1
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El Meouche I, Jain P, Jolly MK, Capp JP. Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity. Transl Oncol 2024; 49:102069. [PMID: 39121829 PMCID: PMC11364053 DOI: 10.1016/j.tranon.2024.102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
A common feature of bacterial, fungal and cancer cell populations upon treatment is the presence of tolerant and persistent cells able to survive, and sometimes grow, even in the presence of usually inhibitory or lethal drug concentrations, driven by non-genetic differences among individual cells in a population. Here we review and compare data obtained on drug survival in bacteria, fungi and cancer cells to unravel common characteristics and cellular pathways, and to point their singularities. This comparative work also allows to cross-fertilize ideas across fields. We particularly focus on the role of gene expression variability in the emergence of cell-cell non-genetic heterogeneity because it represents a possible common basic molecular process at the origin of most persistence phenomena and could be monitored and tuned to help improve therapeutic interventions.
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Affiliation(s)
- Imane El Meouche
- Université Paris Cité, Université Sorbonne Paris Nord, INSERM, IAME, F-75018 Paris, France.
| | - Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France.
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2
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Yan P, Jimenez ER, Li Z, Bui T, Seehawer M, Nishida J, Foidart P, Stevens LE, Xie Y, Gomez MM, Park SY, Long HW, Polyak K. Midkine as a driver of age-related changes and increase in mammary tumorigenesis. Cancer Cell 2024:S1535-6108(24)00350-7. [PMID: 39366375 DOI: 10.1016/j.ccell.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
Aging is a pivotal risk factor for cancer, yet the underlying mechanisms remain poorly defined. Here, we explore age-related changes in the rat mammary gland by single-cell multiomics. Our findings include increased epithelial proliferation, loss of luminal identity, and decreased naive B and T cells with age. We discover a luminal progenitor population unique to old rats with profiles reflecting precancerous changes and identify midkine (Mdk) as a gene upregulated with age and a regulator of age-related luminal progenitors. Midkine treatment of young rats mimics age-related changes via activating PI3K-AKT-SREBF1 pathway and promotes nitroso-N-methylurea-induced mammary tumorigenesis. Midkine levels increase with age in human blood and mammary epithelium, and higher MDK in normal breast tissue is associated with higher breast cancer risk in younger women. Our findings reveal a link between aging and susceptibility to tumor initiation and identify midkine as a mediator of age-dependent increase in breast tumorigenesis.
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Affiliation(s)
- Pengze Yan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ernesto Rojas Jimenez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Triet Bui
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pierre Foidart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Munoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - So Yeon Park
- Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea; Harvard Stem Cell Institute, Cambridge, MA 02142, USA.
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3
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Xue J, Liu Z, Xie B, Dong R, Wu J, Wu Y, Xu Z, Tian Y, Wei Y, Geng Z, Lu L, Liu Y, Xie J, Yang P. Probiotic nucleotides increase IL-10 expression in airway macrophages to mitigate airway allergy. Inflamm Res 2024:10.1007/s00011-024-01940-2. [PMID: 39235607 DOI: 10.1007/s00011-024-01940-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 08/16/2024] [Accepted: 08/25/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Dysfunctional immune regulation plays a crucial role in the pathogenesis of airway allergies. Macrophages are one of the components of the immune regulation cells. The aim of this study is to elucidate the role of lysine demethylase 5 A (KDM5A) in maintaining macrophages' immune regulatory ability. METHODS DNA was extracted from Lactobacillus rhamnosus GG to be designated as LgDNA. LgDNA was administered to the mice through nasal instillations. M2 macrophages (M2 cells) were isolated from the airway tissues using flow cytometry. RESULTS We found that airway M2 cells of mice with airway Th2 polarization had reduced amounts of IL-10 and KDM5A. Mice with Kdm5a deficiency in M2 cells showed the airway Th2 polarization. The expression of Kdm5a in airway M2 cells was enhanced by nasal instillations containing LgDNA. KDM5A mediated the effects of LgDNA on inducing the Il10 expression in airway M2 cells. Administration of LgDNA mitigated experimental airway allergy. CONCLUSIONS M2 macrophages in the airway tissues of mice with airway allergy show low levels of KDM5A. By upregulating KDM5A expression, LgDNA can increase Il10 expression and reconcile airway Th2 polarization.
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Affiliation(s)
- Jinmei Xue
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, 030001, China
| | - Bailing Xie
- State Key Laboratory of Respiratory Diseases Allergy Division at Shenzhen University and Institute of Allergy and Immunology, Shenzhen University School of Medicine, Room A7-509 at Lihu Campus. 1066 Xueyuan Blvd., Shenzhen, China
| | - Rui Dong
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Juan Wu
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Yisha Wu
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Zhihan Xu
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Yuhe Tian
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Yao Wei
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Zhigang Geng
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Lei Lu
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Rapid Diagnosis and Precision Treatment of Airway Allergic Diseases, Taiyuan, China
| | - Yu Liu
- Department of General Practice Medicine, Third Hospital of Shenzhen University, Shenzhen, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, 030001, China.
| | - Pingchang Yang
- State Key Laboratory of Respiratory Diseases Allergy Division at Shenzhen University and Institute of Allergy and Immunology, Shenzhen University School of Medicine, Room A7-509 at Lihu Campus. 1066 Xueyuan Blvd., Shenzhen, China.
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4
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Barozzi I, Slaven N, Canale E, Lopes R, Amorim Monteiro Barbosa I, Bleu M, Ivanoiu D, Pacini C, Mensa' E, Chambers A, Bravaccini S, Ravaioli S, Győrffy B, Dieci MV, Pruneri G, Galli GG, Magnani L. A Functional Survey of the Regulatory Landscape of Estrogen Receptor-Positive Breast Cancer Evolution. Cancer Discov 2024; 14:1612-1630. [PMID: 38753319 PMCID: PMC11372371 DOI: 10.1158/2159-8290.cd-23-1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/12/2024] [Accepted: 05/14/2024] [Indexed: 09/05/2024]
Abstract
Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer, potentially explaining ∼40% of relapses. If other mechanisms underlie the evolution of hormone-dependent breast cancer under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CRE) to cancer evolution by focusing on 12 megabases of noncoding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of noncoding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies trigger the emergence of transient features which could ultimately be exploited to hinder the adaptive process. Significance: This study shows that cells adapting to endocrine therapies undergo changes in the usage or regulatory regions. Dormant cells are less vulnerable to regulatory perturbation but gain transient dependencies which can be exploited to decrease the formation of dormant persisters.
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Affiliation(s)
- Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Rui Lopes
- Disease area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | | | - Melusine Bleu
- Disease area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Claudia Pacini
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Emanuela Mensa'
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Alfie Chambers
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sara Bravaccini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
- Faculty of Medicine and Surgery, "Kore" University of Enna, Enna, Italy
| | - Sara Ravaioli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
- Cancer Biomarker Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
| | - Maria Vittoria Dieci
- Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giancarlo Pruneri
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer, Research, London, United Kingdom
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5
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Yu S, Wu R, Si Y, Fan Z, Wang Y, Yao C, Sun R, Xue Y, Chen Y, Wang Z, Dong S, Wang N, Ling X, Liang Z, Bi C, Yang Y, Dong W, Sun H. Alternative splicing of ALDOA confers tamoxifen resistance in breast cancer. Oncogene 2024; 43:2901-2913. [PMID: 39164523 DOI: 10.1038/s41388-024-03134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024]
Abstract
The cancer-associated alternative splicing (AS) events generate cancer-related transcripts which are involved in uncontrolled cell proliferation and drug resistance. However, the key AS variants implicated in tamoxifen (TAM) resistance in breast cancer remain elusive. In the current study, we investigated the landscape of AS events in nine pairs of primary and relapse breast tumors from patients receiving TAM-based therapy. We unrevealed a notable association between the inclusion of exon 7.2 in the 5'untranslated region (5'UTR) of ALDOA mRNA and TAM resistance. Mechanistically, the inclusion of ALDOA exon 7.2 enhances the translation efficiency of the transcript, resulting in increased ALDOA protein expression, mTOR pathway activity, and the promotion of TAM resistance in breast cancer cells. Moreover, the inclusion of exon 7.2 in ALDOA mRNA is mediated by MSI1 via direct interaction. In addition, elevated inclusion of ALDOA exon 7.2 or expression of MSI1 is associated with an unfavorable prognosis in patients undergoing endocrine therapy. Notably, treatment with Aldometanib, an ALDOA inhibitor, effectively restrains the growth of TAM-resistant breast cancer cells in vitro and in vivo. The present study unveils the pivotal role of an AS event in ALDOA, under the regulation of MSI1, in driving TAM resistance in breast cancer. Therefore, this study provides a promising therapeutic avenue targeting ALDOA to combat TAM resistance.
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Affiliation(s)
- Shiyi Yu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Rui Wu
- School of Life Science, Liaoning Normal University, Dalian, China
| | - Yue Si
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zhehao Fan
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Ying Wang
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Chang Yao
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Rongmao Sun
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yaji Xue
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Yongli Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zheng Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Shuangshuang Dong
- Department of Pathology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Xinyue Ling
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zhengyan Liang
- School of Basic Medical Science, Guangdong Medical University, Dongguan, China
| | - Caili Bi
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Yi Yang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China.
| | - Weibing Dong
- School of Life Science, Liaoning Normal University, Dalian, China.
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China.
- Haian Hospital of Traditional Chinese Medicine, Haian, China.
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6
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Cheng YC, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald TO, Michor F. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proc Natl Acad Sci U S A 2024; 121:e2406842121. [PMID: 39093947 PMCID: PMC11317558 DOI: 10.1073/pnas.2406842121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the EED and EZH2 genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing ITGB4, LAMA3, and LAMB3 as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that CENPF, CKS1B, and MKI67 showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories.
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Affiliation(s)
- Yu-Chen Cheng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Yun Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100021, China
| | - Shubham Tripathi
- Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale School of Medicine, New Haven, CT06510
| | - B. V. Harshavardhan
- Interdisciplinary Mathematics Initiative, Indian Institute of Science, Bangalore560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BCV6T 1Z2, Canada
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
| | - Thomas O. McDonald
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02138
- The Ludwig Center at Harvard, Boston, MA02115
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7
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Izumi M, Costa DB, Kobayashi SS. Targeting of drug-tolerant persister cells as an approach to counter drug resistance in non-small cell lung cancer. Lung Cancer 2024; 194:107885. [PMID: 39002493 PMCID: PMC11305904 DOI: 10.1016/j.lungcan.2024.107885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
The advent of targeted therapies revolutionized treatments of advanced oncogene-driven non-small cell lung cancer (NSCLC). Nonetheless, despite initial dramatic responses, development of drug resistance is inevitable. Although mechanisms underlying acquired resistance, such as on-target mutations, bypass pathways, or lineage transformation, have been described, overcoming drug resistance remains challenging. Recent evidence suggests that drug-tolerant persister (DTP) cells, which are tumor cells tolerant to initial drug exposure, give rise to cells that acquire drug resistance. Thus, the possibility of eradicating cancer by targeting DTP cells is under investigation, and various strategies are proposed. Here, we review overall features of DTP cells, current efforts to define DTP markers, and potential therapeutic strategies to target and eradicate DTP cells in oncogene-driven NSCLC. We also discuss future challenges in the field.
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Affiliation(s)
- Motohiro Izumi
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel B Costa
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Susumu S Kobayashi
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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8
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Hu D, Zhao T, Xu C, Pan X, Zhou Z, Wang S. Epigenetic Modifiers in Cancer Metastasis. Biomolecules 2024; 14:916. [PMID: 39199304 PMCID: PMC11352731 DOI: 10.3390/biom14080916] [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: 06/03/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 09/01/2024] Open
Abstract
Metastasis is the primary cause of cancer-related death, with the dissemination and colonization of primary tumor cells at the metastatic site facilitated by various molecules and complex pathways. Understanding the biological mechanisms underlying the metastatic process is critical for the development of effective interventions. Several epigenetic modifications have been identified that play critical roles in regulating cancer metastasis. This review aims to provide a comprehensive summary of recent advances in understanding the role of epigenetic modifiers, including histone modifications, DNA methylation, non-coding RNAs, enhancer reprogramming, chromatin accessibility, and N6-methyladenosine, in metastasis-associated processes, such as epithelial-mesenchymal transition (EMT), cancer cell migration, and invasion. In particular, this review provides a detailed and in-depth description of the role of crosstalk between epigenetic regulators in tumor metastasis. Additionally, we explored the potential and limitations of epigenetics-related target molecules in the diagnosis, treatment, and prognosis of cancer metastasis.
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Affiliation(s)
- Die Hu
- Key Laboratory of Molecular Genetics between Kangda College of Nanjing Medical University and Suzhou Medical College of Soochow University, Suzhou 215123, China;
- Department of Basic Medicine, Kangda College of Nanjing Medical University, Lianyungang 222000, China; (C.X.); (X.P.)
| | - Tianci Zhao
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China;
| | - Chenxing Xu
- Department of Basic Medicine, Kangda College of Nanjing Medical University, Lianyungang 222000, China; (C.X.); (X.P.)
| | - Xinyi Pan
- Department of Basic Medicine, Kangda College of Nanjing Medical University, Lianyungang 222000, China; (C.X.); (X.P.)
| | - Zhengyu Zhou
- Key Laboratory of Molecular Genetics between Kangda College of Nanjing Medical University and Suzhou Medical College of Soochow University, Suzhou 215123, China;
- Laboratory Animal Center, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Shengjie Wang
- Key Laboratory of Molecular Genetics between Kangda College of Nanjing Medical University and Suzhou Medical College of Soochow University, Suzhou 215123, China;
- Department of Basic Medicine, Kangda College of Nanjing Medical University, Lianyungang 222000, China; (C.X.); (X.P.)
- Laboratory Animal Center, Suzhou Medical College of Soochow University, Suzhou 215123, China
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9
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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10
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Zhang J, Liu J, Yue Y, Wang L, He Q, Xu S, Li J, Liao Y, Chen Y, Wang S, Xie Y, Zhang B, Bian Y, Dimitrov DS, Yuan Y, Zhu J. The immunotoxin targeting PRLR increases tamoxifen sensitivity and enhances the efficacy of chemotherapy in breast cancer. J Exp Clin Cancer Res 2024; 43:173. [PMID: 38898487 PMCID: PMC11188579 DOI: 10.1186/s13046-024-03099-4] [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: 03/26/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Though tamoxifen achieves success in treating estrogen receptor α (ERα)-positive breast cancer, the followed development of tamoxifen resistance is a common challenge in clinic. Signals downstream of prolactin receptor (PRLR) could synergize with ERα in breast cancer progression. However, the potential effect of targeting PRL-PRLR axis combined with tamoxifen has not been thoroughly investigated. METHODS High-throughput RNA-seq data obtained from TCGA, Metabric and GEO datasets were analyzed to explore PRLR expression in breast cancer cell and the association of PRLR expression with tamoxifen treatment. Exogenous or PRL overexpression cell models were employed to investigate the role of activated PRLR pathway in mediating tamoxifen insensitivity. Immunotoxin targeting PRLR (N8-PE24) was constructed with splicing-intein technique, and the efficacy of N8-PE24 against breast cancer was evaluated using in vitro and in vivo methods, including analysis of cells growth or apoptosis, 3D spheroids culture, and animal xenografts. RESULTS PRLR pathway activated by PRL could significantly decrease sensitivity of ERα-positive breast cancer cells to tamoxifen. Tamoxifen treatment upregulated transcription of PRLR and could induce significant accumulation of PRLR protein in breast cancer cells by alkalizing lysosomes. Meanwhile, tamoxifen-resistant MCF7 achieved by long-term tamoxifen pressure exhibited both upregulated transcription and protein level of PRLR. Immunotoxin N8-PE24 enhanced sensitivity of breast cancer cells to tamoxifen both in vitro and in vivo. In xenograft models, N8-PE24 significantly enhanced the efficacy of tamoxifen and paclitaxel when treating PRLR-positive triple-negative breast cancer. CONCLUSIONS PRL-PRLR axis potentially associates with tamoxifen insensitivity in ERα-positive breast cancer cells. N8-PE24 could inhibit cell growth of the breast cancers and promote drug sensitivity of PRLR-positive breast cancer cells to tamoxifen and paclitaxel. Our study provides a new perspective for targeting PRLR to treat breast cancer.
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Affiliation(s)
- Jiawei Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Junjun Liu
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Yali Yue
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Lei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Qunye He
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Shuyi Xu
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Junyan Li
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Yunji Liao
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Yu Chen
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | | | - Yueqing Xie
- Jecho Laboratories, Inc, Frederick, MD, 21704, USA
- Jecho Biopharmaceuticals Co., Ltd, Tianjin, 300467, China
| | - Baohong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Yanlin Bian
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China
| | - Dimiter S Dimitrov
- University of Pittsburgh Department of Medicine, Pittsburgh, PA, 15261, USA
| | - Yunsheng Yuan
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China.
| | - Jianwei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Building 6, Room 208, 800 Dongchuan road, Shanghai, 200240, China.
- Jecho Laboratories, Inc, Frederick, MD, 21704, USA.
- Jecho Biopharmaceuticals Co., Ltd, Tianjin, 300467, China.
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11
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Whiting FJH, Househam J, Baker AM, Sottoriva A, Graham TA. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biol 2024; 34:451-464. [PMID: 37968225 DOI: 10.1016/j.tcb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023]
Abstract
Non-genetic alterations can produce changes in a cell's phenotype. In cancer, these phenomena can influence a cell's fitness by conferring access to heritable, beneficial phenotypes. Herein, we argue that current discussions of 'phenotypic plasticity' in cancer evolution ignore a salient feature of the original definition: namely, that it occurs in response to an environmental change. We suggest 'phenotypic noise' be used to distinguish non-genetic changes in phenotype that occur independently from the environment. We discuss the conceptual and methodological techniques used to identify these phenomena during cancer evolution. We propose that the distinction will guide efforts to define mechanisms of phenotype change, accelerate translational work to manipulate phenotypes through treatment, and, ultimately, improve patient outcomes.
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Affiliation(s)
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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12
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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13
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Lenz G. Heterogeneity generating capacity in tumorigenesis and cancer therapeutics. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167226. [PMID: 38734320 DOI: 10.1016/j.bbadis.2024.167226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Cells of multicellular organisms generate heterogeneity in a controlled and transient fashion during embryogenesis, which can be reactivated in pathologies such as cancer. Although genomic heterogeneity is an important part of tumorigenesis, continuous generation of phenotypic heterogeneity is central for the adaptation of cancer cells to the challenges of tumorigenesis and response to therapy. Here I discuss the capacity of generating heterogeneity, hereafter called cell hetness, in cancer cells both as the activation of hetness oncogenes and inactivation of hetness tumor suppressor genes, which increase the generation of heterogeneity, ultimately producing an increase in adaptability and cell fitness. Transcriptomic high hetness states in therapy-tolerant cell states denote its importance in cancer resistance to therapy. The definition of the concept of hetness will allow the understanding of its origins, its control during embryogenesis, its loss of control in tumorigenesis and cancer therapeutics and its active targeting.
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Affiliation(s)
- Guido Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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14
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Li CY, Wang W, Leung CH, Yang GJ, Chen J. KDM5 family as therapeutic targets in breast cancer: Pathogenesis and therapeutic opportunities and challenges. Mol Cancer 2024; 23:109. [PMID: 38769556 PMCID: PMC11103982 DOI: 10.1186/s12943-024-02011-0] [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: 02/23/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Breast cancer (BC) is the most frequent malignant cancer diagnosis and is a primary factor for cancer deaths in women. The clinical subtypes of BC include estrogen receptor (ER) positive, progesterone receptor (PR) positive, human epidermal growth factor receptor 2 (HER2) positive, and triple-negative BC (TNBC). Based on the stages and subtypes of BC, various treatment methods are available with variations in the rates of progression-free disease and overall survival of patients. However, the treatment of BC still faces challenges, particularly in terms of drug resistance and recurrence. The study of epigenetics has provided new ideas for treating BC. Targeting aberrant epigenetic factors with inhibitors represents a promising anticancer strategy. The KDM5 family includes four members, KDM5A, KDM5B, KDM5C, and KDMD, all of which are Jumonji C domain-containing histone H3K4me2/3 demethylases. KDM5 proteins have been extensively studied in BC, where they are involved in suppressing or promoting BC depending on their specific upstream and downstream pathways. Several KDM5 inhibitors have shown potent BC inhibitory activity in vitro and in vivo, but challenges still exist in developing KDM5 inhibitors. In this review, we introduce the subtypes of BC and their current therapeutic options, summarize KDM5 family context-specific functions in the pathobiology of BC, and discuss the outlook and pitfalls of KDM5 inhibitors in this disease.
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Affiliation(s)
- Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China.
- Macao Centre for Research and Development in Chinese Medicine, University of Macau, Macau, China.
- MoE Frontiers Science Centre for Precision Oncology, University of Macau, Macau, China.
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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15
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Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024; 14:866-889. [PMID: 38527495 PMCID: PMC11061610 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs. See related commentary by Llinas-Bertran et al., p. 704. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F. Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D. Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
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16
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Toska E. Epigenetic mechanisms of cancer progression and therapy resistance in estrogen-receptor (ER+) breast cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189097. [PMID: 38518961 DOI: 10.1016/j.bbcan.2024.189097] [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: 01/08/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Estrogen receptor-positive (ER+) breast cancer is the most frequent breast cancer subtype. Agents targeting the ER signaling pathway have been successful in reducing mortality from breast cancer for decades. However, mechanisms of resistance to these treatments arise, especially in the metastatic setting. Recently, it has been recognized that epigenetic dysregulation is a common feature that facilitates the acquisition of cancer hallmarks across cancer types, including ER+ breast cancer. Alterations in epigenetic regulators and transcription factors (TF) coupled with changes to the chromatin landscape have been found to orchestrate breast oncogenesis, metastasis, and the development of a resistant phenotype. Here, we review recent advances in our understanding of how the epigenome dictates breast cancer tumorigenesis and resistance to targeted therapies and discuss novel therapeutic interventions for overcoming resistance.
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Affiliation(s)
- Eneda Toska
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA.
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17
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Reid SE, Pantaleo J, Bolivar P, Bocci M, Sjölund J, Morsing M, Cordero E, Larsson S, Malmberg M, Seashore-Ludlow B, Pietras K. Cancer-associated fibroblasts rewire the estrogen receptor response in luminal breast cancer, enabling estrogen independence. Oncogene 2024; 43:1113-1126. [PMID: 38388711 PMCID: PMC10997519 DOI: 10.1038/s41388-024-02973-x] [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: 08/11/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
Advanced breast cancers represent a major therapeutic challenge due to their refractoriness to treatment. Cancer-associated fibroblasts (CAFs) are the most abundant constituents of the tumor microenvironment and have been linked to most hallmarks of cancer. However, the influence of CAFs on therapeutic outcome remains largely unchartered. Here, we reveal that spatial coincidence of abundant CAF infiltration with malignant cells was associated with reduced estrogen receptor (ER)-α expression and activity in luminal breast tumors. Notably, CAFs mediated estrogen-independent tumor growth by selectively regulating ER-α signaling. Whereas most prototypical estrogen-responsive genes were suppressed, CAFs maintained gene expression related to therapeutic resistance, basal-like differentiation, and invasion. A functional drug screen in co-cultures identified effector pathways involved in the CAF-induced regulation of ER-α signaling. Among these, the Transforming Growth Factor-β and the Janus kinase signaling cascades were validated as actionable targets to counteract the CAF-induced modulation of ER-α activity. Finally, genes that were downregulated in cancer cells by CAFs were predictive of poor response to endocrine treatment. In conclusion, our work reveals that CAFs directly control the luminal breast cancer phenotype by selectively modulating ER-α expression and transcriptional function, and further proposes novel targets to disrupt the crosstalk between CAFs and tumor cells to reinstate treatment response to endocrine therapy in patients.
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Affiliation(s)
- Steven E Reid
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Jessica Pantaleo
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Paulina Bolivar
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Matteo Bocci
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Jonas Sjölund
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Mikkel Morsing
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Eugenia Cordero
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Sara Larsson
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Maria Malmberg
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden
| | - Brinton Seashore-Ludlow
- Department of Oncology-Pathology, SciLifeLab, Stockholm, Sweden
- Chemical Biology Consortium Sweden (CBCS), Karolinska Institute, Stockholm, Sweden
| | - Kristian Pietras
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, Lund, Sweden.
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18
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Bose A, Datta S, Mandal R, Ray U, Dhar R. Increased heterogeneity in expression of genes associated with cancer progression and drug resistance. Transl Oncol 2024; 41:101879. [PMID: 38262110 PMCID: PMC10832509 DOI: 10.1016/j.tranon.2024.101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024] Open
Abstract
Fluctuations in the number of regulatory molecules and differences in timings of molecular events can generate variation in gene expression among genetically identical cells in the same environmental condition. This variation, termed as expression noise, can create differences in metabolic state and cellular functions, leading to phenotypic heterogeneity. Expression noise and phenotypic heterogeneity have been recognized as important contributors to intra-tumor heterogeneity, and have been associated with cancer growth, progression, and therapy resistance. However, how expression noise changes with cancer progression in actual cancer patients has remained poorly explored. Such an analysis, through identification of genes with increasing expression noise, can provide valuable insights into generation of intra-tumor heterogeneity, and could have important implications for understanding immune-suppression, drug tolerance and therapy resistance. In this work, we performed a genome-wide identification of changes in gene expression noise with cancer progression using single-cell RNA-seq data of lung adenocarcinoma patients at different stages of cancer. We identified 37 genes in epithelial cells that showed an increasing noise trend with cancer progression, many of which were also associated with cancer growth, EMT and therapy resistance. We found that expression of several of these genes was positively associated with expression of mitochondrial genes, suggesting an important role of mitochondria in generation of heterogeneity. In addition, we uncovered substantial differences in sample-specific noise profiles which could have implications for personalized prognosis and treatment.
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Affiliation(s)
- Anwesha Bose
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Subhasis Datta
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Rakesh Mandal
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Upasana Ray
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India.
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19
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Liu CC, Chen L, Cai YW, Chen YF, Liu YM, Zhou YJ, Shao ZM, Yu KD. Targeting EMSY-mediated methionine metabolism is a potential therapeutic strategy for triple-negative breast cancer. Cell Rep Med 2024; 5:101396. [PMID: 38290515 PMCID: PMC10897545 DOI: 10.1016/j.xcrm.2024.101396] [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: 05/26/2023] [Revised: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
Cancer stem cells (CSCs) are the most intractable subpopulation of triple-negative breast cancer (TNBC) cells, which have been associated with a high risk of relapse and poor prognosis. However, eradication of CSCs continues to be difficult. Here, we integrate the multiomics data of a TNBC cohort (n = 360) to identify vital markers of CSCs. We discover that EMSY, inducing a BRCAness phenotype, is preferentially expressed in breast CSCs, promotes ALDH+ cells enrichment, and is positively correlated with poor relapse-free survival. Mechanistically, EMSY competitively binds to the Jmjc domain, which is critical for KDM5B enzyme activity, to reshape methionine metabolism, and to promote CSC self-renewal and tumorigenesis in an H3K4 methylation-dependent manner. Moreover, EMSY accumulation in TNBC cells sensitizes them to PARP inhibitors against bulk cells and methionine deprivation against CSCs. These findings indicate that clinically relevant eradication of CSCs could be achieved with a strategy that targets CSC-specific vulnerabilities in amino acid metabolism.
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Affiliation(s)
- Cui-Cui Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Lie Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Wen Cai
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Fei Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yi-Ming Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Jie Zhou
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ke-Da Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China.
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20
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Schniewind I, Besso MJ, Klicker S, Schwarz FM, Hadiwikarta WW, Richter S, Löck S, Linge A, Krause M, Dubrovska A, Baumann M, Kurth I, Peitzsch C. Epigenetic Targeting to Overcome Radioresistance in Head and Neck Cancer. Cancers (Basel) 2024; 16:730. [PMID: 38398123 PMCID: PMC10886471 DOI: 10.3390/cancers16040730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background: The sensitivity of head and neck squamous cell carcinoma (HNSCC) to ionizing radiation, among others, is determined by the number of cells with high clonogenic potential and stem-like features. These cellular characteristics are dynamically regulated in response to treatment and may lead to an enrichment of radioresistant cells with a cancer stem cell (CSC) phenotype. Epigenetic mechanisms, particularly DNA and histone methylation, are key regulators of gene-specific transcription and cellular plasticity. Therefore, we hypothesized that specific epigenetic targeting may prevent irradiation-induced plasticity and may sensitize HNSCC cells to radiotherapy. (2) Methods: We compared the DNA methylome and intracellular concentrations of tricarboxylic acid cycle metabolites in radioresistant FaDu and Cal33 cell lines with their parental controls, as well as aldehyde dehydrogenase (ALDH)-positive CSCs with negative controls. Moreover, we conducted a screen of a chemical library targeting enzymes involved in epigenetic regulation in combination with irradiation and analyzed the clonogenic potential, sphere formation, and DNA repair capacity to identify compounds with both radiosensitizing and CSC-targeting potential. (3) Results: We identified the histone demethylase inhibitor GSK-J1, which targets UTX (KDM6A) and JMJD3 (KDM6B), leading to increased H3K27 trimethylation, heterochromatin formation, and gene silencing. The clonogenic survival assay after siRNA-mediated knock-down of both genes radiosensitized Cal33 and SAS cell lines. Moreover, high KDM6A expression in tissue sections of patients with HNSCC was associated with improved locoregional control after primary (n = 137) and post-operative (n = 187) radio/chemotherapy. Conversely, high KDM6B expression was a prognostic factor for reduced overall survival. (4) Conclusions: Within this study, we investigated cellular and molecular mechanisms underlying irradiation-induced cellular plasticity, a key inducer of radioresistance, with a focus on epigenetic alterations. We identified UTX (KDM6A) as a putative prognostic and therapeutic target for HNSCC patients treated with radiotherapy.
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Affiliation(s)
- Iñaki Schniewind
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- Department of Neurology, Carl Gustav Carus University Hospital, Dresden University of Technology, 01307 Dresden, Germany
| | - Maria José Besso
- German Cancer Research Center (DKFZ), Division Radiooncology/Radiobiology, 69120 Heidelberg, Germany
| | - Sebastian Klicker
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
| | - Franziska Maria Schwarz
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Institute of Radiooncology—OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Wahyu Wijaya Hadiwikarta
- German Cancer Research Center (DKFZ), Division Radiooncology/Radiobiology, 69120 Heidelberg, Germany
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany
| | - Steffen Löck
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Annett Linge
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Mechthild Krause
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Institute of Radiooncology—OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Anna Dubrovska
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Institute of Radiooncology—OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Michael Baumann
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), Division Radiooncology/Radiobiology, 69120 Heidelberg, Germany
| | - Ina Kurth
- German Cancer Research Center (DKFZ), Division Radiooncology/Radiobiology, 69120 Heidelberg, Germany
| | - Claudia Peitzsch
- National Center for Tumor Diseases (NCT), Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (I.S.)
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf, 01307 Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Dresden University of Technology, 01307 Dresden, Germany
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21
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Ullrich V, Ertmer S, Baginska A, Dorsch M, Gull HH, Cima I, Berger P, Dobersalske C, Langer S, Meyer L, Dujardin P, Kebir S, Glas M, Blau T, Keyvani K, Rauschenbach L, Sure U, Roesch A, Grüner BM, Scheffler B. KDM5B predicts temozolomide-resistant subclones in glioblastoma. iScience 2024; 27:108596. [PMID: 38174322 PMCID: PMC10762356 DOI: 10.1016/j.isci.2023.108596] [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: 04/25/2023] [Revised: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Adaptive plasticity to the standard chemotherapeutic temozolomide (TMZ) leads to glioblastoma progression. Here, we examine early stages of this process in patient-derived cellular models, exposing the human lysine-specific demethylase 5B (KDM5B) as a prospective indicator for subclonal expansion. By integration of a reporter, we show its preferential activity in rare, stem-like ALDH1A1+ cells, immediately increasing expression upon TMZ exposure. Naive, genetically unmodified KDM5Bhigh cells phosphorylate AKT (pAKT) and act as slow-cycling persisters under TMZ. Knockdown of KDM5B reverses pAKT levels, simultaneously increasing PTEN expression and TMZ sensitivity. Pharmacological inhibition of PTEN rescues the effect. Interference with KDM5B subsequent to TMZ decreases cellular vitality, and clonal tracing with DNA barcoding demonstrates high individual levels of KDM5B to predict subclonal expansion already before TMZ exposure. Thus, KDM5Bhigh treatment-naive cells preferentially contribute to the dynamics of drug resistance under TMZ. These findings may serve as a cornerstone for future biomarker-assisted clinical trials.
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Affiliation(s)
- Vivien Ullrich
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Ertmer
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Anna Baginska
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Madeleine Dorsch
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Hanah H. Gull
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, 45147 Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, 45147 Essen, Germany
| | - Igor Cima
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Pia Berger
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Celia Dobersalske
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Langer
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Loona Meyer
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Philip Dujardin
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Sied Kebir
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, 45147 Essen, Germany
- Division of Clinical Neurooncology, Department of Neurology, University Hospital Essen, 45147 Essen, Germany
| | - Martin Glas
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, 45147 Essen, Germany
- Division of Clinical Neurooncology, Department of Neurology, University Hospital Essen, 45147 Essen, Germany
| | - Tobias Blau
- Department of Neuropathology, University Hospital Essen, 45147 Essen, Germany
| | - Kathy Keyvani
- Department of Neuropathology, University Hospital Essen, 45147 Essen, Germany
| | - Laurèl Rauschenbach
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, 45147 Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, 45147 Essen, Germany
| | - Ulrich Sure
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, 45147 Essen, Germany
- Center for Translational Neuroscience and Behavioral Science (C-TNBS), University of Duisburg-Essen, 45147 Essen, Germany
| | - Alexander Roesch
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Dermatology, University Hospital Essen, 45147 Essen, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Barbara M. Grüner
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Björn Scheffler
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, a partnership between DKFZ and University Hospital Essen, Germany
- West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Center of Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
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22
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Li D, Liang H, Wei Y, Xiao H, Peng X, Pan W. Exploring the potential of histone demethylase inhibition in multi-therapeutic approaches for cancer treatment. Eur J Med Chem 2024; 264:115999. [PMID: 38043489 DOI: 10.1016/j.ejmech.2023.115999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
Histone demethylases play a critical role in gene transcription regulation and have been implicated in cancer. Numerous reports have highlighted the overexpression of histone demethylases, such as LSD1 and JmjC, in various malignant tumor tissues, identifying them as effective therapeutic targets for cancer treatment. Despite many histone demethylase inhibitors entering clinical trials, their clinical efficacy has been limited. Therefore, combination therapies based on histone demethylase inhibitors, along with other modulators like dual-acting inhibitors, have gained significant attention and made notable progress in recent years. In this review, we provide an overview of recent advances in drug discovery targeting histone demethylases, focusing specifically on drug combination therapy and histone demethylases-targeting dual inhibitors. We discuss the rational design, pharmacodynamics, pharmacokinetics, and clinical status of these approaches. Additionally, we summarize the co-crystal structures of LSD1 inhibitors and their target proteins as well as describe the corresponding binding interactions. Finally, we also provided the challenges and future directions for utilizing histone demethylases in cancer therapy, such as PROTACs and molecular glue etc.
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Affiliation(s)
- Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Hailiu Liang
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China
| | - Yifei Wei
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China
| | - Hao Xiao
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
| | - Xiaopeng Peng
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
| | - Wanyi Pan
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
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23
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Koncz M, Jimenez MAL, Piebes DGE, Postma M, Verschure PJ. Single-Molecule Analysis of Transcription Dynamics to Understand the Relationship Between Epigenetic Alterations and Transcriptional Variability. Methods Mol Biol 2024; 2842:449-460. [PMID: 39012610 DOI: 10.1007/978-1-0716-4051-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Heterogeneity in gene expression largely stems from the discontinuous nature of transcription, with transcripts being produced in bursts with defined frequencies. This cell-to-cell variability in transcription within isogenic cell populations is a known phenomenon across numerous genes. Multiple gene regulatory and epigenetic factors have been identified as key contributors to this pulsatile gene activity. Understanding the effects of epigenetic modulation on transcriptional cell-to-cell variability and kinetics of transcriptional activity is crucial for interpreting changes in treatment responsiveness. We present a detailed protocol that guides the assessment of fluctuations in gene expression induced by epigenetic modulation using single-molecule RNA in situ hybridization (smRNA FISH) combined with confocal microscopy imaging, data analysis, and quantification in breast cancer cells. Through smRNA FISH labeling, both mature and nascent transcripts are identified. Subsequently, the number of mature transcripts and the intensity and frequency of nascent transcripts are quantified, and these measurements are used to calculate the burst size and frequency for the labeled gene. By following this step-by-step methodology, insights are obtained into the intricate relationship between epigenetic alterations and the dynamic nature of gene expression in breast cancer cells.
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Affiliation(s)
- Mihály Koncz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Diewertje G E Piebes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Marten Postma
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Pernette J Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
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24
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Xiao M, Kondo S, Nomura M, Kato S, Nishimura K, Zang W, Zhang Y, Akashi T, Viny A, Shigehiro T, Ikawa T, Yamazaki H, Fukumoto M, Tanaka A, Hayashi Y, Koike Y, Aoyama Y, Ito H, Nishikawa H, Kitamura T, Kanai A, Yokoyama A, Fujiwara T, Goyama S, Noguchi H, Lee SC, Toyoda A, Hinohara K, Abdel-Wahab O, Inoue D. BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nat Commun 2023; 14:8372. [PMID: 38102116 PMCID: PMC10724271 DOI: 10.1038/s41467-023-44081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF (ncBAF). While cBAF and PBAF regulate fates of multiple cell types, roles for ncBAF in hematopoietic stem cells (HSCs) have not been investigated. Motivated by recent discovery of disrupted expression of BRD9, an essential component of ncBAF, in multiple cancers, including clonal hematopoietic disorders, we evaluate here the role of BRD9 in normal and malignant HSCs. BRD9 loss enhances chromatin accessibility, promoting myeloid lineage skewing while impairing B cell development. BRD9 significantly colocalizes with CTCF, whose chromatin recruitment is augmented by BRD9 loss, leading to altered chromatin state and expression of myeloid-related genes within intact topologically associating domains. These data uncover ncBAF as critical for cell fate specification in HSCs via three-dimensional regulation of gene expression and illuminate roles for ncBAF in normal and malignant hematopoiesis.
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Affiliation(s)
- Muran Xiao
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinji Kondo
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, National Institute of Genetics, Mishima, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yifan Zhang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Akashi
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Systems Biology, Center for Neurological Diseases and Cancer, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Aaron Viny
- Department of Medicine, Division of Hematology and Oncology, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Tsukasa Shigehiro
- Division of Immunobiology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Tomokatsu Ikawa
- Division of Immunobiology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yumi Aoyama
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Ito
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Toshio Kitamura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akinori Kanai
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Yamagata, Japan
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Laboratory Diagnostics, Tohoku University Hospital, Sendai, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, National Institute of Genetics, Mishima, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Stanley C Lee
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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25
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Beumers L, Vlachavas EI, Borgoni S, Schwarzmüller L, Penso-Dolfin L, Michels BE, Sofyali E, Burmester S, Heiss D, Wilhelm H, Yarden Y, Helm D, Will R, Goncalves A, Wiemann S. Clonal heterogeneity in ER+ breast cancer reveals the proteasome and PKC as potential therapeutic targets. NPJ Breast Cancer 2023; 9:97. [PMID: 38042915 PMCID: PMC10693625 DOI: 10.1038/s41523-023-00604-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Intratumoral heterogeneity impacts the success or failure of anti-cancer therapies. Here, we investigated the evolution and mechanistic heterogeneity in clonal populations of cell models for estrogen receptor positive breast cancer. To this end, we established barcoded models of luminal breast cancer and rendered them resistant to commonly applied first line endocrine therapies. By isolating single clones from the resistant cell pools and characterizing replicates of individual clones we observed inter- (between cell lines) and intra-tumor (between different clones from the same cell line) heterogeneity. Molecular characterization at RNA and phospho-proteomic levels revealed private clonal activation of the unfolded protein response and respective sensitivity to inhibition of the proteasome, and potentially shared sensitivities for repression of protein kinase C. Our in vitro findings are consistent with tumor-heterogeneity that is observed in breast cancer patients thus highlighting the need to uncover heterogeneity at an individual patient level and to adjust therapies accordingly.
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Affiliation(s)
- Lukas Beumers
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
| | - Efstathios-Iason Vlachavas
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Luisa Schwarzmüller
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Luca Penso-Dolfin
- Division of Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Birgitta E Michels
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Emre Sofyali
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sara Burmester
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Daniela Heiss
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Rainer Will
- Cellular Tools Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Angela Goncalves
- Division of Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
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26
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Ravindran Menon D, Hammerlindl H, Gimenez G, Hammerlindl S, Zuegner E, Torrano J, Bordag N, Emran AA, Giam M, Denil S, Pavelka N, Tan AC, Sturm RA, Haass NK, Rancati G, Herlyn M, Magnes C, Eccles MR, Fujita M, Schaider H. H3K4me3 remodeling induced acquired resistance through O-GlcNAc transferase. Drug Resist Updat 2023; 71:100993. [PMID: 37639774 PMCID: PMC10719180 DOI: 10.1016/j.drup.2023.100993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
AIMS Drivers of the drug tolerant proliferative persister (DTPP) state have not been well investigated. Histone H3 lysine-4 trimethylation (H3K4me3), an active histone mark, might enable slow cycling drug tolerant persisters (DTP) to regain proliferative capacity. This study aimed to determine H3K4me3 transcriptionally active sites identifying a key regulator of DTPPs. METHODS Deploying a model of adaptive cancer drug tolerance, H3K4me3 ChIP-Seq data of DTPPs guided identification of top transcription factor binding motifs. These suggested involvement of O-linked N-acetylglucosamine transferase (OGT), which was confirmed by metabolomics analysis and biochemical assays. OGT impact on DTPPs and adaptive resistance was explored in vitro and in vivo. RESULTS H3K4me3 remodeling was widespread in CPG island regions and DNA binding motifs associated with O-GlcNAc marked chromatin. Accordingly, we observed an upregulation of OGT, O-GlcNAc and its binding partner TET1 in chronically treated cancer cells. Inhibition of OGT led to loss of H3K4me3 and downregulation of genes contributing to drug resistance. Genetic ablation of OGT prevented acquired drug resistance in in vivo models. Upstream of OGT, we identified AMPK as an actionable target. AMPK activation by acetyl salicylic acid downregulated OGT with similar effects on delaying acquired resistance. CONCLUSION Our findings uncover a fundamental mechanism of adaptive drug resistance that governs cancer cell reprogramming towards acquired drug resistance, a process that can be exploited to improve response duration and patient outcomes.
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Affiliation(s)
- Dinoop Ravindran Menon
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Department of Dermatology, University of Colorado Denver, Aurora, CO, USA; Department of Medical Oncology, University of Colorado Denver, Aurora, CO, USA
| | - Heinz Hammerlindl
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Department of Pharmaceutical Chemistry, The University of California, San Francisco, San Francisco, CA, USA
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sabrina Hammerlindl
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Department of Pharmaceutical Chemistry, The University of California, San Francisco, San Francisco, CA, USA
| | - Elmar Zuegner
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, Austria
| | - Joachim Torrano
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Natalie Bordag
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, Austria
| | - Abdullah Al Emran
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Maybelline Giam
- Institute of Medical Biology, Agency for Science, Technology and Research, Immunos Singapore, Singapore
| | - Simon Denil
- Institute of Medical Biology, Agency for Science, Technology and Research, Immunos Singapore, Singapore
| | - Norman Pavelka
- SIgN, the Singapore Institute for Immunology, Agency for Science, Technology and Research, Immunos Singapore, Singapore
| | - Aik-Choon Tan
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Richard A Sturm
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Nikolas K Haass
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Giulia Rancati
- Institute of Medical Biology, Agency for Science, Technology and Research, Immunos Singapore, Singapore
| | | | - Christoph Magnes
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, Austria
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Denver, Aurora, CO, USA; Denver VA Medical Center, Denver, CO, USA; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO, USA
| | - Helmut Schaider
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Department of Dermatology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia.
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27
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Pu Y, Li L, Peng H, Liu L, Heymann D, Robert C, Vallette F, Shen S. Drug-tolerant persister cells in cancer: the cutting edges and future directions. Nat Rev Clin Oncol 2023; 20:799-813. [PMID: 37749382 DOI: 10.1038/s41571-023-00815-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.
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Affiliation(s)
- Yi Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Haoning Peng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Nantes, France
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
- Nantes Université, INSERM, U1307, CRCI2NA, Nantes, France.
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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28
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Kozłowska E, Swierniak A. Mathematical Model of Intrinsic Drug Resistance in Lung Cancer. Int J Mol Sci 2023; 24:15801. [PMID: 37958784 PMCID: PMC10650033 DOI: 10.3390/ijms242115801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/25/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Drug resistance is a bottleneck in cancer treatment. Commonly, a molecular treatment for cancer leads to the emergence of drug resistance in the long term. Thus, some drugs, despite their initial excellent response, are withdrawn from the market. Lung cancer is one of the most mutated cancers, leading to dozens of targeted therapeutics available against it. Here, we have developed a mechanistic mathematical model describing sensitization to nine groups of targeted therapeutics and the emergence of intrinsic drug resistance. As we focus only on intrinsic drug resistance, we perform the computer simulations of the model only until clinical diagnosis. We have utilized, for model calibration, the whole-exome sequencing data combined with clinical information from over 1000 non-small-cell lung cancer patients. Next, the model has been applied to find an answer to the following questions: When does intrinsic drug resistance emerge? And how long does it take for early-stage lung cancer to grow to an advanced stage? The results show that drug resistance is inevitable at diagnosis but not always detectable and that the time interval between early and advanced-stage tumors depends on the selection advantage of cancer cells.
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Affiliation(s)
| | - Andrzej Swierniak
- Department of Systems Biology and Engineering, Silesian University of Technology, 44100 Gliwie, Poland;
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29
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Wang XC, Tang YL, Liang XH. Tumour follower cells: A novel driver of leader cells in collective invasion (Review). Int J Oncol 2023; 63:115. [PMID: 37615176 PMCID: PMC10552739 DOI: 10.3892/ijo.2023.5563] [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: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
Collective cellular invasion in malignant tumours is typically characterized by the cooperative migration of multiple cells in close proximity to each other. Follower cells are led away from the tumour by specialized leader cells, and both cell populations play a crucial role in collective invasion. Follower cells form the main body of the migration system and depend on intercellular contact for migration, whereas leader cells indicate the direction for the entire cell population. Although collective invasion can occur in epithelial and non‑epithelial malignant neoplasms, such as medulloblastoma and rhabdomyosarcoma, the present review mainly provided an extensive analysis of epithelial tumours. In the present review, the cooperative mechanisms of contact inhibition locomotion between follower and leader cells, where follower cells coordinate and direct collective movement through physical (mechanical) and chemical (signalling) interactions, is summarised. In addition, the molecular mechanisms of follower cell invasion and metastasis during remodelling and degradation of the extracellular matrix and how chemotaxis and lateral inhibition mediate follower cell behaviour were analysed. It was also demonstrated that follower cells exhibit genetic and metabolic heterogeneity during invasion, unlike leader cells.
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Affiliation(s)
- Xiao-Chen Wang
- Departments of Oral and Maxillofacial Surgery, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ya-Ling Tang
- Departments of Oral Pathology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin-Hua Liang
- Departments of Oral and Maxillofacial Surgery, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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30
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Longbotham JE, Kelly MJS, Fujimori DG. Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A. ACS Chem Biol 2023; 18:1915-1925. [PMID: 33621062 PMCID: PMC8380758 DOI: 10.1021/acschembio.0c00976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PHD reader domains are chromatin binding modules often responsible for the recruitment of large protein complexes that contain histone modifying enzymes, chromatin remodelers, and DNA repair machinery. A majority of PHD domains recognize N-terminal residues of histone H3 and are sensitive to the methylation state of Lys4 in histone H3 (H3K4). Histone demethylase KDM5A, an epigenetic eraser enzyme that contains three PHD domains, is often overexpressed in various cancers, and its demethylation activity is allosterically enhanced when its PHD1 domain is bound to the H3 tail. The allosteric regulatory function of PHD1 expands roles of reader domains, suggesting unique features of this chromatin interacting module. Our previous studies determined the H3 binding site of PHD1, although it remains unclear how the H3 tail interacts with the N-terminal residues of PHD1 and how PHD1 discriminates against H3 tails with varying degrees of H3K4 methylation. Here, we have determined the solution structure of apo and H3 bound PHD1. We observe conformational changes occurring in PHD1 in order to accommodate H3, which interestingly binds in a helical conformation. We also observe differential interactions of binding residues with differently methylated H3K4 peptides (me0, me1, me2, or me3), providing a rationale for PHD1's preference for lower methylation states of H3K4. We further assessed the contributions of various H3 interacting residues in the PHD1 domain to the binding of H3 peptides. The structural details of the H3 binding site could provide useful information to aid the development of allosteric small molecule modulators of KDM5A.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
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31
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Song YQ, Yang GJ, Ma DL, Wang W, Leung CH. The role and prospect of lysine-specific demethylases in cancer chemoresistance. Med Res Rev 2023; 43:1438-1469. [PMID: 37012609 DOI: 10.1002/med.21955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Histone methylation plays a key function in modulating gene expression, and preserving genome integrity and epigenetic inheritance. However, aberrations of histone methylation are commonly observed in human diseases, especially cancer. Lysine methylation mediated by histone methyltransferases can be reversed by lysine demethylases (KDMs), which remove methyl marks from histone lysine residues. Currently, drug resistance is a main impediment for cancer therapy. KDMs have been found to mediate drug tolerance of many cancers via altering the metabolic profile of cancer cells, upregulating the ratio of cancer stem cells and drug-tolerant genes, and promoting the epithelial-mesenchymal transition and metastatic ability. Moreover, different cancers show distinct oncogenic addictions for KDMs. The abnormal activation or overexpression of KDMs can alter gene expression signatures to enhance cell survival and drug resistance in cancer cells. In this review, we describe the structural features and functions of KDMs, the KDMs preferences of different cancers, and the mechanisms of drug resistance resulting from KDMs. We then survey KDM inhibitors that have been used for combating drug resistance in cancer, and discuss the opportunities and challenges of KDMs as therapeutic targets for cancer drug resistance.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
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32
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Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
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Howland KK, Brock A. Cellular barcoding tracks heterogeneous clones through selective pressures and phenotypic transitions. Trends Cancer 2023; 9:591-601. [PMID: 37105856 PMCID: PMC10339273 DOI: 10.1016/j.trecan.2023.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023]
Abstract
Genomic DNA barcoding has emerged as a sensitive and flexible tool to measure the fates of clonal subpopulations within a heterogeneous cancer cell population. Coupling cellular barcoding with single-cell transcriptomics permits the longitudinal analysis of molecular mechanisms with detailed clone-level resolution. Numerous recent studies have employed these tools to track clonal cell states in cancer progression and treatment response. With these new technologies comes the opportunity to examine longstanding questions about the origins and contributions of tumor cell heterogeneity and the roles of selection and phenotypic plasticity in disease progression and treatment.
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Affiliation(s)
- Kennedy K Howland
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78734, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78734, USA.
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34
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Kravitz CJ, Yan Q, Nguyen DX. Epigenetic markers and therapeutic targets for metastasis. Cancer Metastasis Rev 2023; 42:427-443. [PMID: 37286865 PMCID: PMC10595046 DOI: 10.1007/s10555-023-10109-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
The last few years have seen an increasing number of discoveries which collectively demonstrate that histone and DNA modifying enzyme modulate different stages of metastasis. Moreover, epigenomic alterations can now be measured at multiple scales of analysis and are detectable in human tumors or liquid biopsies. Malignant cell clones with a proclivity for relapse in certain organs may arise in the primary tumor as a consequence of epigenomic alterations which cause a loss in lineage integrity. These alterations may occur due to genetic aberrations acquired during tumor progression or concomitant to therapeutic response. Moreover, evolution of the stroma can also alter the epigenome of cancer cells. In this review, we highlight current knowledge with a particular emphasis on leveraging chromatin and DNA modifying mechanisms as biomarkers of disseminated disease and as therapeutic targets to treat metastatic cancers.
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Affiliation(s)
- Carolyn J Kravitz
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT, 06520, USA.
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Ferro A, Generali D, Caffo O, Caldara A, De Lisi D, Dipasquale M, Lorenzi M, Monteverdi S, Fedele P, Ciribilli Y. Oral selective estrogen receptor degraders (SERDs): The new emperors in breast cancer clinical practice? Semin Oncol 2023; 50:90-101. [PMID: 37673696 DOI: 10.1053/j.seminoncol.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
Endocrine therapy (ET) targeting estrogen receptor (ER) signaling is still the mainstay treatment option for early or advanced ER-positive breast cancer (BC) and may involve suppressing estrogen production by means of aromatase inhibitors or directly blocking the ER pathway through selective estrogen receptor modulators such as tamoxifen or selective estrogen receptor degraders such as fulvestrant. However, despite the availability of this armamentarium in clinical practice, de novo or acquired resistance to ET is the main cause of endocrine-based treatment failure leading to the progression of the BC. Recent advances in targeting, modulating, and degrading ERs have led to the development of new drugs capable of overcoming intrinsic or acquired ET resistance related to alterations in the ESR1 gene. The new oral selective estrogen receptor degraders, which are capable of reducing ER protein expression and blocking estrogen-dependent and -independent ER signaling, have a broader spectrum of activity against ESR1 mutations and seem to be a promising means of overcoming the failure of standard ET. The aim of this review is to summarize the development of oral selective estrogen receptor degraders, their current status, and their future perspectives.
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Affiliation(s)
- Antonella Ferro
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy.
| | - Daniele Generali
- UO Patologia Mammaria, Cremona Hospital, ASST Cremona, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, Italy
| | - Orazio Caffo
- Medical Oncology Unit, Santa Chiara Hospital, APSS Trento, Italy
| | - Alessia Caldara
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy
| | - Delia De Lisi
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy
| | - Mariachiara Dipasquale
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy
| | - Martina Lorenzi
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy
| | - Sara Monteverdi
- Medical Oncology, Breast Unit Santa Chiara Hospital, APSS Trento, Largo Medaglie D'Oro, Trento, Italy
| | - Palma Fedele
- Oncology Unit, Dario Camberlingo Hospital, ASL Brindisi, Francavilla Fontana, Italy
| | - Yari Ciribilli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Italy.
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36
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Grody EI, Abraham A, Shukla V, Goyal Y. Toward a systems-level probing of tumor clonality. iScience 2023; 26:106574. [PMID: 37192968 PMCID: PMC10182304 DOI: 10.1016/j.isci.2023.106574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Cancer has been described as a genetic disease that clonally evolves in the face of selective pressures imposed by cell-intrinsic and extrinsic factors. Although classical models based on genetic data predominantly propose Darwinian mechanisms of cancer evolution, recent single-cell profiling of cancers has described unprecedented heterogeneity in tumors providing support for alternative models of branched and neutral evolution through both genetic and non-genetic mechanisms. Emerging evidence points to a complex interplay between genetic, non-genetic, and extrinsic environmental factors in shaping the evolution of tumors. In this perspective, we briefly discuss the role of cell-intrinsic and extrinsic factors that shape clonal behaviors during tumor progression, metastasis, and drug resistance. Taking examples of pre-malignant states associated with hematological malignancies and esophageal cancer, we discuss recent paradigms of tumor evolution and prospective approaches to further enhance our understanding of this spatiotemporally regulated process.
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Affiliation(s)
- Emanuelle I. Grody
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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37
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Yang FF, Xu XL, Hu T, Liu JQ, Zhou JZ, Ma LY, Liu HM. Lysine-Specific Demethylase 1 Promises to Be a Novel Target in Cancer Drug Resistance: Therapeutic Implications. J Med Chem 2023; 66:4275-4293. [PMID: 37014989 DOI: 10.1021/acs.jmedchem.2c01527] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chemotherapy, targeted therapy, and immunotherapy are effective against most tumors, but drug resistance remains a barrier to successful treatment. Lysine-specific demethylase 1 (LSD1), a member of histone demethylation modifications, can regulate invasion, metastasis, apoptosis, and immune escape of tumor cells, which are associated with tumorigenesis and tumor progression. Recent studies suggest that LSD1 ablation regulates resensitivity of tumor cells to anticarcinogens containing immune checkpoint inhibitors (ICIs) via multiple upstream and downstream pathways. In this review, we describe the recent findings about LSD1 biology and its role in the development and progression of cancer drug resistance. Further, we summarize LSD1 inhibitors that have a reversal or resensitive effect on drug resistance and discuss the possibility of targeting LSD1 in combination with other agents to surmount resistance.
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Affiliation(s)
- Fei-Fei Yang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xue-Li Xu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ting Hu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jian-Quan Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jin-Zhu Zhou
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Li-Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- Key Laboratory of Cardio-Cerebrovascular Drug, China Meheco Topfond Pharmaceutical Company, Zhumadian 463000, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
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38
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Kato S, Maeda Y, Sugiyama D, Watanabe K, Nishikawa H, Hinohara K. The cancer epigenome: Non-cell autonomous player in tumor immunity. Cancer Sci 2023; 114:730-740. [PMID: 36468774 PMCID: PMC9986067 DOI: 10.1111/cas.15681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of the tumor-intrinsic epigenetic circuit is a key driver event for the development of cancer. Accumulating evidence suggests that epigenetic and/or genetic drivers stimulate intrinsic oncogenic pathways as well as extrinsic factors that modulate the immune system. These modulations indeed shape the tumor microenvironment (TME), allowing pro-oncogenic factors to become oncogenic, thereby contributing to cancer development and progression. Here we review the epigenetic dysregulation arising in cancer cells that disseminates throughout the TME and beyond. Recent CRISPR screening has elucidated key epigenetic drivers that play important roles in the proliferation of cancer cells (intrinsic) and inhibition of antitumor immunity (extrinsic), which lead to the development and progression of cancer. These epigenetic players can serve as promising targets for cancer therapy as a dual (two-in-one)-targeted approach. Considering the interplay between cancer and the immune system as a key determinant of immunotherapy, we discuss a novel lineage-tracing technology that enables longitudinal monitoring of cancer and immune phenotypic heterogeneity and fate paths during cancer development, progression, and therapeutic interventions.
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Affiliation(s)
- Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Watanabe
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
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Rational combinations of targeted cancer therapies: background, advances and challenges. Nat Rev Drug Discov 2023; 22:213-234. [PMID: 36509911 DOI: 10.1038/s41573-022-00615-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
Over the past two decades, elucidation of the genetic defects that underlie cancer has resulted in a plethora of novel targeted cancer drugs. Although these agents can initially be highly effective, resistance to single-agent therapies remains a major challenge. Combining drugs can help avoid resistance, but the number of possible drug combinations vastly exceeds what can be tested clinically, both financially and in terms of patient availability. Rational drug combinations based on a deep understanding of the underlying molecular mechanisms associated with therapy resistance are potentially powerful in the treatment of cancer. Here, we discuss the mechanisms of resistance to targeted therapies and how effective drug combinations can be identified to combat resistance. The challenges in clinically developing these combinations and future perspectives are considered.
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40
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Dormancy, stemness, and therapy resistance: interconnected players in cancer evolution. Cancer Metastasis Rev 2023; 42:197-215. [PMID: 36757577 PMCID: PMC10014678 DOI: 10.1007/s10555-023-10092-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023]
Abstract
The biological complexity of cancer represents a tremendous clinical challenge, resulting in the frequent failure of current treatment protocols. In the rapidly evolving scenario of a growing tumor, anticancer treatments impose a drastic perturbation not only to cancer cells but also to the tumor microenvironment, killing a portion of the cells and inducing a massive stress response in the survivors. Consequently, treatments can act as a double-edged sword by inducing a temporary response while laying the ground for therapy resistance and subsequent disease progression. Cancer cell dormancy (or quiescence) is a central theme in tumor evolution, being tightly linked to the tumor's ability to survive cytotoxic challenges, metastasize, and resist immune-mediated attack. Accordingly, quiescent cancer cells (QCCs) have been detected in virtually all the stages of tumor development. In recent years, an increasing number of studies have focused on the characterization of quiescent/therapy resistant cancer cells, unveiling QCCs core transcriptional programs, metabolic plasticity, and mechanisms of immune escape. At the same time, our partial understanding of tumor quiescence reflects the difficulty to identify stable QCCs biomarkers/therapeutic targets and to control cancer dormancy in clinical settings. This review focuses on recent discoveries in the interrelated fields of dormancy, stemness, and therapy resistance, discussing experimental evidences in the frame of a nonlinear dynamics approach, and exploring the possibility that tumor quiescence may represent not only a peril but also a potential therapeutic resource.
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41
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Liu X, Peng S, Tang G, Xu G, Xie Y, Shen D, Zhu M, Huang Y, Wang X, Yu H, Huang M, Luo Y. Fasting-mimicking diet synergizes with ferroptosis against quiescent, chemotherapy-resistant cells. EBioMedicine 2023; 90:104496. [PMID: 36863257 PMCID: PMC9996234 DOI: 10.1016/j.ebiom.2023.104496] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND More than ten randomized clinical trials are being tested to evaluate the efficacy, effectiveness and safety of a fasting-mimicking diet (FMD) combined with different antitumor agents. METHODS UMI-mRNA sequencing, Cell-cycle analysis, Label retention, metabolomics, Multilabeling et al. were used to explore mechanisms. A tandem mRFP-GFP-tagged LC3B, Annexin-V-FITC Apoptosis, TUNEL, H&E, Ki-67 and animal model was used to search for synergistic drugs. FINDINGS Here we showed that fasting or FMD retards tumor growth more effectively but does not increase 5-fluorouracil/oxaliplatin (5-FU/OXA) sensitivity to apoptosis in vitro and in vivo. Mechanistically, we demonstrated that CRC cells would switch from an active proliferative to a slow-cycling state during fasting. Furthermore, metabolomics shows cell proliferation was decreased to survive nutrient stress in vivo, as evidenced by a low level of adenosine and deoxyadenosine monophosphate. CRC cells would decrease proliferation to achieve increased survival and relapse after chemotherapy. In addition, these fasting-induced quiescent cells were more prone to develop drug-tolerant persister (DTP) tumor cells postulated to be responsible for cancer relapse and metastasis. Then, UMI-mRNA sequencing uncovered the ferroptosis pathway as the pathway most influenced by fasting. Combining fasting with ferroptosis inducer treatment leads to tumor inhibition and eradication of quiescent cells by boosting autophagy. INTERPRETATION Our results suggest that ferroptosis could improve the antitumor activity of FMD + chemotherapy and highlight a potential therapeutic opportunity to avoid DTP cells-driven tumor relapse and therapy failure. FUNDING A full list of funding bodies can be found in the Acknowledgements section.
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Affiliation(s)
- Xiaoxia Liu
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China.
| | - Shaoyong Peng
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guannan Tang
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Gaopo Xu
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Yumo Xie
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Dingcheng Shen
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Mingxuan Zhu
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Yaoyi Huang
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaolin Wang
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Huichuan Yu
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Meijin Huang
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanxin Luo
- Department of Colorectal Surgery, Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China.
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42
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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43
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Fang S, Zheng L, Shen L, Su Y, Ding J, Chen W, Chen X, Chen W, Shu G, Chen M, Zhao Z, Tu J, Ji J. Inactivation of KDM5A suppresses growth and enhances chemosensitivity in liver cancer by modulating ROCK1/PTEN/AKT pathway. Eur J Pharmacol 2023; 940:175465. [PMID: 36566915 DOI: 10.1016/j.ejphar.2022.175465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Liver cancer is a kind of malignant tumor with poor sensitivity to chemotherapy. It is urgent to investigate approaches to improve the outcome of chemotherapy. KDM5A has been reported to be an oncogene in various cancers and is associated with drug resistance. However, the functions of KDM5A in chemotherapeutic sensitivity of liver cancer not been well illustrated. In this study, we found that KDM5A was upregulated in liver cancer tissue and cell lines. KDM5A knockdown using a gene interference strategy suppressed the growth of liver cancer in vitro and in vivo. CPI-455, a pharmacological inactivation of KDM5A enhanced the cytotoxicity of cisplatin (CDDP) in liver cells. CPI-455 and CDDP cotreatment resulted in apoptosis and mitochondrial dysfunction. We also found that knockdown or inactivation of KDM5A resulted in the downregulation of ROCK1, an oncogene regulating the activation of the PTEN/AKT signaling pathway. In particular, overexpression of ROCK1 or SF1670, a pharmacological inhibitor of PTEN, alleviated the cytotoxicity of CPI-455 and CDDP cotreatment. In HCCLM3 xenografts, CPI-455 and CDDP cotreatment dramatically inhibited the growth of xenograft tumor compared to CPI-455 or CDDP treatment alone. In conclusion, this study suggested that targeting the inactivation of KDM5A is an efficient strategy to enhance the chemosensitivity of liver cancer cells to CDDP by modulating the ROCK1/PTEN/AKT signaling pathway.
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Affiliation(s)
- Shiji Fang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China
| | - Liyun Zheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China
| | - Lin Shen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China
| | - Yanping Su
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Jiayi Ding
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Weiyue Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Xiaoxiao Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Weiqian Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China
| | - Gaofeng Shu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Minjiang Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Zhongwei Zhao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China
| | - Jianfei Tu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China.
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China; Interventional Diagnosis and Treatment Center, Lishui Hospital of Zhejiang University, Lishui, 323000, China.
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Di Nisio E, Licursi V, Mannironi C, Buglioni V, Paiardini A, Robusti G, Noberini R, Bonaldi T, Negri R. A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression. Cancer Gene Ther 2023:10.1038/s41417-022-00584-w. [PMID: 36697763 DOI: 10.1038/s41417-022-00584-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023]
Abstract
KDM5B histone demethylase is overexpressed in many cancers and plays an ambivalent role in oncogenesis, depending on the specific context. This ambivalence could be explained by the expression of KDM5B protein isoforms with diverse functional roles, which could be present at different levels in various cancer cell lines. We show here that one of these isoforms, namely KDM5B-NTT, accumulates in breast cancer cell lines due to remarkable protein stability relative to the canonical PLU-1 isoform, which shows a much faster turnover. This isoform is the truncated and catalytically inactive product of an mRNA with a transcription start site downstream of the PLU-1 isoform, and the consequent usage of an alternative ATG for translation initiation. It also differs from the PLU-1 transcript in the inclusion of an additional exon (exon-6), previously attributed to other putative isoforms. Overexpression of this isoform in MCF7 cells leads to an increase in bulk H3K4 methylation and induces derepression of a gene cluster, including the tumor suppressor Cav1 and several genes involved in the interferon-alpha and -gamma response. We discuss the relevance of this finding considering the hypothesis that KDM5B may possess regulatory roles independent of its catalytic activity.
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Affiliation(s)
- Elena Di Nisio
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Sir James Black Centre, Dow Street, DD1 5EH, Dundee, Scotland, UK
| | - Valerio Licursi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy
| | - Valentina Buglioni
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome, p.le Aldo Moro 5, 00185, Rome, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.,Department of Oncology and Hematology-Oncology, University of Milan, Milan, 20122, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy. .,Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy.
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45
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Hao F. Entanglement of Methylation Changes and cGAS-STING Signaling in Non-Small-Cell Lung Cancer. Comb Chem High Throughput Screen 2023; 26:224-235. [PMID: 35585823 DOI: 10.2174/1386207325666220517095503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND cGAS-STING signaling has been primarily discovered as an important DNA sensing machinery, bridging innate immunity and adaptive immunity. Beyond its antiviral response, recent evidence expanded its complicated role in cancer therapy. METHODS UALCAN, The TCGA Wander, GEPIA, SMART, TIMER, Kaplan-Meier plotter, TCGA Data, and cBioPortal were utilized in the investigation. RESULTS We evaluated the expression of four key molecules (MB21D1, TMEM173, TBK1, and IRF3) in the cGAS-STING pathway and found that the TMEM173 gene was significantly downregulated in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Not only immunostimulatory cells but also regulatory T cells were triggered by the DNA sensing pathway. With gene enrichment analysis, we revealed that cell cycle and mechanotransduction/cytoskeleton signals were most closely connected with cGAS-STING signal alterations in non-small-cell lung cancer (NSCLC). cGAS-STING signaling was robustly correlated with methylation changes, especially histone H3K4 lysine demethylase KDM5s. Transient activation of cGAS-STING was found to exert tumor surveillance effect, and inhibition of STING signaling co-opt elevated KDM5 demethylases might inadvertently worsen clinical outcomes. CONCLUSION cGAS-STING signaling and KDM5 demethylases have the potential to be used as targets for evaluating an effective immune response in the tumor microenvironment.
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Affiliation(s)
- Fang Hao
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, China
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46
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Liao C, Liu X, Zhang C, Zhang Q. Tumor hypoxia: From basic knowledge to therapeutic implications. Semin Cancer Biol 2023; 88:172-186. [PMID: 36603793 PMCID: PMC9929926 DOI: 10.1016/j.semcancer.2022.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/07/2022] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
Diminished oxygen availability, termed hypoxia, within solid tumors is one of the most common characteristics of cancer. Hypoxia shapes the landscape of the tumor microenvironment (TME) into a pro-tumorigenic and pro-metastatic niche through arrays of pathological alterations such as abnormal vasculature, altered metabolism, immune-suppressive phenotype, etc. In addition, emerging evidence suggests that limited efficacy or the development of resistance towards antitumor therapy may be largely due to the hypoxic TME. This review will focus on summarizing the knowledge about the molecular machinery that mediates the hypoxic cellular responses and adaptations, as well as highlighting the effects and consequences of hypoxia, especially for angiogenesis regulation, cellular metabolism alteration, and immunosuppressive response within the TME. We also outline the current advances in novel therapeutic implications through targeting hypoxia in TME. A deep understanding of the basics and the role of hypoxia in the tumor will help develop better therapeutic avenues in cancer treatment.
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Affiliation(s)
- Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
| | - Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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47
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Qi R, Zou Q. Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level. RESEARCH (WASHINGTON, D.C.) 2023; 6:0050. [PMID: 36930772 PMCID: PMC10013796 DOI: 10.34133/research.0050] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023]
Abstract
Cancer treatments always face challenging problems, particularly drug resistance due to tumor cell heterogeneity. The existing datasets include the relationship between gene expression and drug sensitivities; however, the majority are based on tissue-level studies. Study drugs at the single-cell level are perspective to overcome minimal residual disease caused by subclonal resistant cancer cells retained after initial curative therapy. Fortunately, machine learning techniques can help us understand how different types of cells respond to different cancer drugs from the perspective of single-cell gene expression. Good modeling using single-cell data and drug response information will not only improve machine learning for cell-drug outcome prediction but also facilitate the discovery of drugs for specific cancer subgroups and specific cancer treatments. In this paper, we review machine learning and deep learning approaches in drug research. By analyzing the application of these methods on cancer cell lines and single-cell data and comparing the technical gap between single-cell sequencing data analysis and single-cell drug sensitivity analysis, we hope to explore the trends and potential of drug research at the single-cell data level and provide more inspiration for drug research at the single-cell level. We anticipate that this review will stimulate the innovative use of machine learning methods to address new challenges in precision medicine more broadly.
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Affiliation(s)
- Ren Qi
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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48
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Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
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Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
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49
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Vegliante R, Pastushenko I, Blanpain C. Deciphering functional tumor states at single-cell resolution. EMBO J 2022; 41:e109221. [PMID: 34918370 PMCID: PMC8762559 DOI: 10.15252/embj.2021109221] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/19/2023] Open
Abstract
Within a tumor, cancer cells exist in different states that are associated with distinct tumor functions, including proliferation, differentiation, invasion, metastasis, and resistance to anti-cancer therapy. The identification of the gene regulatory networks underpinning each state is essential for better understanding functional tumor heterogeneity and revealing tumor vulnerabilities. Here, we review the different studies identifying tumor states by single-cell sequencing approaches and the mechanisms that promote and sustain these functional states and regulate their transitions. We also describe how different tumor states are spatially distributed and interact with the specific stromal cells that compose the tumor microenvironment. Finally, we discuss how the understanding of tumor plasticity and transition states can be used to develop new strategies to improve cancer therapy.
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Affiliation(s)
- Rolando Vegliante
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
| | | | - Cédric Blanpain
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
- WELBIOUniversité Libre de BruxellesBrusselsBelgium
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50
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Serrano A, Berthelet J, Naik SH, Merino D. Mastering the use of cellular barcoding to explore cancer heterogeneity. Nat Rev Cancer 2022; 22:609-624. [PMID: 35982229 DOI: 10.1038/s41568-022-00500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 11/09/2022]
Abstract
Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.
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Affiliation(s)
- Antonin Serrano
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Jean Berthelet
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Shalin H Naik
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Delphine Merino
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia.
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