Citation: Manjunath, M.; Swaroop, S.; Pradhan, S.S.; Rao K, R.; Mahadeva, R.; Sivaramakrishnan, V.; Choudhary, B. Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor. Genes 2022, 13, 1208. https://doi.org/ 10.3390/genes13071208 Academic Editor: Seppo Ylä-Herttuala Received: 20 May 2022 Accepted: 29 June 2022 Published: 6 July 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). genes G C A T T A C G G C A T Article Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor Meghana Manjunath 1,2 , Sai Swaroop 3 , Sai Sanwid Pradhan 3 , Raksha Rao K 1,† , Raghunandan Mahadeva 1,† , Venketesh Sivaramakrishnan 3 and Bibha Choudhary 1, * 1 Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India; mmeghana@ibab.in (M.M.); raksharaok@gmail.com (R.R.K.); raghunandan.hunsur@gmail.com (R.M.) 2 Manipal Academy of Higher Education, Manipal 576104, Karnataka, India 3 Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur 515001, Andhra Pradesh, India; saiswaroopr@sssihl.edu.in (S.S.); saisanwidpradhan@sssihl.edu.in (S.S.P.); svenketesh@sssihl.edu.in(V.S.) * Correspondence: vibha@ibab.ac.in † These authors contributed equally to this work. Abstract: Transcriptomic profiling of several drugs in cancer cell lines has been utilised to obtain drug-specific signatures and guided combination therapy to combat drug resistance and toxicity. Global metabolomics reflects changes due to altered activity of enzymes, environmental factors, etc. Integrating transcriptomics and metabolomics can provide genotype-phenotype correlation, providing meaningful insights into alterations in gene expression and its outcome to understand differential metabolism and guide therapy. This study uses a multi-omics approach to understand the global gene expression and metabolite changes induced by Disarib, a novel Bcl2-specific inhibitor in the Ehrlich adenocarcinoma (EAC) breast cancer mouse model. RNAseq analysis was performed on EAC mouse tumours treated with Disarib and compared to the controls. The expression of 6 oncogenes and 101 tumour suppressor genes interacting with Bcl2 and Bak were modulated upon Disarib treatment. Cancer hallmark pathways like DNA repair, Cell cycle, angiogenesis, and mito- chondrial metabolism were downregulated, and programmed cell death platelet-related pathways were upregulated. Global metabolomic profiling using LC-MS revealed that Oncometabolites like carnitine, oleic acid, glycine, and arginine were elevated in tumour mice compared to normal and were downregulated upon Disarib treatment. Integrated transcriptomic and metabolomic profiles identified arginine metabolism, histidine, and purine metabolism to be altered upon Disarib treat- ment. Pro-angiogenic metabolites, arginine, palmitic acid, oleic acid, and myristoleic acid were downregulated in Disarib-treated mice. We further validated the effect of Disarib on angiogenesis by qRT-PCR analysis of genes in the VEGF pathway. Disarib treatment led to the downregulation of pro-angiogenic markers. Furthermore, the chorioallantoic membrane assay displayed a reduction in the formation of the number of secondary blood vessels upon Disarib treatment. Disarib reduces tumours by reducing oncometabolite and activating apoptosis and downregulating angiogenesis. Keywords: transcriptomics; metabolomics; Bcl2 inhibitors; gene expression; LC-MS; oncometabolite; angiogenesis 1. Introduction Breast cancer is a heterogeneous disease with a high diversity between and within subtypes. Recent advances in cancer development have led to selective targeting of deregu- lated molecules and pathways to achieve a rational cancer therapy. Such targets include mutant kinases, cancer stem cells, and tumour microenvironment, etc. [1]. The Bcl2 family of proteins are central regulators of the mitochondrial pathway of apoptosis, and more Genes 2022, 13, 1208. https://doi.org/10.3390/genes13071208 https://www.mdpi.com/journal/genes