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Sehgal M, Nayak SP, Sahoo S, Somarelli JA, Jolly MK. Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma. Cancer Biol Ther 2024; 25:2301802. [PMID: 38230570 PMCID: PMC10795782 DOI: 10.1080/15384047.2024.2301802] [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: 09/08/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a "teams-like" behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism between NOR and MES phenotypes was also associated with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2 as well as with experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, these "teams-like" patterns were seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Sonali Priyadarshini Nayak
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Max Planck School Matter to Life, University of Göttingen, Göttingen, Germany
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
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2
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Kiri S, Ryba T. Cancer, metastasis, and the epigenome. Mol Cancer 2024; 23:154. [PMID: 39095874 DOI: 10.1186/s12943-024-02069-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: 04/30/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Cancer is the second leading cause of death worldwide and disease burden is expected to increase globally throughout the next several decades, with the majority of cancer-related deaths occurring in metastatic disease. Cancers exhibit known hallmarks that endow them with increased survival and proliferative capacities, frequently as a result of de-stabilizing mutations. However, the genomic features that resolve metastatic clones from primary tumors are not yet well-characterized, as no mutational landscape has been identified as predictive of metastasis. Further, many cancers exhibit no known mutation signature. This suggests a larger role for non-mutational genome re-organization in promoting cancer evolution and dissemination. In this review, we highlight current critical needs for understanding cell state transitions and clonal selection advantages for metastatic cancer cells. We examine links between epigenetic states, genome structure, and misregulation of tumor suppressors and oncogenes, and discuss how recent technologies for understanding domain-scale regulation have been leveraged for a more complete picture of oncogenic and metastatic potential.
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Affiliation(s)
- Saurav Kiri
- College of Medicine, University of Central Florida, 6850 Lake Nona Blvd., Orlando, 32827, Florida, USA.
| | - Tyrone Ryba
- Department of Natural Sciences, New College of Florida, 5800 Bay Shore Rd., Sarasota, 34243, Florida, USA.
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3
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Lopez-Cerda M, Lorenzo-Sanz L, da Silva-Diz V, Llop S, Penin RM, Bermejo JO, de Goeij-de Haas R, Piersma SR, Pham TV, Jimenez CR, Martin-Liberal J, Muñoz P. IGF1R signaling induces epithelial-mesenchymal plasticity via ITGAV in cutaneous carcinoma. J Exp Clin Cancer Res 2024; 43:211. [PMID: 39075581 PMCID: PMC11285232 DOI: 10.1186/s13046-024-03119-3] [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: 03/11/2024] [Accepted: 07/07/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Early cutaneous squamous cell carcinomas (cSCCs) generally show epithelial differentiation features and good prognosis, whereas advanced cSCCs present mesenchymal traits associated with tumor relapse, metastasis, and poor survival. Currently, the mechanisms involved in cSCC progression are unclear, and the established markers are suboptimal for accurately predicting the clinical course of the disease. METHODS Using a mouse model of cSCC progression, expression microarray analysis, immunofluorescence and flow cytometry assays, we have identified a prognostic biomarker of tumor relapse, which has been evaluated in a cohort of cSCC patient samples. Phosphoproteomic analysis have revealed signaling pathways induced in epithelial plastic cancer cells that promote epithelial-mesenchymal plasticity (EMP) and tumor progression. These pathways have been validated by genetic and pharmacological inhibition assays. RESULTS We show that the emergence of epithelial cancer cells expressing integrin αV (ITGAV) promotes cSCC progression to a mesenchymal state. Consistently, ITGAV expression allows the identification of patients at risk of cSCC relapse above the currently employed clinical histopathological parameters. We also demonstrate that activation of insulin-like growth factor-1 receptor (IGF1R) pathway in epithelial cancer cells is necessary to induce EMP and mesenchymal state acquisition in response to tumor microenvironment-derived factors, while promoting ITGAV expression. Likewise, ITGAV knockdown in epithelial plastic cancer cells also blocks EMP acquisition, generating epithelial tumors. CONCLUSIONS Our results demonstrate that ITGAV is a prognostic biomarker of relapse in cSCCs that would allow improved patient stratification. ITGAV also collaborates with IGF1R to induce EMP in epithelial cancer cells and promotes cSCC progression, revealing a potential therapeutic strategy to block the generation of advanced mesenchymal cSCCs.
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Affiliation(s)
- Marta Lopez-Cerda
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Laura Lorenzo-Sanz
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victoria da Silva-Diz
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
- Rutgers Cancer Institute of New Jersey, Rutgers University, 08901, New Brunswick, NJ, USA
| | - Sandra Llop
- Medical Oncology Department, Catalan Institute of Oncology (ICO) L'Hospitalet, 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rosa M Penin
- Pathology Service, Bellvitge University Hospital/IDIBELL, 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep Oriol Bermejo
- Plastic Surgery Unit, Bellvitge University Hospital/IDIBELL, 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam UMC, 1081HV, Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam UMC, 1081HV, Amsterdam, the Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam UMC, 1081HV, Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam UMC, 1081HV, Amsterdam, the Netherlands
| | - Juan Martin-Liberal
- Medical Oncology Department, Catalan Institute of Oncology (ICO) L'Hospitalet, 08908, L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Purificación Muñoz
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain.
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4
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Sanjaya A, Ratnawati H, Adhika OA, Rahmatilah FR. The heterogeneity of breast cancer metastasis: a bioinformatics analysis utilizing single-cell RNA sequencing data. Breast Cancer Res Treat 2024:10.1007/s10549-024-07428-1. [PMID: 38992286 DOI: 10.1007/s10549-024-07428-1] [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: 04/07/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
PURPOSE Breast cancer is a common malignancy in women, and its metastasis is a leading cause of cancer-related deaths. Single-cell RNA sequencing (scRNA-seq) can distinguish the molecular characteristics of metastasis and identify predictor genes for patient prognosis. This article explores gene expression in primary breast cancer tumor tissue against metastatic cells in the lymph node and liver using scRNA-seq. METHODS Breast cancer scRNA-seq data from the Gene Expression Omnibus were used. The data were processed using R and the Seurat package. The cells were clustered and identified using Metascape. InferCNV is used to analyze the variation in copy number. Differential expression analysis was conducted for the cancer cells using Seurat and was enriched using Metascape. RESULTS We identified 18 distinct cell clusters, 6 of which were epithelial. CNV analysis identified significant alterations with duplication of chromosomes 1, 8, and 19. Differential gene analysis resulted in 17 upregulated and 171 downregulated genes for the primary tumor in the primary tumor vs. liver metastasis comparison and 43 upregulated and 4 downregulated genes in the primary tumor in the primary tumor vs lymph node metastasis comparison. Several enriched terms include Ribosome biogenesis, NTP synthesis, Epithelial dedifferentiation, Autophagy, and genes associated with epithelial-to-mesenchymal transitions. CONCLUSION No single gene or pathway can clearly explain the mechanisms behind tumor metastasis. Several mechanisms contribute to lymph node and liver metastasis, such as the loss of differentiation, epithelial-to-mesenchymal transition, and autophagy. These findings necessitate further study of metastatic tissue for effective drug development.
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Affiliation(s)
- Ardo Sanjaya
- Department of Anatomy, Faculty of Medicine, Maranatha Christian University, Jl. Surya Sumantri No. 65, Bandung, 40164, West Java, Indonesia.
- Biomedical Research Laboratory, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia.
| | - Hana Ratnawati
- Biomedical Research Laboratory, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
- Department of Histology, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
| | - Oeij Anindita Adhika
- Department of Anatomy, Faculty of Medicine, Maranatha Christian University, Jl. Surya Sumantri No. 65, Bandung, 40164, West Java, Indonesia
| | - Faiz Rizqy Rahmatilah
- Undergraduate Program in Medicine, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
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Huang B, Yu Z, Cui D, Du F. MAPKAP1 orchestrates macrophage polarization and lipid metabolism in fatty liver-enhanced colorectal cancer. Transl Oncol 2024; 45:101941. [PMID: 38692197 PMCID: PMC11070763 DOI: 10.1016/j.tranon.2024.101941] [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: 12/09/2023] [Revised: 03/02/2024] [Accepted: 03/16/2024] [Indexed: 05/03/2024] Open
Abstract
Various factors, including fatty liver and macrophage alterations, influence colorectal cancer (CRC). This study explores the mechanistic role of fatty liver in CRC progression, focusing on macrophage polarization and lipid metabolism. A murine fatty liver model was created with a high-fat diet (HFD), and CRC was induced using AOM and DSS. Single-cell transcriptome sequencing (scRNA-seq) identified MAPKAP1 as a critical gene promoting CRC via M2 macrophage polarization and lipid metabolism reprogramming. Prognosis analysis on the TCGA-CRC dataset confirmed MAPKAP1's significance. In vitro and in vivo experiments demonstrated that EVs from fatty liver cells enhanced MAPKAP1 expression, accelerating CRC development and metastasis. HFD exacerbated CRC, but fatty acid inhibitors delayed progression. Fatty liver upregulates MAPKAP1, driving M2 macrophage polarization and lipid metabolism changes, worsening CRC. These findings suggest potential therapeutic strategies for CRC, particularly targeting lipid metabolism and macrophage-mediated tumor promotion.
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Affiliation(s)
- Bo Huang
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China.
| | - Zhenqiu Yu
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China.
| | - Dejun Cui
- Department of Gastroenterology, Guizhou Provincial People's Hospital, PR China.
| | - Fawang Du
- Department of Hypertension, The Affiliated Hospital of Guizhou Medical University, No.28, Guimedical Street, Yunyan District, Guiyang City, Guizhou Province, PR China
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6
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Gao Y, Feder AF. Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601073. [PMID: 39005367 PMCID: PMC11244928 DOI: 10.1101/2024.06.27.601073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Understanding cellular birth rate differences is crucial for predicting cancer progression and interpreting tumor-derived genetic data. Lineage tracing experiments enable detailed reconstruction of cellular genealogies, offering new opportunities to measure branching rate heterogeneity. However, the lineage tracing process can introduce complex tree features that complicate this effort. Here, we examine tree characteristics in lineage tracing-derived genealogies and find that editing window placement leads to multifurcations at a tree's root or tips. We propose several ways in which existing tree topology-based metrics can be extended to test for rate heterogeneity on trees even in the presence of lineage-tracing associated distortions. Although these methods vary in power and robustness, a test based on the J 1 statistic effectively detects branching rate heterogeneity in simulated lineage tracing data. Tests based on other common statistics ( ŝ and the Sackin index) show interior performance to J 1 . We apply our validated methods to xenograft experimental data and find widespread rate heterogeneity across multiple study systems. Our results demonstrate the potential of tree topology statistics in analyzing lineage tracing data, and highlight the challenges associated with adapting phylogenetic methods to these systems.
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7
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Bracken CP, Goodall GJ, Gregory PA. RNA regulatory mechanisms controlling TGF-β signaling and EMT in cancer. Semin Cancer Biol 2024; 102-103:4-16. [PMID: 38917876 DOI: 10.1016/j.semcancer.2024.06.001] [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: 12/15/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Epithelial-mesenchymal transition (EMT) is a major contributor to metastatic progression and is prominently regulated by TGF-β signalling. Both EMT and TGF-β pathway components are tightly controlled by non-coding RNAs - including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) - that collectively have major impacts on gene expression and resulting cellular states. While miRNAs are the best characterised regulators of EMT and TGF-β signaling and the miR-200-ZEB1/2 feedback loop plays a central role, important functions for lncRNAs and circRNAs are also now emerging. This review will summarise our current understanding of the roles of non-coding RNAs in EMT and TGF-β signaling with a focus on their functions in cancer progression.
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Affiliation(s)
- Cameron P Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia.
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8
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Bolondi A, Law BK, Kretzmer H, Gassaloglu SI, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet JV, Meissner A, Smith ZD, Chan MM. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Dev Cell 2024; 59:1489-1505.e14. [PMID: 38579718 PMCID: PMC11187653 DOI: 10.1016/j.devcel.2024.03.024] [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: 08/15/2023] [Revised: 12/13/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.
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Affiliation(s)
- Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin K Law
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - René Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Dian Yang
- Department of Molecular Pharmacology and Therapeutics & Systems Biology, Columbia University, New York, NY 10032, USA
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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9
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Stehbens SJ, Scarpa E, White MD. Perspectives in collective cell migration - moving forward. J Cell Sci 2024; 137:jcs261549. [PMID: 38904172 DOI: 10.1242/jcs.261549] [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: 06/22/2024] Open
Abstract
Collective cell migration, where cells move as a cohesive unit, is a vital process underlying morphogenesis and cancer metastasis. Thanks to recent advances in imaging and modelling, we are beginning to understand the intricate relationship between a cell and its microenvironment and how this shapes cell polarity, metabolism and modes of migration. The use of biophysical and mathematical models offers a fresh perspective on how cells migrate collectively, either flowing in a fluid-like state or transitioning to more static states. Continuing to unite researchers in biology, physics and mathematics will enable us to decode more complex biological behaviours that underly collective cell migration; only then can we understand how this coordinated movement of cells influences the formation and organisation of tissues and directs the spread of metastatic cancer. In this Perspective, we highlight exciting discoveries, emerging themes and common challenges that have arisen in recent years, and possible ways forward to bridge the gaps in our current understanding of collective cell migration.
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Affiliation(s)
- Samantha J Stehbens
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, St Lucia, Brisbane, QLD 4072, Australia
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, QLD 4072, Australia
| | - Elena Scarpa
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - Melanie D White
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, QLD 4072, Australia
- The University of Queensland, School of Biomedical Sciences, St Lucia, Brisbane, QLD 4072, Australia
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10
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Jindal K, Adil MT, Yamaguchi N, Yang X, Wang HC, Kamimoto K, Rivera-Gonzalez GC, Morris SA. Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes. Nat Biotechnol 2024; 42:946-959. [PMID: 37749269 PMCID: PMC11180607 DOI: 10.1038/s41587-023-01931-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.
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Affiliation(s)
- Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mohd Tayyab Adil
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Naoto Yamaguchi
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Helen C Wang
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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11
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Ferrer CM, Cho HM, Boon R, Bernasocchi T, Wong LP, Cetinbas M, Haggerty ER, Mitsiades I, Wojtkiewicz GR, McLoughlin DE, Aboushousha R, Abdelhamid H, Kugel S, Rheinbay E, Sadreyev R, Juric D, Janssen-Heininger YMW, Mostoslavsky R. The glutathione S-transferase Gstt1 drives survival and dissemination in metastases. Nat Cell Biol 2024; 26:975-990. [PMID: 38862786 DOI: 10.1038/s41556-024-01426-7] [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: 12/21/2022] [Accepted: 04/18/2024] [Indexed: 06/13/2024]
Abstract
Identifying the adaptive mechanisms of metastatic cancer cells remains an elusive question in the treatment of metastatic disease, particularly in pancreatic cancer (pancreatic adenocarcinoma, PDA). A loss-of-function shRNA targeted screen in metastatic-derived cells identified Gstt1, a member of the glutathione S-transferase superfamily, as uniquely required for dissemination and metastasis, but dispensable for primary tumour growth. Gstt1 is expressed in latent disseminated tumour cells (DTCs), is retained within a subpopulation of slow-cycling cells within existing metastases, and its inhibition leads to complete regression of macrometastatic tumours. This distinct Gstt1high population is highly metastatic and retains slow-cycling phenotypes, epithelial-mesenchymal transition features and DTC characteristics compared to the Gstt1low population. Mechanistic studies indicate that in this subset of cancer cells, Gstt1 maintains metastases by binding and glutathione-modifying intracellular fibronectin, in turn promoting its secretion and deposition into the metastatic microenvironment. We identified Gstt1 as a mediator of metastasis, highlighting the importance of heterogeneity and its influence on the metastatic tumour microenvironment.
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Affiliation(s)
- Christina M Ferrer
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- University of Maryland School of Medicine and the Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Hyo Min Cho
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ruben Boon
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Galapagos NV, 2800 Mechelen, Belgium
| | - Tiziano Bernasocchi
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth R Haggerty
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Irene Mitsiades
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Daniel E McLoughlin
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | - Reem Aboushousha
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Hend Abdelhamid
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Sita Kugel
- Fred Hutchison Cancer Research Center, Seattle, WA, USA
| | - Esther Rheinbay
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Dejan Juric
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | | | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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12
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Yoon B, Kim H, Jung SW, Park J. Single-cell lineage tracing approaches to track kidney cell development and maintenance. Kidney Int 2024; 105:1186-1199. [PMID: 38554991 DOI: 10.1016/j.kint.2024.01.045] [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: 09/08/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 04/02/2024]
Abstract
The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.
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Affiliation(s)
- Baul Yoon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hayoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Su Woong Jung
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea; Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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13
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Lenz G. Heterogeneity generating capacity in tumorigenesis and cancer therapeutics. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167226. [PMID: 38734320 DOI: 10.1016/j.bbadis.2024.167226] [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: 12/08/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Cells of multicellular organisms generate heterogeneity in a controlled and transient fashion during embryogenesis, which can be reactivated in pathologies such as cancer. Although genomic heterogeneity is an important part of tumorigenesis, continuous generation of phenotypic heterogeneity is central for the adaptation of cancer cells to the challenges of tumorigenesis and response to therapy. Here I discuss the capacity of generating heterogeneity, hereafter called cell hetness, in cancer cells both as the activation of hetness oncogenes and inactivation of hetness tumor suppressor genes, which increase the generation of heterogeneity, ultimately producing an increase in adaptability and cell fitness. Transcriptomic high hetness states in therapy-tolerant cell states denote its importance in cancer resistance to therapy. The definition of the concept of hetness will allow the understanding of its origins, its control during embryogenesis, its loss of control in tumorigenesis and cancer therapeutics and its active targeting.
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Affiliation(s)
- Guido Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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14
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Wang X, Zhou Y, Wang L, Haseeb A, Li H, Zheng X, Guo J, Cheng X, Yin W, Sun N, Sun P, Zhang Z, Yang H, Fan K. Fascin-1 Promotes Cell Metastasis through Epithelial-Mesenchymal Transition in Canine Mammary Tumor Cell Lines. Vet Sci 2024; 11:238. [PMID: 38921985 PMCID: PMC11209228 DOI: 10.3390/vetsci11060238] [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: 04/12/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Canine mammary tumors (CMTs) are the most common type of tumor in female dogs. In this study, we obtained a metastatic key protein, Fascin-1, by comparing the proteomics data of in situ tumor and metastatic cell lines from the same individual. However, the role of Fascin-1 in the CMT cell line is still unclear. Firstly, proteomics was used to analyze the differential expression of Fascin-1 between the CMT cell lines CHMm and CHMp. Then, the overexpression (CHMm-OE and CHMp-OE) and knockdown (CHMm-KD and CHMp-KD) cell lines were established by lentivirus transduction. Finally, the differentially expressed proteins (DEPs) in CHMm and CHMm-OE cells were identified through proteomics. The results showed that the CHMm cells isolated from CMT abdominal metastases exhibited minimal expression of Fascin-1. The migration, adhesion, and invasion ability of CHMm-OE and CHMp-OE cells increased, while the migration, adhesion, and invasion ability of CHMm-KD and CHMp-KD cells decreased. The overexpression of Fascin-1 can upregulate the Tetraspanin 4 (TSPAN4) protein in CHMm cells and increase the number of migrations. In conclusion, re-expressed Fascin-1 could promote cell EMT and increase lamellipodia formation, resulting in the enhancement of CHMm cell migration, adhesion, and invasion in vitro. This may be beneficial to improve female dogs' prognosis of CMT.
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Affiliation(s)
- Xin Wang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Ye Zhou
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Linhao Wang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Abdul Haseeb
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Hongquan Li
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Xiaozhong Zheng
- Medical Research Council (MRC) Centre for Inflammation Research, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Jianhua Guo
- Department of Veterinary Pathobiology, Schubot Exotic Bird Health Center, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoliang Cheng
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Wei Yin
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Na Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Panpan Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Zhenbiao Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Huizhen Yang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
| | - Kuohai Fan
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.)
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15
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Holze H, Talarmain L, Fennell KA, Lam EY, Dawson MA, Vassiliadis D. Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools. CELL REPORTS METHODS 2024; 4:100763. [PMID: 38670101 PMCID: PMC11133760 DOI: 10.1016/j.crmeth.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/25/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.
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Affiliation(s)
- Henrietta Holze
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Katie A Fennell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Enid Y Lam
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia; The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia.
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16
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Que X, Ren L, Yang L, Wang L, Li J, Wu R, Chen Q. Long noncoding RNA BMPR1B-AS1 stability regulated by IGF2BP2 affects the decidualization in endometriosis patients through the SMAD1/5/9 pathway. FASEB J 2024; 38:e23622. [PMID: 38703029 DOI: 10.1096/fj.202302195r] [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: 10/25/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 05/06/2024]
Abstract
Endometriosis (EMs)-related infertility commonly has decreased endometrial receptivity and normal decidualization is the basis for establishing and maintaining endometrial receptivity. However, the potential molecular regulatory mechanisms of impaired endometrial decidualization in patients with EMs have not been fully clarified. We confirmed the existence of reduced endometrial receptivity in patients with EMs by scanning electron microscopy and quantitative real-time PCR. Here we identified an lncRNA, named BMPR1B-AS1, which is significantly downregulated in eutopic endometrium in EMs patients and plays an essential role in decidual formation. Furthermore, RNA pull-down, mass spectrometry, RNA immunoprecipitation, and rescue analyses revealed that BMPR1B-AS1 positively regulates decidual formation through interaction with the RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Downregulation of IGF2BP2 led to a decreased stability of BMPR1B-AS1 and inhibition of activation of the SMAD1/5/9 pathway, an inhibitory effect which diminished decidualization in human endometrial stromal cells (hESCs) decidualization. In conclusion, our identified a novel regulatory mechanism in which the IGF2BP2-BMPR1B-AS1-SMAD1/5/9 axis plays a key role in the regulation of decidualization, providing insights into the potential link between abnormal decidualization and infertility in patients with EMs, which will be of clinical significance for the management and treatment of infertility in patients with EMs.
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Affiliation(s)
- Xiaohong Que
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
| | - Lulu Ren
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- Reproductive Medical Center, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Lin Yang
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Lemeng Wang
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Junzui Li
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Rongfeng Wu
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- Reproductive Medical Center, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qionghua Chen
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
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17
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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [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] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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18
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Jakab M, Lee KH, Uvarovskii A, Ovchinnikova S, Kulkarni SR, Jakab S, Rostalski T, Spegg C, Anders S, Augustin HG. Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency. NATURE CANCER 2024; 5:716-730. [PMID: 38308117 PMCID: PMC11136671 DOI: 10.1038/s43018-023-00716-7] [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: 11/22/2022] [Accepted: 12/15/2023] [Indexed: 02/04/2024]
Abstract
In metastasis, cancer cells travel around the circulation to colonize distant sites. Due to the rarity of these events, the immediate fates of metastasizing tumor cells (mTCs) are poorly understood while the role of the endothelium as a dissemination interface remains elusive. Using a newly developed combinatorial mTC enrichment approach, we provide a transcriptional blueprint of the early colonization process. Following their arrest at the metastatic site, mTCs were found to either proliferate intravascularly or extravasate, thereby establishing metastatic latency. Endothelial-derived angiocrine Wnt factors drive this bifurcation, instructing mTCs to follow the extravasation-latency route. Surprisingly, mTC responsiveness towards niche-derived Wnt was established at the epigenetic level, which predetermined tumor cell behavior. Whereas hypomethylation enabled high Wnt activity leading to metastatic latency, methylated mTCs exhibited low activity and proliferated intravascularly. Collectively the data identify the predetermined methylation status of disseminated tumor cells as a key regulator of mTC behavior in the metastatic niche.
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Affiliation(s)
- Moritz Jakab
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Ki Hong Lee
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexey Uvarovskii
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Evotec SE, Göttingen, Germany
| | - Svetlana Ovchinnikova
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Shubhada R Kulkarni
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Sevinç Jakab
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Till Rostalski
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Carleen Spegg
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Hellmut G Augustin
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
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19
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Karras P, Black JRM, McGranahan N, Marine JC. Decoding the interplay between genetic and non-genetic drivers of metastasis. Nature 2024; 629:543-554. [PMID: 38750233 DOI: 10.1038/s41586-024-07302-6] [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: 06/24/2022] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.
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Affiliation(s)
- Panagiotis Karras
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - James R M Black
- Cancer Genome Evolution Research Group, UCL Cancer Institute, London, UK
| | | | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium.
- Department of Oncology, KU Leuven, Leuven, Belgium.
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20
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Nathans JF, Ayers JL, Shendure J, Simpson CL. Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin. J Invest Dermatol 2024; 144:936-949. [PMID: 38643988 PMCID: PMC11034889 DOI: 10.1016/j.jid.2024.02.006] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 04/23/2024]
Abstract
The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.
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Affiliation(s)
- Jenny F Nathans
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica L Ayers
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Dermatology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Department of Dermatology, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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21
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Wang K, Hou L, Wang X, Zhai X, Lu Z, Zi Z, Zhai W, He X, Curtis C, Zhou D, Hu Z. PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes. Nat Biotechnol 2024; 42:778-789. [PMID: 37524958 DOI: 10.1038/s41587-023-01887-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for studying cellular differentiation, but accurately tracking cell fate transitions can be challenging, especially in disease conditions. Here we introduce PhyloVelo, a computational framework that estimates the velocity of transcriptomic dynamics by using monotonically expressed genes (MEGs) or genes with expression patterns that either increase or decrease, but do not cycle, through phylogenetic time. Through integration of scRNA-seq data with lineage information, PhyloVelo identifies MEGs and reconstructs a transcriptomic velocity field. We validate PhyloVelo using simulated data and Caenorhabditis elegans ground truth data, successfully recovering linear, bifurcated and convergent differentiations. Applying PhyloVelo to seven lineage-traced scRNA-seq datasets, generated using CRISPR-Cas9 editing, lentiviral barcoding or immune repertoire profiling, demonstrates its high accuracy and robustness in inferring complex lineage trajectories while outperforming RNA velocity. Additionally, we discovered that MEGs across tissues and organisms share similar functions in translation and ribosome biogenesis.
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Affiliation(s)
- Kun Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- School of Mathematical Sciences, Xiamen University, Xiamen, China
| | - Liangzhen Hou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xin Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiangwei Zhai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhaolian Lu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhike Zi
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weiwei Zhai
- CAS Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Da Zhou
- School of Mathematical Sciences, Xiamen University, Xiamen, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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22
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Liang G, Cao W, Tang D, Zhang H, Yu Y, Ding J, Karges J, Xiao H. Nanomedomics. ACS NANO 2024; 18:10979-11024. [PMID: 38635910 DOI: 10.1021/acsnano.3c11154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Nanomaterials have attractive physicochemical properties. A variety of nanomaterials such as inorganic, lipid, polymers, and protein nanoparticles have been widely developed for nanomedicine via chemical conjugation or physical encapsulation of bioactive molecules. Superior to traditional drugs, nanomedicines offer high biocompatibility, good water solubility, long blood circulation times, and tumor-targeting properties. Capitalizing on this, several nanoformulations have already been clinically approved and many others are currently being studied in clinical trials. Despite their undoubtful success, the molecular mechanism of action of the vast majority of nanomedicines remains poorly understood. To tackle this limitation, herein, this review critically discusses the strategy of applying multiomics analysis to study the mechanism of action of nanomedicines, named nanomedomics, including advantages, applications, and future directions. A comprehensive understanding of the molecular mechanism could provide valuable insight and therefore foster the development and clinical translation of nanomedicines.
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Affiliation(s)
- Ganghao Liang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wanqing Cao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Dongsheng Tang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yingjie Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Johannes Karges
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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23
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Liu X, Wang X, Yang Q, Luo L, Liu Z, Ren X, Lei K, Li S, Xie Z, Zheng G, Zhang Y, Hao Y, Zhou Q, Hou Y, Fang F, Song W, Cui J, Ma J, Xie W, Shen S, Tang C, Peng S, Yu J, Kuang M, Song X, Wang F, Xu L. Th17 Cells Secrete TWEAK to Trigger Epithelial-Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis. Cancer Res 2024; 84:1352-1371. [PMID: 38335276 DOI: 10.1158/0008-5472.can-23-2123] [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: 07/16/2023] [Revised: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Liver metastasis is the leading cause of mortality in patients with colorectal cancer. Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in colorectal cancer liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multiomics analysis of 130 samples from 18 patients with synchronous CRLM integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of nonmalignant cells between primary tumors from patients with metastatic colorectal cancer (mCRC) and non-metastatic colorectal cancer, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared with wild-type mice, while cotransfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in patients with colorectal cancer. In addition, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM. SIGNIFICANCE TWEAK secreted by Th17 cells promotes EMT by binding to Fn14 on colorectal cancer cells, suggesting that blocking the TWEAK-Fn14 interaction may be a promising therapeutic approach to inhibit liver metastasis.
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Affiliation(s)
- Xin Liu
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xin Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qingxia Yang
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Li Luo
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ziqin Liu
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiaoxue Ren
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Kai Lei
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shangru Li
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zonglin Xie
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Gaomin Zheng
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yifan Zhang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yijie Hao
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qianying Zhou
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yingdong Hou
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fei Fang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wu Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ji Cui
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jinping Ma
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wenxuan Xie
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shunli Shen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ce Tang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xinming Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fang Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Lixia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
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24
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Wang R, Yan Z. Cancer spreading patterns based on epithelial-mesenchymal plasticity. Front Cell Dev Biol 2024; 12:1259953. [PMID: 38665432 PMCID: PMC11043583 DOI: 10.3389/fcell.2024.1259953] [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: 07/17/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction: Metastasis is a major cause of cancer-related deaths, underscoring the necessity to discern the rules and patterns of cancer cell spreading. Epithelial-mesenchymal plasticity contributes to cancer aggressiveness and metastasis. Despite establishing key determinants of cancer aggressiveness and metastatic ability, a comprehensive understanding of the underlying mechanism is unknown. We aimed to propose a classification system for cancer cells based on epithelial-mesenchymal plasticity, focusing on hysteresis of the epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype. Methods: We extensively reviewed the concept of epithelial-mesenchymal plasticity, specifically considering the hysteresis of the epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype. Results: In this review and hypothesis article, based on epithelial-mesenchymal plasticity, especially the hysteresis of epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype, we proposed a classification of cancer cells, indicating that cancer cells with epithelial-mesenchymal plasticity potential could be classified into four types: irreversible hysteresis, weak hysteresis, strong hysteresis, and hybrid epithelial/mesenchymal phenotype. These four types of cancer cells had varied biology, spreading features, and prognoses. Discussion: Our results highlight that the proposed classification system offers insights into the diverse behaviors of cancer cells, providing implications for cancer aggressiveness and metastasis.
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Affiliation(s)
- Rui Wang
- Department of Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaopeng Yan
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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25
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Pellecchia S, Franchini M, Viscido G, Arnese R, Gambardella G. Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer. Genome Med 2024; 16:55. [PMID: 38605363 PMCID: PMC11008053 DOI: 10.1186/s13073-024-01327-2] [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: 05/02/2023] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Most primary Triple Negative Breast Cancers (TNBCs) show amplification of the Epidermal Growth Factor Receptor (EGFR) gene, leading to increased protein expression. However, unlike other EGFR-driven cancers, targeting this receptor in TNBC yields inconsistent therapeutic responses. METHODS To elucidate the underlying mechanisms of this variability, we employ cellular barcoding and single-cell transcriptomics to reconstruct the subclonal dynamics of EGFR-amplified TNBC cells in response to afatinib, a tyrosine kinase inhibitor (TKI) that irreversibly inhibits EGFR. RESULTS Integrated lineage tracing analysis revealed a rare pre-existing subpopulation of cells with distinct biological signature, including elevated expression levels of Insulin-Like Growth Factor Binding Protein 2 (IGFBP2). We show that IGFBP2 overexpression is sufficient to render TNBC cells tolerant to afatinib treatment by activating the compensatory insulin-like growth factor I receptor (IGF1-R) signalling pathway. Finally, based on reconstructed mechanisms of resistance, we employ deep learning techniques to predict the afatinib sensitivity of TNBC cells. CONCLUSIONS Our strategy proved effective in reconstructing the complex signalling network driving EGFR-targeted therapy resistance, offering new insights for the development of individualized treatment strategies in TNBC.
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Affiliation(s)
- Simona Pellecchia
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Scuola Superiore Meridionale, Genomics and Experimental Medicine Program, Naples, Italy
| | - Melania Franchini
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
| | - Gaetano Viscido
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Chemical, Materials and Industrial Engineering , University of Naples Federico II, Naples, Italy
| | - Riccardo Arnese
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
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26
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Ren Z, Dharmaratne M, Liang H, Benard O, Morales-Gallego M, Suyama K, Kumar V, Fard AT, Kulkarni AS, Prystowsky M, Mar JC, Norton L, Hazan RB. Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1α. Br J Cancer 2024; 130:908-924. [PMID: 38238426 PMCID: PMC10951347 DOI: 10.1038/s41416-023-02522-5] [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: 03/16/2023] [Revised: 11/08/2023] [Accepted: 11/24/2023] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Redox signaling caused by knockdown (KD) of Glutathione Peroxidase 2 (GPx2) in the PyMT mammary tumour model promotes metastasis via phenotypic and metabolic reprogramming. However, the tumour cell subpopulations and transcriptional regulators governing these processes remained unknown. METHODS We used single-cell transcriptomics to decipher the tumour cell subpopulations stimulated by GPx2 KD in the PyMT mammary tumour and paired pulmonary metastases. We analyzed the EMT spectrum across the various tumour cell clusters using pseudotime trajectory analysis and elucidated the transcriptional and metabolic regulation of the hybrid EMT state. RESULTS Integration of single-cell transcriptomics between the PyMT/GPx2 KD primary tumour and paired lung metastases unraveled a basal/mesenchymal-like cluster and several luminal-like clusters spanning an EMT spectrum. Interestingly, the luminal clusters at the primary tumour gained mesenchymal gene expression, resulting in epithelial/mesenchymal subpopulations fueled by oxidative phosphorylation (OXPHOS) and glycolysis. By contrast, at distant metastasis, the basal/mesenchymal-like cluster gained luminal and mesenchymal gene expression, resulting in a hybrid subpopulation using OXPHOS, supporting adaptive plasticity. Furthermore, p63 was dramatically upregulated in all hybrid clusters, implying a role in regulating partial EMT and MET at primary and distant sites, respectively. Importantly, these effects were reversed by HIF1α loss or GPx2 gain of function, resulting in metastasis suppression. CONCLUSIONS Collectively, these results underscored a dramatic effect of redox signaling on p63 activation by HIF1α, underlying phenotypic and metabolic plasticity leading to mammary tumour metastasis.
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Affiliation(s)
- Zuen Ren
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Malindrie Dharmaratne
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Huizhi Liang
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | | | | | - Kimita Suyama
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Viney Kumar
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Ameya S Kulkarni
- Department of Endocrinology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Michael Prystowsky
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Larry Norton
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, 10021, USA
| | - Rachel B Hazan
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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27
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Eisele AS, Tarbier M, Dormann AA, Pelechano V, Suter DM. Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets. Nat Commun 2024; 15:2744. [PMID: 38553478 PMCID: PMC10980719 DOI: 10.1038/s41467-024-47158-y] [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: 01/29/2024] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in time-resolution, and most scRNA-seq datasets are devoid of lineage information. Here we introduce Gene Expression Memory-based Lineage Inference (GEMLI), a computational tool allowing to robustly identify small to medium-sized cell lineages solely from scRNA-seq datasets. GEMLI allows to study heritable gene expression, to discriminate symmetric and asymmetric cell fate decisions and to reconstruct individual multicellular structures from pooled scRNA-seq datasets. In human breast cancer biopsies, GEMLI reveals previously unknown gene expression changes at the onset of cancer invasiveness. The universal applicability of GEMLI allows studying the role of small cell lineages in a wide range of physiological and pathological contexts, notably in vivo. GEMLI is available as an R package on GitHub ( https://github.com/UPSUTER/GEMLI ).
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Affiliation(s)
- A S Eisele
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
| | - M Tarbier
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - A A Dormann
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland
| | - V Pelechano
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - D M Suter
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
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28
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Abdullah L, Emiliani FE, Vaidya CM, Stuart H, Kolling FW, Ackerman ME, Song L, McKenna A, Huang YH. Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586160. [PMID: 38585810 PMCID: PMC10996474 DOI: 10.1101/2024.03.21.586160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Generating balanced populations of CD8 effector and memory T cells is necessary for immediate and durable immunity to infections and cancer. Yet, a definitive understanding of CD8 differentiation remains unclear. We used CARLIN, a processive lineage recording mouse model with single-cell RNA-seq and TCR-seq to track endogenous antigen-specific CD8 T cells during acute viral infection. We identified a diverse repertoire of expanded T-cell clones represented by seven transcriptional states. TCR enrichment analysis revealed differential memory- or effector-fate biases within clonal populations. Shared Vb segments and amino acid motifs were found within biased categories despite high TCR diversity. Using single-cell CARLIN barcode-seq we tracked multi-generational clones and found that unlike unbiased or memory-biased clones, which stably retain their fate profiles, effector-biased clones could adopt memory- or effector-bias within subclones. Collectively, our study demonstrates that a heterogenous T-cell repertoire specific for a shared antigen is composed of clones with distinct TCR-intrinsic fate-biases.
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Affiliation(s)
- Leena Abdullah
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Francesco E. Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chinmay M. Vaidya
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Hannah Stuart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Li Song
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Yina H. Huang
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology and Laboratory Medicine, Dartmouth Health, Lebanon, NH 03756, USA
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29
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Rodriguez-Tirado C, Sosa MS. How much do we know about the metastatic process? Clin Exp Metastasis 2024:10.1007/s10585-023-10248-0. [PMID: 38520475 DOI: 10.1007/s10585-023-10248-0] [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: 08/13/2023] [Accepted: 11/17/2023] [Indexed: 03/25/2024]
Abstract
Cancer cells can leave their primary sites and travel through the circulation to distant sites, where they lodge as disseminated cancer cells (DCCs), even during the early and asymptomatic stages of tumor progression. In experimental models and clinical samples, DCCs can be detected in a non-proliferative state, defined as cellular dormancy. This state can persist for extended periods until DCCs reawaken, usually in response to niche-derived reactivation signals. Therefore, their clinical detection in sites like lymph nodes and bone marrow is linked to poor survival. Current cancer therapy designs are based on the biology of the primary tumor and do not target the biology of the dormant DCC population and thus fail to eradicate the initial or subsequent waves of metastasis. In this brief review, we discuss the current methods for detecting DCCs and highlight new strategies that aim to target DCCs that constitute minimal residual disease to reduce or prevent metastasis formation. Furthermore, we present current evidence on the relevance of DCCs derived from early stages of tumor progression in metastatic disease and describe the animal models available for their study. We also discuss our current understanding of the dissemination mechanisms utilized by genetically less- and more-advanced cancer cells, which include the functional analysis of intermediate or hybrid states of epithelial-mesenchymal transition (EMT). Finally, we raise some intriguing questions regarding the clinical impact of studying the crosstalk between evolutionary waves of DCCs and the initiation of metastatic disease.
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Affiliation(s)
- Carolina Rodriguez-Tirado
- Department of Microbiology and Immunology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Cancer Dormancy and Tumor Microenvironment Institute/Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
| | - Maria Soledad Sosa
- Department of Microbiology and Immunology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
- Cancer Dormancy and Tumor Microenvironment Institute/Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10461, USA.
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30
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Guo Z, Ashrafizadeh M, Zhang W, Zou R, Sethi G, Zhang X. Molecular profile of metastasis, cell plasticity and EMT in pancreatic cancer: a pre-clinical connection to aggressiveness and drug resistance. Cancer Metastasis Rev 2024; 43:29-53. [PMID: 37453022 DOI: 10.1007/s10555-023-10125-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The metastasis is a multistep process in which a small proportion of cancer cells are detached from the colony to enter into blood cells for obtaining a new place for metastasis and proliferation. The metastasis and cell plasticity are considered major causes of cancer-related deaths since they improve the malignancy of cancer cells and provide poor prognosis for patients. Furthermore, enhancement in the aggressiveness of cancer cells has been related to the development of drug resistance. Metastasis of pancreatic cancer (PC) cells has been considered one of the major causes of death in patients and their undesirable prognosis. PC is among the most malignant tumors of the gastrointestinal tract and in addition to lifestyle, smoking, and other factors, genomic changes play a key role in its progression. The stimulation of EMT in PC cells occurs as a result of changes in molecular interaction, and in addition to increasing metastasis, EMT participates in the development of chemoresistance. The epithelial, mesenchymal, and acinar cell plasticity can occur and determines the progression of PC. The major molecular pathways including STAT3, PTEN, PI3K/Akt, and Wnt participate in regulating the metastasis of PC cells. The communication in tumor microenvironment can provide by exosomes in determining PC metastasis. The components of tumor microenvironment including macrophages, neutrophils, and cancer-associated fibroblasts can modulate PC progression and the response of cancer cells to chemotherapy.
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Affiliation(s)
- Zhenli Guo
- Department of Oncology, First Affiliated Hospital, Gannan Medical University, 128 Jinling Road, Ganzhou City, Jiangxi Province, 341000, China
| | - Milad Ashrafizadeh
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Wei Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Gautam Sethi
- Department of Pharmacology, National University of Singapore, 16 Medical Drive, Singapore, 117600, Singapore.
| | - Xianbin Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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31
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Bose A, Datta S, Mandal R, Ray U, Dhar R. Increased heterogeneity in expression of genes associated with cancer progression and drug resistance. Transl Oncol 2024; 41:101879. [PMID: 38262110 PMCID: PMC10832509 DOI: 10.1016/j.tranon.2024.101879] [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: 10/27/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024] Open
Abstract
Fluctuations in the number of regulatory molecules and differences in timings of molecular events can generate variation in gene expression among genetically identical cells in the same environmental condition. This variation, termed as expression noise, can create differences in metabolic state and cellular functions, leading to phenotypic heterogeneity. Expression noise and phenotypic heterogeneity have been recognized as important contributors to intra-tumor heterogeneity, and have been associated with cancer growth, progression, and therapy resistance. However, how expression noise changes with cancer progression in actual cancer patients has remained poorly explored. Such an analysis, through identification of genes with increasing expression noise, can provide valuable insights into generation of intra-tumor heterogeneity, and could have important implications for understanding immune-suppression, drug tolerance and therapy resistance. In this work, we performed a genome-wide identification of changes in gene expression noise with cancer progression using single-cell RNA-seq data of lung adenocarcinoma patients at different stages of cancer. We identified 37 genes in epithelial cells that showed an increasing noise trend with cancer progression, many of which were also associated with cancer growth, EMT and therapy resistance. We found that expression of several of these genes was positively associated with expression of mitochondrial genes, suggesting an important role of mitochondria in generation of heterogeneity. In addition, we uncovered substantial differences in sample-specific noise profiles which could have implications for personalized prognosis and treatment.
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Affiliation(s)
- Anwesha Bose
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Subhasis Datta
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Rakesh Mandal
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Upasana Ray
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India.
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32
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Celentano M, DeWitt WS, Prillo S, Song YS. Exact and efficient phylodynamic simulation from arbitrarily large populations. ARXIV 2024:arXiv:2402.17153v1. [PMID: 38463501 PMCID: PMC10925381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Many biological studies involve inferring the genealogical history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a comprehensive population tree and is distorted by survivorship and sampling biases. Inferring evolutionary parameters from ascertained trees requires modeling both the underlying population dynamics and the ascertainment process. A crucial component of this phylodynamic modeling involves tree simulation, which is used to benchmark probabilistic inference methods. To simulate an ascertained tree, one must first simulate the full population tree and then prune unobserved lineages. Consequently, the computational cost is determined not by the size of the final simulated tree, but by the size of the population tree in which it is embedded. In most biological scenarios, simulations of the entire population are prohibitively expensive due to computational demands placed on lineages without sampled descendants. Here, we address this challenge by proving that, for any partially ascertained process from a general multi-type birth-death-mutation-sampling (BDMS) model, there exists an equivalent pure birth process (i.e., no death) with mutation and complete sampling. The final trees generated under these processes have exactly the same distribution. Leveraging this property, we propose a highly efficient algorithm for simulating trees under a general BDMS model. Our algorithm scales linearly with the size of the final simulated tree and is independent of the population size, enabling simulations from extremely large populations beyond the reach of current methods but essential for various biological applications. We anticipate that this unprecedented speedup will significantly advance the development of novel inference methods that require extensive training data.
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Affiliation(s)
| | | | | | - Yun S Song
- Computer Science Division, University of California, Berkeley
- Department of Statistics, University of California, Berkeley
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33
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Thiery JP, Sheng G, Shu X, Runyan R. How studies in developmental epithelial-mesenchymal transition and mesenchymal-epithelial transition inspired new research paradigms in biomedicine. Development 2024; 151:dev200128. [PMID: 38300897 DOI: 10.1242/dev.200128] [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: 02/03/2024]
Abstract
Epithelial-mesenchymal transition (EMT) and its reverse mechanism, mesenchymal-epithelial transition (MET), are evolutionarily conserved mechanisms initially identified in studies of early metazoan development. EMT may even have been established in choanoflagellates, the closest unicellular relative of Metazoa. These crucial morphological transitions operate during body plan formation and subsequently in organogenesis. These findings have prompted an increasing number of investigators in biomedicine to assess the importance of such mechanisms that drive epithelial cell plasticity in multiple diseases associated with congenital disabilities and fibrosis, and, most importantly, in the progression of carcinoma. EMT and MET also play crucial roles in regenerative medicine, notably by contributing epigenetic changes in somatic cells to initiate reprogramming into stem cells and their subsequent differentiation into distinct lineages.
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Affiliation(s)
| | - Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Xiaodong Shu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Raymond Runyan
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
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34
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Pan X, Zhang X. Studying temporal dynamics of single cells: expression, lineage and regulatory networks. Biophys Rev 2024; 16:57-67. [PMID: 38495440 PMCID: PMC10937865 DOI: 10.1007/s12551-023-01090-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 03/19/2024] Open
Abstract
Learning how multicellular organs are developed from single cells to different cell types is a fundamental problem in biology. With the high-throughput scRNA-seq technology, computational methods have been developed to reveal the temporal dynamics of single cells from transcriptomic data, from phenomena on cell trajectories to the underlying mechanism that formed the trajectory. There are several distinct families of computational methods including Trajectory Inference (TI), Lineage Tracing (LT), and Gene Regulatory Network (GRN) Inference which are involved in such studies. This review summarizes these computational approaches which use scRNA-seq data to study cell differentiation and cell fate specification as well as the advantages and limitations of different methods. We further discuss how GRNs can potentially affect cell fate decisions and trajectory structures. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-023-01090-5.
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Affiliation(s)
- Xinhai Pan
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Xiuwei Zhang
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
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35
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Celià-Terrassa T, Kang Y. How important is EMT for cancer metastasis? PLoS Biol 2024; 22:e3002487. [PMID: 38324529 PMCID: PMC10849258 DOI: 10.1371/journal.pbio.3002487] [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] [Indexed: 02/09/2024] Open
Abstract
Epithelial-to-mesenchymal transition (EMT), a biological phenomenon of cellular plasticity initially reported in embryonic development, has been increasingly recognized for its importance in cancer progression and metastasis. Despite tremendous progress being made in the past 2 decades in our understanding of the molecular mechanism and functional importance of EMT in cancer, there are several mysteries around EMT that remain unresolved. In this Unsolved Mystery, we focus on the variety of EMT types in metastasis, cooperative and collective EMT behaviors, spatiotemporal characterization of EMT, and strategies of therapeutically targeting EMT. We also highlight new technical advances that will facilitate the efforts to elucidate the unsolved mysteries of EMT in metastasis.
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Affiliation(s)
- Toni Celià-Terrassa
- Cancer Research Program, Hospital del Mar Research Institute, Barcelona, Spain
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, New Jersey, United States of America
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36
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Mei S, Alchahin AM, Tsea I, Kfoury Y, Hirz T, Jeffries NE, Zhao T, Xu Y, Zhang H, Sarkar H, Wu S, Subtelny AO, Johnsen JI, Zhang Y, Salari K, Wu CL, Randolph MA, Scadden DT, Dahl DM, Shin J, Kharchenko PV, Saylor PJ, Sykes DB, Baryawno N. Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions. Genome Med 2024; 16:1. [PMID: 38281962 PMCID: PMC10823713 DOI: 10.1186/s13073-023-01272-6] [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: 10/10/2022] [Accepted: 12/11/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present with bone metastasis at the time of diagnosis. However, the bone metastatic niche in humans, including the immune and stromal microenvironments, has not been well-defined, hindering progress towards identification of therapeutic targets. METHODS We collected fresh patient samples and performed single-cell transcriptomic profiling of solid metastatic tissue (Bone Met), liquid bone marrow at the vertebral level of spinal cord compression (Involved), and liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal), as well as bone marrow from patients undergoing hip replacement surgery (Benign). In addition, we incorporated single-cell data from primary ccRCC tumors (ccRCC Primary) for comparative analysis. RESULTS The bone marrow of metastatic patients is immune-suppressive, featuring increased, exhausted CD8 + cytotoxic T cells, T regulatory cells, and tumor-associated macrophages (TAM) with distinct transcriptional states in metastatic lesions. Bone marrow stroma from tumor samples demonstrated a tumor-associated mesenchymal stromal cell population (TA-MSC) that appears to be supportive of epithelial-to mesenchymal transition (EMT), bone remodeling, and a cancer-associated fibroblast (CAFs) phenotype. This stromal subset is associated with poor progression-free and overall survival and also markedly upregulates bone remodeling through the dysregulation of RANK/RANKL/OPG signaling activity in bone cells, ultimately leading to bone resorption. CONCLUSIONS These results provide a comprehensive analysis of the bone marrow niche in the setting of human metastatic cancer and highlight potential therapeutic targets for both cell populations and communication channels.
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Affiliation(s)
- Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Adele M Alchahin
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Ioanna Tsea
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Youmna Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nathan Elias Jeffries
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ting Zhao
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Hirak Sarkar
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Alexander O Subtelny
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Keyan Salari
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Mark A Randolph
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Douglas M Dahl
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - John Shin
- Department of Neurosurgery, Harvard Medical School, Boston, MA, 02115, USA.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Present: Altos Labs, San Diego, CA, 92121, USA.
| | - Philip J Saylor
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02114, USA.
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden.
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37
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Fontana R, Mestre-Farrera A, Yang J. Update on Epithelial-Mesenchymal Plasticity in Cancer Progression. ANNUAL REVIEW OF PATHOLOGY 2024; 19:133-156. [PMID: 37758242 PMCID: PMC10872224 DOI: 10.1146/annurev-pathmechdis-051222-122423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular process by which epithelial cells lose their characteristics and acquire mesenchymal traits to promote cell movement. This program is aberrantly activated in human cancers and endows tumor cells with increased abilities in tumor initiation, cell migration, invasion, metastasis, and therapy resistance. The EMT program in tumors is rarely binary and often leads to a series of gradual or intermediate epithelial-mesenchymal states. Functionally, epithelial-mesenchymal plasticity (EMP) improves the fitness of cancer cells during tumor progression and in response to therapies. Here, we discuss the most recent advances in our understanding of the diverse roles of EMP in tumor initiation, progression, metastasis, and therapy resistance and address major clinical challenges due to EMP-driven phenotypic heterogeneity in cancer. Uncovering novel molecular markers and key regulators of EMP in cancer will aid the development of new therapeutic strategies to prevent cancer recurrence and overcome therapy resistance.
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Affiliation(s)
- Rosa Fontana
- Department of Pharmacology, Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, California, USA;
| | - Aida Mestre-Farrera
- Department of Pharmacology, Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, California, USA;
| | - Jing Yang
- Department of Pharmacology, Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, California, USA;
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA
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38
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Stanger BZ, Wahl GM. Cancer as a Disease of Development Gone Awry. ANNUAL REVIEW OF PATHOLOGY 2024; 19:397-421. [PMID: 37832945 DOI: 10.1146/annurev-pathmechdis-031621-025610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
In the 160 years since Rudolf Virchow first postulated that neoplasia arises by the same law that regulates embryonic development, scientists have come to recognize the striking overlap between the molecular and cellular programs used by cancers and embryos. Advances in cancer biology and molecular techniques have further highlighted the similarities between carcinogenesis and embryogenesis, where cellular growth, differentiation, motility, and intercellular cross talk are mediated by common drivers and regulatory networks. This review highlights the many connections linking cancer biology and developmental biology to provide a deeper understanding of how a tissue's developmental history may both enable and constrain cancer cell evolution.
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Affiliation(s)
- Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, Abramson Family Cancer Research Institute, and Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA;
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39
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Mehta A, Stanger BZ. Lineage Plasticity: The New Cancer Hallmark on the Block. Cancer Res 2024; 84:184-191. [PMID: 37963209 PMCID: PMC10841583 DOI: 10.1158/0008-5472.can-23-1067] [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: 04/19/2023] [Revised: 09/12/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Plasticity refers to the ability of cells to adopt a spectrum of states or phenotypes. In cancer, it is a critical contributor to tumor initiation, progression, invasiveness, and therapy resistance, and it has recently been recognized as an emerging cancer hallmark. Plasticity can occur as a result of cell-intrinsic factors (e.g., genetic, transcriptional, or epigenetic fluctuations), or through cell-extrinsic cues (e.g., signaling from components of the tumor microenvironment or selective pressure from therapy). Over the past decade, technological advances, analysis of patient samples, and studies in mouse model systems have led to a deeper understanding of how such plastic states come about. In this review, we discuss: (i) the definition of plasticity; (ii) methods to measure and quantify plasticity; (iii) the clinical relevance of plasticity; and (iv) therapeutic hypotheses to modulate plasticity in the clinic.
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Affiliation(s)
- Arnav Mehta
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ben Z. Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Cell and Developmental Biology, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
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40
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Wang L, Dong W, Yin Z, Sheng J, Ezeana CF, Yang L, Yu X, Wong SSY, Wan Z, Danforth RL, Han K, Gao D, Wong STC. Charting Single Cell Lineage Dynamics and Mutation Networks via Homing CRISPR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574236. [PMID: 38260351 PMCID: PMC10802354 DOI: 10.1101/2024.01.05.574236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Single cell lineage tracing, essential for unraveling cellular dynamics in disease evolution is critical for developing targeted therapies. CRISPR-Cas9, known for inducing permanent and cumulative mutations, is a cornerstone in lineage tracing. The novel homing guide RNA (hgRNA) technology enhances this by enabling dynamic retargeting and facilitating ongoing genetic modifications. Charting these mutations, especially through successive hgRNA edits, poses a significant challenge. Our solution, LINEMAP, is a computational framework designed to trace and map these mutations with precision. LINEMAP meticulously discerns mutation alleles at single-cell resolution and maps their complex interrelationships through a mutation evolution network. By utilizing a Markov Process model, we can predict mutation transition probabilities, revealing potential mutational routes and pathways. Our reconstruction algorithm, anchored in the Markov model's attributes, reconstructs cellular lineage pathways, shedding light on the cell's evolutionary journey to the minutiae of single-cell division. Our findings reveal an intricate network of mutation evolution paired with a predictive Markov model, advancing our capability to reconstruct single-cell lineage via hgRNA. This has substantial implications for advancing our understanding of biological mechanisms and propelling medical research forward.
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Affiliation(s)
- Lin Wang
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Wenjuan Dong
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Zheng Yin
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
- Biostatistics and Bioinformatics Shared Resource, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Jianting Sheng
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Chika F. Ezeana
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Li Yang
- T.T. and W. F. Chao Center for BRAIN, Houston Methodist Research Institute, Houston, Texas 77030
| | - Xiaohui Yu
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | | | - Zhihao Wan
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Rebecca L. Danforth
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Kun Han
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
| | - Dingcheng Gao
- Department of Cell & Development Biology, Weill Cornell Medical College, New York, NY 10065
| | - Stephen T. C. Wong
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, Texas 77030
- Departments of Radiology, Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College, Houston, TX 77030
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41
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Li Z, Yang W, Wu P, Shan Y, Zhang X, Chen F, Yang J, Yang JR. Reconstructing cell lineage trees with genomic barcoding: approaches and applications. J Genet Genomics 2024; 51:35-47. [PMID: 37269980 DOI: 10.1016/j.jgg.2023.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 06/05/2023]
Abstract
In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs. Here we review the existing experimental approaches to the reconstruction of CLT, which are broadly categorized as either image-based or DNA barcode-based methods. In addition, we present a summary of the related literature based on the biological insight provided by the obtained CLTs. Moreover, we discuss the challenges that will arise as more and better CLT data become available in the near future. Genomic barcoding-based CLT reconstructions and analyses, due to their wide applicability and high scalability, offer the potential for novel biological discoveries, especially those related to general and systemic properties of the developmental process.
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Affiliation(s)
- Zizhang Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wenjing Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Peng Wu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yuyan Shan
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaoyu Zhang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Feng Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Junnan Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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42
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Wang T, Wagner RT, Hlady RA, Pan X, Zhao X, Kim S, Wang L, Lee J, Luo H, Castle EP, Lake DF, Ho TH, Robertson KD. SETD2 loss in renal epithelial cells drives epithelial-to-mesenchymal transition in a TGF-β-independent manner. Mol Oncol 2024; 18:44-61. [PMID: 37418588 PMCID: PMC10766198 DOI: 10.1002/1878-0261.13487] [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: 04/21/2023] [Revised: 05/25/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023] Open
Abstract
Histone-lysine N-methyltransferase SETD2 (SETD2), the sole histone methyltransferase that catalyzes trimethylation of lysine 36 on histone H3 (H3K36me3), is often mutated in clear cell renal cell carcinoma (ccRCC). SETD2 mutation and/or loss of H3K36me3 is linked to metastasis and poor outcome in ccRCC patients. Epithelial-to-mesenchymal transition (EMT) is a major pathway that drives invasion and metastasis in various cancer types. Here, using novel kidney epithelial cell lines isogenic for SETD2, we discovered that SETD2 inactivation drives EMT and promotes migration, invasion, and stemness in a transforming growth factor-beta-independent manner. This newly identified EMT program is triggered in part through secreted factors, including cytokines and growth factors, and through transcriptional reprogramming. RNA-seq and assay for transposase-accessible chromatin sequencing uncovered key transcription factors upregulated upon SETD2 loss, including SOX2, POU2F2 (OCT2), and PRRX1, that could individually drive EMT and stemness phenotypes in SETD2 wild-type (WT) cells. Public expression data from SETD2 WT/mutant ccRCC support the EMT transcriptional signatures derived from cell line models. In summary, our studies reveal that SETD2 is a key regulator of EMT phenotypes through cell-intrinsic and cell-extrinsic mechanisms that help explain the association between SETD2 loss and ccRCC metastasis.
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Affiliation(s)
- Tianchu Wang
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMNUSA
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan T. Wagner
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xiaoyu Pan
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xia Zhao
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Sungho Kim
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science ResearchMayo ClinicRochesterMNUSA
| | - Jeong‐Heon Lee
- Epigenomics Development LaboratoryMayo ClinicRochesterMNUSA
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Huijun Luo
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | | | | | - Thai H. Ho
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
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43
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Wrenn ED, Apfelbaum AA, Rudzinski ER, Deng X, Jiang W, Sud S, Van Noord RA, Newman EA, Garcia NM, Miyaki A, Hoglund VJ, Bhise SS, Kanaan SB, Waltner OG, Furlan SN, Lawlor ER. Cancer-Associated Fibroblast-Like Tumor Cells Remodel the Ewing Sarcoma Tumor Microenvironment. Clin Cancer Res 2023; 29:5140-5154. [PMID: 37471463 PMCID: PMC10801911 DOI: 10.1158/1078-0432.ccr-23-1111] [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: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. EXPERIMENTAL DESIGN Single-cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining. RESULTS We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAF), and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution was detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci. CONCLUSIONS EwS tumor cells can adopt CAF-like properties, and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment. See related commentary by Kuo and Amatruda, p. 5002.
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Affiliation(s)
- Emma D. Wrenn
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - April A. Apfelbaum
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, Michigan
| | - Erin R. Rudzinski
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Xuemei Deng
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Wei Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Sudha Sud
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | | | - Erika A. Newman
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Nicolas M. Garcia
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Aya Miyaki
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Virginia J. Hoglund
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Shruti S. Bhise
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sami B. Kanaan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Olivia G. Waltner
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Scott N. Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
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44
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Yakubovich E, Cook DP, Rodriguez GM, Vanderhyden BC. Mesenchymal ovarian cancer cells promote CD8 + T cell exhaustion through the LGALS3-LAG3 axis. NPJ Syst Biol Appl 2023; 9:61. [PMID: 38086828 PMCID: PMC10716312 DOI: 10.1038/s41540-023-00322-4] [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: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cancer cells often metastasize by undergoing an epithelial-mesenchymal transition (EMT). Although abundance of CD8+ T-cells in the tumor microenvironment correlates with improved survival, mesenchymal cancer cells acquire greater resistance to antitumor immunity in some cancers. We hypothesized the EMT modulates the immune response to ovarian cancer. Here we show that cancer cells from infiltrated/inflamed tumors possess more mesenchymal cells, than excluded and desert tumors. We also noted high expression of LGALS3 is associated with EMT in vivo, a finding validated with in vitro EMT models. Dissecting the cellular communications among populations in the tumor revealed that mesenchymal cancer cells in infiltrated tumors communicate through LGALS3 to LAG3 receptor expressed by CD8+ T cells. We found CD8+ T cells express high levels of LAG3, a marker of T cell exhaustion. The results indicate that EMT in ovarian cancer cells promotes interactions between cancer cells and T cells through the LGALS3 - LAG3 axis, which could increase T cell exhaustion in infiltrated tumors, dampening antitumor immunity.
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Affiliation(s)
- Edward Yakubovich
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.
| | - David P Cook
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Galaxia M Rodriguez
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Barbara C Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
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45
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Wang X, Eichhorn PJA, Thiery JP. TGF-β, EMT, and resistance to anti-cancer treatment. Semin Cancer Biol 2023; 97:1-11. [PMID: 37944215 DOI: 10.1016/j.semcancer.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/08/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Transforming growth factor-β (TGF-β) signaling regulates cell-specific programs involved in embryonic development, wound-healing, and immune homeostasis. Yet, during tumor progression, these TGF-β-mediated programs are altered, leading to epithelial cell plasticity and a reprogramming of epithelial cells into mesenchymal lineages through epithelial-to-mesenchymal transition (EMT), a critical developmental program in morphogenesis and organogenesis. These changes, in turn, lead to enhanced carcinoma cell invasion, metastasis, immune cell differentiation, immune evasion, and chemotherapy resistance. Here, we discuss EMT as one of the critical programs associated with carcinoma cell plasticity and the influence exerted by TGF-β on carcinoma status and function. We further explore the composition of carcinoma and other cell populations within the tumor microenvironment, and consider the relevant outcomes related to the programs associated with cancer treatment resistance.
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Affiliation(s)
- Xuecong Wang
- Guangzhou National Laboratory, Guangzhou, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Pieter Johan Adam Eichhorn
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia; Curtin Medical School, Curtin University, GPO Box U1987, Perth, WA 6845, Australia; Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
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46
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Affiliation(s)
- Bushra Raj
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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47
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Delamonica B, Balázsi G, Shub M. Cusp bifurcation in a metastatic regulatory network. J Theor Biol 2023; 575:111630. [PMID: 37804940 PMCID: PMC11132523 DOI: 10.1016/j.jtbi.2023.111630] [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: 08/23/2022] [Revised: 06/28/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
Abstract
Understanding the potential for cancers to metastasize is still relatively unknown. While many predictive methods may use deep learning or stochastic processes, we highlight a long standing mathematical concept that may be useful for modeling metastatic breast cancer systems. Ordinary differential equations (ODEs) can model cell state transitions by considering the pertinent environmental variables as well as the paths systems take over time. Bifurcation theory is a branch of dynamical systems which studies changes in the behavior of an ODE system while one or more parameters are varied. Many studies have applied concepts in one-parameter bifurcation theory to model biological network dynamics, and cell division. However, studies of two-parameter bifurcations are much more rare. Two-parameter bifurcations have not been studied in metastatic systems. Here we show how a specific two-parameter bifurcation phenomenon called a cusp bifurcation separates two qualitatively different metastatic cell state transitions modalities and propose a new perspective on defining such transitions based on mathematical theory. We hope the observations and verification methods detailed here may help in the understanding of metastatic potential from a basic biological perspective and in clinical settings.
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Affiliation(s)
- Brenda Delamonica
- Applied Mathematics and Statistics Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Michael Shub
- Department of Mathematics,City College and the Graduate Center of CUNY, New York, NY 10031, USA.
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48
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Bhatia S, Gunter JH, Burgess JT, Adams MN, O'Byrne K, Thompson EW, Duijf PH. Stochastic epithelial-mesenchymal transitions diversify non-cancerous lung cell behaviours. Transl Oncol 2023; 37:101760. [PMID: 37611490 PMCID: PMC10466920 DOI: 10.1016/j.tranon.2023.101760] [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: 05/15/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) is a hallmark of cancer. By enabling cells to shift between different morphological and functional states, EMP promotes invasion, metastasis and therapy resistance. We report that near-diploid non-cancerous human epithelial lung cells spontaneously shift along the EMP spectrum without genetic changes. Strikingly, more than half of single cell-derived clones adopt a mesenchymal morphology. We independently characterise epithelial-like and mesenchymal-like clones. Mesenchymal clones lose epithelial markers, display larger cell aspect ratios and lower motility, with mostly unaltered proliferation rates. Stemness marker expression and metabolic rewiring diverge independently of phenotypes. In 3D culture, more epithelial clones become mesenchymal-like. Thus, non-cancerous epithelial cells may acquire cancer metastasis-associated features prior to genetic alterations and cancerous transformation.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia.
| | - Jennifer H Gunter
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Queensland University of Technology, Woolloongabba 4102, Australia
| | - Joshua T Burgess
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Mark N Adams
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Kenneth O'Byrne
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Princess Alexandra Hospital, Woolloongabba 4102, QLD, Australia
| | - Erik W Thompson
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Pascal Hg Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide SA, 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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49
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Ma X, Chen L, Chen T, Chen K, Zhang H, Huang K, Zheng H, Jin H, Cheng Z, Xiao K, Guo J. Identification of a 24-gene panel and a novel marker of PODXL2 essential for the pathological diagnosis of early prostate cancer. Comput Struct Biotechnol J 2023; 21:5476-5490. [PMID: 38022698 PMCID: PMC10663703 DOI: 10.1016/j.csbj.2023.10.044] [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: 07/20/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Precise diagnosis of early prostate cancer (PCa) is critical for preventing tumor progression. However, the diagnostic outcomes of currently used markers are far from satisfactory due to the low sensitivity or specificity. Here, we identified a diagnostic subpopulation in PCa tissue with the integrating analysis of single-cell and bulk RNA-seq. The representative markers of this subpopulation were extracted to perform intersection analysis with early-PCa-related gene module generated from weighted correlation network analysis (WGCNA). A total of 24 overlapping genes were obtained, the diagnostic roles of which were validated by distinguishing normal and tumorous prostate samples from the public dataset. A least absolute shrinkage and selection operator (LASSO) model was constructed based on these genes and the obtained 24-gene panel showed high sensitivity and specificity for PCa diagnosis, with better identifying capability of PCa than the commercially used gene panel of Oncotype DX. The top two risk factors, TRPM4 and PODXL2, were verified to be highly expressed in early PCa tissues by multiplex immunostaining, and PODXL2 was more sensitive and specific compared to TRPM4 and the pathologically used marker AMACR for early PCa diagnosis, suggesting a novel and promising pathology marker.
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Affiliation(s)
- Xiaoshi Ma
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Lipeng Chen
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Tao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kun Chen
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Huirong Zhang
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Kaipeng Huang
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Han Zheng
- Department of Urology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu 241000, Anhui, China
| | - Hongtao Jin
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Zhiqiang Cheng
- Department of Pathology, Third People’s Hospital of Shenzhen (The Second Affiliated Hospital of Southern University of Science and Technology), Shenzhen 518100, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
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50
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Zhou Y, Tashiro J, Kamatani S, Irie N, Suzuki A, Ishikawa T, Warita K, Oltvai ZN, Warita T. HMG-CoA reductase degrader, SR-12813, counteracts statin-induced upregulation of HMG-CoA reductase and augments the anticancer effect of atorvastatin. Biochem Biophys Res Commun 2023; 677:13-19. [PMID: 37541087 DOI: 10.1016/j.bbrc.2023.07.056] [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: 06/06/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
Statins are cholesterol-lowering drugs that have exhibited potential as cancer therapeutic agents. However, as some cancer cells are resistant to statins, broadening an anticancer spectrum of statins is desirable. The upregulated expression of the statin target enzyme, 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase (HMGCR), in statin-treated cancer cells is a well-known mechanism of statin resistance, which can be counteracted by the downregulation of HMGCR gene expression, or degradation of the HMGCR protein. However, the mechanism by which HMGCR degradation influences the anticancer effects of statins remain unreported. We tested the effect of the HMGCR degrader compound SR-12813 at a concentration that did not affect the growth of eight diverse tumor cell lines. Combined treatment with atorvastatin and a low concentration of SR-12813 led to lowering of increased HMGCR expression, and augmented the cytostatic effect of atorvastatin in both statin-resistant and -sensitive cancer cells compared with that of atorvastatin treatment alone. Dual-targeting of HMGCR using statins and SR-12813 (or similar compounds) could provide an improved anticancer therapeutic approach.
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Affiliation(s)
- Yaxuan Zhou
- Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Jiro Tashiro
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori, 680-8553, Japan
| | - Shiori Kamatani
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori, 680-8553, Japan
| | - Nanami Irie
- Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Akito Suzuki
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori, 680-8553, Japan
| | - Takuro Ishikawa
- Department of Anatomy, School of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Katsuhiko Warita
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori, 680-8553, Japan.
| | - Zoltán N Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA.
| | - Tomoko Warita
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
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