1
|
Guo W, Duan Z, Wu J, Zhou BP. Epithelial-mesenchymal transition promotes metabolic reprogramming to suppress ferroptosis. Semin Cancer Biol 2025; 112:20-35. [PMID: 40058616 DOI: 10.1016/j.semcancer.2025.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 02/05/2025] [Accepted: 02/28/2025] [Indexed: 03/22/2025]
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process that provides cells with the increased plasticity and stem cell-like traits required during embryonic development, tissue remodeling, wound healing and metastasis. Morphologically, EMT confers tumor cells with fibroblast-like properties that lead to the rearrangement of cytoskeleton (loss of stiffness) and decrease of membrane rigidity by incorporating high level of poly-unsaturated fatty acids (PUFA) in their phospholipid membrane. Although large amounts of PUFA in membrane reduces rigidity and offers capabilities for tumor cells with the unbridled ability to stretch, bend and twist in metastasis, these PUFA are highly susceptible to lipid peroxidation, which leads to the breakdown of membrane integrity and, ultimately results in ferroptosis. To escape the ferroptotic risk, EMT also triggers the rewiring of metabolic program, particularly in lipid metabolism, to enforce the epigenetic regulation of EMT and mitigate the potential damages from ferroptosis. Thus, the interplay among EMT, lipid metabolism, and ferroptosis highlights a new layer of intricated regulation in cancer biology and metastasis. Here we summarize the latest findings and discuss these mutual interactions. Finally, we provide perspectives of how these interplays contribute to cellular plasticity and ferroptosis resistance in metastatic tumor cells that can be explored for innovative therapeutic interventions.
Collapse
Affiliation(s)
- Wenzheng Guo
- Departments of Molecular and Cellular Biochemistry, and the Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY 40506, United States
| | - Zhibing Duan
- Departments of Molecular and Cellular Biochemistry, and the Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY 40506, United States
| | - Jingjing Wu
- Departments of Molecular and Cellular Biochemistry, and the Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY 40506, United States
| | - Binhua P Zhou
- Departments of Molecular and Cellular Biochemistry, and the Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY 40506, United States.
| |
Collapse
|
2
|
Hu J, Chen J, Zhao C, Yu P, Xu W, Yin Y, Yang L, Zhang Z, Kong L, Zhang C. Icariside II inhibits Epithelial-Mesenchymal transition in metastatic osteosarcoma by antagonizing the miR-194/215 cluster via PGK1. Biochem Pharmacol 2025; 236:116838. [PMID: 40023448 DOI: 10.1016/j.bcp.2025.116838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 01/31/2025] [Accepted: 02/27/2025] [Indexed: 03/04/2025]
Abstract
Osteosarcoma, the most prevalent malignant bone tumor in adolescents, is characterized by its aggressiveness and tendency to metastasize. Despite the advancements in treatment that have improved survival rates for localized cases, metastatic osteosarcoma remains challenging to treat due to the limited efficacy of current therapies and the severe side effects of chemotherapy. Epithelial-mesenchymal transition (EMT) is a key factor in osteosarcoma metastasis, and the miR-194/215 cluster, which is upregulated in osteosarcoma, promotes this process. This study sought to investigate natural compounds that could counteract the miR-194/215 cluster's effects and inhibit osteosarcoma metastasis. By analyzing miRNA databases and clinical data, a signature gene set for the miR-194/215 cluster was established, and the LINCS database was screened to find natural compounds with antagonistic effects. Icariside II, an active component of Epimedium, was identified as a potential inhibitor and was shown to reduce the migration and invasion of osteosarcoma cells in vitro and lung metastasis in vivo. The study utilized various techniques, including Gene Set Enrichment Analysis (GSEA), Drug Affinity Responsive Target Stability (DARTS), Cellular Thermal Shift Assay (CETSA), molecular docking, and enzyme activity assays, to identify phosphoglycerate kinase 1 (PGK1) as the target protein of Icariside II. It was found that Icariside II competitively inhibits PGK1 by binding to its ADP binding pocket, reducing its activity and thus antagonizing the miR-194/215 cluster's promotion of EMT in metastatic osteosarcoma. The results suggest that Icariside II could be a promising therapeutic agent for metastatic osteosarcoma, providing new targets and strategies for clinical treatment.
Collapse
Affiliation(s)
- Jianping Hu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinhu Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Caili Zhao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Pei Yu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenjun Xu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yong Yin
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhenzhen Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China.
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Chao Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
3
|
Shi R, Farnsworth DA, Febres-Aldana CA, Chow JLM, Sheena R, Atwal T, Gomez Marti JL, Li S, Thomas KN, Lee CM, Awrey SJ, McDonald PC, Somwar R, Dedhar S, Ladanyi M, Bennewith KL, Lockwood WW. Drug tolerance and persistence to EGFR inhibitor treatment are mediated by an ILK-SFK-YAP signaling axis in lung adenocarcinoma. Oncogene 2025:10.1038/s41388-025-03461-6. [PMID: 40450112 DOI: 10.1038/s41388-025-03461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 05/09/2025] [Accepted: 05/20/2025] [Indexed: 06/03/2025]
Abstract
Combating resistance to targeted therapy remains a major challenge to improving lung cancer care. Epithelial-mesenchymal transition (EMT) in tumour cells is an established non-genetic resistance mechanism to EGFR tyrosine kinase inhibitors (TKI) that is also associated with worse outcome in patients. Here we demonstrate that integrin-linked kinase (ILK) is an important driver of EMT-mediated TKI resistance in lung adenocarcinoma (LUAD) by promoting a drug-tolerant persister (DTP) cell phenotype. Our results indicate that high ILK expression is associated with EMT in LUAD patients and that genetic suppression of ILK can limit EMT progression and reduce the viability of DTP cells by impairing YAP activation, ultimately improving osimertinib (Osi) sensitivity in LUAD cells. Importantly, LUAD cells with high ILK expression are able to persist during EGFR-TKI treatment, acquiring additional genetic and phenotypic alterations to develop EGFR-TKI resistance. To improve clinical translatability of our findings, we showed that pharmacological inhibition of ILK can suppress EMT and improve Osi response in LUAD cells. Lastly, we found that strong immunohistochemistry staining of ILK in patient biopsies was significantly associated with and may be used to predict receptor tyrosine kinase-independent mechanisms of EGFR-TKI resistance. Overall, our results suggest that ILK is an important regulator of EGFR-TKI response and may be exploited as a predictor for acquired resistance, providing evidence for co-targeting ILK with EGFR to better control minimal residual disease and EGFR-TKI resistance in lung cancer.
Collapse
Affiliation(s)
- Rocky Shi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Dylan A Farnsworth
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Christopher A Febres-Aldana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justine L M Chow
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Ravinder Sheena
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Tejveer Atwal
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Juan Luis Gomez Marti
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samantha Li
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Kiersten N Thomas
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Che-Min Lee
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Shannon J Awrey
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Romel Somwar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin L Bennewith
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada.
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
4
|
Chandraganti S, Sams C, Sahoo S, Feng B, O’Connell I, Li L, Nepal S, Pulukuri S, Bakhle K, Thiru P, Simian C, Bell GW, Jolly MK, Dongre A. CD4 + T-cells sensitize quasi-mesenchymal breast tumors lacking CD73 to anti-CTLA4 immune checkpoint blockade therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.05.12.653467. [PMID: 40463168 PMCID: PMC12132553 DOI: 10.1101/2025.05.12.653467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2025]
Abstract
Although immune checkpoint blockade therapy has generated dramatic responses in certain cancer types, breast tumors are largely unresponsive. Epithelial-mesenchymal plasticity leads to the assembly of an immunosuppressive tumor microenvironment and drives resistance of breast tumors to immunotherapies. Importantly, targeting CD73 completely sensitizes quasi-mesenchymal breast tumors to anti-CTLA4 immune checkpoint blockade therapy. However, the mechanism(s) of sensitization remained unknown. We demonstrate that targeting CD73 in quasi-mesenchymal breast tumors sensitizes them to anti-CTLA4 immune checkpoint blockade therapy in a CD4 + T-cell dependent manner. Moreover, epithelial-mesenchymal plasticity results in elevated expression of cancer cell-intrinsic CD73 in human triple negative breast cancers. Given the ability of quasi-mesenchymal cancer cells to metastasize and resist multiple therapies, these findings can instruct the formation of novel translational strategies for the treatment of human breast cancers. These findings also bring to the forefront the attractive possibility of utilizing the phenotypic plasticity of cancer cells along with CD73 and CD4 + T-cells as a predictive criterion for immunotherapy responsiveness. Teaser Targeting CD73 sensitizes breast cancer cells with mesenchymal traits to anti-CTLA4 therapy in a CD4 + T-cell dependent manner.
Collapse
Affiliation(s)
- Shiney Chandraganti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Caitlyn Sams
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Brian Feng
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Isabel O’Connell
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lynna Li
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sunita Nepal
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Siddhartha Pulukuri
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Kimaya Bakhle
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Corina Simian
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, 02120, USA
| | - George W. Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Anushka Dongre
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
5
|
Takai Y, Naito S, Ito H, Horie S, Ushijima M, Narisawa T, Yagi M, Ichiyanagi O, Tsuchiya N. Ankrd1 Promotes Lamellipodia Formation and Cell Motility via Interaction with Talin-1 in Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2025; 26:4232. [PMID: 40362467 PMCID: PMC12072362 DOI: 10.3390/ijms26094232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/19/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
Ankyrin repeat domain 1 (Ankrd1), a transcriptional target of Yes-associated protein (YAP), is linked to cardiomyopathy. However, its role in cancer, particularly in clear cell renal cell carcinoma (ccRCC), remains vague. In this study, we examined the expression, regulation, and function of Ankrd1 in ccRCC. High Ankrd1 expression was related to poor prognosis in patients with ccRCC in The Cancer Genome Atlas cohort. Ankrd1 expression was regulated by YAP in all ccRCC cell lines examined and also by ERK5 in a subset of ccRCC cell lines. Moreover, silencing of Ankrd1 in ccRCC cell lines resulted in decreased cell motility, whereas its overexpression increased the cell motility. Ankrd1 colocalized with F-actin in lamellipodia upon phorbol ester stimulation. Ankrd1 silencing resulted in alterations in the shape of RCC cells and caused a decrease in lamellipodia formation. Ankrd1 also colocalized with talin-1 in lamellipodia. Ankrd1 depletion repressed talin-1-mediated activation of the integrin pathway. Immunohistochemical examination of surgical specimens revealed high expression of Ankrd1 in metastatic RCC tissues compared with that in primary RCC tissues from the same patients. Collectively, these findings suggest that Ankrd1 plays a critical role in the motility of ccRCC cells through lamellipodia formation.
Collapse
Affiliation(s)
- Yuki Takai
- Department of Urology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990-9585, Japan; (S.N.); (H.I.); (S.H.); (M.U.); (T.N.); (M.Y.); (O.I.); (N.T.)
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
McDermott M, Mehta R, Roussos Torres ET, MacLean AL. Modeling the dynamics of EMT reveals genes associated with pan-cancer intermediate states and plasticity. NPJ Syst Biol Appl 2025; 11:31. [PMID: 40210876 PMCID: PMC11986130 DOI: 10.1038/s41540-025-00512-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 03/28/2025] [Indexed: 04/12/2025] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a cell state transition co-opted by cancer that drives metastasis via stable intermediate states. Here we study EMT dynamics to identify marker genes of highly metastatic intermediate cells via mathematical modeling with single-cell RNA sequencing (scRNA-seq) data. Across multiple tumor types and stimuli, we identified genes consistently upregulated in EMT intermediate states, many previously unrecognized as EMT markers. Bayesian parameter inference of a simple EMT mathematical model revealed tumor-specific transition rates, providing a framework to quantify EMT progression. Consensus analysis of differential expression, RNA velocity, and model-derived dynamics highlighted SFN and NRG1 as key regulators of intermediate EMT. Independent validation confirmed SFN as an intermediate state marker. Our approach integrates modeling and inference to identify genes associated with EMT dynamics, offering biomarkers and therapeutic targets to modulate tumor-promoting cell state transitions driven by EMT.
Collapse
Affiliation(s)
- MeiLu McDermott
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Riddhee Mehta
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Evanthia T Roussos Torres
- Department of Medicine, Division of Medical Oncology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Adam L MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
7
|
Perelli L, Zhang L, Mangiameli S, Giannese F, Mahadevan KK, Peng F, Citron F, Khan H, Le C, Gurreri E, Carbone F, Russell AJC, Soeung M, Lam TNA, Lundgren S, Marisetty S, Zhu C, Catania D, Mohamed AMT, Feng N, Augustine JJ, Sgambato A, Tortora G, Draetta GF, Tonon G, Futreal A, Giuliani V, Carugo A, Viale A, Kim MP, Heffernan TP, Wang L, Kalluri R, Cittaro D, Chen F, Genovese G. Evolutionary fingerprints of epithelial-to-mesenchymal transition. Nature 2025; 640:1083-1092. [PMID: 40044861 DOI: 10.1038/s41586-025-08671-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/17/2025] [Indexed: 04/13/2025]
Abstract
Mesenchymal plasticity has been extensively described in advanced epithelial cancers; however, its functional role in malignant progression is controversial1-5. The function of epithelial-to-mesenchymal transition (EMT) and cell plasticity in tumour heterogeneity and clonal evolution is poorly understood. Here we clarify the contribution of EMT to malignant progression in pancreatic cancer. We used somatic mosaic genome engineering technologies to trace and ablate malignant mesenchymal lineages along the EMT continuum. The experimental evidence clarifies the essential contribution of mesenchymal lineages to pancreatic cancer evolution. Spatial genomic analysis, single-cell transcriptomic and epigenomic profiling of EMT clarifies its contribution to the emergence of genomic instability, including events of chromothripsis. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross-species analysis of pancreatic and other human solid tumours. Mechanistically, we identified that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, in turn resulting in delayed mitosis and catastrophic cell division. Thus, EMT favours the emergence of genomic-unstable, highly fit tumour cells, which strongly supports the concept of cell-state-restricted patterns of evolution, whereby cancer cell speciation is propagated to progeny within restricted functional compartments. Restraining the evolutionary routes through ablation of clones capable of mesenchymal plasticity, and extinction of the derived lineages, halts the malignant potential of one of the most aggressive forms of human cancer.
Collapse
Affiliation(s)
- Luigi Perelli
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Li Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Mangiameli
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Krishnan K Mahadevan
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francesca Citron
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hania Khan
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney Le
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enrico Gurreri
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Medical Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Andrew J C Russell
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sebastian Lundgren
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sujay Marisetty
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cihui Zhu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Desiree Catania
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alaa M T Mohamed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ningping Feng
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jithesh Jose Augustine
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Sgambato
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Multiplex Spatial Imaging Facility, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giampaolo Tortora
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Medical Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Virginia Giuliani
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center, UT Health Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy.
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Giannicola Genovese
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
8
|
Kulkarni AM, Gayam PKR, Baby BT, Aranjani JM. Epithelial-Mesenchymal Transition in Cancer: A Focus on Itraconazole, a Hedgehog Inhibitor. Biochim Biophys Acta Rev Cancer 2025; 1880:189279. [PMID: 39938662 DOI: 10.1016/j.bbcan.2025.189279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 01/24/2025] [Accepted: 02/04/2025] [Indexed: 02/14/2025]
Abstract
Cancer, and the resulting mortality from it, is an ever-increasing concern in global health. Cancer mortality stems from the metastatic progression of the disease, by dissemination of the tumor cells. Epithelial-Mesenchymal Transition, the major hypothesis purported to be the origin of metastasis, confers mesenchymal phenotype to epithelial cells in a variety of contexts, physiological and pathological. EMT in cancer leads to rise of cancer-stem-like cells, drug resistance, relapse, and progression of malignancy. Inhibition of EMT could potentially attenuate the mortality. While novel molecules for inhibiting EMT are underway, repurposing drugs is also being considered as a viable strategy. In this review, Itraconazole is focused upon, as a repurposed molecule to mitigate EMT. Itraconazole is known to inhibit Hedgehog signaling, and light is shed upon the existing evidence, as well as the questions remaining to be answered.
Collapse
Affiliation(s)
- Aniruddha Murahar Kulkarni
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka 576104, India.
| | - Prasanna Kumar Reddy Gayam
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka 576104, India.
| | - Beena Thazhackavayal Baby
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka 576104, India.
| |
Collapse
|
9
|
Ko CC, Yang PM. Hypoxia-induced MIR31HG expression promotes partial EMT and basal-like phenotype in pancreatic ductal adenocarcinoma based on data mining and experimental analyses. J Transl Med 2025; 23:305. [PMID: 40065368 PMCID: PMC11895263 DOI: 10.1186/s12967-025-06292-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 02/23/2025] [Indexed: 03/14/2025] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is the most common and aggressive type of pancreatic cancer, with a five-year survival rate below 8%. Its high mortality is largely due to late diagnosis, metastatic potential, and resistance to therapy. Epithelial-mesenchymal transition (EMT) plays a key role in metastasis, enabling cancer cells to become mobile. Partial EMT, where cells maintain both epithelial and mesenchymal traits, is more frequent in tumors than complete EMT and contributes to cancer progression. The long non-coding RNA MIR31 host gene (MIR31HG) has recently emerged as a critical factor in PDAC oncogenesis. This study aimed to investigate MIR31HG's role in partial EMT and its association with the basal-like PDAC subtype. METHODS We analyzed the relationship between MIR31HG expression, partial EMT, and the basal-like subtype of PDAC by integrating data from public databases. We reanalyzed public data from PDAC patient-derived organoids to assess MIR31HG expression and gene signatures under hypoxic and normoxic conditions. RNA sequencing and bioinformatics analyses, including gene set enrichment analysis (GSEA), were used to investigate differentially expressed genes and pathway enrichments. EMT, partial EMT, and hypoxia scores were calculated based on the expression levels of specific gene sets. RESULTS We observed that MIR31HG overexpression strongly correlates with higher partial EMT scores and the stabilization of the epithelial phenotype in PDAC. MIR31HG is highly expressed in the basal-like subtype of PDAC, which exhibits partial EMT traits. Hypoxia, a hallmark of basal-like PDAC, was shown to significantly induce MIR31HG expression, thereby promoting the basal-like phenotype and partial EMT. In patient-derived organoids, hypoxic conditions increased MIR31HG expression and enhanced basal-like and partial EMT gene signatures, while normoxia reduced these expressions. These findings suggest that hypoxia-induced MIR31HG expression plays a crucial role in driving the aggressive basal-like subtype of PDAC. CONCLUSIONS Our results indicate that MIR31HG is crucial in regulating PDAC progression, particularly in the aggressive basal-like subtype associated with hypoxia and partial EMT. Targeting the MIR31HG-mediated network may offer a novel therapeutic approach to combat hypoxia-driven PDAC.
Collapse
Affiliation(s)
- Ching-Chung Ko
- Department of Medical Imaging, Chi Mei Medical Center, Tainan, 71004, Taiwan
- Department of Health and Nutrition, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Pei-Ming Yang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, No. 301, Yuantong Rd., Zhonghe Dist., New Taipei City, 235603, Taiwan.
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11031, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei, 11031, Taiwan.
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, 11696, Taiwan.
- Taipei Cancer Center, Taipei Medical University (TMU) and Affiliated Hospitals Pancreatic Cancer Groups, Taipei Medical University, Taipei, 11031, Taiwan.
| |
Collapse
|
10
|
Chen Z, Gong Y, Chen F, Lee HJ, Qian J, Zhao J, Zhang W, Li Y, Zhou Y, Xu Q, Xia Y, Zhou L, Cheng J. Orchestrated desaturation reprogramming from stearoyl-CoA desaturase to fatty acid desaturase 2 in cancer epithelial-mesenchymal transition and metastasis. Cancer Commun (Lond) 2025; 45:245-280. [PMID: 39722173 PMCID: PMC11947613 DOI: 10.1002/cac2.12644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 11/21/2024] [Accepted: 12/06/2024] [Indexed: 12/28/2024] Open
Abstract
BACKGROUND Adaptative desaturation in fatty acid (FA) is an emerging hallmark of cancer metabolic plasticity. Desaturases such as stearoyl-CoA desaturase (SCD) and fatty acid desaturase 2 (FADS2) have been implicated in multiple cancers, and their dominant and compensatory effects have recently been highlighted. However, how tumors initiate and sustain their self-sufficient FA desaturation to maintain phenotypic transition remains elusive. This study aimed to explore the molecular orchestration of SCD and FADS2 and their specific reprogramming mechanisms in response to cancer progression. METHODS The potential interactions between SCD and FADS2 were explored by bioinformatics analyses across multiple cancer cohorts, which guided subsequent functional and mechanistic investigations. The expression levels of desaturases were investigated with online datasets and validated in both cancer tissues and cell lines. Specific desaturation activities were characterized through various isomer-resolved lipidomics methods and sensitivity assays using desaturase inhibitors. In-situ lipid profiling was conducted using multiplex stimulated Raman scattering imaging. Functional assays were performed both in vitro and in vivo, with RNA-sequencing employed for the mechanism verification. RESULTS After integration of the RNA-protein-metabolite levels, the data revealed that a reprogramming from SCD-dependent to FADS2-dependent desaturation was linked to cancer epithelial-mesenchymal transition (EMT) and progression in both patients and cell lines. FADS2 overexpression and SCD suppression concurrently maintained EMT plasticity. A FADS2/β-catenin self-reinforcing feedback loop facilitated the degree of lipid unsaturation, membrane fluidity, metastatic potential and EMT signaling. Moreover, SCD inhibition triggered a lethal apoptosis but boosted survival plasticity by inducing EMT and enhancing FA uptake via adenosine monophosphate-activated protein kinase activation. Notably, this desaturation reprogramming increased transforming growth factor-β2, effectively sustaining aggressive phenotypes and metabolic plasticity during EMT. CONCLUSIONS These findings revealed a metabolic reprogramming from SCD-dependent to FADS2-dependent desaturation during cancer EMT and progression, which concurrently supports EMT plasticity. Targeting desaturation reprogramming represents a potential vulnerability for cancer metabolic therapy.
Collapse
Affiliation(s)
- Zhicong Chen
- Department of Obstetrics and GynecologyCenter for Reproductive MedicineGuangdong Provincial Key Laboratory of Major Obstetric DiseasesGuangdong Provincial Clinical Research Center for Obstetrics and GynecologyGuangdong‐Hong Kong‐Macao Greater Bay Area Higher Education Joint Laboratory of Maternal‐Fetal MedicineThe Third Affiliated HospitalGuangzhou Medical UniversityGuangzhouGuangdongP. R. China
- Department of Biomedical EngineeringDepartment of Electrical and Computer EngineeringPhotonics CenterBoston UniversityBostonMassachusettsUSA
- Department of UrologyPeking University First HospitalBeijingP. R. China
| | - Yanqing Gong
- Department of UrologyPeking University First HospitalBeijingP. R. China
| | - Fukai Chen
- Department of Biomedical EngineeringDepartment of Electrical and Computer EngineeringPhotonics CenterBoston UniversityBostonMassachusettsUSA
| | - Hyeon Jeong Lee
- Department of Biomedical EngineeringDepartment of Electrical and Computer EngineeringPhotonics CenterBoston UniversityBostonMassachusettsUSA
- College of Biomedical Engineering & Instrument ScienceKey Laboratory for Biomedical Engineering of Ministry of EducationZhejiang UniversityHangzhouZhejiangP. R. China
| | - Jinqin Qian
- Department of UrologyPeking University First HospitalBeijingP. R. China
| | - Jing Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyDepartment of ChemistryTsinghua UniversityBeijingP. R. China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and InstrumentsDepartment of Precision InstrumentTsinghua UniversityBeijingP. R. China
| | - Yamin Li
- Department of Biomedical EngineeringTufts UniversityMedfordMassachusettsUSA
| | - Yihui Zhou
- College of Biomedical Engineering & Instrument ScienceKey Laboratory for Biomedical Engineering of Ministry of EducationZhejiang UniversityHangzhouZhejiangP. R. China
| | - Qiaobing Xu
- Department of Biomedical EngineeringTufts UniversityMedfordMassachusettsUSA
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyDepartment of ChemistryTsinghua UniversityBeijingP. R. China
| | - Liqun Zhou
- Department of UrologyPeking University First HospitalBeijingP. R. China
| | - Ji‐Xin Cheng
- Department of Biomedical EngineeringDepartment of Electrical and Computer EngineeringPhotonics CenterBoston UniversityBostonMassachusettsUSA
| |
Collapse
|
11
|
Hu S, Lu Y, Yu G, Zheng Z, Wang W, Ni K, Giri A, Zhang J, Zhang Y, Watanabe K, Yao G, Xing J. Epithelial-mesenchymal transition couples with cell cycle arrest at various stages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639880. [PMID: 40060597 PMCID: PMC11888286 DOI: 10.1101/2025.02.24.639880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Abstract
Numerous computational approaches have been developed to infer cell state transition trajectories from snapshot single-cell data. Most approaches first require projecting high-dimensional data onto a low-dimensional representation, raising the question of whether the dynamics of the system become distorted. Using epithelial-to-mesenchymal transition (EMT) as a test system, we show that both biology-guided low-dimensional representations and stochastic trajectory simulations in high-dimensional state space, not representations obtained with brute force dimension-reduction methods, reveal multiple distinct paths of TGF-β-induced EMT. The paths arise from coupling between EMT and cell cycle arrest at either the G1/S, G2/M or M checkpoints, contributing to cell-cycle related EMT heterogeneity. The present study emphasizes that caution should be taken when inferring transition dynamics from snapshot single-cell data in two- or three-dimensional representations, and that incorporating dynamical information can improve prediction accuracy.
Collapse
Affiliation(s)
- Sophia Hu
- Department of Computational and Systems Biology, University of Pittsburgh, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, USA
| | - Yong Lu
- Department of Computational and Systems Biology, University of Pittsburgh, USA
| | - Gaohan Yu
- Department of Physics and Astronomy, University of Pittsburgh, USA
| | - Zhiqian Zheng
- Department of Computational and Systems Biology, University of Pittsburgh, USA
| | - Weikang Wang
- CAS Key Laboratory for Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Ni
- Department of Computational and Systems Biology, University of Pittsburgh, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, USA
| | - Amitava Giri
- Department of Computational and Systems Biology, University of Pittsburgh, USA
| | - Jingyu Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, USA
| | - Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, USA
| | | | - Guang Yao
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
- Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, USA
- Department of Physics and Astronomy, University of Pittsburgh, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, USA
| |
Collapse
|
12
|
Fernandez-Muñoz KV, Sánchez-Barrera CÁ, Meraz-Ríos M, Reyes JL, Pérez-Yépez EA, Ortiz-Melo MT, Terrazas LI, Mendoza-Rodriguez MG. Natural Alternatives in the Treatment of Colorectal Cancer: A Mechanisms Perspective. Biomolecules 2025; 15:326. [PMID: 40149862 PMCID: PMC11940303 DOI: 10.3390/biom15030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 02/16/2025] [Accepted: 02/19/2025] [Indexed: 03/29/2025] Open
Abstract
Colorectal cancer (CRC) is one of the deadliest neoplasia. Intrinsic or acquired resistance is the main cause of failure of therapy regimens that leads to relapse and death in CRC patients. The widely used chemotherapeutic agent 5-fluorouracil (5-FU) remains the mainstay for therapeutic combinations. Unfortunately, chemotherapeutic resistance and side effects are frequent events that compromise the success of these therapies; the dysregulation of enzymes that regulate 5-FU metabolism increases the expression and activity of efflux pumps. Additional tumor cell adaptations such as epithelial-mesenchymal transition (EMT), autophagy shaping of the tumor microenvironment, and inflammation contribute to chemoresistance. Finding new strategies and alternatives to enhance conventional chemotherapies has become necessary. Recently, the study of natural compounds has been gaining strength as an alternative to chemotherapeutics in different cancers. Curcumin, trimethylglycine, resveratrol, artemisinin, and some helminth-derived molecules, among others, are some natural compounds studied in the context of CRC. This review discusses the main benefits, mechanisms, advances, and dark side of conventional chemotherapeutics currently evaluated in CRC treatment. We also analyzed the landscape of alternative non-conventional compounds and their underlying mechanisms of action, which could, in the short term, provide fundamental knowledge to harness their anti-tumor effects and allow them to be used as alternative adjuvant therapies.
Collapse
Affiliation(s)
- Karen Vanessa Fernandez-Muñoz
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Avenida Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - Cuauhtémoc Ángel Sánchez-Barrera
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
| | - Marco Meraz-Ríos
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Avenida Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - Jose Luis Reyes
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
| | | | - Maria Teresa Ortiz-Melo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
| | - Luis I. Terrazas
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
- Laboratorio Nacional en Salud, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico
| | - Monica Graciela Mendoza-Rodriguez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (K.V.F.-M.); (C.Á.S.-B.); (M.T.O.-M.)
| |
Collapse
|
13
|
Schoenfeld JD, Azad NS, Gross J, Chen L, Overman MJ, Kao K, Jackson L, Brunnquell D, Bu X, Coppola C, Guan P, Lee J, Sims D, Fuchs R, Weirather JL, Pfaff KL, Gunasti L, Ranasinghe S, Hamilton SR, Wang V, O’Dwyer PJ, Wu CJ, Rodig SJ, Patton DR, Harris L. Next-Generation Sequencing-Based MSI Scoring Predicts Benefit in Mismatch Repair-Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D. Clin Cancer Res 2025; 31:667-677. [PMID: 39670863 PMCID: PMC11831103 DOI: 10.1158/1078-0432.ccr-24-0427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/17/2024] [Accepted: 12/10/2024] [Indexed: 12/14/2024]
Abstract
PURPOSE Mismatch repair-deficient (dMMR) tumors have demonstrated favorable responses to immune checkpoint inhibition targeting PD-1. However, more in-depth identification of predictors of response could further refine patient selection for immunotherapy treatment. PATIENTS AND METHODS We undertook integrated evaluation performed on samples collected from 28 of 42 patients enrolled on the NCI-Molecular Analysis for Therapy Choice arm Z1D trial that evaluated PD-1 inhibition treatment with nivolumab in patients with noncolorectal dMMR tumors. Genomic analyses were performed using next-generation sequencing (NGS), whole-exome sequencing, and RNA sequencing and supplemented by multiplex immunofluorescence performed on tissue samples. RESULTS In this dMMR population, more extensive alterations of microsatellites as assessed by measures of NGS were associated with clinical benefit and tumor mutational burden. RNA sequencing further revealed associations between clinical benefit and immune infiltration index. Gene sets enriched in patients with clinical benefit included IFN signaling, antigen processing, and PI3K-AKT-mTOR signaling, whereas hedgehog signaling was found to be enriched in subjects lacking clinical benefit. CONCLUSIONS These genomic data highlight the importance of immune infiltration and antigen presentation in dMMR tumors that respond to immune checkpoint blockade. In addition, they suggest that, even within a dMMR population, NGS-based measures of microsatellite instability could serve as biomarkers of immunotherapy response.
Collapse
Affiliation(s)
- Jonathan D. Schoenfeld
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nilofer S. Azad
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Jacob Gross
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Li Chen
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland
| | - Michael J. Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Katrina Kao
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Latifa Jackson
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Donna Brunnquell
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xiangning Bu
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christina Coppola
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ping Guan
- Cancer Diagnosis Program, National Cancer Institute, Bethesda, Maryland
| | - Jennifer Lee
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Sims
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rebecca Fuchs
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jason L. Weirather
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren Gunasti
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Srin Ranasinghe
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Victoria Wang
- Dana-Farber Cancer Institute–ECOG-ACRIN Biostatistics Center, Boston, Massachusetts
| | - Peter J. O’Dwyer
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Catherine J. Wu
- Center for Hematologic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott J. Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David R. Patton
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lyndsay Harris
- Cancer Diagnosis Program, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
14
|
Roshan P, Biswas A, Ahmed S, Anagnos S, Luebbers R, Harish K, Li M, Nguyen N, Zhou G, Tedeschi F, Hathuc V, Lin Z, Hamilton Z, Origanti S. Sequestration of ribosomal subunits as inactive 80S by targeting eIF6 limits mitotic exit and cancer progression. Nucleic Acids Res 2025; 53:gkae1272. [PMID: 39727167 PMCID: PMC11879136 DOI: 10.1093/nar/gkae1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 10/25/2024] [Accepted: 12/12/2024] [Indexed: 12/28/2024] Open
Abstract
Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A factor crucial for modulating the 60S ribosomal subunit is eukaryotic translation initiation factor-6 (eIF6). Release of eIF6 from the 60S subunit is essential to permit 60S interactions with the 40S subunit. Here, using the eIF6-N106S mutant, we show that disrupting eIF6 interaction with the 60S subunit leads to an increase in vacant 80S ribosomes. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S subunit biogenesis and shows that nucleolar localization of eIF6 is not dependent on BCCIP chaperone and uL14. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-seq analysis of eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3' untranslated regions. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S ribosome availability for translation, mitosis and cancer progression.
Collapse
Affiliation(s)
- Poonam Roshan
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Aparna Biswas
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Sinthyia Ahmed
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Stella Anagnos
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Riley Luebbers
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Kavya Harish
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Megan Li
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Nicholas Nguyen
- Division of Urologic Surgery, Saint Louis University School of Medicine, 6400 Clayton Road, Saint Louis, MO 63117, USA
| | - Gao Zhou
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Frank Tedeschi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Vivian Hathuc
- Department of Pathology, Saint Louis University School of Medicine,1402 S. Grand Blvd., Saint Louis, MO 63104, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| | - Zachary Hamilton
- Division of Urologic Surgery, Saint Louis University School of Medicine, 6400 Clayton Road, Saint Louis, MO 63117, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, 3507 Laclede Ave, Saint Louis, MO 63103, USA
| |
Collapse
|
15
|
Muller L, Fauvet F, Chassot C, Angileri F, Coutant A, Dégletagne C, Tonon L, Saintigny P, Puisieux A, Morel AP, Ouzounova M, Martinez P. EMT-driven plasticity prospectively increases cell-cell variability to promote therapeutic adaptation in breast cancer. Cancer Cell Int 2025; 25:32. [PMID: 39901189 PMCID: PMC11789407 DOI: 10.1186/s12935-025-03637-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 01/07/2025] [Indexed: 02/05/2025] Open
Abstract
Cellular plasticity enables cancer cells to adapt non-genetically, thereby preventing therapeutic success. The epithelial-mesenchymal transition (EMT) is a type of plasticity linked to resistance and metastasis. However, its exact impact on population diversity and its dynamics under chemotherapy is unknown. We used single-cell transcriptomics to investigate phenotypic diversity dynamics upon treatment in two in vitro models of triple negative breast cancer (TNBC), where EMT-driven plasticity is either induced or spontaneously occurring. We report that EMT-driven plasticity confers higher phenotypic cell-cell variability (p < 0.001) while enriching for stem-like cells. Genetic and phenotypic cell-cell variability were not consistently correlated. High-plasticity populations displayed more pre-adapted cells before treatment (p = 0.03). In a population displaying spontaneous EMT and phenotypic variation, pre-adapted cells were a rare minority of high-scoring outliers whose expression patterns correlated with survival in TNBC patients subjected to chemotherapy (p = 0.03). Higher plasticity was not associated with a partial EMT status. Our results provide novel insights on how EMT-driven plasticity promotes a prospective diversification process increasing population phenotypic diversity, which can yield rare pre-adapted states before treatment. This highlights the need to tackle phenotypic diversity prior to treatment in high-plasticity tumours.
Collapse
Affiliation(s)
- Lauriane Muller
- Integrated Analyses of Cancer Dynamics Team, Centre de Recherche en Cancérologie de Lyon (CRCL), Institut Convergence PlasCan, INSERM U1052, CNRSUMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
| | - Frédérique Fauvet
- EMT and Cancer Cell Plasticity Team, Centre Léon Bérard, Lyon, France
| | | | - Francesca Angileri
- Integrated Analyses of Cancer Dynamics Team, Centre de Recherche en Cancérologie de Lyon (CRCL), Institut Convergence PlasCan, INSERM U1052, CNRSUMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
- Département de Pharmacologie, Physiologie et Toxicologie, Institut des Sciences Pharmaceutiques Et Biologiques (ISPB), Université Claude Bernard Lyon I, Lyon, France
- Unité de recherche 3738 CICLY (Centre Pour l'Innovation en Cancérologie de Lyon), Faculté de Médecine et de Maïeutique Lyon Sud - Charles Mérieux, Université Claude Bernard Lyon I, Lyon, France
| | - Angèle Coutant
- Integrated Analyses of Cancer Dynamics Team, Centre de Recherche en Cancérologie de Lyon (CRCL), Institut Convergence PlasCan, INSERM U1052, CNRSUMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
| | - Cyril Dégletagne
- Plateforme de Génomique des Cancers, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurie Tonon
- Plateforme de Bioinformatique Gilles Thomas, Synergie Lyon Cancer, Centre Léon Bérard, Lyon, France
| | - Pierre Saintigny
- Integrated Analyses of Cancer Dynamics Team, Centre de Recherche en Cancérologie de Lyon (CRCL), Institut Convergence PlasCan, INSERM U1052, CNRSUMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
- CASTING - Cancer dynamics, adaptation and modeling, Inria, Inserm, Ecole Normale Supérieure de Lyon, Centre Léon Bérard, Cnrs, Université Claude Bernard Lyon 1, Lyon, France
| | - Alain Puisieux
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
- Institut Curie, PSL Research University, Paris, France
| | - Anne-Pierre Morel
- EMT and Cancer Cell Plasticity Team, Centre Léon Bérard, Lyon, France
| | - Maria Ouzounova
- EMT and Cancer Cell Plasticity Team, Centre Léon Bérard, Lyon, France
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
| | - Pierre Martinez
- Integrated Analyses of Cancer Dynamics Team, Centre de Recherche en Cancérologie de Lyon (CRCL), Institut Convergence PlasCan, INSERM U1052, CNRSUMR 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France.
- CASTING - Cancer dynamics, adaptation and modeling, Inria, Inserm, Ecole Normale Supérieure de Lyon, Centre Léon Bérard, Cnrs, Université Claude Bernard Lyon 1, Lyon, France.
| |
Collapse
|
16
|
Drápela S, Kvokačková B, Slabáková E, Kotrbová A, Gömöryová K, Fedr R, Kurfürstová D, Eliáš M, Študent V, Lenčéšová F, Ranjani GS, Pospíchalová V, Bryja V, van Weerden WM, Puhr M, Culig Z, Bouchal J, Souček K. Pre-existing cell subpopulations in primary prostate cancer tumors display surface fingerprints of docetaxel-resistant cells. Cell Oncol (Dordr) 2025; 48:205-218. [PMID: 39162992 PMCID: PMC11850551 DOI: 10.1007/s13402-024-00982-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
PURPOSE Docetaxel resistance is a significant obstacle in the treatment of prostate cancer (PCa), resulting in unfavorable patient prognoses. Intratumoral heterogeneity, often associated with epithelial-to-mesenchymal transition (EMT), has previously emerged as a phenomenon that facilitates adaptation to various stimuli, thus promoting cancer cell diversity and eventually resistance to chemotherapy, including docetaxel. Hence, understanding intratumoral heterogeneity is essential for better patient prognosis and the development of personalized treatment strategies. METHODS To address this, we employed a high-throughput single-cell flow cytometry approach to identify a specific surface fingerprint associated with docetaxel-resistance in PCa cells and complemented it with proteomic analysis of extracellular vesicles. We further validated selected antigens using docetaxel-resistant patient-derived xenografts in vivo and probed primary PCa specimens to interrogate of their surface fingerprint. RESULTS Our approaches revealed a 6-molecule surface fingerprint linked to docetaxel resistance in primary PCa specimens. We observed consistent overexpression of CD95 (FAS/APO-1), and SSEA-4 surface antigens in both in vitro and in vivo docetaxel-resistant models, which was also observed in a cell subpopulation of primary PCa tumors exhibiting EMT features. Furthermore, CD95, along with the essential enzymes involved in SSEA-4 synthesis, ST3GAL1, and ST3GAL2, displayed a significant increase in patients with PCa undergoing docetaxel-based therapy, correlating with poor survival outcomes. CONCLUSION In summary, we demonstrate that the identified 6-molecule surface fingerprint associated with docetaxel resistance pre-exists in a subpopulation of primary PCa tumors before docetaxel treatment. Thus, this fingerprint warrants further validation as a promising predictive tool for docetaxel resistance in PCa patients prior to therapy initiation.
Collapse
Affiliation(s)
- Stanislav Drápela
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, 602 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, FL, 33612, Tampa, USA
| | - Barbora Kvokačková
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, 602 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Eva Slabáková
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Anna Kotrbová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Radek Fedr
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, 602 00, Czech Republic
| | - Daniela Kurfürstová
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, 779 00, Czech Republic
| | - Martin Eliáš
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, 779 00, Czech Republic
| | - Vladimír Študent
- Department of Urology, University Hospital Olomouc, Olomouc, 779 00, Czech Republic
| | - Frederika Lenčéšová
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, 779 00, Czech Republic
| | - Ganji Sri Ranjani
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Vendula Pospíchalová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Wytske M van Weerden
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Martin Puhr
- Department of Urology, Experimental Urology, Medical University of Innsbruck, Anich Strasse 35, Innsbruck, A-6020, Austria
| | - Zoran Culig
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, 602 00, Czech Republic
- Department of Urology, Experimental Urology, Medical University of Innsbruck, Anich Strasse 35, Innsbruck, A-6020, Austria
| | - Jan Bouchal
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, 779 00, Czech Republic
| | - Karel Souček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 00, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, 602 00, Czech Republic.
| |
Collapse
|
17
|
Carbone L, Incognito GG, Incognito D, Nibid L, Caruso G, Berretta M, Taffon C, Palumbo M, Perrone G, Roviello F, Marrelli D. Clinical implications of epithelial-to-mesenchymal transition in cancers which potentially spread to peritoneum. Clin Transl Oncol 2025:10.1007/s12094-024-03837-2. [PMID: 39775727 DOI: 10.1007/s12094-024-03837-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a biological process by which epithelial cells increase their motility and acquire invasive capacity. It represents a crucial driver of cancer metastasis and peritoneal dissemination. EMT plasticity, with cells exhibiting hybrid epithelial/mesenchymal states, and its reverse process, mesenchymal-to-epithelial transition (MET), allows them to adapt to different microenvironments and evade therapeutic intervention. Resistance to conventional treatments, including chemotherapy, is a major problem. Therapies targeting EMT may inhibit tumour cell migration and invasion, while affecting normal cells and repair mechanisms, resulting in potential side effects. This paper addresses the question of the impact of EMT status on cancers with potential spread to the peritoneum, which has remained unclear in literature. Relevant studies were selected from 2000 to 2024. Three macrosections were analysed: (i) pathological characteristics, (ii) surgical implications and (iii) oncological therapies. The focus was on survival and peritoneal recurrence time in patients who underwent surgical treatment.
Collapse
Affiliation(s)
- Ludovico Carbone
- Unit of Surgical Oncology, Department of Medicine Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100, Siena, Italy.
| | - Giosuè Giordano Incognito
- Department of General Surgery and Medical Surgical Specialties, University of Catania, 95123, Catania, Italy
| | - Dalila Incognito
- Department of Human Pathology "G. Barresi", School of Specialization in Medical Oncology Unit, University of Messina, 98122, Messina, Italy
| | - Lorenzo Nibid
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, 00128, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128, Roma, Italy
| | - Giuseppe Caruso
- Department of General Surgery and Medical Surgical Specialties, University of Catania, 95123, Catania, Italy
| | - Massimiliano Berretta
- Department of Human Pathology "G. Barresi", School of Specialization in Medical Oncology Unit, University of Messina, 98122, Messina, Italy
- Department of Clinical and Experimental Medicine, University of Messina, 98122, Messina, Italy
| | - Chiara Taffon
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, 00128, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128, Roma, Italy
| | - Marco Palumbo
- Department of General Surgery and Medical Surgical Specialties, University of Catania, 95123, Catania, Italy
| | - Giuseppe Perrone
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, 00128, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128, Roma, Italy
| | - Franco Roviello
- Unit of Surgical Oncology, Department of Medicine Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100, Siena, Italy
| | - Daniele Marrelli
- Unit of Surgical Oncology, Department of Medicine Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100, Siena, Italy
| |
Collapse
|
18
|
Tian XJ, Zhang R, Ferro MV, Goetz H. Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology. Methods Mol Biol 2025; 2883:139-154. [PMID: 39702707 DOI: 10.1007/978-1-0716-4290-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Noncoding RNAs (ncRNAs) play critical roles in essential cell fate decisions. However, the exact molecular mechanisms underlying ncRNA-mediated bistable switches remain elusive and controversial. In recent years, systematic mathematical and quantitative experimental analyses have made significant contributions to elucidating the molecular mechanisms of controlling ncRNA-mediated cell fate decision processes. In this chapter, we review and summarize the general framework of mathematical modeling of ncRNA in a pedagogical way and the application of this general framework to real biological processes. We discuss the emerging properties resulting from the reciprocal regulation between mRNA, miRNA, and competing endogenous mRNA (ceRNA). We also explore the efforts within the synthetic biology approach to understand the fundamental design principles underlying cell fate decisions. Both the positive feedback loops between ncRNAs and transcription factors and the emerging properties from the miRNA-mRNA reciprocal regulation enable bistable switches to direct cell fate decisions.
Collapse
Affiliation(s)
- Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
| | - Rong Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Manuela Vanegas Ferro
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Hanah Goetz
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
19
|
Sigalotti L, Frezza AM, Sbaraglia M, Del Savio E, Baldazzi D, Valenti B, Bellan E, De Benedictis I, Doni M, Gambarotti M, Vincenzi B, Brunello A, Baldi GG, Palmerini E, Pasquali S, Ciuffetti ME, Varano V, Cappello F, Appolloni V, Pastrello C, Jurisica I, Gronchi A, Stacchiotti S, Casali PG, Dei Tos AP, Maestro R. Proximal and Classic Epithelioid Sarcomas are Distinct Molecular Entities Defined by MYC/GATA3 and SOX17/Endothelial Markers, Respectively. Mod Pathol 2025; 38:100647. [PMID: 39491746 DOI: 10.1016/j.modpat.2024.100647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/25/2024] [Accepted: 10/25/2024] [Indexed: 11/05/2024]
Abstract
Epithelioid sarcoma (ES) is a rare tumor hallmarked by the loss of INI1/SMARCB1 expression. Apart from this alteration, little is known about the biology of ES. Despite recent advances in treatment, the prognosis of ES remains unsatisfactory. To elucidate the molecular underpinnings of ES, and to identify diagnostic biomarkers and potential therapeutic vulnerabilities, we performed an integrated omics profiling (RNA sequencing and methylation array) of 24 primary, untreated ESs. Transcriptome and methylome analysis identified 2 distinct molecular clusters that essentially corresponded to the morphologic variants of ES, classic ES (C-ES) and the more aggressive proximal ES (P-ES). The P-ES group was characterized by hyperactivation of GATA3 and MYC pathways, with extensive epigenetic rewiring associated with EZH2 overexpression. Both DNA methylation and gene expression analysis indicated a striking similarity with the "MYC subgroup" of atypical teratoid/rhabdoid tumor, another SMARCB1-deficient tumor, implying a shared molecular background and potential therapeutic vulnerabilities. Conversely, the C-ES group exhibited an endothelial-like molecular profile, with expression of vascular genes and elevated proangiogenic SOX17 signaling. Immunohistochemistry validated the overexpression of the chromatin regulators GATA3 (9/12 vs 0/16) and EZH2 (7/7 vs 2/6) in P-ESs, and of the vascular factors SOX17 (8/8 vs 1/10) and N-cadherin (5/9 vs 0/10) in C-ESs. Therefore, these molecules emerge as potential diagnostic tools to fill the gap represented by the lack of ES subtype-specific biomarkers. In summary, our study shows that P-ES and C-ES represent distinct molecular entities defined by MYC/GATA3 and SOX17/endothelial molecular traits, respectively. Besides providing insights into the biology of ES, our study pinpoints subtype-specific biomarkers and potential therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Luca Sigalotti
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Anna Maria Frezza
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marta Sbaraglia
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Elisa Del Savio
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Davide Baldazzi
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Beatrice Valenti
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Elena Bellan
- Department of Pathology, Azienda Ospedale Università Padova, Padua, Italy
| | - Ilaria De Benedictis
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Michele Doni
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Marco Gambarotti
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Università Campus Biomedico di Roma, Rome, Italy
| | - Antonella Brunello
- Department of Oncology, Medical Oncology 1 Unit, Istituto Oncologico Veneto IOV, IRCCS, Padua, Italy
| | - Giacomo Giulio Baldi
- Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sandro Pasquali
- Department of Applied Research and Technological Development, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Elena Ciuffetti
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Veronica Varano
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - Filippo Cappello
- Department of Pathology, Azienda Ospedale Università Padova, Padua, Italy
| | - Viviana Appolloni
- Italian Sarcoma Group, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Pastrello
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada
| | - Igor Jurisica
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alessandro Gronchi
- Department of Sarcoma Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Stacchiotti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Giovanni Casali
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy
| | - Angelo Paolo Dei Tos
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Roberta Maestro
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy.
| |
Collapse
|
20
|
Lazzari N, Rigotto G, Montini B, Del Bianco P, Moretto E, Palladino F, Cappellesso R, Tonello M, Cenzi C, Scapinello A, Piano MA, Rossi CR, Dalerba P, Pilati P, Sommariva A, Calabrò ML. Stemness and hybrid epithelial-mesenchymal profiles guide peritoneal dissemination of malignant mesothelioma and pseudomyxoma peritonei. Int J Cancer 2025; 156:201-215. [PMID: 39146488 DOI: 10.1002/ijc.35137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]
Abstract
Intrabdominal dissemination of malignant mesothelioma (MM) and pseudomyxoma peritonei (PMP) is poorly characterized with respect to the stemness window which malignant cells activate during their reshaping on the epithelial-mesenchymal (E/M) axis. To gain insights into stemness properties and their prognostic significance in these rarer forms of peritoneal metastases (PM), primary tumor cultures from 55 patients selected for cytoreductive surgery with hyperthermic intraperitoneal chemotherapy were analyzed for cancer stem cells (CSC) by aldehyde dehydrogenase 1 (ALDH1) and spheroid formation assays, and for expression of a set of plasticity-related genes to measure E/M transition (EMT) score. Intratumor heterogeneity was also analyzed. Samples from PM of colorectal cancer were included for comparison. Molecular data were confirmed using principal component and cluster analyses. Associations with survival were evaluated using Kaplan-Meier and Cox regression models. The activity of acetylsalicylic acid (ASA), a stemness modifier, was tested in five cultures. Significantly increased amounts of ALDH1bright-cells identified high-grade PMP, and discriminated solid masses from ascitic/mucin-embedded tumor cells in both forms of PM. Epithelial/early hybrid EMT scores and an early hybrid expression pattern correlated with pluripotency factors were significantly associated with early peritoneal progression (p = .0343 and p = .0339, respectively, log-rank test) in multivariable models. ASA impaired spheroid formation and increased cisplatin sensitivity in all five cultures. These data suggest that CSC subpopulations and hybrid E/M states may guide peritoneal spread of MM and PMP. Stemness could be exploited as targetable vulnerability to increase chemosensitivity and improve patient outcomes. Additional research is needed to confirm these preliminary data.
Collapse
Affiliation(s)
- Nayana Lazzari
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Giulia Rigotto
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Barbara Montini
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Paola Del Bianco
- Clinical Research Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Elena Moretto
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Federica Palladino
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Marco Tonello
- Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Carola Cenzi
- Clinical Research Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
- Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Antonio Scapinello
- Anatomy and Histopathology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Maria Assunta Piano
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Piero Dalerba
- Center for Discovery and Innovation (CDI), Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Pierluigi Pilati
- Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Antonio Sommariva
- Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
- Surgical Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
- Advanced Surgical Oncology Unit, Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Maria Luisa Calabrò
- Immunology and Molecular Oncology, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| |
Collapse
|
21
|
Roy N, Lodh R, Mandal S, Kumar Jolly M, Sarma A, Bhattacharyya DK, Barah P. Comparative transcriptomic analysis uncovers molecular heterogeneity in hepatobiliary cancers. Transl Oncol 2025; 51:102192. [PMID: 39546955 PMCID: PMC11613176 DOI: 10.1016/j.tranon.2024.102192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/25/2024] [Accepted: 11/05/2024] [Indexed: 11/17/2024] Open
Abstract
Hepatobiliary cancers (HBCs) pose a major global health challenge, with a lack of effective targeted biomarkers. Due to their complex anatomical locations, shared risk factors, and the limitations of targeted therapies, generalized treatment strategies are often used for gallbladder cancer (GBC), hepatocellular carcinoma (HCC), and intrahepatic cholangiocarcinoma (ICC). This study aimed to identify specific transcriptomic signatures in GBC, HCC, and ICC. The transcriptomic data analysis revealed distinct expression profiles, highlighting complex molecular heterogeneity within these cancers, even within the same organ system. Functional annotation revealed distinct biological pathways associated with each type of HBCs. GBC was linked to cell cycle regulation, HCC was associated with immune system modulation, and ICC was involved in metabolic dysregulation, particularly lipid metabolism. Gene co-expression network (GCN) and protein-protein interaction (PPI) network analyses identified potential key genes, such as MAPK3 and ERBB2 in GBC, AC069287.1 and ACTN2 in HCC, and TRPC1 and BACE1 in ICC. The FOX family of transcription factors (TFs) was conserved across all three cancer types. To further explore the relationship between Epithelial-Mesenchymal Transition (EMT) and the identified hub genes and TFs, an EMT score analysis was conducted. This analysis revealed distinct phenotypic characteristics in each cancer type, with TFs identified in GBC and ICC showing a stronger correlation with EMT compared to those in HCC. External validation using The Cancer Genome Atlas (TCGA) databases confirmed the expression of candidate genes, underscoring their potential as therapeutic targets. These findings provide valuable insights into the molecular heterogeneity and complexity of HBCs, opening new avenues for personalized therapeutic interventions.
Collapse
Affiliation(s)
- Nabanita Roy
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam, 784028, India
| | - Ria Lodh
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam, 784028, India
| | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Anupam Sarma
- Department of Onco-pathology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, 781016, India
| | - Dhruba Kumar Bhattacharyya
- Department of Computer Science and Engineering, Tezpur University, Napaam, Sonitpur, Assam, 784028, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam, 784028, India.
| |
Collapse
|
22
|
Duran GA. Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs. Eur J Breast Health 2025; 21:63-73. [PMID: 39744927 PMCID: PMC11706122 DOI: 10.4274/ejbh.galenos.2024.2024-11-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 12/25/2024] [Indexed: 01/11/2025]
Abstract
Objective The prevalence of breast cancer and gynaecological cancers is high, and these cancer types can occur consecutively as secondary cancers. The aim of our study is to determine the genes commonly expressed in these cancers and to identify the common hub genes and drug components. Materials and Methods Gene intensity values of breast cancer, gynaecological cancers such as cervical, ovarian and endometrial cancers were used from the Gene Expression Omnibus database Affymetrix Human Genome U133 Plus 2.0 Array project. Using the linear modelling method included in the R LIMMA package, genes that differ between healthy individuals and cancer patients were identified. Hub genes were determined using cytoHubba in Cytoscape program. "ShinyGo 0.80" tool was used to determine the disease-specific biological KEGG pathways. Drug.MATADOR from the ShinyGo 0.80 tool was used to predict drug-target relationships. Results The RecQ Like Helicase 4 and Family with Sequence Similarity 13 Member C genes were found to be similarly expressed in breast cancer and gynaecological cancers. Upon KEGG pathway analyses with hub genes, Drug.MATADOR analysis with hub genes related to cancer related pathways was performed. We have determined these gene/drug interactions: NBN (targeted by Hydroxyurea), EP300 (targeted by Acetylcarnitine) and MAPK14 (targeted by Salicylate and Dibutyryl cyclic AMP). Conclusion The drugs associated with hub genes determined in our study are not routinely used in cancer treatment. Our study offers the opportunity to identify the target genes of drugs used in breast and gynaecological cancers with the drug repurposing approach.
Collapse
Affiliation(s)
- Gizem Ayna Duran
- Department of Biomedical Engineering Faculty of Engineering, İzmir University of Economics, İzmir, Turkey
| |
Collapse
|
23
|
Withnell E, Secrier M. SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer. Genome Biol 2024; 25:289. [PMID: 39529126 PMCID: PMC11552145 DOI: 10.1186/s13059-024-03428-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 10/24/2024] [Indexed: 11/16/2024] Open
Abstract
Spatial transcriptomics is revolutionizing the exploration of intratissue heterogeneity in cancer, yet capturing cellular niches and their spatial relationships remains challenging. We introduce SpottedPy, a Python package designed to identify tumor hotspots and map spatial interactions within the cancer ecosystem. Using SpottedPy, we examine epithelial-mesenchymal plasticity in breast cancer and highlight stable niches associated with angiogenic and hypoxic regions, shielded by CAFs and macrophages. Hybrid and mesenchymal hotspot distribution follows transformation gradients reflecting progressive immunosuppression. Our method offers flexibility to explore spatial relationships at different scales, from immediate neighbors to broader tissue modules, providing new insights into tumor microenvironment dynamics.
Collapse
Affiliation(s)
- Eloise Withnell
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
24
|
Martínez-Espinosa I, Serrato JA, Cabello-Gutiérrez C, Carlos-Reyes Á, Ortiz-Quintero B. Mechanisms of microRNA Regulation of the Epithelial-Mesenchymal Transition (EMT) in Lung Cancer. Life (Basel) 2024; 14:1431. [PMID: 39598229 PMCID: PMC11595801 DOI: 10.3390/life14111431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 11/04/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024] Open
Abstract
Lung cancer remains the cancer with the highest mortality worldwide, largely due to a limited understanding of the precise molecular mechanisms that drive its progression. microRNAs (miRNAs) have emerged as crucial regulators of lung cancer progression by influencing key cellular processes, notably the epithelial-mesenchymal transition (EMT). EMT is a complex and potentially reversible process where epithelial cells lose their polarity and adhesion, reorganize their cytoskeleton, and transition to a mesenchymal phenotype, enhancing their migratory and invasive capacities. While EMT plays an essential role in normal physiological contexts such as tissue development and wound healing, it is also a critical mechanism underlying the progression and metastasis of lung cancer. This review aims to summarize the latest research findings on the role of endogenous and exosome-derived microRNAs in regulating EMT in lung cancer, focusing on studies conducted over the past five years. It also provides an overview of EMT's essential molecular mechanisms to better understand how miRNAs regulate EMT in lung cancer.
Collapse
Affiliation(s)
- Israel Martínez-Espinosa
- Department of Molecular Biomedicine and Translational Research, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - José A. Serrato
- Department of Molecular Biomedicine and Translational Research, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Carlos Cabello-Gutiérrez
- Department of Research in Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Ángeles Carlos-Reyes
- Laboratory of Onco-Immunobiology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Blanca Ortiz-Quintero
- Department of Molecular Biomedicine and Translational Research, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
| |
Collapse
|
25
|
Youssef KK, Narwade N, Arcas A, Marquez-Galera A, Jiménez-Castaño R, Lopez-Blau C, Fazilaty H, García-Gutierrez D, Cano A, Galcerán J, Moreno-Bueno G, Lopez-Atalaya JP, Nieto MA. Two distinct epithelial-to-mesenchymal transition programs control invasion and inflammation in segregated tumor cell populations. NATURE CANCER 2024; 5:1660-1680. [PMID: 39414946 PMCID: PMC11584407 DOI: 10.1038/s43018-024-00839-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/06/2024] [Indexed: 10/18/2024]
Abstract
Epithelial-to-mesenchymal transition (EMT) triggers cell plasticity in embryonic development, adult injured tissues and cancer. Combining the analysis of EMT in cell lines, embryonic neural crest and mouse models of renal fibrosis and breast cancer, we find that there is not a cancer-specific EMT program. Instead, cancer cells dedifferentiate and bifurcate into two distinct and segregated cellular trajectories after activating either embryonic-like or adult-like EMTs to drive dissemination or inflammation, respectively. We show that SNAIL1 acts as a pioneer factor in both EMT trajectories, and PRRX1 drives the progression of the embryonic-like invasive trajectory. We also find that the two trajectories are plastic and interdependent, as the abrogation of the EMT invasive trajectory by deleting Prrx1 not only prevents metastasis but also enhances inflammation, increasing the recruitment of antitumor macrophages. Our data unveil an additional role for EMT in orchestrating intratumor heterogeneity, driving the distribution of functions associated with either inflammation or metastatic dissemination.
Collapse
Grants
- This work was supported by grants MICIU RTI2018-096501-B-I00 and MCI PID2021-125682NB-I00 to MAN, RTI2018-102260-B-I00 to JPLA, and PID2022-136854OB-I00 to GMB all funded by MICIU/AEI /10.13039/501100011033 and by FEDER, UE. Funds were also provided by the AECC Scientific Foundation (FC_AECC PROYE19073NIE to MAN and PROYE19036MOR to GMB), Instituto de Salud Carlos III (CIBERONC, CB16/12/00295 to GMB and AC; CIBERER, CB19/07/00038 to MAN), Generalitat Valenciana (Prometeo 2021/45) and the European Research Council (ERC AdG 322694) to MAN, who also acknowledges financial support from Centro de Excelencia Severo Ochoa» Grant CEX2021-001165-S funded by MCIN/AEI/ 10.13039/501100011033. KKY was holder of an EMBO Long-Term fellowship, a “Severo Ochoa Excellence Programme” Postdoctoral contract and currently holds an investigator contract from the AECC Scientific Foundation (Ayudas AECC investigador 2022). N.N held a contract associated with NEUcrest European Union’s Horizon 2020 Research and Innovation Program under Marie Sklodowska-Curie (grant agreement No 860635, ITN NEUcrest to MAN). R.J.C. holds a “Severo Ochoa Excellence Programme” PhD contract (PRE2020-091888).
- MCI PID2021-125682NB-I00
- NEUcrest European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska-Curie (grant agreement No 860635, ITN NEUcrest to MAN
- RTI2018-102260-B-I00
- MICIU RTI2018-096501-B-I00
- PID2022-136854OB-I00
Collapse
Affiliation(s)
| | - Nitin Narwade
- Instituto de Neurociencias (CSIC-UMH), Alicante, Spain
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Alicante, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | | | | | - Hassan Fazilaty
- Instituto de Neurociencias (CSIC-UMH), Alicante, Spain
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Amparo Cano
- Instituto de Investigaciones Biomédicas 'Sols-Morreale' CSIC-UAM, Madrid, Spain
- CIBERONC, Centro de Investigación Biomédica en Red de Cancer, Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Alicante, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Moreno-Bueno
- Instituto de Investigaciones Biomédicas 'Sols-Morreale' CSIC-UAM, Madrid, Spain
- CIBERONC, Centro de Investigación Biomédica en Red de Cancer, Instituto de Salud Carlos III, Madrid, Spain
- MD Anderson Cancer Center International Foundation, Madrid, Spain
| | | | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Alicante, Spain.
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
26
|
Cin M, Akyıldız İğdem A, Bektaş S, Gündoğar Ö, Cin S, Komut N, Çetin B. Is Immunohistochemical Galectin-3 Expression Associated with the Epithelial-Mesenchymal Transition in High- and Low-Grade Invasive Urothelial Carcinomas of the Bladder? Diagnostics (Basel) 2024; 14:2270. [PMID: 39451592 PMCID: PMC11506668 DOI: 10.3390/diagnostics14202270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/06/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024] Open
Abstract
Background/Objectives: Bladder cancer, predominantly urothelial carcinoma, is an important malignancy of the urinary system. Despite the same histologic grade and stage, some patients seem to have a worse prognosis. In this context, the epithelial-mesenchymal transition (EMT), characterized by the loss of E-cadherin and gain of vimentin expression, is an important process in tumor progression. Galectin-3, a lactose-binding protein involved in various cellular processes, has been associated with increased tumor cell migration, invasion, and treatment resistance. Methods: In this study, 223 bladder cancer cases were examined, and E-cadherin, vimentin, and galectin-3 expression was evaluated by immunohistochemical staining in tumor budding areas and invasive components. These markers were also correlated with clinicopathological parameters, including tumor grade and stage. Results: The results indicated a significant decrease in E-cadherin expression and an increase in vimentin staining in higher-grade and higher-stage tumors, supporting EMT involvement. Galectin-3 expression was notably higher in T1 high-grade tumors but decreased in T2 stage tumors. Despite this, no significant correlation was found between galectin-3 and E-cadherin or vimentin, suggesting a complex role of galectin-3 in EMT. Conclusions: High galectin-3 expression in T1 high-grade tumors highlights its potential role in early tumor progression and as a therapeutic target. However, the decrease in its expression in advanced stages underscores the need for further research to understand its multifaceted involvement in bladder cancer. These findings suggest that while galectin-3 may contribute to the EMT and early tumor progression, its exact role and potential as a therapeutic target require more detailed investigation.
Collapse
Affiliation(s)
- Merve Cin
- Department of Pathology, Istanbul Training and Research Hospital, University of Health Sciences, 34098 Istanbul, Turkey
| | | | - Sibel Bektaş
- Department of Pathology, Gaziosmanspasa Education and Research Hospital, University of Health Sciences, 34255 Istanbul, Turkey; (S.B.); (Ö.G.)
| | - Özgecan Gündoğar
- Department of Pathology, Gaziosmanspasa Education and Research Hospital, University of Health Sciences, 34255 Istanbul, Turkey; (S.B.); (Ö.G.)
| | - Selçuk Cin
- Department of Pathology, Bagcilar Training and Research Hospital, University of Health Sciences, 34200 Istanbul, Turkey;
| | - Neslihan Komut
- Department of Pathology, Tekirdag Dr. Ismail Fehmi Cumalioglu City Hospital, 59030 Tekirdag, Turkey;
| | - Buğra Çetin
- Department of Urology, Bahcelievler Medicalpark Hospital, Altinbas University, 34180 Istanbul, Turkey;
| |
Collapse
|
27
|
Cavazzoni A, Salamon I, Fumarola C, Gallerani G, Laprovitera N, Gelsomino F, Riefolo M, Rihawi K, Porcellini E, Rossi T, Mazzeschi M, Naddeo M, Serravalle S, Broseghini E, Agostinis F, Deas O, Roncarati R, Durante G, Pace I, Lauriola M, Garajova I, Calin GA, Bonafè M, D'Errico A, Petronini PG, Cairo S, Ardizzoni A, Sales G, Ferracin M. Synergic activity of FGFR2 and MEK inhibitors in the treatment of FGFR2-amplified cancers of unknown primary. Mol Ther 2024; 32:3650-3668. [PMID: 39033323 PMCID: PMC11489551 DOI: 10.1016/j.ymthe.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/30/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Patients with cancer of unknown primary (CUP) carry the double burden of an aggressive disease and reduced access to therapies. Experimental models are pivotal for CUP biology investigation and drug testing. We derived two CUP cell lines (CUP#55 and #96) and corresponding patient-derived xenografts (PDXs), from ascites tumor cells. CUP cell lines and PDXs underwent histological, immune-phenotypical, molecular, and genomic characterization confirming the features of the original tumor. The tissue-of-origin prediction was obtained from the tumor microRNA expression profile and confirmed by single-cell transcriptomics. Genomic testing and fluorescence in situ hybridization analysis identified FGFR2 gene amplification in both models, in the form of homogeneously staining region (HSR) in CUP#55 and double minutes in CUP#96. FGFR2 was recognized as the main oncogenic driver and therapeutic target. FGFR2-targeting drug BGJ398 (infigratinib) in combination with the MEK inhibitor trametinib proved to be synergic and exceptionally active, both in vitro and in vivo. The effects of the combined treatment by single-cell gene expression analysis revealed a remarkable plasticity of tumor cells and the greater sensitivity of cells with epithelial phenotype. This study brings personalized therapy closer to CUP patients and provides the rationale for FGFR2 and MEK targeting in metastatic tumors with FGFR2 pathway activation.
Collapse
MESH Headings
- Animals
- Female
- Humans
- Mice
- Cell Line, Tumor
- Drug Synergism
- Gene Amplification
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Neoplasms, Unknown Primary/drug therapy
- Neoplasms, Unknown Primary/genetics
- Neoplasms, Unknown Primary/pathology
- Phenylurea Compounds/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Pyridones/pharmacology
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Pyrimidinones/pharmacology
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Andrea Cavazzoni
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Irene Salamon
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Claudia Fumarola
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Giulia Gallerani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Noemi Laprovitera
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | - Mattia Riefolo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Karim Rihawi
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Elisa Porcellini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola 47014, Italy
| | - Martina Mazzeschi
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Maria Naddeo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | | | | | | | - Roberta Roncarati
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM)- Consiglio Nazionale delle Ricerche (CNR), 40136 Bologna, Italy
| | - Giorgio Durante
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Pace
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ingrid Garajova
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Massimiliano Bonafè
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Antonia D'Errico
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | | | | | - Andrea Ardizzoni
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, 35031 Padua, Italy
| | - Manuela Ferracin
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy.
| |
Collapse
|
28
|
Fernando W, Cruickshank BM, Arun RP, MacLean MR, Cahill HF, Morales-Quintanilla F, Dean CA, Wasson MCD, Dahn ML, Coyle KM, Walker OL, Power Coombs MR, Marcato P. ALDH1A3 is the switch that determines the balance of ALDH + and CD24 -CD44 + cancer stem cells, EMT-MET, and glucose metabolism in breast cancer. Oncogene 2024; 43:3151-3169. [PMID: 39251846 PMCID: PMC11493680 DOI: 10.1038/s41388-024-03156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/11/2024]
Abstract
Plasticity is an inherent feature of cancer stem cells (CSCs) and regulates the balance of key processes required at different stages of breast cancer progression, including epithelial-to-mesenchymal transition (EMT) versus mesenchymal-to-epithelial transition (MET), and glycolysis versus oxidative phosphorylation. Understanding the key factors that regulate the switch between these processes could lead to novel therapeutic strategies that limit tumor progression. We found that aldehyde dehydrogenase 1A3 (ALDH1A3) regulates these cancer-promoting processes and the abundance of the two distinct breast CSC populations defined by high ALDH activity and CD24-CD44+ cell surface expression. While ALDH1A3 increases ALDH+ breast cancer cells, it inversely suppresses the CD24-CD44+ population by retinoic acid signaling-mediated gene expression changes. This switch in CSC populations induced by ALDH1A3 was paired with decreased migration but increased invasion and an intermediate EMT phenotype. We also demonstrate that ALDH1A3 increases oxidative phosphorylation and decreases glycolysis and reactive oxygen species (ROS). The effects of ALDH1A3 reduction were countered with the glycolysis inhibitor 2-deoxy-D-glucose (2DG). In cell culture and tumor xenograft models, 2DG suppresses the increase in the CD24-CD44+ population and ROS induced by ALDH1A3 knockdown. Combined inhibition of ALDH1A3 and glycolysis best reduces breast tumor growth and tumor-initiating cells, suggesting that the combination of targeting ALDH1A3 and glycolysis has therapeutic potential for limiting CSCs and tumor progression. Together, these findings identify ALDH1A3 as a key regulator of processes required for breast cancer progression and depletion of ALDH1A3 makes breast cancer cells more susceptible to glycolysis inhibition.
Collapse
Affiliation(s)
- Wasundara Fernando
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Acadia University, Wolfville, NS, Canada
| | - Brianne M Cruickshank
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Surgery, Dalhousie University, Halifax, NS, Canada
| | - Raj Pranap Arun
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Maya R MacLean
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Hannah F Cahill
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | | | - Cheryl A Dean
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | | | - Margaret L Dahn
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Krysta M Coyle
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Olivia L Walker
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Melanie R Power Coombs
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Acadia University, Wolfville, NS, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada.
- Nova Scotia Health Authority, Halifax, NS, Canada.
| |
Collapse
|
29
|
Shi J, Duan Y. Knowledge-map and research trends of circulating tumor cells in breast cancer: a scientometric analysis. Discov Oncol 2024; 15:506. [PMID: 39340703 PMCID: PMC11438760 DOI: 10.1007/s12672-024-01385-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024] Open
Abstract
Assessing circulating tumor cells (CTCs) in early-stage breast cancer patients can help identify relapse risk for timely interventions. Molecular analysis of CTCs can reveal vulnerabilities for personalized treatment options in metastatic breast cancer. This study aims to summarize CTCs in breast cancer research understanding and evaluate research trends. Extracted from the Web of Science Core Collection, publications on CTCs in breast cancer studies spanning from January 1, 2008, to December 21, 2023, were included. Co-authorships, references, and keywords were analyzed using Bibliometrix R packages and VOSviewer software. References and keywords burst detection were conducted with CiteSpace, and BICOMB was utilized to generate high-frequency keyword layouts. Biclustering analysis of the binary co-keyword matrix was performed using gCLUTO. 1747 articles focusing on CTCs in breast cancer were identified. The USA and the University of Texas MD Anderson Cancer Center demonstrated the highest productivity at the national and institutional levels, respectively. The journal "CANCERS" had the highest publication outputs on this subject. Pantel K emerged as the foremost author with the highest publication and co-citation counts. Analysis of co-keywords unveiled five prominent research areas concerning CTCs in breast cancer. The prognostic and predictive roles of CTCs in breast cancer have substantial implications for clinical practice. Nevertheless, precise assessment of CTCs, encompassing its quantities and attributes through advanced technologies, and its role in detecting minimal residual disease in breast cancer, continue to pose notable challenges. In conclusion, recent advancements and trends in CTCs research in breast cancer are examined through scientometric analysis in this study. The results provide valuable insights for the formulation of novel approaches in CTCs research, emphasizing the current research frontiers.
Collapse
Affiliation(s)
- Jinan Shi
- Department of Medical Oncology, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Yin Duan
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
| |
Collapse
|
30
|
Zhang J, Liu L, Wei X, Zhao C, Luo Y, Li J, Le TD. Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data. BMC Biol 2024; 22:218. [PMID: 39334271 PMCID: PMC11438147 DOI: 10.1186/s12915-024-02020-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 09/24/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND RNA-sequencing technology provides an effective tool for understanding miRNA regulation in complex human diseases, including cancers. A large number of computational methods have been developed to make use of bulk and single-cell RNA-sequencing data to identify miRNA regulations at the resolution of multiple samples (i.e. group of cells or tissues). However, due to the heterogeneity of individual samples, there is a strong need to infer miRNA regulation specific to individual samples to uncover miRNA regulation at the single-sample resolution level. RESULTS Here, we develop a framework, Scan, for scanning sample-specific miRNA regulation. Since a single network inference method or strategy cannot perform well for all types of new data, Scan incorporates 27 network inference methods and two strategies to infer tissue-specific or cell-specific miRNA regulation from bulk or single-cell RNA-sequencing data. Results on bulk and single-cell RNA-sequencing data demonstrate the effectiveness of Scan in inferring sample-specific miRNA regulation. Moreover, we have found that incorporating the prior information of miRNA targets can generally improve the accuracy of miRNA target prediction. In addition, Scan can contribute to construct cell/tissue correlation networks and recover aggregate miRNA regulatory networks. Finally, the comparison results have shown that the performance of network inference methods is likely to be data-specific, and selecting optimal network inference methods is required for more accurate prediction of miRNA targets. CONCLUSIONS Scan provides a useful method to help infer sample-specific miRNA regulation for new data, benchmark new network inference methods and deepen the understanding of miRNA regulation at the resolution of individual samples.
Collapse
Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, 671003, Yunnan, China.
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Yanbi Luo
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia.
| |
Collapse
|
31
|
Das P, San Martin R, Hong T, McCord RP. Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609227. [PMID: 39229150 PMCID: PMC11370564 DOI: 10.1101/2024.08.23.609227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Breast cancer cells exhibit organotropism during metastasis, showing preferential homing to certain organs such as bone, lung, liver, and brain. One potential explanation for this organotropic behavior is that cancer cells gain properties that enable thriving in certain microenvironments. Such specific metastatic traits may arise from gene regulation at the primary tumor site. Spatial genome organization plays a crucial role in oncogenic transformation and progression, but the extent to which chromosome architecture contributes to organ-specific metastatic traits is unclear. This work characterizes chromosome architecture changes associated with organotropic metastatic traits. By comparing a collection of genomic data from different subtypes of localized and lung metastatic breast cancer cells with both normal and cancerous lung cells, we find important trends of genomic reorganization. The most striking differences in 3D genome compartments segregate cell types according to their epithelial vs. mesenchymal status. This EMT compartment signature occurs at genomic regions distinct from transcription-defined EMT signatures, suggesting a separate layer of regulation. Specifically querying organotropism, we find 3D genome changes consistent with adaptations needed to survive in a new microenvironment, with lung metastatic breast cells exhibiting compartment switch signatures that shift the genome architecture to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state. TCGA patient data reveals gene expression changes concordant with these organ-permissive compartment changes. These results suggest that genome architecture provides an additional level of cell fate specification informing organotropism and enabling survival at the metastatic site.
Collapse
|
32
|
Lien HC, Yu HC, Yu WH, Lin SF, Chen TWW, Chen IC, Hsiao LP, Yeh LC, Li YC, Lo C, Lu YS. Characteristics and transcriptional regulators of spontaneous epithelial-mesenchymal transition in genetically unperturbed patient-derived non-spindled breast carcinoma. Breast Cancer Res 2024; 26:130. [PMID: 39256881 PMCID: PMC11385830 DOI: 10.1186/s13058-024-01888-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Although tumor cells undergoing epithelial-mesenchymal transition (EMT) typically exhibit spindle morphology in experimental models, such histomorphological evidence of EMT has predominantly been observed in rare primary spindle carcinomas. The characteristics and transcriptional regulators of spontaneous EMT in genetically unperturbed non-spindled carcinomas remain underexplored. METHODS We used primary culture combined with RNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), and in situ RNA-seq to explore the characteristics and transcription factors (TFs) associated with potential spontaneous EMT in non-spindled breast carcinoma. RESULTS Our primary culture revealed carcinoma cells expressing diverse epithelial-mesenchymal traits, consistent with epithelial-mesenchymal plasticity. Importantly, carcinoma cells undergoing spontaneous EMT did not necessarily exhibit spindle morphology, even when undergoing complete EMT. EMT was a favored process, whereas mesenchymal-epithelial transition appeared to be crucial for secondary tumor growth. Through scRNA-seq, we identified TFs that were sequentially and significantly upregulated as carcinoma cells progressed through the EMT process, which correlated with increasing VIM expression. Once upregulated, the TFs remained active throughout the EMT process. ZEB1 was a key initiator and sustainer of EMT, as indicated by its earliest significant upregulation in the EMT process, its exact correlation with VIM expression, and the reversal of EMT and downregulation of EMT-upregulated TFs upon ZEB1 knockdown. The correlation between ZEB1 and vimentin expression in triple-negative breast cancer and metaplastic breast carcinoma tumor cohorts further highlighted its role. The immediate upregulation of ZEB2 following that of ZEB1, along with the observation that the knockdown of ZEB1 or ZEB2 downregulates both ZEB1 and ZEB2 concomitant with the reversal of EMT, suggests their functional cooperation in EMT. This finding, together with that of a lack of correlation of SNAI1, SNAI2, and TWIST1 expression with the mesenchymal phenotype, indicated EMT-TFs have a context-dependent role in EMT. Upregulation of EMT-related gene signatures during EMT correlated with poor patient outcomes, highlighting the biological importance of the model. Elevated EMT gene signatures and increased ZEB1 and ZEB2 expression in vimentin-positive compared to vimentin-negative carcinoma cells within the corresponding primary tumor tissue confirmed ZEB1 and ZEB2 as intrinsic, instead of microenvironmentally-induced, EMT regulators, and vimentin as an in vivo indicator of EMT. CONCLUSIONS Our findings provide insights into the characteristics and transcriptional regulators of spontaneous EMT in primary non-spindled carcinoma.
Collapse
Affiliation(s)
- Huang-Chun Lien
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
| | - Hui-Chieh Yu
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan
| | - Wen-Hsuan Yu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Tom Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center Hospital, Taipei, Taiwan
| | - Li-Ping Hsiao
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan
| | - Ling-Chun Yeh
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan
| | - Yu-Chia Li
- Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
| | - Chiao Lo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, No. 1, Changde St., Zhongzheng District, Taipei City, Taiwan.
| |
Collapse
|
33
|
Winkler J, Tan W, Diadhiou CM, McGinnis CS, Abbasi A, Hasnain S, Durney S, Atamaniuc E, Superville D, Awni L, Lee JV, Hinrichs JH, Wagner PS, Singh N, Hein MY, Borja M, Detweiler AM, Liu SY, Nanjaraj A, Sitarama V, Rugo HS, Neff N, Gartner ZJ, Oliveira Pisco A, Goga A, Darmanis S, Werb Z. Single-cell analysis of breast cancer metastasis reveals epithelial-mesenchymal plasticity signatures associated with poor outcomes. J Clin Invest 2024; 134:e164227. [PMID: 39225101 PMCID: PMC11364385 DOI: 10.1172/jci164227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/11/2024] [Indexed: 09/04/2024] Open
Abstract
Metastasis is the leading cause of cancer-related deaths. It is unclear how intratumor heterogeneity (ITH) contributes to metastasis and how metastatic cells adapt to distant tissue environments. The study of these adaptations is challenged by the limited access to patient material and a lack of experimental models that appropriately recapitulate ITH. To investigate metastatic cell adaptations and the contribution of ITH to metastasis, we analyzed single-cell transcriptomes of matched primary tumors and metastases from patient-derived xenograft models of breast cancer. We found profound transcriptional differences between the primary tumor and metastatic cells. Primary tumors upregulated several metabolic genes, whereas motility pathway genes were upregulated in micrometastases, and stress response signaling was upregulated during progression. Additionally, we identified primary tumor gene signatures that were associated with increased metastatic potential and correlated with patient outcomes. Immune-regulatory control pathways were enriched in poorly metastatic primary tumors, whereas genes involved in epithelial-mesenchymal transition were upregulated in highly metastatic tumors. We found that ITH was dominated by epithelial-mesenchymal plasticity (EMP), which presented as a dynamic continuum with intermediate EMP cell states characterized by specific genes such as CRYAB and S100A2. Elevated expression of an intermediate EMP signature correlated with worse patient outcomes. Our findings identified inhibition of the intermediate EMP cell state as a potential therapeutic target to block metastasis.
Collapse
Affiliation(s)
- Juliane Winkler
- Department of Anatomy and
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Weilun Tan
- Chan Zuckerberg Biohub SF, San Francisco, California, USA
| | | | | | | | | | - Sophia Durney
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
| | - Elena Atamaniuc
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
| | - Daphne Superville
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
| | | | - Joyce V. Lee
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
| | - Johanna H. Hinrichs
- Department of Anatomy and
- Institute of Internal Medicine D, Medical Cell Biology, University Hospital Münster, Münster, Germany
| | - Patrick S. Wagner
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Namrata Singh
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Y. Hein
- Chan Zuckerberg Biohub SF, San Francisco, California, USA
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria
| | - Michael Borja
- Chan Zuckerberg Biohub SF, San Francisco, California, USA
| | | | | | | | | | - Hope S. Rugo
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Norma Neff
- Chan Zuckerberg Biohub SF, San Francisco, California, USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, California, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, California, USA
| | | | - Andrei Goga
- Department of Cell and Tissue Biology, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Spyros Darmanis
- Chan Zuckerberg Biohub SF, San Francisco, California, USA
- Genentech, South San Francisco, California, USA
| | | |
Collapse
|
34
|
Ambeskovic A, McCall MN, Woodsmith J, Juhl H, Land H. Exon-Skipping-Based Subtyping of Colorectal Cancers. Gastroenterology 2024:S0016-5085(24)05357-5. [PMID: 39181169 DOI: 10.1053/j.gastro.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/24/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND & AIMS The identification of colorectal cancer (CRC) molecular subtypes has prognostic and potentially diagnostic value for patients, yet reliable subtyping remains unavailable in the clinic. The current consensus molecular subtype (CMS) classification in CRCs is based on complex RNA expression patterns quantified at the gene level. The clinical application of these methods, however, is challenging due to high uncertainty of single-sample classification and associated costs. Alternative splicing, which strongly contributes to transcriptome diversity, has rarely been used for tissue type classification. Here, we present an AS-based CRC subtyping framework sensitive to differential exon use that can be adapted for clinical application. METHODS Unsupervised clustering was used to measure the strength of association between different categories of alternative splicing and CMSs. To build a classifier, the ground truth for CMS labels was derived from expression data quantified at the gene level. Feature selection was achieved through bootstrapping and L1-penalized estimation. The resulting feature space was used to construct a subtype prediction framework applicable to single and multiple samples. The performance of the models was evaluated on unseen CRCs from 2 independent sources (Indivumed, n = 129; The Cancer Genome Atlas, n = 99). RESULTS We developed a CRC subtype identifier based on 29 exon-skipping events that accurately classifies unseen tumors and enables more precise differentiation of subtypes characterized by distinct biological and prognostic features as compared to classifiers based on gene expression. CONCLUSIONS Here, we demonstrate that a small number of exon-skipping events can reliably classify CRC subtypes using individual patient specimens in a manner suitable to clinical application.
Collapse
Affiliation(s)
- Aslihan Ambeskovic
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York
| | - Matthew N McCall
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York; Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | | | | | - Hartmut Land
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York; Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York.
| |
Collapse
|
35
|
Li SY, Zhang N, Zhang H, Wang N, Du YY, Li HN, Huang CS, Li XR. Deciphering the TCF19/miR-199a-5p/SP1/LOXL2 pathway: Implications for breast cancer metastasis and epithelial-mesenchymal transition. Cancer Lett 2024; 597:216995. [PMID: 38851313 DOI: 10.1016/j.canlet.2024.216995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/11/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
Globally, breast cancer (BC) is the predominant malignancy with a significant death rate due to metastasis. The epithelial-mesenchymal transition (EMT) is a fundamental initiator for metastatic progression. Through advanced computational strategies, TCF19 was identified as a critical EMT-associated gene with diagnostic and prognostic significance in BC, based on a novel EMT score. Molecular details and the pro-EMT impact of the TCF19/miR-199a-5p/SP1/LOXL2 axis were explored in BC cell lines through in vitro validations, and the oncogenic and metastatic potential of TCF19 and LOXL2 were investigated using subcutaneous and tail-vein models. Additionally, BC-specific enrichment of TCF19 and LOXL2 was measured using a distribution landscape driven by diverse genomic analysis techniques. Molecular pathways revealed that TCF19-induced LOXL2 amplification facilitated migratory, invasive, and EMT activities of BC cells in vitro, and promoted the growth and metastatic establishment of xenografts in vivo. TCF19 decreases the expression of miR-199a-5p and alters the nuclear dynamics of SP1, modulating SP1's affinity for the LOXL2 promoter, leading to increased LOXL2 expression and more malignant characteristics in BC cells. These findings unveil a novel EMT-inducing pathway, the TCF19/miR-199a-5P/SP1/LOXL2 axis, highlighting the pivotal role of TCF19 and suggesting potential for novel therapeutic approaches for more focused BC interventions.
Collapse
Affiliation(s)
- Shu-Yu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, PR China
| | - Ning Wang
- Huzhou Central Hospital, Affiliated Hospital of Zhejiang University, Huzhou, PR China
| | - Ya-Ying Du
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Han-Ning Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
| | - Chen-Shen Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, PR China.
| | - Xing-Rui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
| |
Collapse
|
36
|
Wei C, Ma Y, Wang M, Wang S, Yu W, Dong S, Deng W, Bie L, Zhang C, Shen W, Xia Q, Luo S, Li N. Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census. NPJ Precis Oncol 2024; 8:176. [PMID: 39117688 PMCID: PMC11310399 DOI: 10.1038/s41698-024-00660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across nine cancer types and identified distinct monocyte/TAM composition patterns. Using spatial analysis from clinical study tissues, we assessed TAM functions in shaping the tumor microenvironment (TME) and influencing immunotherapy. Two specific TAM clusters (pro-inflammatory and pro-tumor) and four TME subtypes showed distinct immunological features, genomic profiles, immunotherapy responses, and cancer prognosis. Pro-inflammatory TAMs resided in immune-enriched niches with exhausted CD8+ T cells, while pro-tumor TAMs were restricted to niches associated with a T-cell-excluded phenotype and hypoxia. We developed a machine learning model to predict immune checkpoint blockade response by integrating TAMs and clinical data. Our study comprehensively characterizes the common features of TAMs and highlights their interaction with the TME.
Collapse
Affiliation(s)
- Chen Wei
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yijie Ma
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Mengyu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Siyi Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenyue Yu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shuailei Dong
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenying Deng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Bie
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chi Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Shen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| |
Collapse
|
37
|
Cheng YC, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald TO, Michor F. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proc Natl Acad Sci U S A 2024; 121:e2406842121. [PMID: 39093947 PMCID: PMC11317558 DOI: 10.1073/pnas.2406842121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the EED and EZH2 genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing ITGB4, LAMA3, and LAMB3 as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that CENPF, CKS1B, and MKI67 showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories.
Collapse
Affiliation(s)
- Yu-Chen Cheng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Yun Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100021, China
| | - Shubham Tripathi
- Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale School of Medicine, New Haven, CT06510
| | - B. V. Harshavardhan
- Interdisciplinary Mathematics Initiative, Indian Institute of Science, Bangalore560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BCV6T 1Z2, Canada
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
| | - Thomas O. McDonald
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02138
- The Ludwig Center at Harvard, Boston, MA02115
| |
Collapse
|
38
|
Čugura T, Boštjančič E, Uhan S, Hauptman N, Jeruc J. Epithelial-mesenchymal transition associated markers in sarcomatoid transformation of clear cell renal cell carcinoma. Exp Mol Pathol 2024; 138:104909. [PMID: 38876079 DOI: 10.1016/j.yexmp.2024.104909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Epithelial-mesenchymal transition (EMT) plays a pivotal role in the development and progression of many cancers. Partial EMT (pEMT) could represent a critical step in tumor migration and dissemination. Sarcomatoid renal cell carcinoma (sRCC) is an aggressive form of renal cell carcinoma (RCC) composed of a carcinomatous (sRCC-Ca) and sarcomatous (sRCC-Sa) component. The role of (p)EMT in the progression of RCC to sRCC remains unclear. The aim of this study was to investigate the involvement of (p)EMT in RCC and sRCC. Tissue samples from 10 patients with clear cell RCC (ccRCC) and 10 patients with sRCC were selected. The expression of main EMT markers (miR-200 family, miR-205, SNAI1/2, TWIST1/2, ZEB1/2, CDH1/2, VIM) was analyzed by qPCR in ccRCC, sRCC-Ca, and sRCC-Sa and compared to non-neoplastic tissue and between both groups. Expression of E-cadherin, N-cadherin, vimentin and ZEB2 was analyzed using immunohistochemistry. miR-200c was downregulated in sRCC-Ca compared to ccRCC, while miR-200a was downregulated in sRCC-Sa compared to ccRCC. CDH1 was downregulated in sRCC-Sa when compared to any other group. ZEB2 was downregulated in ccRCC and sRCC compared to corresponding non-neoplastic kidney. A positive correlation was observed between CDH1 expression and miR-200a/b/c. Our results suggest that full EMT is not present in sRCC. Instead, discreet molecular differences exist between ccRCC, sRCC-Ca, and sRCC-Sa, possibly representing distinct intermediary states undergoing pEMT.
Collapse
MESH Headings
- Humans
- Epithelial-Mesenchymal Transition/genetics
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Kidney Neoplasms/pathology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- MicroRNAs/genetics
- Male
- Middle Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Female
- Vimentin/metabolism
- Vimentin/genetics
- Zinc Finger E-box Binding Homeobox 2/genetics
- Zinc Finger E-box Binding Homeobox 2/metabolism
- Aged
- Cadherins/genetics
- Cadherins/metabolism
- Gene Expression Regulation, Neoplastic
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Twist-Related Protein 1/genetics
- Twist-Related Protein 1/metabolism
- Snail Family Transcription Factors/genetics
- Snail Family Transcription Factors/metabolism
- Zinc Finger E-box-Binding Homeobox 1/genetics
- Zinc Finger E-box-Binding Homeobox 1/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Cell Transformation, Neoplastic/metabolism
- Adult
- Nuclear Proteins
Collapse
Affiliation(s)
- Tanja Čugura
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Uhan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jera Jeruc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| |
Collapse
|
39
|
Sahoo S, Ramu S, Nair MG, Pillai M, San Juan BP, Milioli HZ, Mandal S, Naidu CM, Mavatkar AD, Subramaniam H, Neogi AG, Chaffer CL, Prabhu JS, Somarelli JA, Jolly MK. Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer. iScience 2024; 27:110116. [PMID: 38974967 PMCID: PMC11225361 DOI: 10.1016/j.isci.2024.110116] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/04/2024] [Accepted: 05/23/2024] [Indexed: 07/09/2024] Open
Abstract
Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. Decoding the interconnections among different biological axes of plasticity is crucial to understand the molecular origins of phenotypic heterogeneity. Here, we use multi-modal transcriptomic data-bulk, single-cell, and spatial transcriptomics-from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity-two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. Mathematical modeling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and identify interventions to restrict it.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | | | | | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560012, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560012, India
| | - Harini Subramaniam
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Arpita G. Neogi
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Christine L. Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- University of New South Wales, UNSW Medicine, Sydney, NSW 2010, Australia
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
40
|
Mariana Kustiawan P, Siregar KAAK, Syaifie PH, Zein Muttaqin F, Ibadillah D, Miftah Jauhar M, Djamas N, Mardliyati E, Taufiqu Rochman N. Uncovering the anti-breast cancer activity potential of east Kalimantan propolis by In vitro and bioinformatics analysis. Heliyon 2024; 10:e33636. [PMID: 39071605 PMCID: PMC11283153 DOI: 10.1016/j.heliyon.2024.e33636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Numerous side effects of breast cancer drugs have prompted researchers to explore more into new therapeutic approaches derived from natural substances. In this context, our study focused on uncovering the potential of East Kalimantan propolis from Trigona apicalis for breast cancer treatment including the underlying mechanisms through bioinformatics approached. We conducted integrated in vitro and bioinformatics analysis of network pharmacology, molecular docking, molecular dynamics and MM-GBSA analysis. Initially, in vitro cytotoxic assay demonstrated the anti-breast cancer activity potential of ethanol extract of East Kalimantan propolis, particularly its ethyl acetate fraction, which exhibited similar activity to doxorubicin, as indicated by their IC50 value. This study revealed eight propolis compounds, consisting of flavonoids and phenolic acids, in East Kalimantan propolis. By integrating microarray datasets (GSE29431, GSE36295, and GSE42568) analysis with potential targets derived from propolis compounds, 39 shared target genes were identified. Subsequently, GO and KEGG pathway, protein-protein interaction (PPI) network, core hub genes and gene expression analysis revealed three major targets, namely, PTGS2, CXCL2, and MMP9. Among them, only MMP9 was highly expressed in breast cancer than normal. Moreover, molecular docking revealed the six of propolis compounds which exhibited pronounced binding affinity towards MMP-9, better than marimastat as control drug. Dynamic simulation confirmed the stability of chrysin and quercetin as best compounds. Additionally, MM-GBSA analysis revealed a relative binding energy for chrysin (-25.6403 kcal/mol) that was comparable to marimastat (-27.3827 kcal/mol). In conclusion, this study reveals how East Kalimantan Propolis affect breast cancer and emphasizes MMP9 as a key target for future therapeutics.
Collapse
Affiliation(s)
- Paula Mariana Kustiawan
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, East Kalimantan, 75124, Indonesia
| | - Khalish Arsy Al Khairy Siregar
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, East Kalimantan, 75124, Indonesia
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Fauzan Zein Muttaqin
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Bhakti Kencana, Bandung, Indonesia
| | - Delfritama Ibadillah
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | | | - Nailulkamal Djamas
- Research Center for Horticultural and Estate Crops, National Research and Innovation Agency (BRIN), Bogor, 16915, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurul Taufiqu Rochman
- Research Center for Advanced Material, National Research and Innovation Agency (BRIN), PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| |
Collapse
|
41
|
Roshan P, Biswas A, Anagnos S, Luebbers R, Harish K, Ahmed S, Li M, Nguyen N, Zhou G, Tedeschi F, Hathuc V, Lin Z, Hamilton Z, Origanti S. Modulation of ribosomal subunit associations by eIF6 is critical for mitotic exit and cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600220. [PMID: 38979253 PMCID: PMC11230244 DOI: 10.1101/2024.06.24.600220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A factor crucial for modulating the 60S ribosomal subunits is eukaryotic translation initiation factor 6. Release of eIF6 from 60S is essential to permit 60S interactions with 40S. Here, using the N106S mutant of eIF6, we show that disrupting eIF6 interaction with 60S leads to an increase in vacant 80S. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S biogenesis and shows that the nucleolar localization of eIF6 is not dependent on uL14-BCCIP interactions. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-Seq analysis of the eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3'UTRs. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with the overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S availability for mitotic translation and cancer progression.
Collapse
|
42
|
Diao Y, Huang S, Liu F, Liao S, Guan C, Xiong X, Zhang P, Li J, Zhang W, Ying Y. CCL2 promotes EGFR-TKIs resistance in non-small cell lung cancer via the AKT-EMT pathway. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1549-1560. [PMID: 38961814 PMCID: PMC11532253 DOI: 10.3724/abbs.2024106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/11/2024] [Indexed: 07/05/2024] Open
Abstract
Acquired resistance to EGFR tyrosine kinase inhibitors (EGFR-TKIs) represents a primary cause of treatment failure in non-small cell lung cancer (NSCLC) patients. Chemokine (C-C motif) ligand 2 (CCL2) is recently found to play a pivotal role in determining anti-cancer treatment response. However, the role and mechanism of CCL2 in the development of EGFR-TKIs resistance have not been fully elucidated. In the present study, we focus on the function of CCL2 in the development of acquired resistance to EGFR-TKIs in NSCLC cells. Our results show that CCL2 is aberrantly upregulated in EGFR-TKIs-resistant NSCLC cells and that CCL2 overexpression significantly diminishes sensitivity to EGFR-TKIs. Conversely, CCL2 suppression by CCL2 synthesis inhibitor, bindarit, or CCL2 knockdown can reverse this resistance. CCL2 upregulation can also lead to enhanced migration and increased expressions of epithelial-mesenchymal transition (EMT) markers in EGFR-TKI-resistant NSCLC cells, which could also be rescued by CCL2 knockdown or inhibition. Furthermore, our findings suggest that CCL2-dependent EGFR-TKIs resistance involves the AKT-EMT signaling pathway; inhibition of this pathway effectively attenuates CCL2-induced cell migration and EMT marker expression. In summary, CCL2 promotes the development of acquired EGFR-TKIs resistance and EMT while activating AKT signaling in NSCLC. These insights suggest a promising avenue for the development of CCL2-targeted therapies that prevent EGFR-TKIs resistance in NSCLC.
Collapse
Affiliation(s)
- Yunlian Diao
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Shibo Huang
- The Clinical Trial Research Centerthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Fangpeng Liu
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Shu Liao
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Chenxi Guan
- Department of PhysiologySchool of Basic Medical SciencesJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Xiaojian Xiong
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Ping Zhang
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Junyao Li
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Wei Zhang
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| | - Ying Ying
- Jiangxi Provincial Key Laboratory of Prevention and Treatment of Infectious DiseasesJiangxi Medical Center for Major Public Health Eventsthe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
- Jiangxi Provincial Key Laboratory of Respiratory DiseasesJiangxi Institute of Respiratory DiseaseDepartment of Respiratory and Critical Care Medicinethe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang330006China
| |
Collapse
|
43
|
Jeong H, Koh J, Kim S, Song SG, Lee SH, Jeon Y, Lee CH, Keam B, Lee SH, Chung DH, Jeon YK. Epithelial-mesenchymal transition induced by tumor cell-intrinsic PD-L1 signaling predicts a poor response to immune checkpoint inhibitors in PD-L1-high lung cancer. Br J Cancer 2024; 131:23-36. [PMID: 38729997 PMCID: PMC11231337 DOI: 10.1038/s41416-024-02698-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We investigated the role of tumor cell-intrinsic PD-L1 signaling in the epithelial-mesenchymal transition (EMT) in non-small-cell lung cancer (NSCLC) and the role of EMT as a predictive biomarker for immune checkpoint inhibitor (ICI) therapy. METHODS PD-L1-overexpressing or PD-L1-knockdown NSCLC cells underwent RNA-seq and EMT phenotype assessment. Mouse lung cancer LLC cells were injected into nude mice. Two cohorts of patients with NSCLC undergoing ICI therapy were analyzed. RESULTS RNA-seq showed that EMT pathways were enriched in PD-L1-high NSCLC cells. EMT was enhanced by PD-L1 in NSCLC cells, which was mediated by transforming growth factor-β (TGFβ). PD-L1 promoted the activation of p38-MAPK by binding to and inhibiting the protein phosphatase PPM1B, thereby increasing the TGFβ production. Tumor growth and metastasis increased in nude mice injected with PD-L1-overexpressing LLC cells. In the ICI cohort, EMT signature was higher in patients with progressive disease than in those with responses, and EMT was significantly associated with poor survival in PD-L1-high NSCLC. In PD-L1-high NSCLC, EMT was associated with increased M2-macrophage and regulatory T-cell infiltrations and decreased cytotoxic T-cell infiltration. CONCLUSIONS Tumor cell-intrinsic PD-L1 function contributes to NSCLC progression by promoting EMT. EMT may predict an unfavorable outcome after ICI therapy in PD-L1-high NSCLC.
Collapse
Affiliation(s)
- Hyein Jeong
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Interdiscipilinary Program of Cancer Biology, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Jaemoon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sehui Kim
- Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung Geun Song
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Lee
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngjoo Jeon
- Interdiscipilinary Program of Cancer Biology, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Chul-Hwan Lee
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bhumsuk Keam
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
- Interdiscipilinary Program of Cancer Biology, Seoul National University Graduate School, Seoul, Republic of Korea.
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
44
|
Yoshimura A, Horinaka M, Yaoi T, Ono H, Itoh K, Yamada T, Takayama K, Sakai T. Epithelial-mesenchymal transition status is a remarkable biomarker for the combination treatment with avutometinib and defactinib in KRAS-mutated non-small cell lung cancer. Br J Cancer 2024; 131:361-371. [PMID: 38822146 PMCID: PMC11263561 DOI: 10.1038/s41416-024-02727-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Recent therapeutic strategies for KRAS-mutated cancers that inhibit the MAPK pathway have attracted considerable attention. The RAF/MEK clamp avutometinib (VS-6766/CH5126766/RO5126766/CKI27) is promising for patients with KRAS-mutated cancers. Although avutometinib monotherapy has shown clinical activity in patients with KRAS-mutated cancers, effective combination strategies will be important to develop. METHODS Using a phosphorylation kinase array kit, we explored the feedback mechanism of avutometinib in KRAS-mutated NSCLC cells, and investigated the efficacy of combining avutometinib with inhibitors of the feedback signal using in vitro and in vivo experiments. Moreover, we searched for a biomarker for the efficacy of combination therapy through an in vitro study and analysis using the The Cancer Genome Atlas Programme dataset. RESULTS Focal adhesion kinase (FAK) phosphorylation/activation was increased after avutometinib treatment and synergy between avutometinib and FAK inhibitor, defactinib, was observed in KRAS-mutated NSCLC cells with an epithelial rather than mesenchymal phenotype. Combination therapy with avutometinib and defactinib induced apoptosis with upregulation of Bim in cancer cells with an epithelial phenotype in an in vitro and in vivo study. CONCLUSIONS These results demonstrate that the epithelial-mesenchymal transition status may be a promising biomarker for the efficacy of combination therapy with avutometinib and defactinib in KRAS-mutated NSCLC.
Collapse
Affiliation(s)
- Akihiro Yoshimura
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daini Hospital, 355-5, Haruobi-cho, Kamigyo-ku, Kyoto, 602-8026, Japan
| | - Mano Horinaka
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Takeshi Yaoi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hisako Ono
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
- Department of Clinical Oncology, Japanese Red Cross Kyoto Daini Hospital, 355-5, Haruobi-cho, Kamigyo-ku, Kyoto, 602-8026, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Koichi Takayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Toshiyuki Sakai
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| |
Collapse
|
45
|
Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
Collapse
Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
| |
Collapse
|
46
|
Fan W, Xing Y, Yan S, Liu W, Ning J, Tian F, Wang X, Zhan Y, Luo L, Cao M, Huang J, Cai L. DUSP5 regulated by YTHDF1-mediated m6A modification promotes epithelial-mesenchymal transition and EGFR-TKI resistance via the TGF-β/Smad signaling pathway in lung adenocarcinoma. Cancer Cell Int 2024; 24:208. [PMID: 38872157 DOI: 10.1186/s12935-024-03382-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) patients have a dismal survival rate because of cancer metastasis and drug resistance. The study aims to identify the genes that concurrently modulate EMT, metastasis and EGFR-TKI resistance, and to investigate the underlying regulatory mechanisms. METHODS Cox regression and Kaplan-Meier analyses were applied to identify prognostic oncogenes in LUAD. Gene set enrichment analysis (GSEA) was used to indicate the biological functions of the gene. Wound-healing and Transwell assays were used to detect migratory and invasive ability. EGFR-TKI sensitivity was evaluated by assessing the proliferation, clonogenic survival and metastatic capability of cancer cells with treatment with gefitinib. Methylated RNA immunoprecipitation (MeRIP) and RNA immunoprecipitation (RIP) analyses established the level of m6A modification present on the target gene and the protein's capability to interact with RNA, respectively. Single-sample gene set enrichment (ssGSEA) algorithm used to investigate levels of immune cell infiltration. RESULTS Our study identified dual-specificity phosphatase 5 (DUSP5) as a novel and powerful predictor of adverse outcomes for LUAD by using public datasets. Functional enrichment analysis found that DUSP5 was positively enriched in EMT and transforming growth factor-beta (TGF-β) signaling pathway, a prevailing pathway involved in the induction of EMT. As expected, DUSP5 knockdown suppressed EMT via inhibiting the canonical TGF-β/Smad signaling pathway in in vitro experiments. Consistently, knockdown of DUSP5 was first found to inhibit migratory ability and invasiveness of LUAD cells in in vitro and prevent lung metastasis in in vivo. DUSP5 knockdown re-sensitized gefitinib-resistant LUAD cells to gefitinib, accompanying reversion of EMT progress. In LUAD tissue samples, we found 14 cytosine-phosphate-guanine (CpG) sites of DUSP5 that were negatively associated with DUSP5 gene expression. Importantly, 5'Azacytidine (AZA), an FDA-approved DNA methyltransferase inhibitor, restored DUSP5 expression. Moreover, RIP experiments confirmed that YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), a m6A reader protein, could bind DUSP5 mRNA. YTHDF1 promoted DUSP5 expression and the malignant phenotype of LUAD cells. In addition, the DUSP5-derived genomic model revealed the two clusters with distinguishable immune features and tumor mutational burden (TMB). CONCLUSIONS Briefly, our study discovered DUSP5 which was regulated by epigenetic modification, might be a potential therapeutic target, especially in LUAD patients with acquired EGFR-TKI resistance.
Collapse
Affiliation(s)
- Weina Fan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Shi Yan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Jinfeng Ning
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fanglin Tian
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Xin Wang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Yuning Zhan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Lixin Luo
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Mengru Cao
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| | - Jian Huang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| |
Collapse
|
47
|
Nair MG, Mavatkar AD, Naidu CM, V. P. S, C. E. A, Rajarajan S, Sahoo S, Mohan G, Jaikumar VS, Ramesh RS, B. S. S, Jolly MK, Maliekal TT, Prabhu JS. Elucidating the Role of MicroRNA-18a in Propelling a Hybrid Epithelial-Mesenchymal Phenotype and Driving Malignant Progression in ER-Negative Breast Cancer. Cells 2024; 13:821. [PMID: 38786043 PMCID: PMC11119613 DOI: 10.3390/cells13100821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Epigenetic alterations that lead to differential expression of microRNAs (miRNAs/miR) are known to regulate tumour cell states, epithelial-mesenchymal transition (EMT) and the progression to metastasis in breast cancer. This study explores the key contribution of miRNA-18a in mediating a hybrid E/M cell state that is pivotal to the malignant transformation and tumour progression in the aggressive ER-negative subtype of breast cancer. The expression status and associated effects of miR-18a were evaluated in patient-derived breast tumour samples in combination with gene expression data from public datasets, and further validated in in vitro and in vivo breast cancer model systems. The clinical relevance of the study findings was corroborated against human breast tumour specimens (n = 446 patients). The down-regulated expression of miR-18a observed in ER-negative tumours was found to drive the enrichment of hybrid epithelial/mesenchymal (E/M) cells with luminal attributes, enhanced traits of migration, stemness, drug-resistance and immunosuppression. Further analysis of the miR-18a targets highlighted possible hypoxia-inducible factor 1-alpha (HIF-1α)-mediated signalling in these tumours. This is a foremost report that validates the dual role of miR-18a in breast cancer that is subtype-specific based on hormone receptor expression. The study also features a novel association of low miR-18a levels and subsequent enrichment of hybrid E/M cells, increased migration and stemness in a subgroup of ER-negative tumours that may be attributed to HIF-1α mediated signalling. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing miRNA signatures.
Collapse
Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Savitha Rajarajan
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Gayathri Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Vishnu Sunil Jaikumar
- Animal Research Facility, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, Karnataka, India
| | - Srinath B. S.
- Department of Surgical Oncology, Sri Shankara Cancer Hospital and Research Centre, Bangalore 560004, Karnataka, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| |
Collapse
|
48
|
Metge BJ, Alsheikh HAM, Kammerud SC, Chen D, Das D, Nebane NM, Bostwick JR, Shevde LA, Samant RS. Targeting EMT using low-dose Teniposide by downregulating ZEB2-driven activation of RNA polymerase I in breast cancer. Cell Death Dis 2024; 15:322. [PMID: 38719798 PMCID: PMC11079014 DOI: 10.1038/s41419-024-06694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024]
Abstract
Metastatic dissemination from the primary tumor is a complex process that requires crosstalk between tumor cells and the surrounding milieu and involves the interplay between numerous cellular-signaling programs. Epithelial-mesenchymal transition (EMT) remains at the forefront of orchestrating a shift in numerous cellular programs, such as stemness, drug resistance, and apoptosis that allow for successful metastasis. Till date, there is limited success in therapeutically targeting EMT. Utilizing a high throughput screen of FDA-approved compounds, we uncovered a novel role of the topoisomerase inhibitor, Teniposide, in reversing EMT. Here, we demonstrate Teniposide as a potent modulator of the EMT program, specifically through an IRF7-NMI mediated response. Furthermore, Teniposide significantly reduces the expression of the key EMT transcriptional regulator, Zinc Finger E-Box Binding Homeobox 2 (ZEB2). ZEB2 downregulation by Teniposide inhibited RNA polymerase I (Pol I) activity and rRNA biogenesis. Importantly, Teniposide treatment markedly reduced pulmonary colonization of breast cancer cells. We have uncovered a novel role of Teniposide, which when used at a very low concentration, mitigates mesenchymal-like invasive phenotype. Overall, its ability to target EMT and rRNA biogenesis makes Teniposide a viable candidate to be repurposed as a therapeutic option to restrict breast cancer metastases.
Collapse
Affiliation(s)
- Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Sarah C Kammerud
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongquan Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Devika Das
- Birmingham VA Health Care System, Birmingham, AL, USA
- Parexel Biotech, Waltham, MA, USA
| | - N Miranda Nebane
- High-Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - J Robert Bostwick
- High-Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Birmingham VA Health Care System, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
49
|
Liu Z, Yu L, Lai J, Zhang R. Decoding the molecular landscape: A novel prognostic signature for uveal melanoma unveiled through programmed cell death-associated genes. Medicine (Baltimore) 2024; 103:e38021. [PMID: 38701273 PMCID: PMC11062707 DOI: 10.1097/md.0000000000038021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Uveal melanoma (UM) is a rare but aggressive malignant ocular tumor with a high metastatic potential and limited therapeutic options, currently lacking accurate prognostic predictors and effective individualized treatment strategies. Public databases were utilized to analyze the prognostic relevance of programmed cell death-related genes (PCDRGs) in UM transcriptomes and survival data. Consensus clustering and Lasso Cox regression analysis were performed for molecular subtyping and risk feature construction. The PCDRG-derived index (PCDI) was evaluated for its association with clinicopathological features, gene expression, drug sensitivity, and immune infiltration. A total of 369 prognostic PCDRGs were identified, which could cluster UM into 2 molecular subtypes with significant differences in prognosis and clinicopathological characteristics. Furthermore, a risk feature PCDI composed of 11 PCDRGs was constructed, capable of indicating prognosis in UM patients. Additionally, PCDI exhibited correlations with the sensitivity to 25 drugs and the infiltration of various immune cells. Enrichment analysis revealed that PCDI was associated with immune regulation-related biological processes and pathways. Finally, a nomogram for prognostic assessment of UM patients was developed based on PCDI and gender, demonstrating excellent performance. This study elucidated the potential value of PCDRGs in prognostic assessment for UM and developed a corresponding risk feature. However, further basic and clinical studies are warranted to validate the functions and mechanisms of PCDRGs in UM.
Collapse
Affiliation(s)
- Zibin Liu
- Department of Ophthalmology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lili Yu
- Department of Pediatrics, Hangzhou Linping TCM Hospital, Hangzhou, Zhejiang, China
| | - Jian Lai
- Department of Ophthalmology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Rui Zhang
- Department of Ophthalmology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| |
Collapse
|
50
|
Prasad H, Mandal S, Mathew JKK, Cherukunnath A, Duddu AS, Banerjee M, Ramani H, Bhat R, Jolly MK, Visweswariah SS. An Endosomal Acid-Regulatory Feedback System Rewires Cytosolic cAMP Metabolism and Drives Tumor Progression. Mol Cancer Res 2024; 22:465-481. [PMID: 38319300 PMCID: PMC7617132 DOI: 10.1158/1541-7786.mcr-23-0606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/02/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Although suppressed cAMP levels have been linked to cancer for nearly five decades, the molecular basis remains uncertain. Here, we identify endosomal pH as a novel regulator of cytosolic cAMP homeostasis and a promoter of transformed phenotypic traits in colorectal cancer. Combining experiments and computational analysis, we show that the Na+/H+ exchanger NHE9 contributes to proton leak and causes luminal alkalinization, which induces resting [Ca2+], and in consequence, represses cAMP levels, creating a feedback loop that echoes nutrient deprivation or hypoxia. Higher NHE9 expression in cancer epithelia is associated with a hybrid epithelial-mesenchymal (E/M) state, poor prognosis, tumor budding, and invasive growth in vitro and in vivo. These findings point to NHE9-mediated cAMP suppression as a pseudostarvation-induced invasion state and potential therapeutic vulnerability in colorectal cancer. Our observations lay the groundwork for future research into the complexities of endosome-driven metabolic reprogramming and phenotype switching and the biology of cancer progression. IMPLICATIONS Endosomal pH regulator NHE9 actively controls cytosolic Ca2+ levels to downregulate the adenylate cyclase-cAMP system, enabling colorectal cancer cells to acquire hybrid E/M characteristics and promoting metastatic progression.
Collapse
Affiliation(s)
- Hari Prasad
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | | | - Aparna Cherukunnath
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | | | - Mallar Banerjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Harini Ramani
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Ramray Bhat
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Sandhya S. Visweswariah
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| |
Collapse
|