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Chamaria S, Johnson KW, Vengrenyuk Y, Baber U, Shameer K, Divaraniya AA, Glicksberg BS, Li L, Bhatheja S, Moreno P, Maehara A, Mehran R, Dudley JT, Narula J, Sharma SK, Kini AS. Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. Sci Rep 2017; 7:7001. [PMID: 28765529 PMCID: PMC5539108 DOI: 10.1038/s41598-017-07029-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/20/2017] [Indexed: 12/20/2022] Open
Abstract
Residual atherothrombotic risk remains higher in patients with versus without diabetes mellitus (DM) despite statin therapy. The underlying mechanisms are unclear. This is a retrospective post-hoc analysis of the YELLOW II trial, comparing patients with and without DM (non-DM) who received rosuvastatin 40 mg for 8–12 weeks and underwent intracoronary multimodality imaging of an obstructive nonculprit lesion, before and after therapy. In addition, blood samples were drawn to assess cholesterol efflux capacity (CEC) and changes in gene expression in peripheral blood mononuclear cells (PBMC). There was a significant reduction in low density lipoprotein-cholesterol (LDL-C), an increase in CEC and beneficial changes in plaque morphology including increase in fibrous cap thickness and decrease in the prevalence of thin cap fibro-atheroma by optical coherence tomography in DM and non-DM patients. While differential gene expression analysis did not demonstrate differences in PBMC transcriptome between the two groups on the single-gene level, weighted gene coexpression network analysis revealed two modules of coexpressed genes associated with DM, Collagen Module and Platelet Module, related to collagen catabolism and platelet function respectively. Bayesian network analysis revealed key driver genes within these modules. These transcriptomic findings might provide potential mechanisms responsible for the higher cardiovascular risk in DM patients.
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Affiliation(s)
| | - Kipp W Johnson
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA
| | | | - Usman Baber
- Mount Sinai Heart, Mount Sinai Hospital, New York, USA
| | - Khader Shameer
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA
| | - Aparna A Divaraniya
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA
| | - Benjamin S Glicksberg
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA
| | - Li Li
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA
| | | | - Pedro Moreno
- Mount Sinai Heart, Mount Sinai Hospital, New York, USA
| | | | - Roxana Mehran
- Mount Sinai Heart, Mount Sinai Hospital, New York, USA
| | - Joel T Dudley
- Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn Institute for Genetics and Genomic Sciences, Icahn School of Medicine, New York, USA.,Department of Population Health and Health Policy, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jagat Narula
- Mount Sinai Heart, Mount Sinai Hospital, New York, USA
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Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE. EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. Pac Symp Biocomput 2017; 22:120-131. [PMID: 27896968 PMCID: PMC5161348 DOI: 10.1142/9789813207813_0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Network reconstruction algorithms are increasingly being employed in biomedical and life sciences research to integrate large-scale, high-dimensional data informing on living systems. One particular class of probabilistic causal networks being applied to model the complexity and causal structure of biological data is Bayesian networks (BNs). BNs provide an elegant mathematical framework for not only inferring causal relationships among many different molecular and higher order phenotypes, but also for incorporating highly diverse priors that provide an efficient path for incorporating existing knowledge. While significant methodological developments have broadly enabled the application of BNs to generate and validate meaningful biological hypotheses, the reproducibility of BNs in this context has not been systematically explored. In this study, we aim to determine the criteria for generating reproducible BNs in the context of transcription-based regulatory networks. We utilize two unique tissues from independent datasets, whole blood from the GTEx Consortium and liver from the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Team (STARNET) study. We evaluated the reproducibility of the BNs by creating networks on data subsampled at different levels from each cohort and comparing these networks to the BNs constructed using the complete data. To help validate our results, we used simulated networks at varying sample sizes. Our study indicates that reproducibility of BNs in biological research is an issue worthy of further consideration, especially in light of the many publications that now employ findings from such constructs without appropriate attention paid to reproducibility. We find that while edge-to-edge reproducibility is strongly dependent on sample size, identification of more highly connected key driver nodes in BNs can be carried out with high confidence across a range of sample sizes.
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Affiliation(s)
- Ariella Cohain
- Icahn Institute and Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA*Co-first Authors
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