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Sridhar A, More AS, Jadhav AR, Patil K, Mavlankar A, Dixit VM, Bapat SA. Pattern recognition in the landscape of seemingly random chimeric transcripts. Comput Struct Biotechnol J 2023; 21:5153-5164. [PMID: 37920814 PMCID: PMC10618115 DOI: 10.1016/j.csbj.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
The molecular and functional diversity generated by chimeric transcripts (CTs) that are derived from two genes is indicated to contribute to tumor cell survival. Several gaps yet exist. The present research is a systematic study of the spectrum of CTs identified in RNA sequencing datasets of 160 ovarian cancer samples in the The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov). Structural annotation revealed complexities emerging from chromosomal localization of partner genes, differential splicing and inclusion of regulatory, untranslated regions. Identification of phenotype-specific associations further resolved a dynamically modulated mesenchymal signature during transformation. On an evolutionary background, protein-coding CTs were indicated to be highly conserved, while non-coding CTs may have evolved more recently. We also realized that the current premise postulating structural alterations or neighbouring gene readthrough generating CTs is not valid in instances wherein the parental genes are genomically distanced. In addressing this lacuna, we identified the essentiality of specific spatiotemporal arrangements mediated gene proximities in 3D space for the generation of CTs. All these features together suggest non-random mechanisms towards increasing the molecular diversity in a cell through chimera formation either in parallel or with cross-talks with the indigenous regulatory network.
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Affiliation(s)
- Aksheetha Sridhar
- Open Health Systems Laboratory, 9601 Medical Centre Drive, Rockville, MD 20850, US
| | - Ankita S. More
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Amruta R. Jadhav
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Komal Patil
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Anuj Mavlankar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Vaishnavi M. Dixit
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Sharmila A. Bapat
- Open Health Systems Laboratory, 9601 Medical Centre Drive, Rockville, MD 20850, US
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
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More MH, Varankar SS, Naik RR, Dhake RD, Ray P, Bankar RM, Mali AM, Subbalakshmi AR, Chakraborty P, Jolly MK, Bapat SA. A Multistep Tumor Growth Model of High-Grade Serous Ovarian Carcinoma Identifies Hypoxia-Associated Signatures. Cells Tissues Organs 2022; 213:79-95. [PMID: 35970135 DOI: 10.1159/000526432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSC) is associated with late-stage disease presentation and poor prognosis, with a limited understanding of early transformation events. Our study analyzes HGSC tumor progression and organ-specific metastatic dissemination to identify hypoxia-associated molecular, cellular, and histological alterations. Clinical characteristics of the HGSC were replicated in orthotopic xenografts, which involve metastatic dissemination and the prevalence of group B tumors (volume: >0.0625 ≤ 0.5 cm3). Enhanced hyaluronic acid (HA) deposition, expanded tumor vasculature, and increased necrosis contributed to the remodeling of tumor tissue architecture. The proliferative potential of tumor cells and the ability to form glands were also altered during tumor growth. Flow cytometry and label chase-based molecular profiling across the tumor regenerative hierarchy identified the hypoxia-vasculogenic niche and the hybrid epithelial-mesenchymal tumor-cell state as determinants of self-renewal capabilities of progenitors and cancer stem cells. A regulatory network and mathematical model based on tumor histology and molecular signatures predicted hypoxia-inducible factor 1-alpha (HIF1A) as a central node connecting HA synthesis, epithelial-mesenchymal transition, metabolic, vasculogenic, inflammatory, and necrotic pathways in HGSC tumors. Thus, our findings provide a temporal resolution of hypoxia-associated events that sculpt HGSC tumor growth; an in-depth understanding of it may aid in the early detection and treatment of HGSC.
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Affiliation(s)
- Madhuri H More
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Sagar S Varankar
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Rutika R Naik
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Rahul D Dhake
- Department of Histopathology, Inlaks and Budhrani Hospital, Morbai Naraindas Cancer Institute, Pune, India
| | - Pritha Ray
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Rahul M Bankar
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Avinash M Mali
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | | | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
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Kalra RS, Soman GS, Parab PB, Mali AM, Varankar SS, Naik RR, Kamble SC, Dhanjal JK, Bapat SA. A monoclonal antibody against annexin A2 targets stem and progenitor cell fractions in tumors. Transl Oncol 2021; 15:101257. [PMID: 34715620 PMCID: PMC8564672 DOI: 10.1016/j.tranon.2021.101257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
Development of a novel antibody (termed as mAb150) developed in our lab which targets annexin A2. Although there are earlier reports of another monoclonal antibody with the same target, the epitope recognized by mAb150 is novel. mAb150 is specifically recognized to target the achilles heel of cancer viz. cancer stem cells and progenitors that persist after treatments and potentially give rise to minimal residual disease.
The involvement of cancer stem cells (CSCs) in driving tumor dormancy and drug resistance is well established. Most therapeutic regimens however are ineffective in targeting these regenerative populations. We report the development and evaluation of a monoclonal antibody, mAb150, which targets the metastasis associated antigen, Annexin A2 (AnxA2) through recognition of a N-terminal epitope. Treatment with mAb150 potentiated re-entry of CSCs into the cell cycle that perturbed tumor dormancy and facilitated targeting of CSCs as was validated by in vitro and in vivo assays. Epigenetic potentiation further improved mAb150 efficacy in achieving total tumor regression by targeting regenerative populations to achieve tumor regression, specifically in high-grade serous ovarian adenocarcinoma.
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Affiliation(s)
- Rajkumar S Kalra
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India; Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Gaurav S Soman
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Pradeep B Parab
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Avinash M Mali
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Sagar S Varankar
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India; Wellcome-MRC Cambridge Stem Cell Institute, Puddicombe Way, Cambridge, CB2 0AW
| | - Rutika R Naik
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Swapnil C Kamble
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India; Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Jaspreet K Dhanjal
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase III, New Delhi 110020, India
| | - Sharmila A Bapat
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
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Varankar SS, More M, Abraham A, Pansare K, Kumar B, Narayanan NJ, Jolly MK, Mali AM, Bapat SA. Functional balance between Tcf21-Slug defines cellular plasticity and migratory modalities in high grade serous ovarian cancer cell lines. Carcinogenesis 2020; 41:515-526. [PMID: 31241128 DOI: 10.1093/carcin/bgz119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/26/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Cellular plasticity and transitional phenotypes add to complexities of cancer metastasis that can be initiated by single cell epithelial to mesenchymal transition (EMT) or cooperative cell migration (CCM). Our study identifies novel regulatory cross-talks between Tcf21 and Slug in mediating phenotypic and migration plasticity in high-grade serous ovarian adenocarcinoma (HGSC). Differential expression and subcellular localization associate Tcf21, Slug with epithelial, mesenchymal phenotypes, respectively; however, gene manipulation approaches identify their association with additional intermediate phenotypic states, implying the existence of a multistep epithelial-mesenchymal transition program. Live imaging further associated distinct migratory modalities with the Tcf21/Slug status of cell systems and discerned proliferative/passive CCM, active CCM and EMT modes of migration. Tcf21-Slug balance identified across a phenotypic spectrum in HGSC cell lines, associated with microenvironment-induced transitions and the emergence of an epithelial phenotype following drug exposure. Phenotypic transitions and associated functionalities following drug exposure were affirmed to ensue from occupancy of Slug promoter E-box sequences by Tcf21. Our study effectively provides a framework for understanding the relevance of ovarian cancer plasticity as a function of two transcription factors.
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Affiliation(s)
- Sagar S Varankar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Madhuri More
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Ancy Abraham
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Kshama Pansare
- Institute for Plasma Research & Tata Memorial Centre, Kharghar, Navi-Mumbai, India
| | - Brijesh Kumar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Nivedhitha J Narayanan
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Avinash M Mali
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
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Insights into the Multi-Dimensional Dynamic Landscape of Epithelial-Mesenchymal Plasticity through Inter-Disciplinary Approaches. J Clin Med 2020; 9:jcm9061624. [PMID: 32471235 PMCID: PMC7356048 DOI: 10.3390/jcm9061624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
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