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Catalanotto M, Vaz JM, Abshire C, Youngblood R, Chu M, Levine H, Jolly MK, Dragoi AM. Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal transition plasticity (EMP). Transl Oncol 2024; 39:101837. [PMID: 37984255 PMCID: PMC10689956 DOI: 10.1016/j.tranon.2023.101837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Epithelial-to-mesenchymal transition (EMT) is a developmental program that consists of the loss of epithelial features concomitant with the acquisition of mesenchymal features. Activation of EMT in cancer facilitates the acquisition of aggressive traits and cancer invasion. EMT plasticity (EMP), the dynamic transition between multiple hybrid states in which cancer cells display both epithelial and mesenchymal markers, confers survival advantages for cancer cells in constantly changing environments during metastasis. METHODS RNAseq analysis was performed to assess genome-wide transcriptional changes in cancer cells depleted for histone regulators FLASH, NPAT, and SLBP. Quantitative PCR and Western blot were used for the detection of mRNA and protein levels. Computational analysis was performed on distinct sets of genes to determine the epithelial and mesenchymal score in cancer cells and to correlate FLASH expression with EMT markers in the CCLE collection. RESULTS We demonstrate that loss of FLASH in cancer cells gives rise to a hybrid E/M phenotype with high epithelial scores even in the presence of TGFβ, as determined by computational methods using expression of predetermined sets of epithelial and mesenchymal genes. Multiple genes involved in cell-cell junction formation are similarly specifically upregulated in FLASH-depleted cells, suggesting that FLASH acts as a repressor of the epithelial phenotype. Further, FLASH expression in cancer lines is inversely correlated with the epithelial score. Nonetheless, subsets of mesenchymal markers were distinctly up-regulated in FLASH, NPAT, or SLBP-depleted cells. CONCLUSIONS The ZEB1low/SNAILhigh/E-cadherinhigh phenotype described in FLASH-depleted cancer cells is driving a hybrid E/M phenotype in which epithelial and mesenchymal markers coexist.
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Affiliation(s)
| | - Joel Markus Vaz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Reneau Youngblood
- Department of Molecular and Cellular Physiology, LSUHSC, Shreveport, LA, USA
| | - Min Chu
- Feist-Weiller Cancer Center, INLET Core, LSUHSC, Shreveport, LA, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA; Department of Physics, Northeastern University, Boston, MA, USA; Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ana-Maria Dragoi
- Department of Molecular and Cellular Physiology, LSUHSC, Shreveport, LA, USA; Feist-Weiller Cancer Center, INLET Core, LSUHSC, Shreveport, LA, USA.
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Lu W, Eapen MS, Hardikar A, Chia C, Robertson I, Singhera GK, Hackett TL, Sohal SS. Epithelial-mesenchymal transition changes in nonsmall cell lung cancer patients with early COPD. ERJ Open Res 2023; 9:00581-2023. [PMID: 38152085 PMCID: PMC10752287 DOI: 10.1183/23120541.00581-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/06/2023] [Indexed: 12/29/2023] Open
Abstract
Background Epithelial-mesenchymal transition (EMT) might be central to lung cancer development in smokers and COPD. We illustrate EMT changes in a broader demographic of patient groups who were diagnosed with nonsmall cell lung cancer (adenocarcinoma and squamous cell carcinoma). These included COPD current and ex-smokers, patients with small airway disease and normal lung function smokers compared to normal controls. Methods We had access to surgically resected small airway tissue from 46 subjects and assessed for airway wall thickness and immunohistochemically for the EMT biomarkers E-cadherin, N-cadherin, S100A4, vimentin and epidermal growth factor receptor (EGFR). All tissue analysis was done with a computer and microscope-assisted Image-Pro Plus 7.0 software. Results Airway wall thickness significantly increased across all pathological groups (p<0.05) compared to normal controls. Small airway epithelial E-cadherin expression markedly decreased (p<0.01), and increases in N-cadherin, vimentin, S100A4 and EGFR expression were observed in all pathological groups compared to normal controls (p<0.01). Vimentin-positive cells in the reticular basement membrane, lamina propria and adventitia showed a similar trend to epithelium across all pathological groups (p<0.05); however, such changes were only observed in reticular basement membrane for S100A4 (p<0.05). Vimentin was higher in adenocarcinoma versus squamous cell carcinoma; in contrast, S100A4 was higher in the squamous cell carcinoma group. EGFR and N-cadherin expression in both phenotypes was markedly higher than E-cadherin, vimentin and S100A4 (p<0.0001). Conclusion EMT is an active process in the small airway of smokers and COPD diagnosed with nonsmall cell lung cancer, contributing to small airway remodelling and cancer development as seen in these patients.
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Affiliation(s)
- Wenying Lu
- Respiratory Translational Research Group, School of Health Sciences, University of Tasmania, Newnham, TAS, Australia
- Launceston Respiratory and Sleep Centre, Launceston, TAS, Australia
| | - Mathew Suji Eapen
- Respiratory Translational Research Group, School of Health Sciences, University of Tasmania, Newnham, TAS, Australia
| | - Ashutosh Hardikar
- Department of Cardiothoracic Surgery, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Collin Chia
- Respiratory Translational Research Group, School of Health Sciences, University of Tasmania, Newnham, TAS, Australia
- Launceston Respiratory and Sleep Centre, Launceston, TAS, Australia
- Department of Respiratory Medicine, Launceston General Hospital, Launceston, TAS, Australia
| | - Iain Robertson
- Respiratory Translational Research Group, School of Health Sciences, University of Tasmania, Newnham, TAS, Australia
| | - Gurpreet Kaur Singhera
- Department of Anesthesiology, Pharmacology and Therapeutics, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Tillie L. Hackett
- Department of Anesthesiology, Pharmacology and Therapeutics, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Sukhwinder Singh Sohal
- Respiratory Translational Research Group, School of Health Sciences, University of Tasmania, Newnham, TAS, Australia
- Launceston Respiratory and Sleep Centre, Launceston, TAS, Australia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Subhadarshini S, Markus J, Sahoo S, Jolly MK. Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? ACS Omega 2023; 8:11665-11673. [PMID: 37033874 PMCID: PMC10077445 DOI: 10.1021/acsomega.2c07989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) is a key driver of cancer metastasis and therapeutic resistance, through which cancer cells can reversibly and dynamically alter their molecular and functional traits along the epithelial-mesenchymal spectrum. While cells in the epithelial phenotype are usually tightly adherent, less metastatic, and drug-sensitive, those in the hybrid epithelial/mesenchymal and/or mesenchymal state are more invasive, migratory, drug-resistant, and immune-evasive. Single-cell studies have emerged as a powerful tool in gaining new insights into the dynamics of EMP across various cancer types. Here, we review many recent studies that employ single-cell analysis techniques to better understand the dynamics of EMP in cancer both in vitro and in vivo. These single-cell studies have underlined the plurality of trajectories cells can traverse during EMP and the consequent heterogeneity of hybrid epithelial/mesenchymal phenotypes seen at both preclinical and clinical levels. They also demonstrate how diverse EMP trajectories may exhibit hysteretic behavior and how the rate of such cell-state transitions depends on the genetic/epigenetic background of recipient cells, as well as the dose and/or duration of EMP-inducing growth factors. Finally, we discuss the relationship between EMP and patient survival across many cancer types. We also present a next set of questions related to EMP that could benefit much from single-cell observations and pave the way to better tackle phenotypic switching and heterogeneity in clinic.
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Affiliation(s)
| | - Joel Markus
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sarthak Sahoo
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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Zhang L, Tang C, Zhang M, Tong X, Xie Y, Yan R, Wang X, Zhang X, Liu D, Li S. Single cell meta-analysis of EndMT and EMT state in COVID-19. Front Immunol 2022; 13:976512. [PMID: 36248845 PMCID: PMC9558222 DOI: 10.3389/fimmu.2022.976512] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 prognoses suggests that a proportion of patients develop fibrosis, but there is no evidence to indicate whether patients have progression of mesenchymal transition (MT) in the lungs. The role of MT during the COVID-19 pandemic remains poorly understood. Using single-cell RNA sequencing, we profiled the transcriptomes of cells from the lungs of healthy individuals (n = 45), COVID-19 patients (n = 58), and idiopathic pulmonary fibrosis (IPF) patients (n = 64) human lungs to map the entire MT change. This analysis enabled us to map all high-resolution matrix-producing cells and identify distinct subpopulations of endothelial cells (ECs) and epithelial cells as the primary cellular sources of MT clusters during COVID-19. For the first time, we have identied early and late subgroups of endothelial mesenchymal transition (EndMT) and epithelial-mesenchymal transition (EMT) using analysis of public databases for single-cell sequencing. We assessed epithelial subgroups by age, smoking status, and gender, and the data suggest that the proportional changes in EMT in COVID-19 are statistically significant. Further enumeration of early and late EMT suggests a correlation between invasive genes and COVID-19. Finally, EndMT is upregulated in COVID-19 patients and enriched for more inflammatory cytokines. Further, by classifying EndMT as early or late stages, we found that early EndMT was positively correlated with entry factors but this was not true for late EndMT. Exploring the MT state of may help to mitigate the fibrosis impact of SARS-CoV-2 infection.
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Affiliation(s)
- Lanlan Zhang
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, And Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Dan Liu, ; Lanlan Zhang, ; Xin Zhang,
| | - Chuang Tang
- Department of Gastroenterology, West China (Airport) Hospital, Sichuan University, Chengdu, China
| | - Min Zhang
- Oncology Bussiness Department, Novogene Co., Ltd, Beijing, China
| | - Xia Tong
- Department of Gastroenterology, West China (Airport) Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital of Sichuan University, Chengdu, China
| | - Yingying Xie
- Department of Nephrology, Seventh Affiliated Hospital Sun Yat-sen University, Shenzhen, China
| | | | - Xiangjun Wang
- First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xin Zhang
- Department of Gastroenterology, West China (Airport) Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Dan Liu, ; Lanlan Zhang, ; Xin Zhang,
| | - Dan Liu
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, And Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Dan Liu, ; Lanlan Zhang, ; Xin Zhang,
| | - Shasha Li
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
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Sohal SS. Therapeutic Modalities for Asthma, COPD, and Pathogenesis of COVID-19: Insights from the Special Issue. J Clin Med 2022; 11:jcm11154525. [PMID: 35956140 PMCID: PMC9369734 DOI: 10.3390/jcm11154525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/02/2022] [Indexed: 12/10/2022] Open
Affiliation(s)
- Sukhwinder Singh Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7248, Australia
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Parthasarathi KTS, Mandal S, Singh S, Gundimeda S, Jolly MK, Pandey A, Sharma J. In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. Cancers (Basel) 2022; 14:1444. [PMID: 35326596 PMCID: PMC8946083 DOI: 10.3390/cancers14061444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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