrays to atherosclerosis research using monocytes and monocyte-derived macrophages, as these are key cells in all phases of atherosclerosis, from the formation of foam cells to the destabilization and rupture of the atherosclerotic plaque. These studies have provided relevant information on genes involved in atherosclerosis development, contributing to our understanding of the molecular mechanisms that underlie this complex disease.
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Affiliation(s)
- Juan C Laguna
- Pharmacology Department, Faculty of Pharmacy & Institute of Biomedicine (IBUB), University of Barcelona, Spain
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Philibert RA, Beach SRH, Gunter TD, Brody GH, Madan A, Gerrard M. The effect of smoking on MAOA promoter methylation in DNA prepared from lymphoblasts and whole blood. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:619-628. [PMID: 19777560 PMCID: PMC3694401 DOI: 10.1002/ajmg.b.31031] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prior work using lymphoblast DNA prepared from 192 subjects from the Iowa Adoption Studies (IAS) demonstrated that decreased MAOA promoter methylation was associated with lifetime symptom count for nicotine dependence (ND) and provided suggestive evidence that the amount of methylation is genotype dependent. In the current investigation, we replicate and extend these prior findings in three ways using another 289 IAS subjects and the same methodologies. First, we show that methylation is dependent on current smoking status. Second, we introduce a factor analytic approach to DNA methylation, highlighting three distinct regions of the promoter that may function in somewhat different ways for males and females. Third, we directly compare the methylation signatures in DNA prepared from whole blood and lymphoblasts from a subset of these subjects and provide suggestive evidence favoring the use of lymphoblast DNA. We conclude that smoking reliably decreases MAOA methylation, but exact characterization of effects on level of methylation depend on genotype, smoking history, current smoking status, gender, and region of the promoter-associated CpG Island examined.
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Affiliation(s)
- Robert A. Philibert
- Department of Psychiatry, The University of Iowa, Iowa City, IA.
,Neuroscience and Genetics Programs, The University of Iowa, Iowa City, IA.
,To whom correspondence should be addressed. Rm 2-126 MEB Psychiatry Research/MEB, Iowa City, IA, USA. 52242-1000 TEL 319-353-4986, FAX 301-353-3003,
| | - Steven R. H. Beach
- Institute for Behavioral Research, The University of Georgia, Athens, GA
| | - Tracy D. Gunter
- Department of Psychiatry, The University of Iowa, Iowa City, IA
| | - Gene H. Brody
- Institute for Behavioral Research, The University of Georgia, Athens, GA
| | - Anup Madan
- The Swedish Hospital Institute for Neuroscience, Seattle, WA
| | - Meg Gerrard
- Norris Cotton Cancer Center, Dartmouth Medical Center, Lebanon, NH
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Bykhovskaya Y, Mengesha E, Fischel-Ghodsian N. Phenotypic expression of maternally inherited deafness is affected by RNA modification and cytoplasmic ribosomal proteins. Mol Genet Metab 2009; 97:297-304. [PMID: 19482502 PMCID: PMC2728627 DOI: 10.1016/j.ymgme.2009.05.003] [Citation(s) in RCA: 7] [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: 03/30/2009] [Revised: 04/30/2009] [Accepted: 05/02/2009] [Indexed: 01/06/2023]
Abstract
The homoplasmic mitochondrial A1555G mutation in the 12S rRNA gene leads to a mitochondrial translation disorder associated with deafness. The absence of disease in non-cochlear tissues in all patients, and in the cochlea in some patients, is not well understood. We used a system-based approach, including whole genome expression and biological function analysis, to elucidate the pathways underlying tissue specificity and clinical severity of this condition. Levels of over 48K RNA transcripts from EBV-transformed lymphoblasts of deaf and hearing individuals with the A1555G mutation and controls were obtained. Differentially expressed transcripts were functionally grouped using gene set enrichment analysis. Over 50 RNA binding proteins were differentially expressed between deaf and hearing individuals with the A1555G mutation (P-value of 2.56E-7), confirming previous genetic data implicating this pathway in the determination of the severity of hearing loss. Unexpectedly, the majority of cytoplasmic ribosomal genes were up-regulated in a coordinated fashion in individuals with the A1555G mutation versus controls (P-value of 3.91E-135). This finding was verified through real time RT-PCR, and through measuring of protein levels by flow cytometry. Analysis of expression levels of other differentially expressed genes suggests that this coordinated over-expression of cytoplasmic ribosomal proteins might occur through the Myc/Max pathway. We propose that expression levels of RNA binding proteins help determine the severity of the cochlear phenotype, and that coordinated up-regulation of the cytoplasmic translation apparatus operates as a compensation mechanism in unaffected tissues of patients with maternal deafness associated with the A1555G mutation.
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Affiliation(s)
- Yelena Bykhovskaya
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
| | - Emebet Mengesha
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
| | - Nathan Fischel-Ghodsian
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
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Collette JC, Chen XN, Mills DL, Galaburda AM, Reiss AL, Bellugi U, Korenberg JR. William's syndrome: gene expression is related to parental origin and regional coordinate control. J Hum Genet 2009; 54:193-8. [PMID: 19282872 DOI: 10.1038/jhg.2009.5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
William's syndrome (WS) features a spectrum of neurocognitive and behavioral abnormalities due to a rare 1.5 MB deletion that includes about 24-28 genes on chromosome band 7q11.23. Study of the expression of these genes from the single normal copy provides an opportunity to elucidate the genetic and epigenetic controls on these genes as well as their roles in both WS and normal brain development and function. We used quantitative RT-PCR to determine the transcriptional level of 14 WS gene markers in a cohort of 77 persons with WS and 48 normal controls. Results reported here: (1) show that the expression of the genes deleted in WS is decreased in some but not all cases, (2) demonstrate that the parental origin of the deletion contributes to the level of expression of GTF2I independently of age and gender and (3) indicate that the correlation of expression between GTF2I and some other genes in the WS region differs in WS subjects and normal controls, which in turn points toward a regulatory role for this gene. Interspecies comparisons suggest GTF2I may play a key role in normal brain development.
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Affiliation(s)
- Jeremy C Collette
- Division of Neurogenetics, Cedars-Sinai Medical Center and Departments of Human Genetics and Pediatrics, UCLA, Los Angeles, CA, USA
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11
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Llaverias G, Pou J, Ros E, Zambón D, Cofán M, Sánchez A, Vázquez-Carrera M, Sánchez RM, Laguna JC, Alegret M. Monocyte gene-expression profile in men with familial combined hyperlipidemia and its modification by atorvastatin treatment. Pharmacogenomics 2009; 9:1035-54. [PMID: 18681780 DOI: 10.2217/14622416.9.8.1035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The genetic origin of familial combined hyperlipidemia (FCH) is not well understood. We used microarray profiling of peripheral blood monocytes to search novel genes and pathways involved in FCH. METHODS Fasting plasma for determination of lipid profiles, inflammatory molecules and adipokines was obtained and peripheral blood monocytes were isolated from male FCH patients basally and after 4 weeks of atorvastatin treatment. Sex-, age- and adiposity-matched controls were also studied. Gene-expression profiles were analyzed using Affymetrix Human Genome U133A 2.0 GeneChip arrays. RESULTS Analysis of gene expression by cDNA microarrays showed that 82 genes were differentially expressed in FCH monocytes compared with controls. Atorvastatin treatment modified the expression of 86 genes. Pathway analysis revealed the over-representation of the complement and coagulation cascades, the hematopoietic cell lineage and the arachidonic acid metabolism pathways. Changes in the expression of some genes, confirmed by real-time RT-PCR, (CD36, leucine-rich repeats and immunoglobulin-like domains-1, tissue factor pathway inhibitor 2, myeloid cell nuclear differentiation antigen, tumor necrosis factor receptor superfamily, member 25, CD96 and lipoprotein lipase), may be related to a proinflammatory environment in FCH monocytes, which is partially reversed by atorvastatin. Higher plasma levels of triglycerides and free fatty acids and lower levels of adiponectin in FCH patients could also trigger changes in gene expression that atorvastatin cannot modify. CONCLUSION Our results show clear differences in gene expression in FCH monocytes compared with those of matched healthy controls, some of which are influenced by atorvastatin treatment.
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Affiliation(s)
- Gemma Llaverias
- Pharmacology Department, Faculty of Pharmacy and Biomedicine Institute (IBUB), University of Barcelona and Ciber Diabetes y Enfermedades Metabólicas asociadas (CIBERDEM), Instituto de Salud Carlos III, Diagonal 643. E-08028, Spain
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12
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Session 2: Personalised nutrition Transcriptomic signatures that have identified key features of metabolic syndrome. Proc Nutr Soc 2008; 67:395-403. [DOI: 10.1017/s0029665108008756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Human Genome Project and rapid advances in high-throughput molecular technologies are providing an unprecedented opportunity to advance the understanding of the common polygenic diet-related diseases, including obesity, the metabolic syndrome, type 2 diabetes mellitus, CVD and some cancers. In particular, transcriptomic approaches that allow multiple simultaneous gene-expression profiles facilitate the characterisation of metabolic perturbations that underlie diet-related pathologies. The present paper will focus on ‘transcriptomic signatures’ to characterise and understand the molecular mechanisms that accurately reflect ‘metabolic health’.
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13
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Aziz H, Zaas A, Ginsburg GS. Peripheral blood gene expression profiling for cardiovascular disease assessment. Genomic Med 2008; 1:105-12. [PMID: 18923935 DOI: 10.1007/s11568-008-9017-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2008] [Accepted: 01/25/2008] [Indexed: 12/18/2022] Open
Abstract
Whole blood gene expression profiling has the potential to be informative about dynamic changes in disease states and to provide information on underlying disease mechanisms. Having demonstrated proof of concept in animal models, a number of studies have now tried to tackle the complexity of cardiovascular disease in human hosts to develop better diagnostic and prognostic indicators. These studies show that genomic signatures are capable of classifying patients with cardiovascular diseases into finer categories based on the molecular architecture of a patient's disease and more accurately predict the likelihood of a cardiovascular event than current techniques. To highlight the spectrum of potential applications of whole blood gene expression profiling approach in cardiovascular science, we have chosen to review the findings in a number of complex cardiovascular diseases such as atherosclerosis, hypertension and myocardial infarction as well as thromboembolism, aortic aneurysm, and heart transplant.
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Affiliation(s)
- Hamza Aziz
- School of Medicine, Duke University, Durham, USA
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Philibert RA, Crowe R, Ryu GY, Yoon JG, Secrest D, Sandhu H, Madan A. Transcriptional profiling of lymphoblast lines from subjects with panic disorder. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:674-82. [PMID: 17342723 DOI: 10.1002/ajmg.b.30502] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In attempts to isolate genetic vulnerability factors for panic disorder (PD), a number of investigators have used genome-wide linkage or association analyses. But these attempts have been only modestly successful which suggests that alternative approaches may be needed to define the biology of PD. Therefore, using recently developed genome-wide gene expression profiling, we explored whether transcriptional signatures associated with PD are present in lymphoblast cell line. The expression of 2,469 transcripts in lymphoblast cell lines from 16 subjects was arithmetically increased in every line and significantly increased overall and 354 transcripts was arithmetically decreased in every cell line and significantly decreased overall as compared to those lymphoblast lines from 17 subjects without a history of behavioral illness. Further sex specific analyses showed that in those 10 lines derived from female probands, the expression of a further 67 transcripts was arithmetically increased in every line and significantly increased overall and a further 332 transcripts was arithmetically decreased in every cell line and significantly decreased. Conversely, in cell lines from the six male probands, the expression of an additional 212 was arithmetically increased in every line and significantly increased overall and a further 332 transcripts was arithmetically decreased in every cell line. We conclude that lymphoblast cell lines derived from subjects with PD have significant, partially sex dependent changes in gene transcription. Further studies are necessary to correlate these changes in these hemopoetically derived cells with those changes postulated to occur in the CNS in association with PD.
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Affiliation(s)
- Robert A Philibert
- Department of Psychiatry, The University of Iowa, Iowa City, Iowa 52242, USA.
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15
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Philibert RA, Ryu GY, Yoon JG, Sandhu H, Hollenbeck N, Gunter T, Barkhurst A, Adams W, Madan A. Transcriptional profiling of subjects from the Iowa adoption studies. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:683-90. [PMID: 17342724 DOI: 10.1002/ajmg.b.30512] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Transcriptional profiling has been used to identify gene expression patterns indicative of general medical illnesses such as atherosclerosis. However, whether these methods can identify common psychiatric disorders has not been established. To answer this question with respect to nicotine use, we used genome-wide expression profiling lymphoblast cell lines from six actively smoking Iowa Adoption Studies (IAS) subjects and nine "clean" control subjects, followed by real-time PCR (RT-PCR) of gene expression patterns in lymphoblast derived RNA from 94 subjects in the IAS. As compared to those from controls without a history of smoking (n = 9), the expression levels of 579 of 29,098 genes were significantly up-regulated and expression levels of 584 of 29,098 genes were significantly down-regulated in lymphoblast lines from currently smoking subjects (n = 6). RT-PCR confirmation of four select RNA levels confirmed the validity of the overall profile and revealed highly significant relationships between the expression of some of these transcripts and (1) major depression, (2) antisocial personality, (3) nicotine dependence, and (4) cannabis dependence. We conclude that the use of expression profiling may contribute significant insights into the biology of complex behavioral disorders.
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Affiliation(s)
- Robert A Philibert
- Department of Psychiatry, The University of Iowa, Iowa City, Iowa 52242, USA.
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16
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Bykhovskaya Y, Mengesha E, Fischel-Ghodsian N. Pleiotropic effects and compensation mechanisms determine tissue specificity in mitochondrial myopathy and sideroblastic anemia (MLASA). Mol Genet Metab 2007; 91:148-56. [PMID: 17374500 PMCID: PMC1986728 DOI: 10.1016/j.ymgme.2007.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 02/06/2007] [Indexed: 11/30/2022]
Abstract
The tissue specificity of mitochondrial diseases is poorly understood. Recently, tissue-specific quantitative differences of the components of the mitochondrial translation system have been found to correlate with disease presentation in fatal hepatopathy caused by mutations in mitochondrial translation factor EFG1. MLASA is an autosomal recessive inherited progressive oxidative phosphorylation disorder that affects muscle and erythroid cells. The disease is caused by the homozygous point mutation C656T (R116W) in the catalytic domain of the pseudouridylate synthase 1 (PUS1) gene, which leads to a complete lack of pseudouridylation at the expected sites in mitochondrial and cytoplasmic tRNAs. Despite the presence of these altered tRNAs, most tissues are unaffected, and even in muscle and erythroid cells the disease phenotype only slowly emerges over the course of years. In order to elucidate intracellular pathways through which the homozygous mutation leads to tissue-restricted phenotype, we performed microarray expression analysis of EBV-transformed lymphoblasts from MLASA patients, heterozygous parents, and controls using human Beadchip microarray with 47,296 transcripts. Genes coding for proteins involved in DNA transcription and its regulation, and metal binding proteins, demonstrated major differences in expression between patients and all other individuals with normal phenotype. Genes coding for ribosomal proteins differed significantly between individual with at least one copy of the mutated PUS1 gene and controls. These findings indicate that the lack of tRNA pseudouridylation can be overcome by compensatory changes in levels of ribosomal proteins, and that the disease phenotype in affected tissues is likely due to pleiotropic effects of PUS1p on non-tRNA molecules involved in DNA transcription and iron metabolism. Similar combinations of mechanisms may play a role in the tissue specificity of other mitochondrial disorders.
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Affiliation(s)
- Yelena Bykhovskaya
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Emebet Mengesha
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Nathan Fischel-Ghodsian
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Philibert R, Madan A, Andersen A, Cadoret R, Packer H, Sandhu H. Serotonin transporter mRNA levels are associated with the methylation of an upstream CpG island. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:101-5. [PMID: 16958039 DOI: 10.1002/ajmg.b.30414] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The serotonin reuptake transporter (5HTT) is thought to be the principal regulator of serotonergic activity and epigenetic effects at this locus are thought to be important moderators of vulnerability to neuropsychiatric illness. In attempt to understand the basis of this regulation, several gene polymorphisms that affect 5HTT mRNA levels have been described. But to date, no clear mechanism linking these polymorphisms to vulnerability to epigenetic effects have been described. In this communication, we describe a CpG island in the 5' region of the 5HTT gene that contains an alternative exon 1 and possible promoter for 5HTT. We then confirm the existence of this transcript and ascertain the methylation status of this CpG island in 49 lymphoblast cell lines and analyze the relationship between methylation and 5HTT mRNA levels. We demonstrate that methylation at this CpG island is associated with decreased levels of 5HTT mRNA, but that this effect is evident only when 5HTTLPR genotype is taken into account. We suggest that these findings have significant implications for the understanding of the role of this locus in behavioral illness.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, The University of Iowa, Psychiatry Research/MEB, Iowa City, Iowa, USA.
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van der Vleuten GM, Isaacs A, Hijmans A, van Duijn CM, Stalenhoef AFH, de Graaf J. The involvement of upstream stimulatory factor 1 in Dutch patients with familial combined hyperlipidemia. J Lipid Res 2006; 48:193-200. [PMID: 17065663 DOI: 10.1194/jlr.m600184-jlr200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, the upstream stimulatory factor 1 gene (USF1) was proposed as a candidate gene for familial combined hyperlipidemia (FCH). In this study, we examined the previously identified risk haplotype of USF1 with respect to FCH and its related phenotypes in 36 Dutch FCH families. The diagnosis of FCH was based on both the traditional diagnostic criteria and a nomogram. The two polymorphisms, USF1s1 and USF1s2, were in complete linkage disequilibrium. No association was found for the individual single nucleotide polymorphisms (SNPs) with FCH defined by the nomogram (USF1s1, P = 0.53; USF1s2, P = 0.53), whereas suggestive associations were found when using the traditional diagnostic criteria for FCH (USF1s1, P = 0.08; USF1s2, P = 0.07). USF1 was associated with total cholesterol (USF1s1, P = 0.05; USF1s2, P = 0.04) and apolipoprotein B (USF1s1, P = 0.06; USF1s2, P = 0.04). Small dense LDL showed a suggestive association (USF1s1, P = 0.10; USF1s2, P = 0.09). The results from the haplotype analyses supported the results obtained for the individual SNPs. In conclusion, the previously identified risk haplotype of USF1 showed a suggestive association with FCH and contributed to the related lipid traits in our Dutch FCH families.
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Affiliation(s)
- Gerly M van der Vleuten
- Department of Medicine, Division of General Internal Medicine, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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Ma J, Dempsey AA, Stamatiou D, Marshall KW, Liew CC. Identifying leukocyte gene expression patterns associated with plasma lipid levels in human subjects. Atherosclerosis 2006; 191:63-72. [PMID: 16806233 DOI: 10.1016/j.atherosclerosis.2006.05.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 03/22/2006] [Accepted: 05/03/2006] [Indexed: 02/07/2023]
Abstract
Plasma lipid levels have been known to be risk factors for atherosclerosis for decades, and in recent years it has become accepted that inflammation is a crucial event in the pathogenesis of atherosclerosis. In this study, we investigated the relationship between plasma lipids and leukocytes by profiling and analyzing leukocyte gene expression in response to plasma lipid levels. We discovered several interesting patterns of leukocyte gene expression: (1) the expression of a number of immune response- and inflammation-related genes are correlated with plasma lipid levels; (2) genes involved in lipid metabolism and in the electron transport chain were positively correlated with triglycerides and low-density lipoprotein cholesterol (LDL) levels, and negatively correlated with high-density lipoprotein cholesterol (HDL) levels; (3) genes involved in platelet activation were negatively correlated with HDL levels; (4) transcription factors regulating lipogenesis-related genes were correlated with plasma lipid levels; (5) a number of genes correlated with plasma lipid levels were found to be located in the regions of known quantitative trait loci (QTLs) associated with hyperlipemia. Our findings suggest that leukocytes respond to changing plasma lipid levels by regulating a network of genes, including genes involved in immune response, and lipid and fatty acid metabolism.
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Affiliation(s)
- Jun Ma
- ChondroGene, Inc., 800 Petrolia Road, Unit 15, Toronto, Ont., Canada M3J 3K4
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van der Vleuten GM, Hijmans A, Heil S, Blom HJ, Stalenhoef AFH, de Graaf J. Can we exclude theTXNIP gene as a candidate gene for familial combined hyperlipidemia? Am J Med Genet A 2006; 140:1010-2. [PMID: 16575890 DOI: 10.1002/ajmg.a.31181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Familial combined hyperlipidemia (FCHL) constitutes a substantial risk factor for atherosclerosis since it is observed in about 20% of coronary heart disease (CHD) patients under 60 years. FCHL, characterized by elevated levels of total cholesterol (TC) and triglycerides (TGs), or both, is also one of the most common familial hyperlipidemias with a prevalence of 1%-6% in Western populations. Numerous studies have been performed to identify genes contributing to FCHL. The recent linkage and association studies and their replications are beginning to elucidate the genetic variations underlying the susceptibility to FCHL. Three chromosomal regions on 1q21-23, 11p and 16q22-24.1 have been replicated in different study samples, offering targets for gene hunting. In addition, several candidate gene studies have replicated the influence of the lipoprotein lipase (LPL) gene and apolipoprotein A1/C3/A4/A5 (APOA1/C3/A4/A5) gene cluster in FCHL. Recently, the linked region on chromosome 1q21 was successfully fine-mapped and the upstream transcription factor 1 (USF1) gene identified as the underlying gene for FCHL. This finding has now been replicated in independent FCHL samples. However, the total number of variants, the risk related to each variant and their relative contributions to the disease susceptibility are not known yet.
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Affiliation(s)
- Elina Suviolahti
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-7088, USA
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Abstract
AbstractTraditional gene expression studies typically focus on one or a few genes of interest. An important limitation of single-gene studies is that they present a portrait of disease that is essentially static. However, disease is a dynamic process, driven by a combination of genetic, epigenetic and environmental factors. Recently, genomic technologies have permitted better characterization of the dynamic aspect of disease progression. Genome-wide expression profiles of cardiovascular diseases, heart failure in particular, using microarrays have been published and are providing new insights into this complex disease. Tissue biopsies required for traditional microarray studies, however, are often invasive and not readily available. By contrast, blood samples are relatively non-invasive and are readily available. In a number of recent studies, blood cells appear to be a viable substitute for tissue biopsy. Blood cells have the ability to mirror the body's tissues and organs in health and disease; thus, we hypothesize that blood cells can indicate at the molecular level the presence of disease. Here we review microarray gene expression profiling of blood RNA for a number of different diseases. Sieving through gene expression molecular signatures has identified groups of genes characteristic of each and has identified biomarkers associated with specific diseases.
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Affiliation(s)
- Choong Chin Liew
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA.
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