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Liu X, Cortes E, Ji Y, Zhao K, Ho J, Liu YS, Davicioni E, Feng FY, Alumkal JJ, Spratt DE, Sweeney CJ, Yu H, Hu Q, Cheng Z, Zhang D, Chatta G, Nastiuk KL, Goodrich DW, Rycaj K, Jamroze A, Kirk JS, Puzanov I, Liu S, Wang J, Tang DG. Increasing Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.27.650697. [PMID: 40458374 PMCID: PMC12129099 DOI: 10.1101/2025.04.27.650697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/11/2025]
Abstract
Cancer progression involves loss of differentiation and acquisition of stem cell-like traits, broadly referred to as "stemness". Here, we test whether the level of stemness, assessed by a transcriptome-derived Stemness score, can quantitatively track prostate cancer (PCa) development, progression, therapy resistance, metastasis, plasticity, and patient survival. Integrative analysis of transcriptomic data from 87,183 samples across 26 datasets reveals a progressive increase in Stemness and decline in pro-differentiation androgen receptor activity (AR-A) along the PCa continuum, with metastatic castration-resistant PCa (mCRPC) exhibiting the highest Stemness and lowest AR-A. Both the general Stemness score and a newly developed 12-gene "PCa-Stem Signature" correlate with and predict poor clinical outcomes. Mechanistically, increased AR-A may promote Stemness in early-stage PCa while MYC amplification and bi-allelic RB1 loss likely drive greatly elevated Stemness in mCRPC where AR-A is suppressed. Our findings establish Stemness as a robust quantitative measure of PCa aggressiveness and offer a scalable framework for PCa risk stratification.
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2
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Qin Z, Liu S, Zheng Y, Wang Y, Chen Y, Peng X, Jia L. Co-targeting BMI1 and MYC to eliminate cancer stem cells in squamous cell carcinoma. Cell Rep Med 2025; 6:102077. [PMID: 40239645 DOI: 10.1016/j.xcrm.2025.102077] [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: 04/08/2024] [Revised: 10/28/2024] [Accepted: 03/18/2025] [Indexed: 04/18/2025]
Abstract
Bmi1+ tumor cells act as cancer stem cells (CSCs) driving relapse and therapy resistance in head and neck squamous cell carcinoma (HNSCC). Although BMI1 inhibitors reduce CSCs, combined cisplatin treatment targeting non-stem tumor cells is more effective in eliminating CSCs. Non-stem tumor cells may revert to CSCs post-treatment. However, in vivo evidence and underlying mechanisms remain unclear. Here, we demonstrate that BMI1 inhibitors induce temporary tumor regression followed by relapse. Lineage tracing reveals that keratin 16-marked non-stem tumor cells revert to Bmi1+ CSCs, which drive compensatory tumor growth after BMI1 targeting therapy. Mechanistically, BMI1 inhibitors activate DNA damage/nuclear factor κB (NF-κB) signaling and inflammatory cytokine secretion, subsequently stimulating myelocytomatosis viral oncogene homolog (MYC) expression in non-stem tumor cells to promote the reversion process. Genetic and pharmacological inhibition of MYC synergizes with BMI1 targeting, achieving sustained CSC eradication and relapse prevention. These findings provide insights into CSCs' plasticity and suggest dual BMI1/MYC blockade as an effective HNSCC treatment strategy.
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Affiliation(s)
- Zhen Qin
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Shuo Liu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Yunfei Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Yujia Wang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Yiwen Chen
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Xin Peng
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China.
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China; National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing 100081, P.R. China; Beijing Advanced Center of Cellular Homeostasis and Aging-Related Diseases, Institute of Advanced Clinical Medicine, Peking University, Beijing 100091, P.R. China.
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3
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Marefati M, Fernandez-Vallone V, Leprovots M, Vasile G, Libert F, Lefort A, Dinsart G, Weber A, Jetzer J, Garcia MI, Vassart G. A Lgr5-independent developmental lineage is involved in mouse intestinal regeneration. Development 2025; 152:dev204654. [PMID: 40013494 PMCID: PMC12045596 DOI: 10.1242/dev.204654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 02/06/2025] [Indexed: 02/28/2025]
Abstract
Collagenase and dispase treatment of intestinal tissue from adult mice generates cells growing in matrigel as stably replatable cystic spheroids, in addition to differentiated organoids. Contrary to classical EDTA-derived organoids, these spheroids display poor intestinal differentiation and grow independently of Rspondin, noggin and EGF. Their transcriptome strikingly resembles that of fetal intestinal spheroids, with downregulation of crypt base columnar cell (CBC) markers (Lgr5, Ascl2, Smoc2 and Olfm4). In addition, they display upregulation of inflammatory and mesenchymal genetic programs, together with robust expression of YAP target genes. Lineage tracing, cell-sorting and single cell RNA sequencing experiments demonstrate that adult spheroid-generating cells belong to a hitherto undescribed developmental lineage, independent of Lgr5-positive CBCs, and are involved in regeneration of the epithelium following CBC ablation.
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Affiliation(s)
- Maryam Marefati
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Valeria Fernandez-Vallone
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Morgane Leprovots
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Gabriella Vasile
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Frédérick Libert
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Anne Lefort
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Gilles Dinsart
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Achim Weber
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Jasna Jetzer
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
- Institute of Molecular Cancer Research, University of Zurich, CH-8091 Zurich, Switzerland
| | - Marie-Isabelle Garcia
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Gilbert Vassart
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM, https://iribhm.org/), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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4
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Belenki D, Richter-Pechanska P, Shao Z, Bhattacharya A, Lau A, Nabuco Leva Ferreira de Freitas JA, Kandler G, Hick TP, Cai X, Scharnagl E, Bittner A, Schönlein M, Kase J, Pardon K, Brzezicha B, Thiessen N, Bischof O, Dörr JR, Reimann M, Milanovic M, Du J, Yu Y, Chapuy B, Lee S, Leser U, Scheidereit C, Wolf J, Fan DNY, Schmitt CA. Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control. Nat Commun 2025; 16:3079. [PMID: 40159497 PMCID: PMC11955568 DOI: 10.1038/s41467-025-57429-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 02/21/2025] [Indexed: 04/02/2025] Open
Abstract
Cellular senescence is a stress-inducible state switch relevant in aging, tumorigenesis and cancer therapy. Beyond a lasting arrest, senescent cells are characterized by profound chromatin remodeling and transcriptional reprogramming. We show here myeloid-skewed aberrant lineage plasticity and its immunological ramifications in therapy-induced senescence (TIS) of primary human and murine B-cell lymphoma. We find myeloid transcription factor (TF) networks, specifically AP-1-, C/EBPβ- and PU.1-governed transcriptional programs, enriched in TIS but not in equally chemotherapy-exposed senescence-incapable cancer cells. Dependent on these master TF, TIS lymphoma cells adopt a lineage-promiscuous state with properties of monocytic-dendritic cell (DC) differentiation. TIS lymphoma cells are preferentially lysed by T-cells in vitro, and mice harboring DC-skewed Eμ-myc lymphoma experience significantly longer tumor-free survival. Consistently, superior long-term outcome is also achieved in diffuse large B-cell lymphoma patients with high expression of a TIS-related DC signature. In essence, these data demonstrate a therapeutically exploitable, prognostically favorable immunogenic role of senescence-dependent aberrant myeloid plasticity in B-cell lymphoma.
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MESH Headings
- Cellular Senescence/genetics
- Cellular Senescence/immunology
- Humans
- Animals
- Mice
- T-Lymphocytes/immunology
- Dendritic Cells/immunology
- Cell Lineage
- Cell Differentiation
- Cell Line, Tumor
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/pathology
- Lymphoma, B-Cell/genetics
- Gene Expression Regulation, Neoplastic
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Cell Plasticity
- Female
- Mice, Inbred C57BL
- Proto-Oncogene Proteins
- Trans-Activators
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Affiliation(s)
- Dimitri Belenki
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Paulina Richter-Pechanska
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Zhiting Shao
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Animesh Bhattacharya
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Andrea Lau
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | | | - Gregor Kandler
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Timon P Hick
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xiurong Cai
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Eva Scharnagl
- Johannes Kepler University, Medical Faculty, Linz, Austria
| | - Aitomi Bittner
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Martin Schönlein
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Julia Kase
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Katharina Pardon
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | | | - Nina Thiessen
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health, Berlin, Germany
| | - Oliver Bischof
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 - Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil, Créteil, France
| | - Jan R Dörr
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maurice Reimann
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
| | - Maja Milanovic
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Campus Benjamin Franklin, Berlin, Germany
- Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), partner site Berlin, Berlin, Germany
| | - Jing Du
- Medical Research Center and Department of Oncology Binzhou Medical University Hospital, 256600, Binzhou, P.R. China
| | - Yong Yu
- Johannes Kepler University, Medical Faculty, Linz, Austria
| | - Björn Chapuy
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Campus Benjamin Franklin, Berlin, Germany
| | - Soyoung Lee
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Johannes Kepler University, Medical Faculty, Linz, Austria
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claus Scheidereit
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jana Wolf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Dorothy N Y Fan
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), partner site Berlin, Berlin, Germany
| | - Clemens A Schmitt
- Charité - Universitätsmedizin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum - MKFZ, Campus Virchow Klinikum, Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Johannes Kepler University, Medical Faculty, Linz, Austria.
- Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), partner site Berlin, Berlin, Germany.
- Kepler University Hospital, Department of Hematology and Oncology, Krankenhausstraße 9, 4020, Linz, Austria.
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5
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Rolver MG, Camacho-Roda J, Dai Y, Flinck M, Ialchina R, Hindkær J, Dyhr RT, Bodilsen AN, Prasad NS, Baldan J, Yao J, Sandelin A, Arnes L, Pedersen SF. Tumor microenvironment acidosis favors pancreatic cancer stem cell properties and in vivo metastasis. iScience 2025; 28:111956. [PMID: 40083719 PMCID: PMC11904601 DOI: 10.1016/j.isci.2025.111956] [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: 09/06/2024] [Revised: 12/20/2024] [Accepted: 01/31/2025] [Indexed: 03/16/2025] Open
Abstract
The acidic tumor microenvironment (TME) favors cancer aggressiveness via incompletely understood pathways. Here, we asked whether adaptation to environmental acidosis (pH 6.5) selects for human pancreatic cancer stem cell (CSC) properties. RNA sequencing (RNA-seq) of acid-adapted (AA) Panc-1 cells revealed CSC pathway enrichment and upregulation of CSC markers. AA Panc-1 cells exhibited classical CSC characteristics including increased aldehyde dehydrogenase (ALDH) activity and β-catenin activity. Panc-1, PaTu8988s, and MiaPaCa-2 cells all exhibited increased pancreatosphere-forming efficiency after acid adaptation but differed in CSC marker expression and did not exhibit typical flow cytometric CSC populations. However, single-nucleus sequencing revealed the acid adaptation-induced emergence of Panc-1 cell subpopulations with clear CSC characteristics. In orthotopic mouse tumors, AA Panc-1 cells exhibited enhanced aggressiveness, liver and lung metastasis, compared to controls. Collectively, our work suggests that acid adaptation enriches for pancreatic CSC phenotypes with unusual traits via several trajectories, providing new insight into how acidic microenvironments favor cancer aggressiveness.
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Affiliation(s)
- Michala G. Rolver
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Juan Camacho-Roda
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Yifan Dai
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette Flinck
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Renata Ialchina
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Julie Hindkær
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Rigmor T. Dyhr
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - August N. Bodilsen
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nanditha S. Prasad
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Baldan
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jiayi Yao
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luis Arnes
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Stine F. Pedersen
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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6
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Diao S, Zou JY, Wang S, Ghaddar N, Chan JE, Kim H, Poulain N, Koumenis C, Hatzoglou M, Walter P, Sonenberg N, Le Quesne J, Tammela T, Koromilas AE. Lineage plasticity of the integrated stress response is a hallmark of cancer evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.637516. [PMID: 39990365 PMCID: PMC11844398 DOI: 10.1101/2025.02.10.637516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
The link between the "stress phenotype"-a well-established hallmark of cancer-and its role in tumor progression and intratumor heterogeneity remains poorly defined. The integrated stress response (ISR) is a key adaptive pathway that enables tumor survival under oncogenic stress. While ISR has been implicated in promoting tumor growth, its precise role in driving tumor evolution and heterogeneity has not been elucidated. In this study, using a genetically engineered mouse models, we demonstrate that ISR activation-indicated by elevated levels of phosphorylated eIF2 (p-eIF2) and ATF4-is essential for the emergence of dedifferentiated, therapy-resistant cell states. ISR, through the coordinated actions of ATF4 and MYC, facilitates the development of tumor cell populations characterized by high plasticity, stemness, and an epithelial-mesenchymal transition (EMT)-prone phenotype. This process is driven by ISR-mediated expression of genes that maintain mitochondrial integrity and function, critical for sustaining tumor progression. Importantly, genetic, or pharmacological inhibition of the p-eIF2-ATF4 signaling axis leads to mitochondrial dysfunction and significantly impairs tumor growth in mouse models of lung adenocarcinoma (LUAD). Moreover, ISR-driven dedifferentiation is associated with poor prognosis and therapy resistance in advanced human LUAD, underscoring ISR inhibition as a promising therapeutic strategy to disrupt tumor evolution and counteract disease progression.
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7
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Elder E, Lemieux A, Legault LM, Caron M, Bertrand-Lehouillier V, Dupas T, Raynal NM, Bourque G, Sinnett D, Gévry N, McGraw S. Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells. Nucleic Acids Res 2025; 53:gkaf130. [PMID: 39997223 PMCID: PMC11851107 DOI: 10.1093/nar/gkaf130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 12/27/2024] [Accepted: 02/11/2025] [Indexed: 02/26/2025] Open
Abstract
Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. However, only partial reversal could be achieved. Extensive changes in DNA methylation, histone modifications, and gene expression were detected, along with transposable element derepression and genomic instability. Reduction of cellular size, complexity, and proliferation rate were observed, as well as lasting effects in germ layer lineages and embryoid bodies. Interestingly, by analyzing the impact on imprinted regions, we uncovered 20 regions exhibiting imprinted-like signatures. Notably, while many permanent effects persisted throughout Dnmt1 inactivation and rescue, others arose from the rescue intervention. Lastly, rescuing DNMT1 after differentiation initiation worsened outcomes, reinforcing the need for early intervention. Our findings highlight the far-reaching functions of DNMT1 and provide valuable perspectives on the repercussions of epigenetic perturbations during early development and the challenges of rescue interventions.
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Affiliation(s)
- Elizabeth Elder
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
| | - Anthony Lemieux
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
| | - Lisa-Marie Legault
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
| | - Maxime Caron
- University of Montreal Hospital Research Centre, Montreal, Quebec, H2X 0A9, Canada
| | - Virginie Bertrand-Lehouillier
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
| | - Thomas Dupas
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
- Department of Obstetrics and Gynecology, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Noël J-M Raynal
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
- Department of Pharmacology and Physiology, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1Y2, Canada
- McGill Genome Centre, Montreal, Quebec, H3A 0G1, Canada
| | - Daniel Sinnett
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, H3T 1C5, Canada
| | - Nicolas Gévry
- Department of Biology, University of Sherbrooke, Sherbrooke, Quebec, J1K 2R1, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
- Azrieli Research Centre of Sainte-Justine University Hospital, Montreal, Quebec, H3T 1C5, Canada
- Department of Obstetrics and Gynecology, University of Montreal, Montreal, Quebec, H3T 1J4, Canada
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8
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Liang X, Guo J, Wang X, Luo B, Fu R, Chen H, Yang Y, Jin Z, Lin C, Zang A, Jia Y, Feng L, Wang L. Overexpression of ornithine decarboxylase 1 mediates the immune-deserted microenvironment and poor prognosis in diffuse large B-cell lymphoma. JOURNAL OF THE NATIONAL CANCER CENTER 2025; 5:57-74. [PMID: 40040873 PMCID: PMC11873660 DOI: 10.1016/j.jncc.2024.10.001] [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: 10/13/2023] [Revised: 10/08/2024] [Accepted: 10/15/2024] [Indexed: 03/06/2025] Open
Abstract
Background Previous researches mainly focused on whether cancer stem cells exist in diffuse large B-cell lymphoma (DLBCL). However, subgroups with dismal prognosis and stem cell-like characteristics have been overlooked. Methods Using large scale data (n = 2133), we conducted machine learning algorithms to identify a high risk DLBCL subgroup with stem cell-like features, and then investigated the potential mechanisms in shaping this subgroup using transcriptome, genome and single-cell RNA-seq data, and in vitro experiments. Results We identified a high-risk subgroup (25.6 % of DLBCL) with stem cell-like characteristics and dismal prognosis. This high-risk group (HRG) was featured by upregulation of key enzyme (ODC1) in polyamine metabolism and cold tumor microenvironment (TME), and had a poor prognosis with lower 3-year overall survival (OS) (54.3 % vs. 83.6 %, P < 0.0001) and progression-free survival (PFS) (42.8 % vs. 74.7 %, P < 0.0001) rates compared to the low-risk group. HRG also exhibited malignant proliferative phenotypes similar to Burkitt lymphoma. Patients with MYC rearrangement, double-hit, double-expressors, or complete remission might have either favorable or poor prognosis, which could be further distinguished by our risk stratification model. Genomic analysis revealed widespread copy number losses in the chemokine and interferon coding regions 8p23.1 and 9p21.3 in HRG. We identified ODC1 as a therapeutic vulnerability for HRG-DLBCL. Single-cell analysis and in vitro experiments demonstrated that ODC1 overexpression enhanced DLBCL cell proliferation and drove macrophage polarization towards the M2 phenotype. Conversely, ODC1 inhibition reduced DLBCL cell proliferation, induced cell cycle arrest and apoptosis, and promoted macrophage polarization towards the M1 phenotype. Finally, we developed a comprehensive database of DLBCL for clinical application. Conclusions Our study effectively advances the precise risk stratification of DLBCL and reveals that ODC1 and immune-deserted microenvironment jointly shape a group of DLBCL patients with stem cell-like features. Targeting ODC1 regulates immunotherapies in DLBCL, offering new insights for DLBCL treatment.
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Affiliation(s)
- Xiaojie Liang
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jia Guo
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaofang Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Baiwei Luo
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ruiying Fu
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Haiying Chen
- The First School of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Yunong Yang
- The First School of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Zhihao Jin
- The First School of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Chaoran Lin
- The First School of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Aimin Zang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Youchao Jia
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Lin Feng
- School of Mechanical Engineering & Automation, Beihang University, Beijing, China
| | - Liang Wang
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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9
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Faraji F, Ramirez SI, Clubb LM, Sato K, Burghi V, Hoang TS, Officer A, Anguiano Quiroz PY, Galloway WMG, Mikulski Z, Medetgul-Ernar K, Marangoni P, Jones KB, Cao Y, Molinolo AA, Kim K, Sakaguchi K, Califano JA, Smith Q, Goren A, Klein OD, Tamayo P, Gutkind JS. YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution. Nat Commun 2025; 16:498. [PMID: 39779672 PMCID: PMC11711616 DOI: 10.1038/s41467-024-55660-6] [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: 08/24/2024] [Accepted: 12/18/2024] [Indexed: 01/11/2025] Open
Abstract
Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ spatiotemporally controlled oncogene activation and tumor suppressor inhibition together with multiomics to unveil the processes underlying oral epithelial progenitor cell reprogramming into tumor initiating cells at single cell resolution. Tumor initiating cells displayed a distinct stem-like state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal invasive gene programs. YAP-mediated tumor initiating cell programs included activation of oncogenic transcriptional networks and mTOR signaling, and recruitment of myeloid cells to the invasive front contributing to tumor infiltration. Tumor initiating cell transcriptional programs are conserved in human head and neck cancer and associated with poor patient survival. These findings illuminate processes underlying cancer initiation at single cell resolution, and identify candidate targets for early cancer detection and prevention.
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Affiliation(s)
- Farhoud Faraji
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego Health, La Jolla, CA, 92037, USA.
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA.
| | - Sydney I Ramirez
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego Health, La Jolla, CA, 92093, USA
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Lauren M Clubb
- University of California San Diego, Biomedical Sciences Graduate Program, La Jolla, CA, 92093, USA
| | - Kuniaki Sato
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
| | - Valeria Burghi
- Department of Pharmacology, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Thomas S Hoang
- University of California San Diego, Biomedical Sciences Graduate Program, La Jolla, CA, 92093, USA
| | - Adam Officer
- University of California San Diego, Bioinformatics and Systems Biology Graduate Program, La Jolla, CA, 92093, USA
| | - Paola Y Anguiano Quiroz
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
| | - William M G Galloway
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | | | - Kate Medetgul-Ernar
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
| | - Pauline Marangoni
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kyle B Jones
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Yuwei Cao
- University of California San Diego, Biomedical Sciences Graduate Program, La Jolla, CA, 92093, USA
| | - Alfredo A Molinolo
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
| | - Kenneth Kim
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | | | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego Health, La Jolla, CA, 92037, USA
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
| | - Quinton Smith
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, 92697, USA
| | - Alon Goren
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, 90048, USA
| | - Pablo Tamayo
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Novel Therapeutics, University of California San Diego, La Jolla, CA, 92037, USA
| | - J Silvio Gutkind
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92037, USA.
- Department of Pharmacology, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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10
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Pian LL, Song MH, Wang TF, Qi L, Peng TL, Xie KP. Identification and analysis of pancreatic intraepithelial neoplasia: opportunities and challenges. Front Endocrinol (Lausanne) 2025; 15:1401829. [PMID: 39839479 PMCID: PMC11746065 DOI: 10.3389/fendo.2024.1401829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 12/17/2024] [Indexed: 01/23/2025] Open
Abstract
Pancreatic intraepithelial neoplasia (PanIN) is the most common precursor lesion of pancreatic ductal adenocarcinoma (PDAC), which has poor prognosis with a short median overall survival of 6-12 months and a low 5-year survival rate of approximately 3%. It is crucial to remove PanIN lesions to prevent the development of invasive PDAC, as PDAC spreads rapidly outside the pancreas. This review aims to provide the latest knowledge on PanIN risk, pathology, cellular origin, genetic susceptibility, and diagnosis, while identifying research gaps that require further investigation in this understudied area of precancerous lesions. PanINs are classified into PanIN 1, PanIN 2, and PanIN 3, with PanIN 3 having the highest likelihood of developing into invasive PDAC. Differentiating between PanIN 2 and PanIN 3 is clinically significant. Genetic alterations found in PDAC are also present in PanIN and increase with the grade of PanIN. Imaging methods alone are insufficient for distinguishing PanIN, necessitating the use of genetic and molecular tests for identification. In addition, metabolomics technologies and miRNAs are playing an increasingly important role in the field of cancer diagnosis, offering more possibilities for efficient identification of PanIN. Although detecting and stratifying the risk of PanIN poses challenges, the combined utilization of imaging, genetics, and metabolomics holds promise for improving patient survival in this field.
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Affiliation(s)
- Ling-ling Pian
- School of Medicine, The South China University of Technology, Guangzhou, Guangdong, China
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, The Sixth Clinical Medical School, Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, Guangdong, China
| | - Mei-hui Song
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, The Sixth Clinical Medical School, Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, Guangdong, China
| | - Teng-fei Wang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, The Sixth Clinical Medical School, Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, Guangdong, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, China
| | - Ling Qi
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, The Sixth Clinical Medical School, Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, Guangdong, China
| | - Tie-li Peng
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, The Sixth Clinical Medical School, Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, Guangdong, China
| | - Ke-ping Xie
- School of Medicine, The South China University of Technology, Guangzhou, Guangdong, China
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11
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Sarkar H, Lee E, Lopez-Darwin SL, Kang Y. Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges. Genes Dev 2025; 39:64-85. [PMID: 39496456 PMCID: PMC11789490 DOI: 10.1101/gad.351956.124] [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: 11/06/2024]
Abstract
Cancer stem cells (CSCs) often exhibit stem-like attributes that depend on an intricate stemness-promoting cellular ecosystem within their niche. The interplay between CSCs and their niche has been implicated in tumor heterogeneity and therapeutic resistance. Normal stem cells (NSCs) and CSCs share stemness features and common microenvironmental components, displaying significant phenotypic and functional plasticity. Investigating these properties across diverse organs during normal development and tumorigenesis is of paramount research interest and translational potential. Advancements in next-generation sequencing (NGS), single-cell transcriptomics, and spatial transcriptomics have ushered in a new era in cancer research, providing high-resolution and comprehensive molecular maps of diseased tissues. Various spatial technologies, with their unique ability to measure the location and molecular profile of a cell within tissue, have enabled studies on intratumoral architecture and cellular cross-talk within the specific niches. Moreover, delineation of spatial patterns for niche-specific properties such as hypoxia, glucose deprivation, and other microenvironmental remodeling are revealed through multilevel spatial sequencing. This tremendous progress in technology has also been paired with the advent of computational tools to mitigate technology-specific bottlenecks. Here we discuss how different spatial technologies are used to identify NSCs and CSCs, as well as their associated niches. Additionally, by exploring related public data sets, we review the current challenges in characterizing such niches, which are often hindered by technological limitations, and the computational solutions used to address them.
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Affiliation(s)
- Hirak Sarkar
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton, New Jersey 08544, USA
| | - Eunmi Lee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Sereno L Lopez-Darwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA;
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, New Jersey 08544, USA
- Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
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12
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Meng S, Whitt AG, Eaton JW, Yaddanapudi K, Li C. The efficacy of an embryonic stem cell-based vaccine for lung cancer prevention depends on the undifferentiated state of the stem cells. Sci Rep 2024; 14:32127. [PMID: 39739089 PMCID: PMC11685895 DOI: 10.1038/s41598-024-83932-0] [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: 03/27/2024] [Accepted: 12/18/2024] [Indexed: 01/02/2025] Open
Abstract
Based on the antigenic similarity between tumor cells and embryonic stem cells (ESCs), several recent studies report the use of intact murine ESCs or exosomes from murine ESCs as cancer vaccines. Since the capacity for self-renewal is one of the most specialized properties shared between ESCs and a subset of tumor cells, cancer stem cells (CSCs), we investigated whether the undifferentiated state of murine ESCs is essential for the prophylactic effectiveness of an ESC-based vaccine. The undifferentiated state of ES-D3, a murine ESC line, was essential for their anchorage-independent growth potential. Importantly, differentiation of ES-D3 cells decreased their efficacy in preventing the outgrowth of implanted lung tumors. Furthermore, the long-term cancer-preventive potential of this vaccine was also inhibited by the differentiation of these cells. To examine the antigenicity of the ESC-derived vaccine, we performed combined affinity chromatography shotgun immunoproteomic experiments to identify antigens specific to the whole-cell ES vaccine as well as to the ESC-derived exosome vaccine. Our data demonstrate that antibodies against several lung cancer-associated keratin members were enriched in the serum of vaccinated mice. In summary, these data suggest that the tumor-preventing efficacy of ESC-based vaccine is reliant on the differentiation properties of these stem cells.
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Affiliation(s)
- Shuhan Meng
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- Experimental Therapeutics Group, Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Aaron G Whitt
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- Experimental Therapeutics Group, Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - John W Eaton
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- Experimental Therapeutics Group, Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Kavitha Yaddanapudi
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA.
- Immuno-Oncology Program, Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, USA.
- Division of Immunotherapy, Department of Surgery, University of Louisville, Louisville, KY, USA.
| | - Chi Li
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA.
- Experimental Therapeutics Group, Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, USA.
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13
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Mukherjee A, Kakati RT, Van Alsten S, Laws T, Ebbs AL, Hollern DP, Spanheimer PM, Hoadley KA, Troester MA, Simon JM, Baldwin AS. DAB2IP loss in luminal a breast cancer leads to NF-κB-associated aggressive oncogenic phenotypes. JCI Insight 2024; 9:e171705. [PMID: 39418101 PMCID: PMC11623953 DOI: 10.1172/jci.insight.171705] [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: 04/26/2023] [Accepted: 10/11/2024] [Indexed: 10/19/2024] Open
Abstract
Despite proven therapy options for estrogen receptor-positive (ER+) breast tumors, a substantial number of patients with ER+ breast cancer exhibit relapse with associated metastasis. Loss of expression of RasGAPs leads to poor outcomes in several cancers, including breast cancer. Mining the The Cancer Genome Atlas (TCGA) breast cancer RNA-Seq dataset revealed that low expression of the RasGAP DAB2IP was associated with a significant decrease in relapse-free survival in patients with Luminal A breast cancer. Immunostaining demonstrated that DAB2IP loss occurred in grade 2 tumors and higher. Consistent with this, genes upregulated in DAB2IP-low Luminal A tumors were shared with more aggressive tumor subtypes and were associated with proliferation, metastasis, and altered ER signaling. Low DAB2IP expression in ER+ breast cancer cells was associated with increased proliferation, enhanced stemness phenotypes, and activation of IKK, the upstream regulator of the transcription factor NF-κB. Integrating cell-based ChIP-Seq with motif analysis and TCGA RNA-Seq data, we identified a set of candidate NF-κB target genes upregulated with loss of DAB2IP linked with several oncogenic phenotypes, including altered RNA processing. This study provides insight into mechanisms associated with aggressiveness and recurrence within a subset of the typically less aggressive Luminal A breast cancer intrinsic subtype.
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Affiliation(s)
- Angana Mukherjee
- UNC Lineberger Comprehensive Cancer, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine and
| | - Rasha T. Kakati
- Division of Surgical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sarah Van Alsten
- UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tyler Laws
- UNC Lineberger Comprehensive Cancer, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aaron L. Ebbs
- UNC Lineberger Comprehensive Cancer, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Philip M. Spanheimer
- Division of Surgical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Melissa A. Troester
- UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy M. Simon
- Department of Genetics and
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Data Science, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Albert S. Baldwin
- UNC Lineberger Comprehensive Cancer, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina, USA
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14
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Masciale V, Banchelli F, Grisendi G, Samarelli AV, Raineri G, Rossi T, Zanoni M, Cortesi M, Bandini S, Ulivi P, Martinelli G, Stella F, Dominici M, Aramini B. The molecular features of lung cancer stem cells in dedifferentiation process-driven epigenetic alterations. J Biol Chem 2024; 300:107994. [PMID: 39547513 PMCID: PMC11714729 DOI: 10.1016/j.jbc.2024.107994] [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: 03/23/2024] [Revised: 10/30/2024] [Accepted: 11/05/2024] [Indexed: 11/17/2024] Open
Abstract
Cancer stem cells (CSCs) may be dedifferentiated somatic cells following oncogenic processes, representing a subpopulation of cells able to promote tumor growth with their capacities for proliferation and self-renewal, inducing lineage heterogeneity, which may be a main cause of resistance to therapies. It has been shown that the "less differentiated process" may have an impact on tumor plasticity, particularly when non-CSCs may dedifferentiate and become CSC-like. Bidirectional interconversion between CSCs and non-CSCs has been reported in other solid tumors, where the inflammatory stroma promotes cell reprogramming by enhancing Wnt signaling through nuclear factor kappa B activation in association with intracellular signaling, which may induce cells' pluripotency, the oncogenic transformation can be considered another important aspect in the acquisition of "new" development programs with oncogenic features. During cell reprogramming, mutations represent an initial step toward dedifferentiation, in which tumor cells switch from a partially or terminally differentiated stage to a less differentiated stage that is mainly manifested by re-entry into the cell cycle, acquisition of a stem cell-like phenotype, and expression of stem cell markers. This phenomenon typically shows up as a change in the form, function, and pattern of gene and protein expression, and more specifically, in CSCs. This review would highlight the main epigenetic alterations, major signaling pathways and driver mutations in which CSCs, in tumors and specifically, in lung cancer, could be involved, acting as key elements in the differentiation/dedifferentiation process. This would highlight the main molecular mechanisms which need to be considered for more tailored therapies.
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Affiliation(s)
- Valentina Masciale
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Federico Banchelli
- Department of Statistical Sciences "Paolo Fortunati", Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Giulia Grisendi
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Anna Valeria Samarelli
- Laboratory of and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Giulia Raineri
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michele Zanoni
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Cortesi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Sara Bandini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Franco Stella
- Thoracic Surgery Unit, Department of Medical and Surgical Sciences-DIMEC of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy; Division of Oncology, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Beatrice Aramini
- Thoracic Surgery Unit, Department of Medical and Surgical Sciences-DIMEC of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy.
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15
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Pedrosa P, Zhang Z, Nuñez-Quintela V, Macias D, Ge J, Denholm M, Dyas A, Estevez-Souto V, Lado-Fernandez P, Gonzalez P, Gomez M, Martin JE, Da Silva-Alvarez S, Collado M, Muñoz-Espín D. Inhibition of lung tumorigenesis by transient reprogramming in cancer cells. Cell Death Dis 2024; 15:857. [PMID: 39587064 PMCID: PMC11589828 DOI: 10.1038/s41419-024-07207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 10/25/2024] [Accepted: 10/31/2024] [Indexed: 11/27/2024]
Abstract
Oncogenic transformation and Oct4, Sox2, Klf4 and c-Myc (OSKM)-mediated induction of pluripotency are two independent and incompatible cellular fates. While continuous expression of OSKM can convert normal somatic cells into teratogenic pluripotent cells, it remains speculative what is the impact of transient OSKM expression in cancer cells. Here, we find that OSKM expression limits the growth of transformed lung cells by inducing apoptosis and senescence. We identify Oct4 and Klf4 as the main individual reprogramming factors responsible for this effect. Mechanistically, the induction of cell cycle inhibitor p21 downstream of the reprogramming factors acts as mediator of cell death and senescence. Using a variety of in vivo systems, including allografts, orthotopic transplantation and KRAS-driven lung cancer mouse models, we demonstrate that transient reprogramming by OSKM expression in cancer cells impairs tumor growth and reduces tumor burden. Altogether, our results show that the induction of transient reprogramming in cancer cells is antitumorigenic opening novel potential therapeutic avenues in oncology.
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Affiliation(s)
- Pablo Pedrosa
- Cell Senescence, Cancer and Aging Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Zhenguang Zhang
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Victor Nuñez-Quintela
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - David Macias
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jianfeng Ge
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mary Denholm
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anna Dyas
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Valentin Estevez-Souto
- Cell Senescence, Cancer and Aging Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Patricia Lado-Fernandez
- Cell Senescence, Cancer and Aging Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Patricia Gonzalez
- Histopathology Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Maria Gomez
- Histopathology Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jose Ezequiel Martin
- CMDL, Department of Oncology, SMCL, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Sabela Da Silva-Alvarez
- Cell Senescence, Cancer and Aging Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Manuel Collado
- Cell Senescence, Cancer and Aging Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
- Department of Immunology and Oncology (DIO), Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Daniel Muñoz-Espín
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK.
- CRUK Cambridge Centre Thoracic Cancer Programme, University of Cambridge, Cambridge, UK.
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16
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Bai X, Liu J, Zhou S, Wu L, Feng X, Zhang P. METTL14 suppresses the expression of YAP1 and the stemness of triple-negative breast cancer. J Exp Clin Cancer Res 2024; 43:307. [PMID: 39563370 PMCID: PMC11577812 DOI: 10.1186/s13046-024-03225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 11/04/2024] [Indexed: 11/21/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) has pronounced stemness that is associated with relapse. N6-methyladenosine (m6A) plays a crucial role in shaping cellular behavior by modulating transcript expression. However, the role of m6A in TNBC stemness, as well as the mechanisms governing its abundance, has yet to be elucidated. METHODS We analyzed proteomic and transcriptomic data derived from breast cancer cohorts, with an emphasis on m6A regulators. To unravel the role of m6A in TNBC, we employed RNA sequencing, methylated RNA immunoprecipitation sequencing, RNA immunoprecipitation, chromatin immunoprecipitation, and luciferase reporter assays with mesenchymal stem-like (MSL) TNBC models. The clinical relevance was validated using human tissue microarrays and publicly accessible databases. RESULTS Our findings indicate that the global level of m6A modification in MSL TNBC is downregulated primarily due to the loss of methyltransferase-like 14 (METTL14). The diminished m6A modification is crucial for the maintenance of TNBC stemness, as it increases the expression of yes-associated protein 1 (YAP1) by blocking YTH domain-containing family protein 2 (YTHDF2)-mediated transcript decay, thereby promoting the activation of Hippo-independent YAP1 signaling. YAP1 is essential for sustaining the stemness regulated by METTL14. Furthermore, we demonstrated that the loss of METTL14 expression results from lysine-specific demethylase 1 (LSD1)-mediated removal of histone H3 lysine 4 methylation at the promoter region, which is critical for LSD1-driven stemness in TNBC. CONCLUSION These findings present an epi-transcriptional mechanism that maintains Hippo-independent YAP1 signaling and plays a role in preserving the undifferentiated state of TNBC, which indicates the potential for targeting the LSD1-METTL14 axis to address TNBC stemness.
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Affiliation(s)
- Xupeng Bai
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
| | - Jiarui Liu
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Shujie Zhou
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Lingzhi Wu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiaojie Feng
- Department of Gynecologic Oncology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Pumin Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310018, Zhejiang, China.
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17
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Pavlova S, Fab L, Dzarieva F, Ryabova A, Revishchin A, Panteleev D, Antipova O, Usachev D, Kopylov A, Pavlova G. Unite and Conquer: Association of Two G-Quadruplex Aptamers Provides Antiproliferative and Antimigration Activity for Cells from High-Grade Glioma Patients. Pharmaceuticals (Basel) 2024; 17:1435. [PMID: 39598347 PMCID: PMC11597096 DOI: 10.3390/ph17111435] [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: 09/21/2024] [Revised: 10/23/2024] [Accepted: 10/24/2024] [Indexed: 11/29/2024] Open
Abstract
Background: High-grade gliomas remain a virtually incurable form of brain cancer. Current therapies are unable to completely eradicate the tumor, and the tumor cells that survive chemotherapy or radiation therapy often become more aggressive and resistant to further treatment, leading to inevitable relapses. While the antiproliferative effects of new therapeutic molecules are typically the primary focus of research, less attention is given to their influence on tumor cell migratory activity, which can play a significant role in recurrence. A potential solution may lie in the synergistic effects of multiple drugs on the tumor. Objectives: In this study, we investigated the effect of combined exposure to bi-(AID-1-T), an anti-proliferative aptamer, and its analog bi-(AID-1-C), on the migratory activity of human GBM cells. Results: We examined the effects of various sequences of adding bi-(AID-1-T) and bi-(AID-1-C) on five human GBM cell cultures. Our findings indicate that certain sequences significantly reduced the ability of tumor cells to migrate and proliferate. Additionally, the expression of Nestin, PARP1, L1CAM, Caveolin-1, and c-Myc was downregulated in human GBM cells that survived exposure, suggesting that the treatment had a persistent antitumor effect on these cells.
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Affiliation(s)
- Svetlana Pavlova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Lika Fab
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Fatima Dzarieva
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Anastasia Ryabova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander Revishchin
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Dmitriy Panteleev
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Olga Antipova
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry Usachev
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Alexey Kopylov
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Galina Pavlova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
- Institution N. N. Burdenko National Medical Research Center of Neurosurgery of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia
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18
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Faraji F, Ramirez SI, Clubb L, Sato K, Burghi V, Hoang TS, Officer A, Anguiano Quiroz PY, Galloway WM, Mikulski Z, Medetgul-Ernar K, Marangoni P, Jones KB, Molinolo AA, Kim K, Sakaguchi K, Califano JA, Smith Q, Goren A, Klein OD, Tamayo P, Gutkind JS. YAP-Driven Oral Epithelial Stem Cell Malignant Reprogramming at Single Cell Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.24.550427. [PMID: 37546810 PMCID: PMC10402053 DOI: 10.1101/2023.07.24.550427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ spatiotemporally controlled oncogene activation and tumor suppressor inhibition together with multiomics to unveil the processes underlying oral epithelial progenitor cell reprogramming into tumor initiating cells (TIC) at single cell resolution. TIC displayed a distinct stem-like state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal (pEMT) invasive gene programs. YAP-mediated TIC programs included the activation of oncogenic transcriptional networks and mTOR signaling, and the recruitment of myeloid cells to the invasive front contributing to tumor infiltration. TIC transcriptional programs are conserved in human head and neck cancer and associated with poor patient survival. These findings illuminate processes underlying cancer initiation at single cell resolution, and identify candidate targets for early cancer detection and prevention.
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19
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Rosen BP, Li QV, Cho HS, Liu D, Yang D, Graff S, Yan J, Luo R, Verma N, Damodaran JR, Kale HT, Kaplan SJ, Beer MA, Sidoli S, Huangfu D. Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness. Nat Commun 2024; 15:8966. [PMID: 39419994 PMCID: PMC11487130 DOI: 10.1038/s41467-024-53284-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/08/2024] [Indexed: 10/19/2024] Open
Abstract
Pluripotent stem cells have remarkable self-renewal capacity: the ability to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into almost any cell type in the body. To investigate the interplay between these two aspects of self-renewal, we perform four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSCs and the dissolution of primed pluripotent identity during early differentiation. These screens distinguish genes with distinct roles in pluripotency regulation, including mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control pluripotent identity during early differentiation. We further identify a core set of genes controlling both stem cell fitness and pluripotent identity, including a network of chromatin factors. Here, unbiased screening and comparative analyses disentangle two interconnected aspects of pluripotency, provide a valuable resource for exploring pluripotent stem cell identity versus cell fitness, and offer a framework for categorizing gene function.
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Affiliation(s)
- Bess P Rosen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Qing V Li
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tessera Therapeutics, Somerville, MA, USA
| | - Hyein S Cho
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Dingyu Liu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Sarah Graff
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jielin Yan
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nipun Verma
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Hanuman T Kale
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Samuel J Kaplan
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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20
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Jiang W, Liu L, Wang M, Li X, Zhou T, Hou X, Qiao L, Chen C, Zuo D, Liu J, Ren L. KLF15 suppresses stemness of pancreatic cancer by decreasing USP21-mediated Nanog stability. Cell Mol Life Sci 2024; 81:417. [PMID: 39367978 PMCID: PMC11455850 DOI: 10.1007/s00018-024-05442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/08/2024] [Accepted: 08/22/2024] [Indexed: 10/07/2024]
Abstract
The existence of cancer stem cells (CSCs) in pancreatic ductal adenocarcinoma (PDAC) is considered to be the key factor for metastasis and chemoresistance. Thus, novel therapeutic strategies for eradicating CSCs are urgently needed. Here we aimed to explore the role of KLF15 in stemness and the feasibility of using KLF15 to inhibit CSCs and improve chemotherapy sensitivity in PDAC. In this study, we report that KLF15 is negatively associated with poor survival and advanced pathological staging of PDAC. Moreover, tumorous KLF15 suppresses the stemness of PDAC by promoting the degradation of Nanog, and KLF15 directly interacts with Nanog, inhibiting interaction between Nanog with USP21. We also demonstrate that the KLF15/Nanog complex inhibit the stemness in vivo and in PDX cells. Tazemetostat suppresses stemness and sensitizes PDAC cells to gemcitabine by promoting KLF15 expression in PDAC. In summary, the findings of our study confirm the value of KLF15 level in diagnosis and prognosis of PDAC, it is the first time to explore the inhibition role of KLF15 in stemness of PDAC and the regulation mechanism of Nanog, contributing to provide a new therapeutic strategy that using Tazemetostat sensitizes PDAC cells to gemcitabine by promoting KLF15 expression for PDAC.
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Affiliation(s)
- Wenna Jiang
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China
| | - Lin Liu
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China
| | - Meng Wang
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China
| | - Xueyang Li
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Tianxing Zhou
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Xupeng Hou
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Lu Qiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin, China
| | - Chong Chen
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China
| | - Duo Zuo
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China
| | - Jing Liu
- Department of Breast Oncoplastic Surgery, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Li Ren
- Department of Clinical Laboratory, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Hexi District, Huanhuxi Road, Tianjin, 300060, China.
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21
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Peretz CAC, Kennedy VE, Walia A, Delley CL, Koh A, Tran E, Clark IC, Hayford CE, D'Amato C, Xue Y, Fontanez KM, May-Zhang AA, Smithers T, Agam Y, Wang Q, Dai HP, Roy R, Logan AC, Perl AE, Abate A, Olshen A, Smith CC. Multiomic single cell sequencing identifies stemlike nature of mixed phenotype acute leukemia. Nat Commun 2024; 15:8191. [PMID: 39294124 PMCID: PMC11411136 DOI: 10.1038/s41467-024-52317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 08/30/2024] [Indexed: 09/20/2024] Open
Abstract
Despite recent work linking mixed phenotype acute leukemia (MPAL) to certain genetic lesions, specific driver mutations remain undefined for a significant proportion of patients and no genetic subtype is predictive of clinical outcomes. Moreover, therapeutic strategy for MPAL remains unclear, and prognosis is overall poor. We performed multiomic single cell profiling of 14 newly diagnosed adult MPAL patients to characterize the inter- and intra-tumoral transcriptional, immunophenotypic, and genetic landscapes of MPAL. We show that neither genetic profile nor transcriptome reliably correlate with specific MPAL immunophenotypes. Despite this, we find that MPAL blasts express a shared stem cell-like transcriptional profile indicative of high differentiation potential. Patients with the highest differentiation potential demonstrate inferior survival in our dataset. A gene set score, MPAL95, derived from genes highly enriched in the most stem-like MPAL cells, is applicable to bulk RNA sequencing data and is predictive of survival in an independent patient cohort, suggesting a potential strategy for clinical risk stratification.
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Affiliation(s)
- Cheryl A C Peretz
- Division of Hematology and Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Vanessa E Kennedy
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Anushka Walia
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Andrew Koh
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Tran
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iain C Clark
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | | | | | - Yi Xue
- Fluent Biosciences Inc., Watertown, MA, USA
| | | | | | | | - Yigal Agam
- Fluent Biosciences Inc., Watertown, MA, USA
| | - Qian Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China
| | - Hai-Ping Dai
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aaron C Logan
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexander E Perl
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Catherine C Smith
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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22
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Maciejewski K, Giers M, Oleksiewicz U, Czerwinska P. The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors. Int J Mol Sci 2024; 25:7841. [PMID: 39063083 PMCID: PMC11277355 DOI: 10.3390/ijms25147841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/07/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Dysregulation of histone deacetylases (HDACs) is closely associated with cancer development and progression. Here, we comprehensively analyzed the association between all HDAC family members and several clinicopathological and molecular traits of solid tumors across 22 distinct tumor types, focusing primarily on cancer stemness and immunity. To this end, we used publicly available TCGA data and several bioinformatic tools (i.e., GEPIA2, TISIDB, GSCA, Enrichr, GSEA). Our analyses revealed that class I and class II HDAC proteins are associated with distinct cancer phenotypes. The transcriptomic profiling indicated that class I HDAC members, including HDAC2, are positively associated with cancer stemness, while class IIA HDAC proteins, represented by HDAC7, show a negative correlation to cancer stem cell-like phenotypes in solid tumors. In contrast to tumors with high amounts of HDAC7 proteins, the transcriptome signatures of HDAC2-overexpressing cancers are significantly enriched with biological terms previously determined as stemness-associated genes. Moreover, high HDAC2-expressing tumors are depleted with immune-related processes, and HDAC2 expression correlates with tumor immunosuppressive microenvironments. On the contrary, HDAC7 upregulation is significantly associated with enhanced immune responses, followed by enriched infiltration of CD4+ and CD8+ T cells. This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors.
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Affiliation(s)
- Kacper Maciejewski
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
| | - Marek Giers
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Patrycja Czerwinska
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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23
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Chakraborty A, Yang C, Kresak JL, Silver AJ, Feier D, Tian G, Andrews M, Sobanjo OO, Hodge ED, Engelbart MK, Huang J, Harrison JK, Sarkisian MR, Mitchell DA, Deleyrolle LP. KR158 Spheres Harboring Slow-Cycling Cells Recapitulate High-Grade Glioma Features in an Immunocompetent System. Cells 2024; 13:938. [PMID: 38891070 PMCID: PMC11171638 DOI: 10.3390/cells13110938] [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: 03/04/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) poses a significant challenge in clinical oncology due to its aggressive nature, heterogeneity, and resistance to therapies. Cancer stem cells (CSCs) play a critical role in GBM, particularly in treatment resistance and tumor relapse, emphasizing the need to comprehend the mechanisms regulating these cells. Also, their multifaceted contributions to the tumor microenvironment (TME) underline their significance, driven by their unique properties. This study aimed to characterize glioblastoma stem cells (GSCs), specifically slow-cycling cells (SCCs), in an immunocompetent murine GBM model to explore their similarities with their human counterparts. Using the KR158 mouse model, we confirmed that SCCs isolated from this model exhibited key traits and functional properties akin to human SCCs. KR158 murine SCCs, expanded in the gliomasphere assay, demonstrated sphere forming ability, self-renewing capacity, positive tumorigenicity, enhanced stemness and resistance to chemotherapy. Together, our findings validate the KR158 murine model as a framework to investigate GSCs and SCCs in GBM pathology, and explore specifically the SCC-immune system communications, understand their role in disease progression, and evaluate the effect of therapeutic strategies targeting these specific connections.
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Affiliation(s)
- Avirup Chakraborty
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
| | - Changlin Yang
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
| | - Jesse L. Kresak
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Aryeh J. Silver
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
| | - Diana Feier
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
| | - Guimei Tian
- Department of Surgery, University of Florida, Gainesville, FL 32610, USA
| | - Michael Andrews
- College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Olusegun O. Sobanjo
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
| | - Ethan D. Hodge
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
| | - Mia K. Engelbart
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
| | - Jianping Huang
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
| | - Jeffrey K. Harrison
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32603, USA
| | - Matthew R. Sarkisian
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Duane A. Mitchell
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
| | - Loic P. Deleyrolle
- Adam Michael Rosen Neuro-Oncology Laboratories, Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA (A.J.S.)
- Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL 32608, USA
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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24
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Sala-Hamrick KE, Tapaswi A, Polemi KM, Nguyen VK, Colacino JA. High-Throughput Transcriptomics of Nontumorigenic Breast Cells Exposed to Environmentally Relevant Chemicals. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:47002. [PMID: 38568856 PMCID: PMC10990114 DOI: 10.1289/ehp12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND There is a suite of chemicals, including metals, pesticides, and personal care product compounds, which are commonly detected at high levels in US Center for Disease Control's National Health and Nutrition Examination Survey (NHANES) chemical biomarker screens. Whether these chemicals influence development of breast cancer is not well understood. OBJECTIVES The objectives were to perform an unbiased concentration-dependent assessment of these chemicals, to quantify differences in cancer-specific genes and pathways, to describe if these differences occur at human population-relevant concentrations, and to specifically test for differences in markers of stemness and cellular plasticity. METHODS We treated nontumorigenic mammary epithelial cells, MCF10A, with 21 chemicals at four concentrations (25 nM , 250 nM , 2.5 μ M , and 25 μ M ) for 48 h. We conducted RNA-sequencing for these 408 samples, adapting the plexWell plate-based RNA-sequencing method to analyze differences in gene expression. We calculated gene and biological pathway-specific benchmark concentrations (BMCs) using BMDExpress3, identifying differentially expressed genes and generating the best fit benchmark concentration models for each chemical across all genes. We identified enriched biological processes and pathways for each chemical and tested whether chemical exposures change predicted cell type distributions. We contextualized benchmark concentrations relative to human population biomarker concentrations in NHANES. RESULTS We detected chemical concentration-dependent differences in gene expression for thousands of genes. Enrichment and cell type distribution analyses showed benchmark concentration responses correlated with differences in breast cancer-related pathways, including induction of basal-like characteristics for some chemicals, including arsenic, lead, copper, and methyl paraben. Comparison of benchmark data to NHANES chemical biomarker (urine or blood) concentrations indicated an overlap between exposure levels and levels sufficient to cause a gene expression response. DISCUSSION These analyses revealed that many of these 21 chemicals resulted in differences in genes and pathways involved in breast cancer in vitro at human exposure-relevant concentrations. https://doi.org/10.1289/EHP12886.
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Affiliation(s)
| | - Anagha Tapaswi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Katelyn M. Polemi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Vy K. Nguyen
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Program in the Environment, University of Michigan, Ann Arbor, Michigan, USA
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25
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Kang M, Armenteros JJA, Gulati GS, Gleyzer R, Avagyan S, Brown EL, Zhang W, Usmani A, Earland N, Wu Z, Zou J, Fields RC, Chen DY, Chaudhuri AA, Newman AM. Mapping single-cell developmental potential in health and disease with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585637. [PMID: 38562882 PMCID: PMC10983880 DOI: 10.1101/2024.03.19.585637] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cell fate in developmental systems. However, identifying the molecular hallmarks of potency - the capacity of a cell to differentiate into other cell types - has remained challenging. Here, we introduce CytoTRACE 2, an interpretable deep learning framework for characterizing potency and differentiation states on an absolute scale from scRNA-seq data. Across 31 human and mouse scRNA-seq datasets encompassing 28 tissue types, CytoTRACE 2 outperformed existing methods for recovering experimentally determined potency levels and differentiation states covering the entire range of cellular ontogeny. Moreover, it reconstructed the temporal hierarchy of mouse embryogenesis across 62 timepoints; identified pan-tissue expression programs that discriminate major potency levels; and facilitated discovery of cellular phenotypes in cancer linked to survival and immunotherapy resistance. Our results illuminate a fundamental feature of cell biology and provide a broadly applicable platform for delineating single-cell differentiation landscapes in health and disease.
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26
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Wu T, Chen Y, You Q, Jiang Z, Chen X. Targeting bromodomian-containing protein 8 (BRD8): An advanced tool to interrogate BRD8. Eur J Med Chem 2024; 268:116271. [PMID: 38401187 DOI: 10.1016/j.ejmech.2024.116271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Epigenetic modifications play crucial roles in physiological processes, including cell differentiation, proliferation, and death. Bromodomain/Brd-containing proteins (BCPs) regulate abnormal gene expression in various diseases by recognizing the lysine-ε-N-acetylated residues (KAc) or by acting as transcriptional co-activators. Small molecule inhibitors targeting BCPs offer an attractive strategy for modulating aberrant gene expression. Besides the extensive research on the bromodomain and extra-terminal (BET) domain family proteins, the non-BET proteins have gained increasing attention. Bromodomain containing protein 8 (BRD8), a reader of KAc and co-activator of nuclear receptors (NRs), plays a key role in various cancers. This review provides a comprehensive analysis of the structure, disease-related functions, and inhibitor development of BRD8. Opportunities and challenges for future studies targeting BRD8 in disease treatment are discussed.
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Affiliation(s)
- Tingting Wu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yali Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xuetao Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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27
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Xiong G, Xie N, Nie M, Ling R, Yun B, Xie J, Ren L, Huang Y, Wang W, Yi C, Zhang M, Xu X, Zhang C, Zou B, Zhang L, Liu X, Huang H, Chen D, Cao W, Wang C. Single-cell transcriptomics reveals cell atlas and identifies cycling tumor cells responsible for recurrence in ameloblastoma. Int J Oral Sci 2024; 16:21. [PMID: 38424060 PMCID: PMC10904398 DOI: 10.1038/s41368-024-00281-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 03/02/2024] Open
Abstract
Ameloblastoma is a benign tumor characterized by locally invasive phenotypes, leading to facial bone destruction and a high recurrence rate. However, the mechanisms governing tumor initiation and recurrence are poorly understood. Here, we uncovered cellular landscapes and mechanisms that underlie tumor recurrence in ameloblastoma at single-cell resolution. Our results revealed that ameloblastoma exhibits five tumor subpopulations varying with respect to immune response (IR), bone remodeling (BR), tooth development (TD), epithelial development (ED), and cell cycle (CC) signatures. Of note, we found that CC ameloblastoma cells were endowed with stemness and contributed to tumor recurrence, which was dominated by the EZH2-mediated program. Targeting EZH2 effectively eliminated CC ameloblastoma cells and inhibited tumor growth in ameloblastoma patient-derived organoids. These data described the tumor subpopulation and clarified the identity, function, and regulatory mechanism of CC ameloblastoma cells, providing a potential therapeutic target for ameloblastoma.
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Affiliation(s)
- Gan Xiong
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Nan Xie
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Min Nie
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bokai Yun
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jiaxiang Xie
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Linlin Ren
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yaqi Huang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Wenjin Wang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Chen Yi
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Ming Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xiuyun Xu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Caihua Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Leitao Zhang
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiqiang Liu
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongzhang Huang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Demeng Chen
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- Department of Oral and Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Center for Stomatology, National Clinical Research Center for Oral diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China.
| | - Cheng Wang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China.
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28
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Villeneuve C, Hashmi A, Ylivinkka I, Lawson-Keister E, Miroshnikova YA, Pérez-González C, Myllymäki SM, Bertillot F, Yadav B, Zhang T, Matic Vignjevic D, Mikkola ML, Manning ML, Wickström SA. Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture. Nat Cell Biol 2024; 26:207-218. [PMID: 38302719 PMCID: PMC10866703 DOI: 10.1038/s41556-023-01332-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/08/2023] [Indexed: 02/03/2024]
Abstract
Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, which is initiated by the formation of an epithelial invagination-termed placode-that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions and physical compartmentalization of the placode are unknown. Here we identify a key role for coordinated mechanical forces stemming from contractile, proliferative and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which, in collaboration with polarized epithelial myosin activity, promote elongation and local tissue thickening. These mechanical stresses further enhance compartmentalization of Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodelling locally softens the basement membrane to facilitate a release of pressure on the placode, enabling localized cell divisions, tissue fluidification and epithelial invagination into the underlying mesenchyme. Together, our experiments and modelling identify dynamic cell shape transformations and tissue-scale mechanical cooperation as key factors for orchestrating organ formation.
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Affiliation(s)
- Clémentine Villeneuve
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ali Hashmi
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Irene Ylivinkka
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Yekaterina A Miroshnikova
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carlos Pérez-González
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS, Paris, France
| | - Satu-Marja Myllymäki
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Fabien Bertillot
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bhagwan Yadav
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tao Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | | | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - M Lisa Manning
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, NY, USA.
| | - Sara A Wickström
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
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29
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Chakraborty A, Yang C, Kresak JL, Silver A, Feier D, Tian G, Andrews M, Sobanjo OO, Hodge ED, Engelbart MK, Huang J, Harrison JK, Sarkisian MR, Mitchell DA, Deleyrolle LP. KR158 spheres harboring slow-cycling cells recapitulate GBM features in an immunocompetent system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577279. [PMID: 38501121 PMCID: PMC10945590 DOI: 10.1101/2024.01.26.577279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Glioblastoma (GBM) poses a significant challenge in clinical oncology due to its aggressive nature, heterogeneity, and resistance to therapies. Cancer stem cells (CSCs) play a critical role in GBM, particularly in treatment-resistance and tumor relapse, emphasizing the need to comprehend the mechanisms regulating these cells. Also, their multifaceted contributions to the tumor-microenvironment (TME) underline their significance, driven by their unique properties. This study aimed to characterize glioblastoma stem cells (GSCs), specifically slow-cycling cells (SCCs), in an immunocompetent murine GBM model to explore their similarities with their human counterparts. Using the KR158 mouse model, we confirmed that SCCs isolated from this model exhibited key traits and functional properties akin to human SCCs. KR158 murine SCCs, expanded in the gliomasphere assay, demonstrated sphere forming ability, self-renewing capacity, positive tumorigenicity, enhanced stemness and resistance to chemotherapy. Together, our findings validate the KR158 murine model as a framework to investigate GSCs and SCCs in GBM-pathology, and explore specifically the SCC-immune system communications, understand their role in disease progression, and evaluate the effect of therapeutic strategies targeting these specific connections.
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30
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Scott MT, Liu W, Mitchell R, Clarke CJ, Kinstrie R, Warren F, Almasoudi H, Stevens T, Dunn K, Pritchard J, Drotar ME, Michie AM, Jørgensen HG, Higgins B, Copland M, Vetrie D. Activating p53 abolishes self-renewal of quiescent leukaemic stem cells in residual CML disease. Nat Commun 2024; 15:651. [PMID: 38246924 PMCID: PMC10800356 DOI: 10.1038/s41467-024-44771-9] [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: 10/24/2022] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Whilst it is recognised that targeting self-renewal is an effective way to functionally impair the quiescent leukaemic stem cells (LSC) that persist as residual disease in chronic myeloid leukaemia (CML), developing therapeutic strategies to achieve this have proved challenging. We demonstrate that the regulatory programmes of quiescent LSC in chronic phase CML are similar to that of embryonic stem cells, pointing to a role for wild type p53 in LSC self-renewal. In support of this, increasing p53 activity in primitive CML cells using an MDM2 inhibitor in combination with a tyrosine kinase inhibitor resulted in reduced CFC outputs and engraftment potential, followed by loss of multilineage priming potential and LSC exhaustion when combination treatment was discontinued. Our work provides evidence that targeting LSC self-renewal is exploitable in the clinic to irreversibly impair quiescent LSC function in CML residual disease - with the potential to enable more CML patients to discontinue therapy and remain in therapy-free remission.
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Affiliation(s)
- Mary T Scott
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wei Liu
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rebecca Mitchell
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cassie J Clarke
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ross Kinstrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Felix Warren
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Hassan Almasoudi
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Thomas Stevens
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Karen Dunn
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John Pritchard
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark E Drotar
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Michie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Heather G Jørgensen
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David Vetrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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31
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Gutkind JS, Faraji F, Ramirez S, Clubb L, Sato K, Quiroz PA, Galloway W, Mikulski Z, Hoang T, Medetgul-Ernar K, Marangoni P, Jones K, Officer A, Molinolo A, Kim K, Sakaguchi K, Califano J, Smith Q, Klein O, Tamayo P. YAP-Driven Malignant Reprogramming of Epithelial Stem Cells at Single Cell Resolution. RESEARCH SQUARE 2023:rs.3.rs-3426301. [PMID: 37961717 PMCID: PMC10635308 DOI: 10.21203/rs.3.rs-3426301/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ cell tracing approaches with spatiotemporally controlled oncogene activation and tumor suppressor inhibition to unveil the processes underlying oral epithelial progenitor cell reprogramming into cancer stem cells (CSCs) at single cell resolution. This revealed the rapid emergence of a distinct stem-like cell state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal (pEMT) invasive gene programs. Interestingly, CSCs harbor limited cell autonomous invasive capacity, but instead recruit myeloid cells to remodel the basement membrane and ultimately initiate tumor invasion. CSC transcriptional programs are conserved in human carcinomas and associated with poor patient survival. These findings illuminate the process of cancer initiation at single cell resolution, thus identifying candidate targets for early cancer detection and prevention.
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Affiliation(s)
| | - Farhoud Faraji
- University of California San Diego Health Department of Otolaryngology-Head and Neck Surgery and Moores Cancer Center
| | | | - Lauren Clubb
- University of California San Diego Health Moores Cancer Center
| | - Kuniaki Sato
- University of California San Diego Health Moores Cancer Center
| | | | - William Galloway
- University of California Irvine Department of Chemical and Biomolecular Engineering
| | | | - Thomas Hoang
- University of California San Diego Health Moores Cancer Center
| | | | - Pauline Marangoni
- Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco
| | - Kyle Jones
- University of California San Francisco (UCSF)
| | - Adam Officer
- University of California San Diego Health Moores Cancer Center
| | | | | | | | | | - Quinton Smith
- University of California Irvine Department of Chemical and Biomolecular Engineering
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32
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Dickinson MJ, Barba P, Jäger U, Shah NN, Blaise D, Briones J, Shune L, Boissel N, Bondanza A, Mariconti L, Marchal AL, Quinn DS, Yang J, Price A, Sohoni A, Treanor LM, Orlando EJ, Mataraza J, Davis J, Lu D, Zhu X, Engels B, Moutouh-de Parseval L, Brogdon JL, Moschetta M, Flinn IW. A Novel Autologous CAR-T Therapy, YTB323, with Preserved T-cell Stemness Shows Enhanced CAR T-cell Efficacy in Preclinical and Early Clinical Development. Cancer Discov 2023; 13:1982-1997. [PMID: 37249512 PMCID: PMC10481129 DOI: 10.1158/2159-8290.cd-22-1276] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/21/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
CAR T-cell product quality and stemness (Tstem) are major determinants of in vivo expansion, efficacy, and clinical response. Prolonged ex vivo culturing is known to deplete Tstem, affecting clinical outcome. YTB323, a novel autologous CD19-directed CAR T-cell therapy expressing the same validated CAR as tisagenlecleucel, is manufactured using a next-generation platform in <2 days. Here, we report the preclinical development and preliminary clinical data of YTB323 in adults with relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL; NCT03960840). In preclinical mouse models, YTB323 exhibited enhanced in vivo expansion and antitumor activity at lower doses than traditionally manufactured CAR T cells. Clinically, at doses 25-fold lower than tisagenlecleucel, YTB323 showed (i) promising overall safety [cytokine release syndrome (any grade, 35%; grade ≥3, 6%), neurotoxicity (any grade, 25%; grade ≥3, 6%)]; (ii) overall response rates of 75% and 80% for DL1 and DL2, respectively; (iii) comparable CAR T-cell expansion; and (iv) preservation of T-cell phenotype. Current data support the continued development of YTB323 for r/r DLBCL. SIGNIFICANCE Traditional CAR T-cell manufacturing requires extended ex vivo cell culture, reducing naive and stem cell memory T-cell populations and diminishing antitumor activity. YTB323, which expresses the same validated CAR as tisagenlecleucel, can be manufactured in <2 days while retaining T-cell stemness and enhancing clinical activity at a 25-fold lower dose. See related commentary by Wang, p. 1961. This article is featured in Selected Articles from This Issue, p. 1949.
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Affiliation(s)
- Michael J. Dickinson
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Pere Barba
- Hematology Department, Hospital Universitari Vall d'Hebrón, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ulrich Jäger
- Clinical Division of Hematology and Hemostaseology, Department of Medicine I, and Comprehensive Cancer Center, Vienna General Hospital – Medical University of Vienna, Vienna, Austria
| | | | - Didier Blaise
- Département d'Hématologie, Programme de Transplantation et de Thérapie Cellulaire, Centre de Recherche en Cancérologie de Marseille, Aix-Marseille University, Institut Paoli Calmettes, Marseille, France
| | - Javier Briones
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Leyla Shune
- University of Kansas Medical Center, Kansas City, Kansas
| | - Nicolas Boissel
- Hematology Adolescent and Young Adult Unit, Saint-Louis Hospital, APHP, Paris, France
| | | | - Luisa Mariconti
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - David S. Quinn
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jennifer Yang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Andrew Price
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Akash Sohoni
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Louise M. Treanor
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Elena J. Orlando
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jennifer Mataraza
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jaclyn Davis
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Darlene Lu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xu Zhu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Boris Engels
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | | | | | - Ian W. Flinn
- Sarah Cannon Research Institute and Tennessee Oncology Center for Blood Cancers, Nashville, Tennessee
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Liu Y, Chen Y, Zhao Q, Xie T, Xiang C, Guo Q, Zhang W, Zhou Y, Yuan Y, Zhang Y, Xi T, Li X, Zheng L. A positive TGF-β/miR-9 regulatory loop promotes the expansion and activity of tumour-initiating cells in breast cancer. Br J Pharmacol 2023; 180:2280-2297. [PMID: 37060166 DOI: 10.1111/bph.16092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 03/19/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND AND PURPOSE MicroRNA-9 (miR-9) has previously been described as a dual-functional RNA during breast cancer progression and its roles need to be clarified thoroughly. EXPERIMENTAL APPROACH A miR-9 knockout mode of mouse breast cancer, the MMTV-PyMT model (PyMT-miR-9-/- ), combined with different human breast cancer cell lines were used to evaluate the effects of miR-9 on breast cancer initiation, progression and metastasis. Lin-NECs (Neoplastic mammary epithelial cells) and pNECs (Pre-neoplastic mammary epithelial cells) were isolated and subjected to tumour-initiation assay. Whole-mount staining of mammary gland and histology was performed to determine mammary gland growth. Tumour-initiating analysis combining a series of in vitro experiments were carried out to evaluate miR-9 roles in tumour-initiating ability. RNA-sequencing of human breast cancer cells, and mammary glands at hyperplastic stages and established tumours in PyMT and PyMT-miR-9-/- mice, ChIP and luciferase report assays were conducted to reveal the underlying mechanisms. KEY RESULTS MiR-9 is ectopically expressed in breast cancer and its level is negatively correlated with the prognosis, especially in basal-like breast cancer patients. Additionally, miR-9 is essential for breast cancer progression by promoting the expansion and activity of tumour-initiating cells (TICs) in preneoplastic glands, established tumours and xenograft modes. Mechanistically, the activity of TICs hinges on a positive TGF-β/miR-9 regulatory loop mediated by the STARD13/YAP axis. CONCLUSIONS AND IMPLICATIONS These findings demonstrate that miR-9 is an oncogenic miRNA rather than a tumour-suppressor in breast cancer, calling for rectification of the model for this conserved and highly abundant miRNA.
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Affiliation(s)
- Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Ying Chen
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Qiong Zhao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Tianyuan Xie
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Chenxi Xiang
- Department of Pathology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qianqian Guo
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yi Zhou
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Yin Yuan
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Yuxin Zhang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
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Martínez-Illescas NG, Leal S, González P, Graña-Castro O, Muñoz-Oliveira JJ, Cortés-Peña A, Gómez-Gil M, Vega Z, Neva V, Romero A, Quintela-Fandino M, Ciruelos E, Sanz C, Aragón S, Sotolongo L, Jiménez S, Caleiras E, Mulero F, Sánchez C, Malumbres M, Salazar-Roa M. miR-203 drives breast cancer cell differentiation. Breast Cancer Res 2023; 25:91. [PMID: 37542268 PMCID: PMC10401798 DOI: 10.1186/s13058-023-01690-9] [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: 01/24/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
A hallmark of many malignant tumors is dedifferentiated (immature) cells bearing slight or no resemblance to the normal cells from which the cancer originated. Tumor dedifferentiated cells exhibit a higher capacity to survive to chemo and radiotherapies and have the ability to incite tumor relapse. Inducing cancer cell differentiation would abolish their self-renewal and invasive capacity and could be combined with the current standard of care, especially in poorly differentiated and aggressive tumors (with worst prognosis). However, differentiation therapy is still in its early stages and the intrinsic complexity of solid tumor heterogeneity demands innovative approaches in order to be efficiently translated into the clinic. We demonstrate here that microRNA 203, a potent driver of differentiation in pluripotent stem cells (ESCs and iPSCs), promotes the differentiation of mammary gland tumor cells. Combining mouse in vivo approaches and both mouse and human-derived tridimensional organoid cultures, we report that miR-203 influences the self-renewal capacity, plasticity and differentiation potential of breast cancer cells and prevents tumor cell growth in vivo. Our work sheds light on differentiation-based antitumor therapies and offers miR-203 as a promising tool for directly confronting the tumor-maintaining and regeneration capability of cancer cells.
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Affiliation(s)
- Nuria G Martínez-Illescas
- Department of Biochemistry and Molecular Biology, School of Biology, Complutense University, Madrid, Spain
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Cell Division and Cancer Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | | | - Osvaldo Graña-Castro
- Bioinformatics Unit, CNIO, Madrid, Spain
- Department of Basic Medical Sciences, Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), San Pablo-CEU University, Madrid, Spain
| | | | - Alfonso Cortés-Peña
- Flow Cytometry and Fluorescence Microscopy Unit (CAI), Complutense University, Madrid, Spain
| | | | - Zaira Vega
- Histopathology Unit, CNIO, Madrid, Spain
| | | | | | | | - Eva Ciruelos
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Hospital 12 de Octubre, Madrid, Spain
| | - Consuelo Sanz
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Hospital 12 de Octubre, Madrid, Spain
| | - Sofía Aragón
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Hospital 12 de Octubre, Madrid, Spain
| | - Leisy Sotolongo
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Hospital 12 de Octubre, Madrid, Spain
| | - Sara Jiménez
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain
- Hospital 12 de Octubre, Madrid, Spain
| | | | | | - Cristina Sánchez
- Department of Biochemistry and Molecular Biology, School of Biology, Complutense University, Madrid, Spain.
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain.
| | - Marcos Malumbres
- Cell Division and Cancer Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Cancer Cell Cycle Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- ICREA, Passeig Lluís Companys 23, Barcelona, Spain.
| | - María Salazar-Roa
- Department of Biochemistry and Molecular Biology, School of Biology, Complutense University, Madrid, Spain.
- Breast and Gynecologic Cancer Group, Research Institute i+12, Madrid, Spain.
- Cell Division and Cancer Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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Wei M, Nurjanah U, Li J, Luo X, Hosea R, Li Y, Zeng J, Duan W, Song G, Miyagishi M, Kasim V, Wu S. YY2-DRP1 Axis Regulates Mitochondrial Fission and Determines Cancer Stem Cell Asymmetric Division. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207349. [PMID: 37300334 PMCID: PMC10427375 DOI: 10.1002/advs.202207349] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/24/2023] [Indexed: 06/12/2023]
Abstract
Cancer stem cells (CSCs) are associated with tumor progression, recurrence, and therapeutic resistance. To maintain their pool while promoting tumorigenesis, CSCs divide asymmetrically, producing a CSC and a highly proliferative, more differentiated transit-amplifying cell. Exhausting the CSC pool has been proposed as an effective antitumor strategy; however, the mechanism underlying CSC division remains poorly understood, thereby largely limiting its clinical application. Here, through cross-omics analysis, yin yang 2 (YY2) is identified as a novel negative regulator of CSC maintenance. It is shown that YY2 is downregulated in stem-like tumor spheres formed by hepatocarcinoma cells and in liver cancer, in which its expression is negatively correlated with disease progression and poor prognosis. Furthermore, it is revealed that YY2 overexpression suppressed liver CSC asymmetric division, leading to depletion of the CSC pool and decreased tumor-initiating capacity. Meanwhile, YY2 knock-out in stem-like tumor spheres caused enrichment in mitochondrial functions. Mechanistically, it is revealed that YY2 impaired mitochondrial fission, and consequently, liver CSC asymmetric division, by suppressing the transcription of dynamin-related protein 1. These results unravel a novel regulatory mechanism of mitochondrial dynamic-mediated CSCs asymmetric division and highlight the role of YY2 as a tumor suppressor and a therapeutic target in antitumor treatment.
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Affiliation(s)
- Mankun Wei
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Uli Nurjanah
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Juan Li
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Xinxin Luo
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Rendy Hosea
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Yanjun Li
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Jianting Zeng
- Department of Hepatobiliary and Pancreatic OncologyChongqing University Cancer HospitalChongqing UniversityChongqing400030P. R. China
| | - Wei Duan
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Guanbin Song
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
| | - Makoto Miyagishi
- Life Science InnovationSchool of Integrative and Global MajorsUniversity of TsukubaTsukubaIbaraki305‐0006Japan
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing UniversityChongqing400030P. R. China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and TechnologyMinistry of EducationCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- The 111 Project Laboratory of Biomechanics and Tissue RepairCollege of BioengineeringChongqing UniversityChongqing400044P. R. China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing UniversityChongqing400030P. R. China
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Wu Y, Hu SS, Zhang R, Goplen NP, Gao X, Narasimhan H, Shi A, Chen Y, Li Y, Zang C, Dong H, Braciale TJ, Zhu B, Sun J. Single cell RNA sequencing unravels mechanisms underlying senescence-like phenotypes of alveolar macrophages. iScience 2023; 26:107197. [PMID: 37456831 PMCID: PMC10344965 DOI: 10.1016/j.isci.2023.107197] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 12/11/2022] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Alveolar macrophages (AMs) are resident innate immune cells that play vital roles in maintaining lung physiological functions. However, the effects of aging on their dynamics, heterogeneity, and transcriptional profiles remain to be fully elucidated. Through single cell RNA sequencing (scRNA-seq), we identified CBFβ as an indispensable transcription factor that ensures AM self-renewal. Intriguingly, despite transcriptome similarities of proliferating cells, AMs from aged mice exhibited reduced embryonic stem cell-like features. Aged AMs also displayed compromised DNA repair abilities, potentially leading to obstructed cell cycle progression and an elevation of senescence markers. Consistently, AMs from aged mice exhibited impaired self-renewal ability and reduced sensitivity to GM-CSF. Decreased CBFβ was observed in the cytosol of AMs from aged mice. Similar senescence-like phenotypes were also found in human AMs. Taken together, these findings suggest that AMs in aged hosts demonstrate senescence-like phenotypes, potentially facilitated by the abrogated CBF β activity.
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Affiliation(s)
- Yue Wu
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Mayo Clinic Department of Immunology, Rochester, MN 55905, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ruixuan Zhang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Nick P. Goplen
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaochen Gao
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Mayo Clinic Department of Immunology, Rochester, MN 55905, USA
| | - Harish Narasimhan
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Ao Shi
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Yin Chen
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Mayo Clinic Department of Immunology, Rochester, MN 55905, USA
| | - Ying Li
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Haidong Dong
- Mayo Clinic Department of Immunology, Rochester, MN 55905, USA
- Department of Urology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas J. Braciale
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Bibo Zhu
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jie Sun
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Mayo Clinic Department of Immunology, Rochester, MN 55905, USA
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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Oei V, Chuang LSH, Matsuo J, Srivastava S, Teh M, Ito Y. RUNX3 inactivates oncogenic MYC through disruption of MYC/MAX complex and subsequent recruitment of GSK3β-FBXW7 cascade. Commun Biol 2023; 6:689. [PMID: 37400551 DOI: 10.1038/s42003-023-05037-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
MYC is one of the most commonly dysregulated proto-oncogenes in cancer. MYC promotes cancer initiation and maintenance by regulating multiple biological processes, such as proliferation and stem cell function. Here, we show that developmental regulator RUNX3 targets MYC protein for rapid degradation through the glycogen synthase kinase-3 beta-F-box/WD repeat-containing protein 7 (GSK3β-FBXW7) proteolytic pathway. The evolutionarily conserved Runt domain of RUNX3 interacts directly with the basic helix-loop-helix leucine zipper of MYC, resulting in the disruption of MYC/MAX and MYC/MIZ-1 interactions, enhanced GSK3β-mediated phosphorylation of MYC protein at threonine-58 and its subsequent degradation via the ubiquitin-proteasomal pathway. We therefore uncover a previously unknown mode of MYC destabilization by RUNX3 and provide an explanation as to why RUNX3 inhibits early-stage cancer development in gastrointestinal and lung mouse cancer models.
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Affiliation(s)
- Vincent Oei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Graduate School, Integrative Sciences and Engineering Programme, Singapore, Singapore
| | - Linda Shyue Huey Chuang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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38
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Maghsoudi M, Aghdam R, Eslahchi C. Removing the association of random gene sets and survival time in cancers with positive random bias using fixed-point gene set. Sci Rep 2023; 13:8663. [PMID: 37248269 DOI: 10.1038/s41598-023-35588-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/20/2023] [Indexed: 05/31/2023] Open
Abstract
Cancer research aims to identify genes that cause or control disease progression. Although a wide range of gene sets have been published, they are usually in poor agreement with one another. Furthermore, recent findings from a gene-expression cohort of different cancer types, known as positive random bias, showed that sets of genes chosen randomly are significantly associated with survival time much higher than expected. In this study, we propose a method based on Brouwer's fixed-point theorem that employs significantly survival-associated random gene sets and reveals a small fixed-point gene set for cancers with a positive random bias property. These sets significantly correspond to cancer-related pathways with biological relevance for the progression and metastasis of the cancer types they represent. Our findings show that our proposed significant gene sets are biologically related to each cancer type available in the cancer genome atlas with the positive random bias property, and by using these sets, positive random bias is significantly more reduced in comparison with state-of-the-art methods in this field. The random bias property is removed in 8 of these 17 cancer types, and the number of random sets of genes associated with survival time is significantly reduced in the remaining 9 cancers.
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Affiliation(s)
- Maryam Maghsoudi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Rosa Aghdam
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Changiz Eslahchi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.
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Zhang T, Zhuang L, Muaibati M, Wang D, Abasi A, Tong Q, Ma D, Jin L, Huang X. Identification of cervical cancer stem cells using single-cell transcriptomes of normal cervix, cervical premalignant lesions, and cervical cancer. EBioMedicine 2023; 92:104612. [PMID: 37224771 DOI: 10.1016/j.ebiom.2023.104612] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Cervical cancer is the fourth leading cause of mortality among gynecological malignancies. However, the identification of cervical cancer stem cells remains unclear. METHODS We performed single-cell mRNA sequencing on ∼122,400 cells from 20 cervical biopsies, including 5 healthy controls, 4 high-grade intraepithelial neoplasias, 5 microinvasive carcinomas of the cervix, and 6 invasive cervical squamous carcinomas. Bioinformatic results were validated by multiplex immunohistochemistry (mIHC) in cervical cancer tissue microarrays (TMA) (n = 85). FINDINGS We identified cervical cancer stem cells and highlighted the functional changes in cervical stem cells during malignant transformation. The original non-malignant stem cell properties (characterized by high proliferation) gradually diminished, whereas the tumor stem cell properties (characterized by epithelial-mesenchymal transformation and invasion) were enhanced. The mIHC results of our TMA cohort confirmed the existence of stem-like cells and indicated that cluster correlated with neoplastic recurrence. Subsequently, we investigated malignant and immune cell heterogeneity in the cervical multicellular ecosystem across different disease stages. We observed global upregulation of interferon responses in the cervical microenvironment during lesion progression. INTERPRETATION Our results provide more insights into cervical premalignant and malignant lesion microenvironments. FUNDING This research was supported by the Guangdong Provincial Natural Science Foundation of China (2023A1515010382), Grant 2021YFC2700603 from the National Key Research & Development Program of China and the Hubei Provincial Natural Science Foundation of China (2022CFB174 and 2022CFB893).
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Affiliation(s)
- Tao Zhang
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China; Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People's Republic of China
| | - Liang Zhuang
- Department of Oncology, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People's Republic of China
| | - Munawaer Muaibati
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China
| | - Dan Wang
- Department of Ophthalmology, Wuhan Children's Hospital, Tongji Medicine College, Huazhong University of Science and Technology, Wuhan 430015, People's Republic of China
| | - Abuduyilimu Abasi
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China
| | - Qing Tong
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China
| | - Lei Jin
- Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People's Republic of China.
| | - Xiaoyuan Huang
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030; People's Republic of China.
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Peretz CAC, Kennedy VE, Walia A, Delley CL, Koh A, Tran E, Clark IC, Hayford CE, D'Amato C, Xue Y, Fontanez KM, Roy R, Logan AC, Perl AE, Abate A, Olshen A, Smith CC. Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540305. [PMID: 37292835 PMCID: PMC10245585 DOI: 10.1101/2023.05.15.540305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mixed phenotype acute leukemia (MPAL) is a leukemia whose biologic drivers are poorly understood, therapeutic strategy remains unclear, and prognosis is poor. We performed multiomic single cell (SC) profiling of 14 newly diagnosed adult MPAL patients to characterize the immunophenotypic, genetic, and transcriptional landscapes of MPAL. We show that neither genetic profile nor transcriptome reliably correlate with specific MPAL immunophenotypes. However, progressive acquisition of mutations is associated with increased expression of immunophenotypic markers of immaturity. Using SC transcriptional profiling, we find that MPAL blasts express a stem cell-like transcriptional profile distinct from other acute leukemias and indicative of high differentiation potential. Further, patients with the highest differentiation potential demonstrated inferior survival in our dataset. A gene set score, MPAL95, derived from genes highly enriched in this cohort, is applicable to bulk RNA sequencing data and was predictive of survival in an independent patient cohort, suggesting utility for clinical risk stratification.
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Affiliation(s)
- Cheryl A C Peretz
- Divison of Hematology and Oncology, Department of Pediatrics, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Vanessa E Kennedy
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Anushka Walia
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cyrille L Delley
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Andrew Koh
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Tran
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iain C Clark
- Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | | | | | - Yi Xue
- Fluent Biosciences Inc., Watertown, MA
| | | | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Aaron C Logan
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexander E Perl
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Catherine C Smith
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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Martins-Neves SR, Sampaio-Ribeiro G, Gomes CMF. Self-Renewal and Pluripotency in Osteosarcoma Stem Cells' Chemoresistance: Notch, Hedgehog, and Wnt/β-Catenin Interplay with Embryonic Markers. Int J Mol Sci 2023; 24:8401. [PMID: 37176108 PMCID: PMC10179672 DOI: 10.3390/ijms24098401] [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: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Osteosarcoma is a highly malignant bone tumor derived from mesenchymal cells that contains self-renewing cancer stem cells (CSCs), which are responsible for tumor progression and chemotherapy resistance. Understanding the signaling pathways that regulate CSC self-renewal and survival is crucial for developing effective therapies. The Notch, Hedgehog, and Wnt/β-Catenin developmental pathways, which are essential for self-renewal and differentiation of normal stem cells, have been identified as important regulators of osteosarcoma CSCs and also in the resistance to anticancer therapies. Targeting these pathways and their interactions with embryonic markers and the tumor microenvironment may be a promising therapeutic strategy to overcome chemoresistance and improve the prognosis for osteosarcoma patients. This review focuses on the role of Notch, Hedgehog, and Wnt/β-Catenin signaling in regulating CSC self-renewal, pluripotency, and chemoresistance, and their potential as targets for anti-cancer therapies. We also discuss the relevance of embryonic markers, including SOX-2, Oct-4, NANOG, and KLF4, in osteosarcoma CSCs and their association with the aforementioned signaling pathways in overcoming drug resistance.
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Affiliation(s)
- Sara R. Martins-Neves
- iCBR—Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (S.R.M.-N.)
- Institute of Pharmacology and Experimental Therapeutics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Gabriela Sampaio-Ribeiro
- iCBR—Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (S.R.M.-N.)
- Institute of Pharmacology and Experimental Therapeutics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- CIBB—Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
- CACC—Clinical Academic Center of Coimbra, 3000-075 Coimbra, Portugal
| | - Célia M. F. Gomes
- iCBR—Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (S.R.M.-N.)
- Institute of Pharmacology and Experimental Therapeutics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- CIBB—Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
- CACC—Clinical Academic Center of Coimbra, 3000-075 Coimbra, Portugal
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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Xiao M, Wu CH, Meek G, Kelly B, Castillo DB, Young LEA, Martire S, Dhungel S, McCauley E, Saha P, Dube AL, Gentry MS, Banaszynski LA, Sun RC, Kikani CK. PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence. eLife 2023; 12:e81717. [PMID: 37052079 PMCID: PMC10162801 DOI: 10.7554/elife.81717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/11/2023] [Indexed: 04/14/2023] Open
Abstract
Quiescent stem cells are activated in response to a mechanical or chemical injury to their tissue niche. Activated cells rapidly generate a heterogeneous progenitor population that regenerates the damaged tissues. While the transcriptional cadence that generates heterogeneity is known, the metabolic pathways influencing the transcriptional machinery to establish a heterogeneous progenitor population remains unclear. Here, we describe a novel pathway downstream of mitochondrial glutamine metabolism that confers stem cell heterogeneity and establishes differentiation competence by countering post-mitotic self-renewal machinery. We discovered that mitochondrial glutamine metabolism induces CBP/EP300-dependent acetylation of stem cell-specific kinase, PAS domain-containing kinase (PASK), resulting in its release from cytoplasmic granules and subsequent nuclear migration. In the nucleus, PASK catalytically outcompetes mitotic WDR5-anaphase-promoting complex/cyclosome (APC/C) interaction resulting in the loss of post-mitotic Pax7 expression and exit from self-renewal. In concordance with these findings, genetic or pharmacological inhibition of PASK or glutamine metabolism upregulated Pax7 expression, reduced stem cell heterogeneity, and blocked myogenesis in vitro and muscle regeneration in mice. These results explain a mechanism whereby stem cells co-opt the proliferative functions of glutamine metabolism to generate transcriptional heterogeneity and establish differentiation competence by countering the mitotic self-renewal network via nuclear PASK.
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Affiliation(s)
- Michael Xiao
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD ProgramNew YorkUnited States
| | - Chia-Hua Wu
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Graham Meek
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Brian Kelly
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Dara Buendia Castillo
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Lyndsay EA Young
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
| | - Sara Martire
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Sajina Dhungel
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Elizabeth McCauley
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Purbita Saha
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Altair L Dube
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Matthew S Gentry
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Ramon C Sun
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
- Department of Neuroscience, College of Medicine, University of KentuckyLexingtonUnited States
| | - Chintan K Kikani
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
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Niu N, Ye J, Hu Z, Zhang J, Wang Y. Regulative Roles of Metabolic Plasticity Caused by Mitochondrial Oxidative Phosphorylation and Glycolysis on the Initiation and Progression of Tumorigenesis. Int J Mol Sci 2023; 24:ijms24087076. [PMID: 37108242 PMCID: PMC10139088 DOI: 10.3390/ijms24087076] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
One important feature of tumour development is the regulatory role of metabolic plasticity in maintaining the balance of mitochondrial oxidative phosphorylation and glycolysis in cancer cells. In recent years, the transition and/or function of metabolic phenotypes between mitochondrial oxidative phosphorylation and glycolysis in tumour cells have been extensively studied. In this review, we aimed to elucidate the characteristics of metabolic plasticity (emphasizing their effects, such as immune escape, angiogenesis migration, invasiveness, heterogeneity, adhesion, and phenotypic properties of cancers, among others) on tumour progression, including the initiation and progression phases. Thus, this article provides an overall understanding of the influence of abnormal metabolic remodeling on malignant proliferation and pathophysiological changes in carcinoma.
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Affiliation(s)
- Nan Niu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
- College of Physics and Optoelectronic Engineering, Canghai Campus of Shenzhen University, Shenzhen 518060, China
| | - Jinfeng Ye
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Junbin Zhang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Yun Wang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
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45
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Barata T, Duarte I, Futschik ME. Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes. Genes (Basel) 2023; 14:genes14030745. [PMID: 36981016 PMCID: PMC10048104 DOI: 10.3390/genes14030745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Stem cells encompass a variety of different cell types which converge on the dual capacity to self-renew and differentiate into one or more lineages. These characteristic features are key for the involvement of stem cells in crucial biological processes such as development and ageing. To decipher their underlying genetic substrate, it is important to identify so-called stemness genes that are common to different stem cell types and are consistently identified across different studies. In this meta-analysis, 21 individual stemness signatures for humans and another 21 for mice, obtained from a variety of stem cell types and experimental techniques, were compared. Although we observed biological and experimental variability, a highly significant overlap between gene signatures was identified. This enabled us to define integrated stemness signatures (ISSs) comprised of genes frequently occurring among individual stemness signatures. Such integrated signatures help to exclude false positives that can compromise individual studies and can provide a more robust basis for investigation. To gain further insights into the relevance of ISSs, their genes were functionally annotated and connected within a molecular interaction network. Most importantly, the present analysis points to the potential roles of several less well-studied genes in stemness and thus provides promising candidates for further experimental validation.
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Affiliation(s)
- Tânia Barata
- SysBioLab, Centre for Biomedical Research (CBMR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Isabel Duarte
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Matthias E Futschik
- SysBioLab, Centre for Biomedical Research (CBMR), Universidade do Algarve, 8005-139 Faro, Portugal
- School of Biomedical Sciences, Faculty of Health, Derriford Research Facility, University of Plymouth, Plymouth PL6 8BU, UK
- MRC London Institute of Medical Sciences (LMS), Imperial College London, London W12 0NN, UK
- NOVA Medical School, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
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Luo F, Tshering LF, Tutuska K, Szenk M, Rubel D, Rail JG, Russ S, Liu J, Nemajerova A, Balázsi G, Talos F. A luminal intermediate cell state maintains long-term prostate homeostasis and contributes to tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529762. [PMID: 36909551 PMCID: PMC10002646 DOI: 10.1101/2023.02.24.529762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Cellular heterogeneity poses tremendous challenges for developing cell-targeted therapies and biomarkers of clinically significant prostate cancer. The origins of this heterogeneity within normal adult and aging tissue remain unknown, leaving cellular states and transcriptional programs that allow expansions of malignant clones unidentified. To define cell states that contribute to early cancer development, we performed clonal analyses and single cell transcriptomics of normal prostate from genetically-engineered mouse models. We uncovered a luminal transcriptional state with a unique "basal-like" Wnt/p63 signaling ( luminal intermediate , LumI) which contributes to the maintenance of long-term prostate homeostasis. Moreover, LumI cells greatly expand during early stages of tumorigenesis in several mouse models of prostate cancer. Genetic ablation of p63 in vivo in luminal cells reduced the formation of aggressive clones in mouse prostate tumor models. Finally, the LumI cells and Wnt signaling appear to significantly increase in human aging prostate and prostate cancer samples, highlighting the importance of this hybrid cell state for human pathologies with potential translational impact.
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Tafessu A, O’Hara R, Martire S, Dube AL, Saha P, Gant VU, Banaszynski LA. H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells. Genome Biol 2023; 24:25. [PMID: 36782260 PMCID: PMC9926682 DOI: 10.1186/s13059-023-02867-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood. RESULTS We perform genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and find evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 results in reduced chromatin accessibility and transcription factor (TF) binding at promoters of expressed genes in ESCs. Likewise, enrichment of the transcriptional coactivator p300 and downstream histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the acetyl lysine reader BRD4. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TF motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate. CONCLUSIONS H3.3 facilitates DNA accessibility, transcription factor binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it does promote de novo transcription factor binding which may contribute to the dysregulation of cellular differentiation in the absence of H3.3.
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Affiliation(s)
- Amanuel Tafessu
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Ryan O’Hara
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Sara Martire
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Altair L. Dube
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Purbita Saha
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Vincent U. Gant
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Laura A. Banaszynski
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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Patil S, Islam F, Gopalan V. Diagnostic and Prognostic Implications of Cancer Stem Cell Transcription Factors. CANCER STEM CELLS: BASIC CONCEPT AND THERAPEUTIC IMPLICATIONS 2023:325-347. [DOI: 10.1007/978-981-99-3185-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Vanden Bempt M, Debackere K, Demeyer S, Van Thillo Q, Meeuws N, Prieto C, Provost S, Mentens N, Jacobs K, Gielen O, Nittner D, Ogawa S, Kataoka K, Graux C, Tousseyn T, Cools J, Dierickx D. Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T-cell lymphoma. Blood 2022; 140:2463-2476. [PMID: 35960849 PMCID: PMC10653048 DOI: 10.1182/blood.2022016428] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 12/13/2022] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of hematological cancers arising from the malignant transformation of mature T cells. In a cohort of 28 PTCL cases, we identified recurrent overexpression of MYCN, a member of the MYC family of oncogenic transcription factors. Approximately half of all PTCL cases was characterized by a MYC expression signature. Inducible expression of MYCN in lymphoid cells in a mouse model caused T-cell lymphoma that recapitulated human PTCL with an MYC expression signature. Integration of mouse and human expression data identified EZH2 as a key downstream target of MYCN. Remarkably, EZH2 was found to be an essential cofactor for the transcriptional activation of the MYCN-driven gene expression program, which was independent of methyltransferase activity but dependent on phosphorylation by CDK1. MYCN-driven T-cell lymphoma was sensitive to EZH2 degradation or CDK1 inhibition, which displayed synergy with US Food and Drug Administration-approved histone deacetylase (HDAC) inhibitors.
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Affiliation(s)
- Marlies Vanden Bempt
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Koen Debackere
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Quentin Van Thillo
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Nienke Meeuws
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Cristina Prieto
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Sarah Provost
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Nicole Mentens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Kris Jacobs
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - David Nittner
- Histopathology Expertise Center, VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Daan Dierickx
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
- Department of Hematology, University Hospital Leuven, Leuven, Belgium
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