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Parthasarathi KTS, Mandal S, George JP, Gaikwad KB, Sasidharan S, Gundimeda S, Jolly MK, Pandey A, Sharma J. Aberrations in ion channels interacting with lipid metabolism and epithelial-mesenchymal transition in esophageal squamous cell carcinoma. Front Mol Biosci 2023; 10:1201459. [PMID: 37529379 PMCID: PMC10388552 DOI: 10.3389/fmolb.2023.1201459] [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: 04/12/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most prevalent malignant gastrointestinal tumor. Ion channels contribute to tumor growth and progression through interactions with their neighboring molecules including lipids. The dysregulation of membrane ion channels and lipid metabolism may contribute to the epithelial-mesenchymal transition (EMT), leading to metastatic progression. Herein, transcriptome profiles of patients with ESCC were analyzed by performing differential gene expression and weighted gene co-expression network analysis to identify the altered ion channels, lipid metabolism- and EMT-related genes in ESCC. A total of 1,081 differentially expressed genes, including 113 ion channels, 487 lipid metabolism-related, and 537 EMT-related genes, were identified in patients with ESCC. Thereafter, EMT scores were correlated with altered co-expressed genes. The altered co-expressed genes indicated a correlation with EMT signatures. Interactions among 22 ion channels with 3 hub lipid metabolism- and 13 hub EMT-related proteins were determined using protein-protein interaction networks. A pathway map was generated to depict deregulated signaling pathways including insulin resistance and the estrogen receptor-Ca2+ signaling pathway in ESCC. The relationship between potential ion channels and 5-year survival rates in ESCC was determined using Kaplan-Meier plots and Cox proportional hazard regression analysis. Inositol 1,4,5-trisphosphate receptor type 3 (ITPR3) was found to be associated with poor prognosis of patients with ESCC. Additionally, drugs interacting with potential ion channels, including GJA1 and ITPR3, were identified. Understanding alterations in ion channels with lipid metabolism and EMT in ESCC pathophysiology would most likely provide potential targets for the better treatment of patients with ESCC.
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Affiliation(s)
- K. T. Shreya Parthasarathi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Susmita Mandal
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - John Philip George
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Sruthi Sasidharan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Seetaramanjaneyulu Gundimeda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Rochester, MN, United States
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Center for Individualized Medicine, Rochester, MN, United States
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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Omics approaches to discover pathophysiological pathways contributing to human pain. Pain 2022; 163:S69-S78. [PMID: 35994593 PMCID: PMC9557800 DOI: 10.1097/j.pain.0000000000002726] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/19/2022] [Indexed: 10/26/2022]
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In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. Cancers (Basel) 2022; 14:cancers14061444. [PMID: 35326596 PMCID: PMC8946083 DOI: 10.3390/cancers14061444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Breast cancer involves changes in the healthy cells of the breast resulting in rapid and abnormal division of cells that later spread to other parts of the body through the process of metastasis, which involves epithelial mesenchymal transition (EMT). Ion channels play a significant role in the switch from epithelial to mesenchymal transition through their contributions to cellular motility, cell volume regulation and cell cycle progression. Comprehensive computational analyses were performed to understand the role of ion channels in tumor/metastatic samples of breast cancer and their correlation with EMT. Abstract Uncontrolled growth of breast cells due to altered gene expression is a key feature of breast cancer. Alterations in the expression of ion channels lead to variations in cellular activities, thus contributing to attributes of cancer hallmarks. Changes in the expression levels of ion channels were observed as a consequence of EMT. Additionally, ion channels were reported in the activation of EMT and maintenance of a mesenchymal phenotype. Here, to identify altered ion channels in breast cancer patients, differential gene expression and weighted gene co-expression network analyses were performed using transcriptomic data. Protein–protein interactions network analysis was carried out to determine the ion channels interacting with hub EMT-related genes in breast cancer. Thirty-two ion channels were found interacting with twenty-six hub EMT-related genes. The identified ion channels were further correlated with EMT scores, indicating mesenchymal phenotype. Further, the pathway map was generated to represent a snapshot of deregulated cellular processes by altered ion channels and EMT-related genes. Kaplan–Meier five-year survival analysis and Cox regressions indicated the expression of CACNA1B, ANO6, TRPV3, VDAC1 and VDAC2 to be potentially associated with poor survival. Deregulated ion channels correlate with EMT-related genes and have a crucial role in breast cancer-associated tumorigenesis. Most likely, they are potential candidates for the determination of prognosis in patients with breast cancer.
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Munjal NS, Sapra D, Parthasarathi KTS, Goyal A, Pandey A, Banerjee M, Sharma J. Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods. Pathogens 2022; 11:pathogens11020259. [PMID: 35215201 PMCID: PMC8874499 DOI: 10.3390/pathogens11020259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 01/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is accountable for the protracted COVID-19 pandemic. Its high transmission rate and pathogenicity led to health emergencies and economic crisis. Recent studies pertaining to the understanding of the molecular pathogenesis of SARS-CoV-2 infection exhibited the indispensable role of ion channels in viral infection inside the host. Moreover, machine learning (ML)-based algorithms are providing a higher accuracy for host-SARS-CoV-2 protein–protein interactions (PPIs). In this study, PPIs of SARS-CoV-2 proteins with human ion channels (HICs) were trained on the PPI-MetaGO algorithm. PPI networks (PPINs) and a signaling pathway map of HICs with SARS-CoV-2 proteins were generated. Additionally, various U.S. food and drug administration (FDA)-approved drugs interacting with the potential HICs were identified. The PPIs were predicted with 82.71% accuracy, 84.09% precision, 84.09% sensitivity, 0.89 AUC-ROC, 65.17% Matthews correlation coefficient score (MCC) and 84.09% F1 score. Several host pathways were found to be altered, including calcium signaling and taste transduction pathway. Potential HICs could serve as an initial set to the experimentalists for further validation. The study also reinforces the drug repurposing approach for the development of host directed antiviral drugs that may provide a better therapeutic management strategy for infection caused by SARS-CoV-2.
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Affiliation(s)
- Nupur S. Munjal
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (N.S.M.); (D.S.); (K.T.S.P.); (A.G.)
| | - Dikscha Sapra
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (N.S.M.); (D.S.); (K.T.S.P.); (A.G.)
| | - K. T. Shreya Parthasarathi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (N.S.M.); (D.S.); (K.T.S.P.); (A.G.)
| | - Abhishek Goyal
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (N.S.M.); (D.S.); (K.T.S.P.); (A.G.)
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India;
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India;
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (N.S.M.); (D.S.); (K.T.S.P.); (A.G.)
- Manipal Academy of Higher Education (MAHE), Udupi 576104, India
- Correspondence:
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Chen D, Kelly C, Haw TJ, Lombard JM, Nordman IIC, Croft AJ, Ngo DTM, Sverdlov AL. Heart Failure in Breast Cancer Survivors: Focus on Early Detection and Novel Biomarkers. Curr Heart Fail Rep 2021; 18:362-377. [PMID: 34731413 DOI: 10.1007/s11897-021-00535-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE OF REVIEW Breast cancer survival rate has greatly improved in the last two decades due to the emergence of next-generation anti-cancer agents. However, cardiotoxicity remains a significant adverse effect arising from traditional and emerging chemotherapies as well as targeted therapies for breast cancer patients. In this review, we will discuss cardiotoxicities of both traditional and emerging therapies for breast cancer. We will discuss current practices to detect cardiotoxicity of these therapies with the focus on new and emerging biomarkers. We will then focus on 'omics approaches, especially the use of epigenetics to discover novel biomarkers and therapeutics to mitigate cardiotoxicity. RECENT FINDINGS Significant cardiotoxicities of conventional chemotherapies remain and new and unpredictable new forms of cardiac and/or vascular toxicity emerge with the surge in novel and targeted therapies. Yet, there is no clear guidance on detection of cardiotoxicity, except for significant left ventricular systolic dysfunction, and even then, there is no uniform definition of what constitutes cardiotoxicity. The gold standard for detection of cardiotoxicity involves a serial echocardiography in conjunction with blood-based biomarkers to detect early subclinical cardiac dysfunction. However, the ability of these tests to detect early disease remains limited and not all forms of toxicity are detectable with these modalities. There is an unprecedented need to discover novel biomarkers that are sensitive and specific for early detection of subclinical cardiotoxicity. In that space, novel echocardiographic techniques, such as strain, are becoming more common-place and new biomarkers, discovered by epigenetic approaches, seem to become promising alternatives or adjuncts to conventional non-specific cardiac biomarkers.
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Affiliation(s)
- Dongqing Chen
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia
| | - Conagh Kelly
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia
| | - Tatt Jhong Haw
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia.,Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Janine M Lombard
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Ina I C Nordman
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Amanda J Croft
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Doan T M Ngo
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia. .,School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
| | - Aaron L Sverdlov
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia. .,Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia. .,Cardiovascular Department, John Hunter Hospital, Hunter New England Local Health District, NSW, New Lambton Heights, Australia. .,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
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Tripathi A, Kashyap A, Tripathi G, Yadav J, Bibban R, Aggarwal N, Thakur K, Chhokar A, Jadli M, Sah AK, Verma Y, Zayed H, Husain A, Bharti AC, Kashyap MK. Tumor reversion: a dream or a reality. Biomark Res 2021; 9:31. [PMID: 33958005 PMCID: PMC8101112 DOI: 10.1186/s40364-021-00280-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Reversion of tumor to a normal differentiated cell once considered a dream is now at the brink of becoming a reality. Different layers of molecules/events such as microRNAs, transcription factors, alternative RNA splicing, post-transcriptional, post-translational modifications, availability of proteomics, genomics editing tools, and chemical biology approaches gave hope to manipulation of cancer cells reversion to a normal cell phenotype as evidences are subtle but definitive. Regardless of the advancement, there is a long way to go, as customized techniques are required to be fine-tuned with precision to attain more insights into tumor reversion. Tumor regression models using available genome-editing methods, followed by in vitro and in vivo proteomics profiling techniques show early evidence. This review summarizes tumor reversion developments, present issues, and unaddressed challenges that remained in the uncharted territory to modulate cellular machinery for tumor reversion towards therapeutic purposes successfully. Ongoing research reaffirms the potential promises of understanding the mechanism of tumor reversion and required refinement that is warranted in vitro and in vivo models of tumor reversion, and the potential translation of these into cancer therapy. Furthermore, therapeutic compounds were reported to induce phenotypic changes in cancer cells into normal cells, which will contribute in understanding the mechanism of tumor reversion. Altogether, the efforts collectively suggest that tumor reversion will likely reveal a new wave of therapeutic discoveries that will significantly impact clinical practice in cancer therapy.
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Affiliation(s)
- Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Joni Yadav
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Rakhi Bibban
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Nikita Aggarwal
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Kulbhushan Thakur
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Arun Chhokar
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Mohit Jadli
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), India
- Department of Pathology and Laboratory Medicine, Medanta-The Medicity, Haryana, Gurugram, India
| | - Yeshvandra Verma
- Department of Toxicology, C C S University, Meerut, UP, 250004, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER), Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Alok Chandra Bharti
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India.
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
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