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Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [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: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
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Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
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Zahedian S, Hadizadeh M, Farazi MM, Jafarinejad-Farsangi S. MiRNA-miRNA interaction network in peripheral blood of patients with myocardial infarction: a gene expression meta-analysis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-18. [PMID: 38497563 DOI: 10.1080/15257770.2024.2330597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
In recent years, investigations have revealed that microRNAs (miRNAs) can bind together and form a miRNA-miRNA-mRNA regulatory network that alters the consequence of miRNA-mRNA interaction. If we consider the miRNA that binds to mRNA as the primary miRNA and the miRNA that binds to the primary miRNA as the secondary one, secondry miRNAs can act as master regulators upstream of primary miRNAs and their target mRNAs. One of the distinguishing characteristics of secondary miRNAs as master regulators within a diverse set of differentially expressed genes is the absence of direct target mRNA for them. Instead, these master regulators exclusively govern the regulation of miRNAs that target specific mRNAs. Through in silico analysis, we identified 18 miRNAs among 385 differentially expressed miRNAs (DEmiRNAs) with no direct target mRNAs among 58 differentially expressed mRNAs (DEmRNAs) in peripheral blood of patients with myocardial infarction (MI). Instead, these secondary miRNAs targeted 9 primary miRNAs that had 36 direct targets among 58 DEmRNAs. We found that one primary miRNA might be regulated by more than one secondary miRNAs and each secondary miRNA can target more than one primary miRNAs. Among identified miRNA-miRNA-mRNA networks miR-188-5p/miR-299-3p/natural killer cell granule protein (NKG7), miR-200a-3p/miR-199b-5p/granzyme B (GZMB), and miR-377-3p/miR-581/oviductal glycoprotein 1 (OVGP1) exhibited higher scors in terms of expression levels (>2-fold increase or decrease) and strengh of interactions (ΔG < -5). Given the extensive network of miRNA interactions, focusing on master regulators opens up avenues for identifying key regulatory nodes for more effective therapeutic strategies.
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Affiliation(s)
- Setareh Zahedian
- Student Research Committee, Kerman University of Medical Science, Kerman, Iran
| | - Morteza Hadizadeh
- Cardiovascular Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Mojtaba Farazi
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
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Meta-Analysis of RNA-Seq Datasets Identifies Novel Players in Glioblastoma. Cancers (Basel) 2022; 14:cancers14235788. [PMID: 36497269 PMCID: PMC9737249 DOI: 10.3390/cancers14235788] [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: 10/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Glioblastoma is a devastating grade IV glioma with poor prognosis. Identification of predictive molecular biomarkers of disease progression would substantially contribute to better disease management. In the current study, we performed a meta-analysis of different RNA-seq datasets to identify differentially expressed protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs). This meta-analysis aimed to improve power and reproducibility of the individual studies while identifying overlapping disease-relevant pathways. We supplemented the meta-analysis with small RNA-seq on glioblastoma tissue samples to provide an overall transcriptomic view of glioblastoma. Co-expression correlation of filtered differentially expressed PCGs and lncRNAs identified a functionally relevant sub-cluster containing DANCR and SNHG6, with two novel lncRNAs and two novel PCGs. Small RNA-seq of glioblastoma tissues identified five differentially expressed microRNAs of which three interacted with the functionally relevant sub-cluster. Pathway analysis of this sub-cluster identified several glioblastoma-linked pathways, which were also previously associated with the novel cell death pathway, ferroptosis. In conclusion, the current meta-analysis strengthens evidence of an overarching involvement of ferroptosis in glioblastoma pathogenesis and also suggests some candidates for further analyses.
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Kelly J, Berzuini C, Keavney B, Tomaszewski M, Guo H. A review of causal discovery methods for molecular network analysis. Mol Genet Genomic Med 2022; 10:e2055. [PMID: 36087049 PMCID: PMC9544222 DOI: 10.1002/mgg3.2055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND With the increasing availability and size of multi-omics datasets, investigating the casual relationships between molecular phenotypes has become an important aspect of exploring underlying biology andgenetics. There are an increasing number of methodlogies that have been developed and applied to moleular networks to investigate these causal interactions. METHODS We have introduced and reviewed the available methods for building large-scale causal molecular networks that have been developed and applied in the past decade. RESULTS In this review we have identified and summarized the existing methods for infering causality in large-scale causal molecular networks, and discussed important factors that will need to be considered in future research in this area. CONCLUSION Existing methods to infering causal molecular networks have their own strengths and limitations so there is no one best approach, and it is instead down to the discretion of the researcher. This review also to discusses some of the current limitations to biological interpretation of these networks, and important factors to consider for future studies on molecular networks.
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Affiliation(s)
- Jack Kelly
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and HealthUniversity of ManchesterManchesterUK
| | - Carlo Berzuini
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and HealthUniversity of ManchesterManchesterUK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and HealthUniversity of ManchesterManchesterUK
- Division of Cardiology and Manchester Academic Health Science CentreManchester University NHS Foundation TrustManchesterUK
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and HealthUniversity of ManchesterManchesterUK
- Manchester Heart Centre and Manchester Academic Health Science CentreManchester University NHS Foundation TrustManchesterUK
| | - Hui Guo
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and HealthUniversity of ManchesterManchesterUK
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Keel BN, Lindholm-Perry AK. Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq. Front Genet 2022; 13:983043. [PMID: 36199583 PMCID: PMC9527320 DOI: 10.3389/fgene.2022.983043] [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: 06/30/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates. Meta-analysis procedures can be used to integrate and jointly analyze data from multiple independent studies. Meta-analyses increase the sample size, which in turn increase both statistical power and robustness of the results. In this work, we discuss cutting edge approaches to combining results from multiple independent RNA-Seq studies to improve livestock transcriptomics research. We review currently published RNA-Seq meta-analyses in livestock, describe many of the key issues specific to RNA-Seq meta-analysis in livestock species, and discuss future perspectives.
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Ye Z, Mo C, Ke H, Yan Q, Chen C, Kochunov P, Hong LE, Mitchell BD, Chen S, Ma T. Meta-Analysis of Transcriptome-Wide Association Studies across 13 Brain Tissues Identified Novel Clusters of Genes Associated with Nicotine Addiction. Genes (Basel) 2021; 13:37. [PMID: 35052378 PMCID: PMC8775257 DOI: 10.3390/genes13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 12/01/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified and reproduced thousands of diseases associated loci, but many of them are not directly interpretable due to the strong linkage disequilibrium among variants. Transcriptome-wide association studies (TWAS) incorporated expression quantitative trait loci (eQTL) cohorts as a reference panel to detect associations with the phenotype at the gene level and have been gaining popularity in recent years. For nicotine addiction, several important susceptible genetic variants were identified by GWAS, but TWAS that detected genes associated with nicotine addiction and unveiled the underlying molecular mechanism were still lacking. In this study, we used eQTL data from the Genotype-Tissue Expression (GTEx) consortium as a reference panel to conduct tissue-specific TWAS on cigarettes per day (CPD) over thirteen brain tissues in two large cohorts: UK Biobank (UKBB; number of participants (N) = 142,202) and the GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN; N = 143,210), then meta-analyzing the results across tissues while considering the heterogeneity across tissues. We identified three major clusters of genes with different meta-patterns across tissues consistent in both cohorts, including homogenous genes associated with CPD in all brain tissues; partially homogeneous genes associated with CPD in cortex, cerebellum, and hippocampus tissues; and, lastly, the tissue-specific genes associated with CPD in only a few specific brain tissues. Downstream enrichment analyses on each gene cluster identified unique biological pathways associated with CPD and provided important biological insights into the regulatory mechanism of nicotine dependence in the brain.
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Affiliation(s)
- Zhenyao Ye
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Chen Mo
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Hongjie Ke
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD 20742, USA;
| | - Qi Yan
- Irving Medical Center, Department of Obstetrics & Gynecology, Columbia University, New York, NY 10032, USA;
| | - Chixiang Chen
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
| | - L. Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Shuo Chen
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD 20742, USA;
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