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Lopez D, Tyson DR, Hong T. Intercellular signaling reinforces single-cell level phenotypic transitions and facilitates robust re-equilibrium of heterogeneous cancer cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.03.631250. [PMID: 39803530 PMCID: PMC11722408 DOI: 10.1101/2025.01.03.631250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2025]
Abstract
Background Cancer cells within tumors exhibit a wide range of phenotypic states driven by non-genetic mechanisms in addition to extensively studied genetic alterations. Conversions among cancer cell states can result in intratumoral heterogeneity which contributes to metastasis and development of drug resistance. However, mechanisms underlying the initiation and/or maintenance of such phenotypic plasticity are poorly understood. In particular, the role of intercellular communications in phenotypic plasticity remains elusive. Methods In this study, we employ a multiscale inference-based approach using single-cell RNA sequencing (scRNA-seq) data to explore how intercellular interactions influence phenotypic dynamics of cancer cells, particularly cancers undergoing epithelial-mesenchymal transition. In addition, we use mathematical models based on our data-driven findings to interrogate the roles of intercellular communications at the cell populations from the viewpoint of dynamical systems. Results Our inference approach reveals that signaling interactions between cancerous cells in small cell lung cancer (SCLC) result in the reinforcement of the phenotypic transition in single cells and the maintenance of population-level intratumoral heterogeneity. Additionally, we find a recurring signaling pattern across multiple types of cancer in which the mesenchymal-like subtypes utilize signals from other subtypes to support its new phenotype, further promoting the intratumoral heterogeneity. Our models show that inter-subtype communication both accelerates the development of heterogeneous tumor populations and confers robustness to their steady state phenotypic compositions. Conclusions Our work highlights the critical role of intercellular signaling in sustaining intratumoral heterogeneity, and our approach of computational analysis of scRNA-seq data can infer inter- and intra-cellular signaling networks in a holistic manner.
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Affiliation(s)
- Daniel Lopez
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville. Knoxville, Tennessee 37916, USA
| | - Darren R Tyson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Tian Hong
- Department of Biological Sciences, The University of Texas at Dallas. Richardson, Texas 75080, USA
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Kim RT, Whited JL. Putative epithelial-mesenchymal transitions during salamander limb regeneration: Current perspectives and future investigations. Ann N Y Acad Sci 2024; 1540:89-103. [PMID: 39269330 PMCID: PMC11471381 DOI: 10.1111/nyas.15210] [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] [Indexed: 09/15/2024]
Abstract
Previous studies have implicated epithelial-mesenchymal transition (EMT) in salamander limb regeneration. In this review, we describe putative roles for EMT during each stage of limb regeneration in axolotls and other salamanders. We hypothesize that EMT and EMT-like gene expression programs may regulate three main cellular processes during limb regeneration: (1) keratinocyte migration during wound closure; (2) transient invasion of the stump by epithelial cells undergoing EMT; and (3) use of EMT-like programs by non-epithelial blastemal progenitor cells to escape the confines of their niches. Finally, we propose nontraditional roles for EMT during limb regeneration that warrant further investigation, including alternative EMT regulators, stem cell activation, and fibrosis induced by aberrant EMT.
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Affiliation(s)
- Ryan T Kim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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Zhang Z, Jiang X, Li K, Qiao S, Li M, Mei Y, Ding L, Lv Q, Ding Y, Zhao Y, Lv G, Tan G, Yang H, Li G, Gao X, Liu M. KLF7 promotes colon adenocarcinoma progression through the PDGFB signaling pathway. Int J Biol Sci 2024; 20:387-402. [PMID: 38164176 PMCID: PMC10750276 DOI: 10.7150/ijbs.86385] [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: 05/21/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
Colon adenocarcinoma (COAD) is the most common malignancy of the digestive tract, which is characterized by a dismal prognosis. No effective treatment has been established presently, thus there is an urgent need to understand the mechanisms driving COAD progression in order to develop effective therapeutic approaches and enhance clinical outcomes. In this study, we found that KLF7 is overexpressed in COAD tissues and correlated with clinicopathological features of COAD. Both gain-of-function and loss-of-function experiments have unequivocally demonstrated that overexpression of KLF7 promotes the growth and metastasis of COAD in vitro and in vivo, while KLF7 knockdown attenuated these effects. Mechanistically, our findings reveal that KLF7 can specifically bind to the promoter region of PDGFB (TGGGTGGAG), thus promoting the transcription of PDGFB and increasing its secretion. Subsequently, secreted PDGFB facilitates the progression of COAD by activating MAPK/ERK, PI3K/AKT, and JAK/STAT3 signaling pathways through PDGFRβ. Additionally, we found that sunitinib can block PDGFB signaling and inhibit COAD progression, offering a promising therapeutic strategy for COAD treatment.
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Affiliation(s)
- Zhicheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xiaochen Jiang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
- Editorial Board of Harbin Medical University, Harbin Medical University, Harbin 150001, China
| | - Kai Li
- School of Medicine and Health, Harbin Institute of Technology, Harbin, 150001, China
| | - Shupei Qiao
- Heilongjiang Key Laboratory of Children Development and Genetic Research, Harbin Medical University, Harbin,150001, China
| | - Mengmeng Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Yu Mei
- Drug Engineering and Technology Research Center, Harbin University of Commerce, Harbin, 150001, China
| | - Lixian Ding
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qiang Lv
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Yike Ding
- St John's College William Nicholls Drive, Old St Mellons, Cardiff, CF35YX, United Kingdom
| | - Yunhan Zhao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Guixiang Lv
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Gang Tan
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Huanjie Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, 150001, China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin,150001, China
- Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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