Integrating Genes Affecting Coronary Artery Disease in Functional Networks by Multi-OMICs Approach

Vilne, Baiba; Schunkert, Heribert

doi:10.3389/fcvm.2018.00089

Cited by 28 publications

(34 citation statements)

References 100 publications

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“…Therefore, a better understanding of the disease aetiology and more efficient therapies are needed. Genetic predisposition as well as environmental factors and lifestyle are thought to contribute to disease risk 2 . Cardiovascular risk is assessed mainly on the basis of classic risk factors, such as age, gender, smoking status, blood pressure, glucose levels, and lipid levels.…”

Section: Introductionmentioning

confidence: 99%

TREML4 mRNA Expression and Polymorphisms in Blood Leukocytes are Associated with Atherosclerotic Lesion Extension in Coronary Artery Disease

Duarte

Miranda

Cruz

et al. 2019

Sci Rep

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Members of the triggering receptor expressed on myeloid cells (TREM) family are associated with atherosclerosis risk and progression. TREML4 is upregulated in the early phase of acute coronary syndrome. We investigated the relationship between the mRNA expression of 13 genes in blood leukocytes, TREML4 polymorphisms, and coronary artery lesion extension (Friesinger index) in patients with coronary artery disease (CAD) (n = 137). TREML4 rs2803495 (A > G) and rs2803496 (T > C) variants and leukocyte mRNA expression were analysed by qRT-PCR. TREML4 expression was higher in patients with major coronary artery lesions than in subjects without or with low and intermediate lesions ( p < 0.05). However, TREML4 polymorphisms were not associated with coronary lesion extent. Presence of the rs2803495 G allele was not associated with increased TREML4 mRNA expression. Patients carrying the rs2803496 C allele (TC/CC genotypes) were more likely to express TREML4 mRNA than non-C allele carriers (allele C: OR 7.3, and 95% CI 1.9–27.5, p = 0.03). In conclusion, increased TREML4 mRNA expression in blood leukocytes is influenced by gene polymorphisms and is associated with more severe coronary artery lesions, suggesting its potential as a biomarker of the extent of coronary lesions in patients with CAD.

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Section: Introductionmentioning

confidence: 99%

TREML4 mRNA Expression and Polymorphisms in Blood Leukocytes are Associated with Atherosclerotic Lesion Extension in Coronary Artery Disease

Duarte

Miranda

Cruz

et al. 2019

Sci Rep

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“…Integration of multi-omics can generate new information and improve classification accuracy that are not accessible by analysis of single datasets alone [50][51]. For instance, Liu et al demonstrated that the integration of multiple omics improved the validity of functional analysis of differentially expressed miRNAs using intersection genes and constructed a ceRNA relationship network in broody chickens [52].…”

Section: Discussionmentioning

confidence: 99%

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Wang¹,

Chai²,

Zhong³

et al. 2019

Preprint

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Background: the yak (Bos grunniens) is one of the major livestock that can survive the extremely cold, harsh and oxygen-poor conditions and provide meat, milk and transportation for Tibetans living in the Qinghai-Tibetan Plateau, and there are some cattle migrate to yak habitat but cannot survive the extremely conditions well. However, the regulatory mechanisms that drive hypoxic adaptation of yak remain elusive. Results: Thus, we collected heart tissues from Leiwuqi (LWQ) yak and their relatives, the migration cattle in LWQ yak habitat (HAC) and low-altitude cattle (LAC), respectively, for RNA sequencing, 178 co-differentially expressed protein-coding transcripts (CETs) including 6 down-regulated and 172 up-regulated CETs were discovered in both LAC-vs-LWQY and LAC-vs-HAC comparison groups. There were 133, 11 and 3 lncRNA transcripts were specific expressed in LWQY, HAC, and LAC groups, respectively. 2 and 230 lncRNA transcripts differentially expressed in LAC-vs-LWQY and LAC-vs-HAC，respectively, but no lncRNA transcripts co-differentially expressed in those two comparison groups. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and 1 down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiply CETs which are the target genes for miRNAs/lncRNAs were significantly enriched in high-altitude adaptation related processes, for instance, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network by integrating competing relationships among CETs, miRNAs, lncRNAs and circRNAs were constructed. Furthermore, we constructed a hypoxic adaptation related ceRNA network to identified that 8 miRNAs and 15 circRNAs were predicted to regulated MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1 and F2R genes. Conclusion: In conclusion, our data reinforce the view that the molecular network of high-altitude adaptation is composed of several protein-coding transcripts and non-coding transcripts that involved in multiply hypoxic adaptation regulatory pathways. The detailed mechanism for how this network crosstalk each other in heart of Bovidae are worthy of future research efforts.

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“…Secondly, omics data should be seen as a whole, with each type of data being a piece of the puzzle which needs to be integrated with the other pieces in order to fully elucidate the intrinsic mechanisms underlying SC-mediated cardiac protection and regeneration [51,184,185].…”

Section: Challenges In Omics Data Managementmentioning

confidence: 99%

The Winding Road of Cardiac Regeneration—Stem Cell Omics in the Spotlight

Micheu

Scărlătescu

Scafa-Udriște

et al. 2018

Cells

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Despite significant progress in treating ischemic cardiac disease and succeeding heart failure, there is still an unmet need to develop effective therapeutic strategies given the persistent high-mortality rate. Advances in stem cell biology hold great promise for regenerative medicine, particularly for cardiac regeneration. Various cell types have been used both in preclinical and clinical studies to repair the injured heart, either directly or indirectly. Transplanted cells may act in an autocrine and/or paracrine manner to improve the myocyte survival and migration of remote and/or resident stem cells to the site of injury. Still, the molecular mechanisms regulating cardiac protection and repair are poorly understood. Stem cell fate is directed by multifaceted interactions between genetic, epigenetic, transcriptional, and post-transcriptional mechanisms. Decoding stem cells’ “panomic” data would provide a comprehensive picture of the underlying mechanisms, resulting in patient-tailored therapy. This review offers a critical analysis of omics data in relation to stem cell survival and differentiation. Additionally, the emerging role of stem cell-derived exosomes as “cell-free” therapy is debated. Last but not least, we discuss the challenges to retrieve and analyze the huge amount of publicly available omics data.

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Integrating Genes Affecting Coronary Artery Disease in Functional Networks by Multi-OMICs Approach

Cited by 28 publications

References 100 publications

TREML4 mRNA Expression and Polymorphisms in Blood Leukocytes are Associated with Atherosclerotic Lesion Extension in Coronary Artery Disease

TREML4 mRNA Expression and Polymorphisms in Blood Leukocytes are Associated with Atherosclerotic Lesion Extension in Coronary Artery Disease

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

The Winding Road of Cardiac Regeneration—Stem Cell Omics in the Spotlight

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