Omics: a Journal of Integrative Biology

Journal Information
ISSN / EISSN: 15362310 / 15578100
Total articles ≅ 1,329

Latest articles in this journal

Aishwarya Swain,
Published: 3 February 2023
Omics: a Journal of Integrative Biology; https://doi.org/10.1089/omi.2022.0180

Abstract:
Acinetobacter baumannii, an opportunistic gram-negative pathogen responsible for several nosocomial infections, has developed resistance to various antibiotics. Proteins involved in the two-component system (TCS), virulence, and antibiotic resistance (AR), help this pathogen in regulating antibiotic susceptibility and virulence mechanisms. The present study reports a network-based integrative omics approach to drug discovery to identify key regulatory proteins as therapeutic candidates against A. baumannii. We collected data on the TCS, virulence, and AR proteins from various databases (P2CS, VFDB, ARDB, and PAIDB), which were subjected to network, host–pathogen, and gene expression data analysis. Network analysis identified 43 hubs, and 10 proteins were found to be interacting with human proteins associated with vital pathways. Of the 53 (43 + 10) pathogen proteins, 46 had no orthologs in the human host. Twelve proteins, namely, RpfC, Wzc, OmpR, EnvZ, BfmS, PilG, histidine kinase, ABC 3 transport family protein, outer membrane porin OprD family, CsuD, Pgm, and LpxA, were differentially expressed in the resistant strain. We propose these proteins as key regulators that warrant evaluation as therapeutic target candidates in the future. Furthermore, structure prediction of ABC 3 transport family protein was performed as a case study. The findings from this study are poised to facilitate and inform drug discovery and development against A. baumannii.
Abhilash Barpanda, Ankit Halder, Ayushi Dhote, Shashwati Parihari, Chetan Kantharia,
Published: 1 February 2023
Omics: a Journal of Integrative Biology; https://doi.org/10.1089/omi.2022.0169

Abstract:
Colorectal cancer (CRC) is reportedly the second leading cause of cancer death worldwide. By the end of the decade, there will likely be more than one million fatalities worldwide from this cancer, with an estimated 2.2 million additional cases. We need new ways of thinking about cancer research. One approach is to deploy systems science using quantitative proteomics to obtain postgenomic and functional insights into cancer. The present study compares the tissue proteome of CRC (n = 10) with the matched peritumoral controls (n = 10) in samples obtained from the Indian subcontinent. When compared with the controls, a list of 22 substantially altered protein candidates was identified, which were associated with the growth, survival, and metastasis of the tumor. A list of the unique peptides from top significant proteins, including olfactomedin-4, alanyl aminopeptidase, and grancalcin was further validated using a parallel reaction monitoring-based targeted proteomics approach. In addition, biological pathway analysis showed perturbation in key biological processes, including dysregulation in purine metabolism, MYC targets in cancer, DNA repair, and replication, and leukocyte transendothelial migration, among others. The protein panel reported herein is also shown to be dysregulated in CRC and warrants further research toward understanding pathobiology, diagnostics, and therapeutics development in CRC.
, Aditi Mankad, Elizabeth V. Hobman
Published: 27 January 2023
Omics: a Journal of Integrative Biology; https://doi.org/10.1089/omi.2022.0181

Abstract:
Engaging diverse publics on the acceptability of large-scale biology applications such as gene drives is held in high regard by the international research community. The development of gene drives to suppress invasive and pest species and improvements to the sustainability of food systems are examples of integrative biology applications in engineering and ecology with the potential for large-scale research impact. Despite a global collective intention to ensure disruptive technologies are in broad alignment with wider social and public values, evidence of applied research organizations integrating the knowledge acquired from social research is hard to find. Concrete mechanisms to ensure public perspectives affect science decision-making are yet to emerge. We offer avenues for making inroads in what we identify as a remaining gap in public engagement research in the fields of synthetic biology and bioengineering.
Caíque Manóchio, Sabrina Torres-Loureiro, Mariana M. Scudeler, Bruno Miwa, Fernanda C. Souza-Santos,
Published: 4 January 2023
Omics: a Journal of Integrative Biology; https://doi.org/10.1089/omi.2022.0151

Abstract:
Coronavirus disease 2019 (COVID-19) is a systemic disease that impacts multiple organ systems with a complex clinical presentation and outcomes that can vary from person to person and between populations. To optimize COVID-19 treatment outcomes, and in light of the availability of antiviral drugs, there is a need for greater attention to the field of theranostics, the fusion of therapeutics and diagnostics. Theranostics tests would be invaluable, we suggest in this expert review, so as to optimize the efficacy and safety of current and future antiviral drugs against COVID-19. Theranostics would also assist in the design and implementation of clinical trials with antiviral drug candidates. We discuss here theranostics considering drugs such as remdesivir, Paxlovid™, and molnupiravir. All in all, we underscore that theranostics as a concept and practice is essential for efficient and safe health interventions against COVID-19 and other ecological crises in the 21st century.
Pooja Wakchoure, Khizra Momin,
Published: 1 January 2023
Omics: a Journal of Integrative Biology, Volume 27, pp 15-23; https://doi.org/10.1089/omi.2022.0130

Abstract:
Tuberculosis (TB) among patients with human immunodeficiency virus (HIV) is a major global health burden and contributes to a high mortality rate due to HIV-mediated immunosuppression and subsequent susceptibility to TB. It is imperative to understand the pathogenesis of the association between HIV and TB for therapeutic innovation and preventive medicine. In the present study, we employed transcriptomic and bioinformatic analyses of differential gene expression data obtained from Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information. The expression data of Mycobacterium tuberculosis-infected macrophages and blood samples from TB patients (GSE54992, GSE52819, and GSE19435) and blood samples from HIV patients (GSE30310) were accessed for identification of differentially expressed genes (DEGs). Data from 20 healthy subjects and 19 patients with TB and 16 healthy subjects and 16 patients with HIV were analyzed. We report here the DEGs shared by HIV and TB infection. Moreover, HIV and TB host–pathogen interaction data were collected from BIOGRID, v 4.4.210, for identifying significantly modulated genes' targets and their interactions with the host. Host targets, including PLSCR1 (phospholipid scramblase 1), STAT1 (signal transducer and activator of transcription-1 alpha/beta), FBXO6 (F-box only protein 6), ITGAL (integrin alpha-L), and APP (amyloid beta precursor protein), are commonly modulated in both diseases. The function of these targets was screened from and reconciled with the literature to understand their role in the pathogenesis of HIV and TB. Overall, the study results suggest that these targets may potentially be important contributors to the pathogenesis of this comorbidity. Further experimental work is needed for evaluating these new observations, with a view to future therapeutic innovation for patients with HIV and TB.
Muntadher Jihad,
Published: 1 January 2023
Omics: a Journal of Integrative Biology, Volume 27, pp 24-33; https://doi.org/10.1089/omi.2022.0170

Abstract:
Multiomics data integration is one of the leading frontiers of complex disease research and integrative biology. The advances in single-cell sequencing technologies offer yet another crucial dimension in multiomics research. The single-cell studies enable the study and integration of multiomics data simultaneously in the same cell. We report in this study multiomics data integration in single-cell resolution using Bayesian networks (BNs) in a case study of hepatocellular carcinoma (HCC). A BN encodes the conditional dependencies/independencies of variables using a graphical model with an accompanying joint probability. RNA-seq and Reduced Representation Bisulfite Sequencing data were analyzed separately, and copy number variations were estimated by the hidden Markov model method. Several BN models were constructed to reveal omics' causal and associational relationships. These methods were subjected to a validation study using an independent data set. We show the heterogeneity of the multiple cellular layers of HCC at single-cell omics resolution by identifying best-fitted BN models of 295 genes. We also provide novel insights into the multiomics mechanistic relationships in the human lymphocyte antigen class I genes in HCC. To the best of our knowledge, this is the first study to focus on integrating omics data using a machine learning algorithm, BNs, at the single-cell resolution using a case study of HCC.
, Salam Almasri, Yasemin Yuyucu Karabulut, Murat Korkmaz, Öznur Bucak, Sibel Oğuzkan Balcı
Published: 1 January 2023
Omics: a Journal of Integrative Biology, Volume 27, pp 34-44; https://doi.org/10.1089/omi.2022.0175

Abstract:
Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive memory loss and cognitive decline, with hallmark pathologies related to amyloid beta (Aβ) and TAU. Natural phytochemicals show promise for drug discovery to fill the current therapeutic innovation gap in AD. This study investigated the effect of cucurbitacin E (CuE), one of the bioactive components of Ecballium elaterium, on TAU fibril formation in okadaic acid-induced AD in rats. In a randomized design, we assigned 30 female Sprague Dawley rats to one of five experimental groups: (1) control, (2) stereotaxic surgery, (3) stereotaxic surgery + artificial cerebrospinal fluid, (4) stereotaxic surgery + okadaic acid (AD model), and (5) stereotaxic surgery + okadaic acid + CuE treatment. For experimental groups 4 and 5, rats were administered OKA-ICV (200 ng/kg) followed by CuE (4 mg/[kg·day], intraperitoneally) for 20 days. Expression of the MAPK1/3 and MAPK14 genes associated with TAU metabolism, hippocampal protein levels of these genes, cognitive functions of the rats, and histological accumulation of TAU in the brain were evaluated. Our findings in this preclinical model collectively suggest that phytochemical CuE contributes to memory gain by reducing TAU protein accumulation, which warrants further evaluation in future in vitro and in vivo studies.
Published: 27 December 2022
Omics: a Journal of Integrative Biology; https://doi.org/10.1089/omi.2023.29079.ack

Abstract:
OMICS: A Journal of Integrative Biology
Oveis Jamialahmadi, Ehsan Salehabadi, , Ehsan Motamedian, Fatemeh Bagheri, ,
Published: 1 December 2022
Omics: a Journal of Integrative Biology, Volume 26, pp 671-682; https://doi.org/10.1089/omi.2022.0122

Abstract:
Genome-scale metabolic modeling (GEM) is one of the key approaches to unpack cancer metabolism and for discovery of new drug targets. In this study, we report the Transcriptional Regulated Flux Balance Analysis-CORE (TRFBA-), an algorithm for GEM using key growth-correlated reactions using hepatocellular carcinoma (HCC), an important global health burden, as a case study. We generated a HepG2 cell-specific GEM by integrating this cell line transcriptomic data with a generic human metabolic model to forecast potential drug targets for HCC. A total of 108 essential genes for growth were predicted by the TRFBA-CORE. These genes were enriched for metabolic pathways involved in cholesterol, sterol, and steroid biosynthesis. Furthermore, we silenced a predicted essential gene, 11-beta dehydrogenase hydroxysteroid type 2 (HSD11B2), in HepG2 cells resulting in a reduction in cell viability. To further identify novel potential drug targets in HCC, we examined the effect of nine drugs targeting the essential genes, and observed that most drugs inhibited the growth of HepG2 cells. Some of these drugs in this model performed better than Sorafenib, the first-line therapeutic against HCC. A HepG2 cell-specific GEM highlights sterol metabolism to be essential for cell growth. HSD11B2 downregulation results in lower cell growth. Most of the compounds, selected by drug repurposing approach, show a significant inhibitory effect on cell growth in a wide range of concentrations. These findings offer new molecular leads for drug discovery for hepatic cancer while also illustrating the importance of GEM and drug repurposing in cancer therapeutics innovation.
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