101
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Khaliq M, Manikkam M, Martinez ED, Fallahi-Sichani M. Epigenetic modulation reveals differentiation state specificity of oncogene addiction. Nat Commun 2021; 12:1536. [PMID: 33750776 PMCID: PMC7943789 DOI: 10.1038/s41467-021-21784-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
Hyperactivation of the MAPK signaling pathway motivates the clinical use of MAPK inhibitors for BRAF-mutant melanomas. Heterogeneity in differentiation state due to epigenetic plasticity, however, results in cell-to-cell variability in the state of MAPK dependency, diminishing the efficacy of MAPK inhibitors. To identify key regulators of such variability, we screen 276 epigenetic-modifying compounds, individually or combined with MAPK inhibitors, across genetically diverse and isogenic populations of melanoma cells. Following single-cell analysis and multivariate modeling, we identify three classes of epigenetic inhibitors that target distinct epigenetic states associated with either one of the lysine-specific histone demethylases Kdm1a or Kdm4b, or BET bromodomain proteins. While melanocytes remain insensitive, the anti-tumor efficacy of each inhibitor is predicted based on melanoma cells' differentiation state and MAPK activity. Our systems pharmacology approach highlights a path toward identifying actionable epigenetic factors that extend the BRAF oncogene addiction paradigm on the basis of tumor cell differentiation state.
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Affiliation(s)
- Mehwish Khaliq
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Mohan Manikkam
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
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102
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Caswell-Jin JL, Lorenz C, Curtis C. Molecular Heterogeneity and Evolution in Breast Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2021. [DOI: 10.1146/annurev-cancerbio-060220-014137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Breast cancer comprises a heterogeneous group of tumor subtypes, whether defined by immunohistochemistry of key proteins, RNA expression profiles, or genetic alterations, and each of these subtypes may benefit from a distinct treatment approach. However, there can be striking heterogeneity within tumors, which may pose challenges to the development of personalized approaches to therapy. Intratumor heterogeneity can be divided into three main categories: genetic, phenotypic, and microenvironmental. Here, we review technologies to interrogate these three categories of heterogeneity in patient samples, as well as the current state of understanding of these categories in breast cancer, from cell to cell, across different regions of the same tumor mass, across treatment, and across metastasis. Efforts to characterize tumor heterogeneity longitudinally will be crucial to the development of personalized oncology for breast cancer.
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Affiliation(s)
- Jennifer L. Caswell-Jin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carina Lorenz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christina Curtis
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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103
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Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, Ma DL, Chen J. The emerging role of KDM5A in human cancer. J Hematol Oncol 2021; 14:30. [PMID: 33596982 PMCID: PMC7888121 DOI: 10.1186/s13045-021-01041-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Histone methylation is a key posttranslational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Variations in the pattern of histone methylation influence both physiological and pathological events. Lysine-specific demethylase 5A (KDM5A, also known as JARID1A or RBP2) is a KDM5 Jumonji histone demethylase subfamily member that erases di- and tri-methyl groups from lysine 4 of histone H3. Emerging studies indicate that KDM5A is responsible for driving multiple human diseases, particularly cancers. In this review, we summarize the roles of KDM5A in human cancers, survey the field of KDM5A inhibitors including their anticancer activity and modes of action, and the current challenges and potential opportunities of this field.
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Affiliation(s)
- 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, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.,Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Yan-Jun Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, People's Republic of China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, People's Republic of 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, People's Republic of China. .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China. .,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
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104
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Peck B, Bland P, Mavrommati I, Muirhead G, Cottom H, Wai PT, Maguire SL, Barker HE, Morrison E, Kriplani D, Yu L, Gibson A, Falgari G, Brennan K, Farnie G, Buus R, Marlow R, Novo D, Knight E, Guppy N, Kolarevic D, Susnjar S, Milijic NM, Naidoo K, Gazinska P, Roxanis I, Pancholi S, Martin LA, Holgersen EM, Cheang MCU, Noor F, Postel-Vinay S, Quinn G, McDade S, Krasny L, Huang P, Daley F, Wallberg F, Choudhary JS, Haider S, Tutt AN, Natrajan R. 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer. Cancer Res 2021; 81:847-859. [PMID: 33509944 PMCID: PMC7611219 DOI: 10.1158/0008-5472.can-20-1822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/12/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancers (TNBC) are resistant to standard-of-care chemotherapy and lack known targetable driver gene alterations. Identification of novel drivers could aid the discovery of new treatment strategies for this hard-to-treat patient population, yet studies using high-throughput and accurate models to define the functions of driver genes in TNBC to date have been limited. Here, we employed unbiased functional genomics screening of the 200 most frequently mutated genes in breast cancer, using spheroid cultures to model in vivo-like conditions, and identified the histone acetyltransferase CREBBP as a novel tumor suppressor in TNBC. CREBBP protein expression in patient tumor samples was absent in 8% of TNBCs and at a high frequency in other tumors, including squamous lung cancer, where CREBBP-inactivating mutations are common. In TNBC, CREBBP alterations were associated with higher genomic heterogeneity and poorer patient survival and resulted in upregulation and dependency on a FOXM1 proliferative program. Targeting FOXM1-driven proliferation indirectly with clinical CDK4/6 inhibitors (CDK4/6i) selectively impaired growth in spheroids, cell line xenografts, and patient-derived models from multiple tumor types with CREBBP mutations or loss of protein expression. In conclusion, we have identified CREBBP as a novel driver in aggressive TNBC and identified an associated genetic vulnerability in tumor cells with alterations in CREBBP and provide a preclinical rationale for assessing CREBBP alterations as a biomarker of CDK4/6i response in a new patient population. SIGNIFICANCE: This study demonstrates that CREBBP genomic alterations drive aggressive TNBC, lung cancer, and lymphomas and may be selectively treated with clinical CDK4/6 inhibitors.
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Affiliation(s)
- Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Hannah Cottom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Sarah L Maguire
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Stem Cells and Cancer, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Eamonn Morrison
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Divya Kriplani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Amy Gibson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Giulia Falgari
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Keith Brennan
- Faculty of Life Sciences, University of Manchester, Manchester, England, United Kingdom
| | - Gillian Farnie
- SGC Oxford, University of Oxford, Oxford, England, United Kingdom
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Eleanor Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Daniela Kolarevic
- The Royal Marsden NHS Foundation Trust, London, England, United Kingdom
| | - Snezana Susnjar
- Department of Medical Oncology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Natasa Medic Milijic
- Department of Pathology and Cytology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sunil Pancholi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Erle M Holgersen
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Maggie C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, England, United Kingdom
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sophie Postel-Vinay
- Department of Drug Development (DITEP), Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- UMR981, ATIP-Avenir team, INSERM, Villejuif, France
| | - Gerard Quinn
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Paul Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Fredrik Wallberg
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Andrew N Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom.
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
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105
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Peng D, Lin B, Xie M, Zhang P, Guo Q, Li Q, Gu Q, Yang S, Sen L. Histone demethylase KDM5A promotes tumorigenesis of osteosarcoma tumor. Cell Death Discov 2021; 7:9. [PMID: 33436536 PMCID: PMC7803953 DOI: 10.1038/s41420-020-00396-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Osteosarcoma is a primary bone malignancy with a high rate of recurrence and poorer prognosis. Therefore, it is of vital importance to explore novel prognostic molecular biomarkers and targets for more effective therapeutic approaches. Previous studies showed that histone demethylase KDM5A can increase the proliferation and metastasis of several cancers. However, the function of KDM5A in the carcinogenesis of osteosarcoma is not clear. In the current study, KDM5A was highly expressed in osteosarcoma than adjacent normal tissue. Knockdown of KDM5A suppressed osteosarcoma cell proliferation and induced apoptosis. Moreover, knockdown of KDM5A could increase the expression level of P27 (cell-cycle inhibitor) and decrease the expression of Cyclin D1. Furthermore, after knockout of KDM5A in osteosarcoma cells by CRISPR/Cas9 system, the tumor size and growth speed were inhibited in tumor-bearing nude mice. RNA-Seq of KDM5A-KO cells indicated that interferon, epithelial–mesenchymal transition (EMT), IL6/JAK/STAT3, and TNF-α/NF-κB pathway were likely involved in the regulation of osteosarcoma cell viability. Taken together, our research established a role of KDM5A in osteosarcoma tumorigenesis and progression.
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Affiliation(s)
- Daohu Peng
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Birong Lin
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Mingzhong Xie
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Ping Zhang
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - QingXi Guo
- The affiliated hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, 646015, Luzhou City, Sichuan, P. R. China
| | - Qian Li
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Qinwen Gu
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Sijin Yang
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China.
| | - Li Sen
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China.
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106
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Guo L, Lee YT, Zhou Y, Huang Y. Targeting epigenetic regulatory machinery to overcome cancer therapy resistance. Semin Cancer Biol 2021; 83:487-502. [PMID: 33421619 PMCID: PMC8257754 DOI: 10.1016/j.semcancer.2020.12.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
Drug resistance, either intrinsic or acquired, represents a major hurdle to achieving optimal therapeutic outcomes during cancer treatment. In addition to acquisition of resistance-conferring genetic mutations, accumulating evidence suggests an intimate involvement of the epigenetic machinery in this process as well. Recent studies have revealed that epigenetic reprogramming, such as altered expression or relocation of DNA/histone modulators accompanied with chromatin structure remodeling, can lead to transcriptional plasticity in tumor cells, thereby driving their transformation towards a persistent state. These "persisters" represent a pool of slow-growing cells that can either re-expand when treatment is discontinued or acquire permanent resistance. Targeting epigenetic reprogramming or plasticity represents a new strategy to prevent the emergence of drug-refractory populations and to enable more consistent clinical responses. With the growing numbers of drugs or drug candidates developed to target epigenetic regulators, more and more epigenetic therapies are under preclinical evaluation, early clinical trials or approved by FDA as single agent or in combination with existing antitumor drugs. In this review, we highlight latest discoveries in the mechanistic understanding of epigenetically-induced drug resistance. In parallel, we discuss the potential of combining epigenetic drugs with existing anticancer regimens as a promising strategy for overcoming cancer drug resistance.
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Affiliation(s)
- Lei Guo
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yi-Tsang Lee
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
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107
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Chen K, Ozturk K, Contreras RL, Simon J, McCann S, Chen WJ, Carter H, Fraley SI. Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity. iScience 2020; 24:101991. [PMID: 33490901 PMCID: PMC7808958 DOI: 10.1016/j.isci.2020.101991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 12/21/2020] [Indexed: 02/08/2023] Open
Abstract
To better understand cellular communication driving diverse behaviors, we need to uncover the molecular mechanisms of within-cell-type functional heterogeneity. While single-cell RNA sequencing (scRNAseq) has advanced our understanding of cell heterogeneity, linking individual cell phenotypes to transcriptomic data remains challenging. Here, we used a phenotypic cell sorting technique to ask whether phenotypically supervised scRNAseq analysis (pheno-scRNAseq) can provide more insight into heterogeneous cell behaviors than unsupervised scRNAseq. Using a simple 3D in vitro breast cancer (BRCA) model, we conducted pheno-scRNAseq on invasive and non-invasive cells and compared the results to phenotype-agnostic scRNAseq analysis. Pheno-scRNAseq identified unique and more selective differentially expressed genes than unsupervised scRNAseq analysis. Functional studies validated the utility of pheno-scRNAseq in understanding within-cell-type functional heterogeneity and revealed that migration phenotypes were coordinated with specific metabolic, proliferation, stress, and immune phenotypes. This approach lends new insight into the molecular systems underlying BRCA cell phenotypic heterogeneity.
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Affiliation(s)
- Kevin Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kivilcim Ozturk
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryne L Contreras
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica Simon
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sean McCann
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wei Ji Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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108
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Zheng Y, Tang L, Chen G, Liu Z. Comprehensive Bioinformatics Analysis of Key Methyltransferases and Demethylases for Histone Lysines in Hepatocellular Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820983284. [PMID: 33355042 PMCID: PMC7871294 DOI: 10.1177/1533033820983284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background & Aims: Methylation of lysines on histones, controlled by various methyltransferases and demethylases, is an important component of epigenetic modifications, and abnormal regulation of such enzymes serves as common events in hepatocellular carcinoma. We determined to identify important methyltransferases and demethylases that might regulate the development of hepatocellular carcinoma by bioinformatics. Methods: The Oncomine and UALCAN databases were used to retrieve mRNA expression levels of histone lysine methyltransferases and demethylases in hepatocellular carcinoma. Data analyses of genetic alterations, mainly mutations and copy number alterations, were performed on the cBioportal platform. Protein-protein interactions were established in the STRING database. Results: mRNA expression of 8 genes correlated with clinical staging and grading, whereas 4 genes indicated a role in the prognosis, all co-expressed with SEDB1 and WHSC1. Genetically, 12 genes showing an alteration rate higher than 5% were identified, and only 3 were indicative of prognosis. Copy number gains in ASH1L, SETDB1, and KDM5B might partially contribute to the upregulation of their mRNA expression. The close relationship of mutations in MLL2/MLL3 with driver gene mutations in hepatocellular carcinoma provided a rationale for further investigation. Conclusions: We identified 11 methyltransferases and demethylases for major histone lysines that might be promising research targets in the pathogenesis, development, and prediction of prognosis in hepatocellular carcinoma using bioinformatics.
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Affiliation(s)
- Yang Zheng
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
| | - Lili Tang
- Institute of Military Cognition and Brain Sciences, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Guojiang Chen
- Institute of Pharmacology and Toxicology, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Ziling Liu
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
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109
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Baek M, Chang JT, Echeverria GV. Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside. J Mammary Gland Biol Neoplasia 2020; 25:289-304. [PMID: 33300087 PMCID: PMC7960623 DOI: 10.1007/s10911-020-09470-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
There is a major need to overcome therapeutic resistance and metastasis that eventually arises in many breast cancer patients. Therapy resistant and metastatic tumors are increasingly recognized to possess intra-tumoral heterogeneity (ITH), a diversity of cells within an individual tumor. First hypothesized in the 1970s, the possibility that this complex ITH may endow tumors with adaptability and evolvability to metastasize and evade therapies is now supported by multiple lines of evidence. Our understanding of ITH has been driven by recent methodological advances including next-generation sequencing, computational modeling, lineage tracing, single-cell technologies, and multiplexed in situ approaches. These have been applied across a range of specimens, including patient tumor biopsies, liquid biopsies, cultured cell lines, and mouse models. In this review, we discuss these approaches and how they have deepened our understanding of the mechanistic origins of ITH amongst tumor cells, including stem cell-like differentiation hierarchies and Darwinian evolution, and the functional role for ITH in breast cancer progression. While ITH presents a challenge for combating tumor evolution, in-depth analyses of ITH in clinical biopsies and laboratory models hold promise to elucidate therapeutic strategies that should ultimately improve outcomes for breast cancer patients.
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Affiliation(s)
- Mokryun Baek
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey T Chang
- Department of Pharmacology and Integrative Biology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Gloria V Echeverria
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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110
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Wu Z, Lawrence PJ, Ma A, Zhu J, Xu D, Ma Q. Single-Cell Techniques and Deep Learning in Predicting Drug Response. Trends Pharmacol Sci 2020; 41:1050-1065. [PMID: 33153777 PMCID: PMC7669610 DOI: 10.1016/j.tips.2020.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/04/2020] [Accepted: 10/09/2020] [Indexed: 12/19/2022]
Abstract
Rapidly developing single-cell sequencing analyses produce more comprehensive profiles of the genomic, transcriptomic, and epigenomic heterogeneity of tumor subpopulations than do traditional bulk sequencing analyses. Moreover, single-cell techniques allow the response of a tumor to drug exposure to be more thoroughlyinvestigated. Deep learning (DL) models have successfully extracted features from complex bulk sequence data to predict drug responses. We review recent innovations in single-cell technologies and DL-based approaches related to drug sensitivity predictions. We believe that, by using insights from bulk sequencedata, deep transfer learning (DTL) can facilitate the use of single-cell data for training superior DL-based drug prediction models.
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Affiliation(s)
- Zhenyu Wu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick J Lawrence
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Anjun Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA.
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111
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Abstract
Therapeutic resistance continues to be an indominable foe in our ambition for curative cancer treatment. Recent insights into the molecular determinants of acquired treatment resistance in the clinical and experimental setting have challenged the widely held view of sequential genetic evolution as the primary cause of resistance and brought into sharp focus a range of non-genetic adaptive mechanisms. Notably, the genetic landscape of the tumour and the non-genetic mechanisms used to escape therapy are frequently linked. Remarkably, whereas some oncogenic mutations allow the cancer cells to rapidly adapt their transcriptional and/or metabolic programme to meet and survive the therapeutic pressure, other oncogenic drivers convey an inherent cellular plasticity to the cancer cell enabling lineage switching and/or the evasion of anticancer immunosurveillance. The prevalence and diverse array of non-genetic resistance mechanisms pose a new challenge to the field that requires innovative strategies to monitor and counteract these adaptive processes. In this Perspective we discuss the key principles of non-genetic therapy resistance in cancer. We provide a perspective on the emerging data from clinical studies and sophisticated cancer models that have studied various non-genetic resistance pathways and highlight promising therapeutic avenues that may be used to negate and/or counteract the non-genetic adaptive pathways.
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Affiliation(s)
- Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium.
- Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
- Center for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia.
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
- Center for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia.
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112
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Abstract
2-Oxoglutarate-dependent dioxygenases (2OGDDs) are a superfamily of enzymes that play diverse roles in many biological processes, including regulation of hypoxia-inducible factor-mediated adaptation to hypoxia, extracellular matrix formation, epigenetic regulation of gene transcription and the reprogramming of cellular metabolism. 2OGDDs all require oxygen, reduced iron and 2-oxoglutarate (also known as α-ketoglutarate) to function, although their affinities for each of these co-substrates, and hence their sensitivity to depletion of specific co-substrates, varies widely. Numerous 2OGDDs are recurrently dysregulated in cancer. Moreover, cancer-specific metabolic changes, such as those that occur subsequent to mutations in the genes encoding succinate dehydrogenase, fumarate hydratase or isocitrate dehydrogenase, can dysregulate specific 2OGDDs. This latter observation suggests that the role of 2OGDDs in cancer extends beyond cancers that harbour mutations in the genes encoding members of the 2OGDD superfamily. Herein, we review the regulation of 2OGDDs in normal cells and how that regulation is corrupted in cancer.
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Affiliation(s)
- Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA.
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113
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Shao X, Wang Y, Lu X, Hu Y, Liao J, Li J, Chen X, Yu Y, Ai N, Ying M, Fan X. A Clinical Genomics-Guided Prioritizing Strategy Enables Selecting Proper Cancer Cell Lines for Biomedical Research. iScience 2020; 23:101748. [PMID: 33225250 PMCID: PMC7662851 DOI: 10.1016/j.isci.2020.101748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/01/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022] Open
Abstract
Selecting appropriate cell lines to represent a disease is crucial for the success of biomedical research, because the usage of less relevant cell lines could deliver misleading results. However, systematic guidance on cell line selection is unavailable. Here we developed a clinical Genomics-guided Prioritizing Strategy for Cancer Cell Lines (CCL-cGPS) and help to guide this process. Statistical analyses revealed CCL-cGPS selected cell lines were among the most appropriate models. Moreover, we observed a linear correlation between the drug response and CCL-cGPS score of cell lines for breast and thyroid cancers. Using RT4 cells selected by CCL-GPS, we identified mebendazole and digitoxin as candidate drugs against bladder cancer and validate their promising anticancer effect through in vitro and in vivo experiments. Additionally, a web tool was developed. In conclusion, CCL-cGPS bridges the gap between tumors and cell lines, presenting a helpful guide to select the most suitable cell line models. Cell lines were ranked by the resemblance of transcriptional signatures to tumors Among 44 tumor subtypes, CCL-cGPS provides proper cell lines for each subtype CCL-cGPS was verified by the computational analysis, in vitro and in vivo assays A web tool was developed to guide the selection of the most suitable cell lines
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Affiliation(s)
- Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Hu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junying Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuechun Chen
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunru Yu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ni Ai
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meidan Ying
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin 301617, China
- Corresponding author
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114
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Michmerhuizen NL, Klco JM, Mullighan CG. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 2020; 136:2275-2289. [PMID: 32766874 PMCID: PMC7702474 DOI: 10.1182/blood.2020007093] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleoporin 98 (NUP98) fusion oncoproteins are observed in a spectrum of hematologic malignancies, particularly pediatric leukemias with poor patient outcomes. Although wild-type full-length NUP98 is a member of the nuclear pore complex, the chromosomal translocations leading to NUP98 gene fusions involve the intrinsically disordered and N-terminal region of NUP98 with over 30 partner genes. Fusion partners include several genes bearing homeodomains or having known roles in transcriptional or epigenetic regulation. Based on data in both experimental models and patient samples, NUP98 fusion oncoprotein-driven leukemogenesis is mediated by changes in chromatin structure and gene expression. Multiple cofactors associate with NUP98 fusion oncoproteins to mediate transcriptional changes possibly via phase separation, in a manner likely dependent on the fusion partner. NUP98 gene fusions co-occur with a set of additional mutations, including FLT3-internal tandem duplication and other events contributing to increased proliferation. To improve the currently dire outcomes for patients with NUP98-rearranged malignancies, therapeutic strategies have been considered that target transcriptional and epigenetic machinery, cooperating alterations, and signaling or cell-cycle pathways. With the development of more faithful experimental systems and continued study, we anticipate great strides in our understanding of the molecular mechanisms and therapeutic vulnerabilities at play in NUP98-rearranged models. Taken together, these studies should lead to improved clinical outcomes for NUP98-rearranged leukemia.
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Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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115
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Capp JP, Thomas F. Tissue-disruption-induced cellular stochasticity and epigenetic drift: Common origins of aging and cancer? Bioessays 2020; 43:e2000140. [PMID: 33118188 DOI: 10.1002/bies.202000140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023]
Abstract
Age-related and cancer-related epigenomic modifications have been associated with enhanced cell-to-cell gene expression variability that characterizes increased cellular stochasticity. Since gene expression variability appears to be highly reduced by-and epigenetic and phenotypic stability acquired through-direct or long-range cellular interactions during cell differentiation, we propose a common origin for aging and cancer in the failure to control cellular stochasticity by cell-cell interactions. Tissue-disruption-induced cellular stochasticity associated with epigenetic drift would be at the origin of organ dysfunction because of an increase in phenotypic variation among cells, ultimately leading to cell death and organ failure through a loss of coordination in cellular functions, and eventually to cancerization. We propose mechanistic research perspectives to corroborate this hypothesis and explore its evolutionary consequences, highlighting a positive correlation between the median age of mass loss onset (a proxy for the onset of organ aging) and the median age at cancer diagnosis.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC (CREES), UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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116
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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117
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Tripathi S, Kessler DA, Levine H. Biological Networks Regulating Cell Fate Choice Are Minimally Frustrated. PHYSICAL REVIEW LETTERS 2020; 125:088101. [PMID: 32909810 DOI: 10.1103/physrevlett.125.088101] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous studies, focusing on identifying topological features that are present in biological networks but not in random networks, have, however, provided few functional insights. We use a Boolean modeling framework and ideas from the spin glass literature to identify functional differences between five real biological networks and random networks with similar topological features. We show that minimal frustration is a fundamental property that allows biological networks to robustly establish cell types and regulate cell fate choice, and that this property can emerge in complex networks via Darwinian evolution. The study also provides clues regarding how the regulation of cell fate choice can go awry in a disease like cancer and lead to the emergence of aberrant cell types.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - David A Kessler
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
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118
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Fu YD, Huang MJ, Guo JW, You YZ, Liu HM, Huang LH, Yu B. Targeting histone demethylase KDM5B for cancer treatment. Eur J Med Chem 2020; 208:112760. [PMID: 32883639 DOI: 10.1016/j.ejmech.2020.112760] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
KDM5B (Lysine-Specific Demethylase 5B) erases the methyl group from H3K4me2/3, which performs wide regulatory effects on chromatin structure, and represses the transcriptional function of genes. KDM5B functions as an oncogene and associates with human cancers closely. Targeting KDM5B has been a promising direction for curing cancer since the emergence of potent KDM5B inhibitor CPI-455. In this area, most reported KDM5B inhibitors are Fe (Ⅱ) chelators, which also compete with the cofactor 2-OG in the active pockets. Besides, Some KDM5B inhibitors have been identified through high throughput screening or biochemical screening. In this reviewing article, we summarized the pioneering progress in KDM5B to provide a comprehensive realization, including crystal structure, transcriptional regulation function, cancer-related functions, development of inhibitors, and SAR studies. We hope to provide a comprehensive overview of KDM5B and the development of KDM5B inhibitors.
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Affiliation(s)
- Yun-Dong Fu
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ming-Jie Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Jia-Wen Guo
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ya-Zhen You
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-Hua Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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119
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Nam AS, Chaligne R, Landau DA. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics. Nat Rev Genet 2020; 22:3-18. [PMID: 32807900 DOI: 10.1038/s41576-020-0265-5] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 12/17/2022]
Abstract
Cancer represents an evolutionary process through which growing malignant populations genetically diversify, leading to tumour progression, relapse and resistance to therapy. In addition to genetic diversity, the cell-to-cell variation that fuels evolutionary selection also manifests in cellular states, epigenetic profiles, spatial distributions and interactions with the microenvironment. Therefore, the study of cancer requires the integration of multiple heritable dimensions at the resolution of the single cell - the atomic unit of somatic evolution. In this Review, we discuss emerging analytic and experimental technologies for single-cell multi-omics that enable the capture and integration of multiple data modalities to inform the study of cancer evolution. These data show that cancer results from a complex interplay between genetic and non-genetic determinants of somatic evolution.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. .,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA. .,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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120
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Histone Demethylase KDM5B as a Therapeutic Target for Cancer Therapy. Cancers (Basel) 2020; 12:cancers12082121. [PMID: 32751840 PMCID: PMC7465382 DOI: 10.3390/cancers12082121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
Lysine-specific demethylase 5B (KDM5B/PLU1/JARID1B) is found to be overexpressed in numerous malignancies, including breast, lung, skin, liver, and prostate cancer. Identification of molecules targeting the KDM5B enzyme could be a potential lead in cancer research. Although many KDM5B inhibitors with promising outcomes have been developed so far, its further application in clinical practice is limited due to toxicity and lack of target specificity. Here, we summarize the significance of targeting KDM5B in anticancer therapy and report the molecular docking studies of some known anti-viral agents, decitabine, entecavir, abacavir, penciclovir, and 3-deazaneplanocin A in the catalytic domain JmjC of KDM5B. These studies show the repurposing potential of identified anti-viral agents in cancer therapy.
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121
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Ding S, Chen X, Shen K. Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy. Cancer Commun (Lond) 2020; 40:329-344. [PMID: 32654419 PMCID: PMC7427308 DOI: 10.1002/cac2.12078] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
Single‐cell RNA sequencing (scRNA‐seq) is a novel technology that allows transcriptomic analyses of individual cells. During the past decade, scRNA‐seq sensitivity, accuracy, and efficiency have improved due to innovations including more sensitive, automated, and cost‐effective single‐cell isolation methods with higher throughput as well as ongoing technological development of scRNA‐seq protocols. Among the variety of current approaches with distinct features, researchers can choose the most suitable method to carry out their research. By profiling single cells in a complex population mix, scRNA‐seq presents great advantages over traditional sequencing methods in dissecting heterogeneity in cell populations hidden in bulk analysis and exploring rare cell types associated with tumorigenesis and metastasis. scRNA‐seq studies in recent years in the field of breast cancer research have clustered breast cancer cell populations with different molecular subtypes to identify distinct populations that may correlate with poor prognosis and drug resistance. The technology has also been used to explain tumor microenvironment heterogeneity by identifying distinct immune cell subsets that may be associated with immunosurveillance and are potential immunotherapy targets. Moreover, scRNA‐seq has diverse applications in breast cancer research besides exploring heterogeneity, including the analysis of cell‐cell communications, regulatory single‐cell states, immune cell distributions, and more. scRNA‐seq is also a promising tool that can facilitate individualized therapy due to its ability to define cell subsets with potential treatment targets. Although scRNA‐seq studies of therapeutic selection in breast cancer are currently limited, the application of this technology in this field is prospective. Joint efforts and original ideas are needed to better implement scRNA‐seq technologies in breast cancer research to pave the way for individualized treatment management. This review provides a brief introduction on the currently available scRNA‐seq approaches along with their corresponding strengths and weaknesses and may act as a reference for the selection of suitable methods for research. We also discuss the current applications of scRNA‐seq in breast cancer research for tumor heterogeneity analysis, individualized therapy, and the other research directions mentioned above by reviewing corresponding published studies. Finally, we discuss the limitations of current scRNA‐seq technologies and technical problems that remain to be overcome.
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Affiliation(s)
- Shuning Ding
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
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122
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Morinishi L, Kochanowski K, Levine RL, Wu LF, Altschuler SJ. Loss of TET2 Affects Proliferation and Drug Sensitivity through Altered Dynamics of Cell-State Transitions. Cell Syst 2020; 11:86-94.e5. [PMID: 32619551 DOI: 10.1016/j.cels.2020.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/20/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022]
Abstract
A persistent puzzle in cancer biology is how mutations, which neither alter growth signaling pathways nor directly interfere with drug mechanism, can still recur and persist in tumors. One example is the mutation of the DNA demethylase tet methylcytosine dioxygenase 2 (TET2) in acute myeloid leukemias (AMLs) that frequently persists from diagnosis through remission and relapse, but whose fitness advantage in chemotherapy is unclear. Here, we use isogenic human AML cell lines to show that TET2 loss of function alters the dynamics of transitions between differentiated and stem-like states. A conceptual mathematical model and experimental validation suggest that these altered cell-state dynamics can benefit the cell population by slowing population decay during drug treatment and lowering the number of survivor cells needed to re-establish the initial population. These studies shed light on the functional and phenotypic effects of a TET2 mutation in AML and illustrate how a single gene mutation can alter a cells' phenotypic plasticity. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Leanna Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karl Kochanowski
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ross L Levine
- Human Oncology and pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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123
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Shu S, Wu HJ, Ge JY, Zeid R, Harris IS, Jovanović B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F, Polyak K. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Mol Cell 2020; 78:1096-1113.e8. [PMID: 32416067 PMCID: PMC7306005 DOI: 10.1016/j.molcel.2020.04.027] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/11/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight significant heterogeneity among samples and demonstrate that BBDI resistance can be pre-existing or acquired.
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Affiliation(s)
- Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hua-Jun Wu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02215, USA
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Isaac S Harris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Binbin Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer E Endress
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Jaime Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tengfei Xiao
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Evangelia K Papachristou
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Thomas O McDonald
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca J Modiste
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brittany Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA.
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124
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Integrative multi-omics analysis of a colon cancer cell line with heterogeneous Wnt activity revealed RUNX2 as an epigenetic regulator of EMT. Oncogene 2020; 39:5152-5164. [PMID: 32535615 DOI: 10.1038/s41388-020-1351-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/25/2020] [Accepted: 06/03/2020] [Indexed: 12/21/2022]
Abstract
Epithelial-mesenchymal transition (EMT) program, which facilitates tumor metastasis, stemness and therapy resistance, is a reversible biological process that is largely orchestrated at the epigenetic level under the regulation of different cell signaling pathways. EMT state is often heterogeneous within individual tumors, though the epigenetic drivers underlying such heterogeneity remain elusive. In colon cancer, hyperactivation of the Wnt/β-catenin signaling not only drives tumor initiation, but also promotes metastasis in late stage by promoting EMT program. However, it is unknown whether the intratumorally heterogeneous Wnt activity could directly drive EMT heterogeneity, and, if so, what are the underlying epigenetic driver(s). Here, by analyzing a phenotypically and molecularly heterogeneous colon cancer cell line using single-cell RNA sequencing, we identified two distinct cell populations with positively correlated Wnt activity and EMT state. Integrative multi-omics analysis of these two cell populations revealed RUNX2 as a critical transcription factor epigenetically driving the EMT heterogeneity. Both in vitro and in vivo genetic perturbation assays validated the EMT-enhancing effect of RUNX2, which remodeled chromatin landscape and activated a panel of EMT-associated genes through binding to their promoters and/or potential enhancers. Finally, by exploring the clinical data, we showed that RUNX2 expression is positively correlated with metastasis development and poor survival of colon cancer patients, as well as patients afflicted with other types of cancer. Taken together, our work revealed RUNX2 as a new EMT-promoting epigenetic regulator in colon cancer, which may potentially serve as a prognostic marker for tumor metastasis.
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125
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Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single-Cell Genomics. Cancer Cell 2020; 37:456-470. [PMID: 32289270 PMCID: PMC7899145 DOI: 10.1016/j.ccell.2020.03.008] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/01/2020] [Accepted: 03/09/2020] [Indexed: 01/21/2023]
Abstract
Single-cell sequencing (SCS) has impacted many areas of cancer research and improved our understanding of intratumor heterogeneity, the tumor microenvironment, metastasis, and therapeutic resistance. The development and refinement of SCS technologies has led to massive reductions in costs, increased cell throughput, and improved reproducibility, paving the way for clinical applications. However, before translational applications can be realized, there are a number of logistical and technical challenges that must be overcome. This review discusses past cancer research studies, emerging technologies, and future clinical applications that are bound to transform cancer medicine.
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Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiyun Lin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Navin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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126
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Abstract
Advances in our understanding of molecular mechanisms of tumorigenesis have translated into knowledge-based therapies directed against specific oncogenic signaling targets. These therapies often induce dramatic responses in susceptible tumors. Unfortunately, most advanced cancers, including those with robust initial responses, eventually acquire resistance to targeted therapies and relapse. Even though immune-based therapies are more likely to achieve complete cures, acquired resistance remains an obstacle to their success as well. Acquired resistance is the direct consequence of pre-existing intratumor heterogeneity and ongoing diversification during therapy, which enables some tumor cells to survive treatment and facilitates the development of new therapy-resistant phenotypes. In this review, we discuss the sources of intratumor heterogeneity and approaches to capture and account for it during clinical decision making. Finally, we outline potential strategies to improve therapeutic outcomes by directly targeting intratumor heterogeneity.
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Affiliation(s)
- Andriy Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Michalina Janiszewska
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, 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.
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127
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Assessing Cell Activities rather than Identities to Interpret Intra-Tumor Phenotypic Diversity and Its Dynamics. iScience 2020; 23:101061. [PMID: 32361272 PMCID: PMC7195534 DOI: 10.1016/j.isci.2020.101061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022] Open
Abstract
Despite advances in single-cell and molecular techniques, it is still unclear how to best quantify phenotypic heterogeneity in cancer cells that evolved beyond normal, known classifications. We present an approach to phenotypically characterize cells based on their activities rather than static classifications. We validated the detectability of specific activities (epithelial-mesenchymal transition, glycolysis) in single cells, using targeted RT-qPCR analyses and in vitro inductions. We analyzed 50 established activity signatures as a basis for phenotypic description in public data and computed cell-cell distances in 28,513 cells from 85 patients and 8 public datasets. Despite not relying on any classification, our measure correlated with standard diversity indices in populations of known structure. We identified bottlenecks as phenotypic diversity reduced upon colorectal cancer initiation. This suggests that focusing on what cancer cells do rather than what they are can quantify phenotypic diversity in universal fashion, to better understand and predict intra-tumor heterogeneity dynamics. Cells categorized as having the same identity can perform different activities Single-cell expression data can be used to infer the activities cells take part in Activity profiles provide a basis to measure phenotypic cell-cell divergence Cell activity can quantify intra-tumor heterogeneity more fully than identity
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128
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Bell CC, Gilan O. Principles and mechanisms of non-genetic resistance in cancer. Br J Cancer 2019; 122:465-472. [PMID: 31831859 PMCID: PMC7028722 DOI: 10.1038/s41416-019-0648-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
As well as undergoing genetic evolution, cancer cells can alter their epigenetic state to adapt and resist treatment. This non-genetic evolution is emerging as a major component of cancer resistance. Only now are we beginning to acquire the necessary data and tools to establish some of the underlying principles and mechanisms that define when, why and how non-genetic resistance occurs. Preliminary studies suggest that it can exist in a number of forms, including drug persistence, unstable non-genetic resistance and, most intriguingly, stable non-genetic resistance. Exactly how they each arise remains unclear; however, epigenetic heterogeneity and plasticity appear to be important variables. In this review, we provide an overview of these different forms of non-genetic resistance, before exploring how epigenetic heterogeneity and plasticity influence their emergence. We highlight the distinction between non-genetic Darwinian selection and Lamarckian induction and discuss how each is capable of generating resistance. Finally, we discuss the potential interaction between genetic and non-genetic adaptation and propose the idea of ‘the path of most resistance’, which outlines the variables that dictate whether cancers adapt through genetic and/or epigenetic means. Through these discussions, we hope to provide a conceptual framework that focuses future studies, whose insights might help prevent or overcome non-genetic resistance.
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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129
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Zoeller EL, Pedro B, Konen J, Dwivedi B, Rupji M, Sundararaman N, Wang L, Horton JR, Zhong C, Barwick BG, Cheng X, Martinez ED, Torres MP, Kowalski J, Marcus AI, Vertino PM. Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes. J Cell Sci 2019; 132:jcs231514. [PMID: 31515279 PMCID: PMC6803364 DOI: 10.1242/jcs.231514] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
Collective invasion, the coordinated movement of cohesive packs of cells, has become recognized as a major mode of metastasis for solid tumors. These packs are phenotypically heterogeneous and include specialized cells that lead the invasive pack and others that follow behind. To better understand how these unique cell types cooperate to facilitate collective invasion, we analyzed transcriptomic sequence variation between leader and follower populations isolated from the H1299 non-small cell lung cancer cell line using an image-guided selection technique. We now identify 14 expressed mutations that are selectively enriched in leader or follower cells, suggesting a novel link between genomic and phenotypic heterogeneity within a collectively invading tumor cell population. Functional characterization of two phenotype-specific candidate mutations showed that ARP3 enhances collective invasion by promoting the leader cell phenotype and that wild-type KDM5B suppresses chain-like cooperative behavior. These results demonstrate an important role for distinct genetic variants in establishing leader and follower phenotypes and highlight the necessity of maintaining a capacity for phenotypic plasticity during collective cancer invasion.
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Affiliation(s)
- Elizabeth L Zoeller
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Brian Pedro
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Jessica Konen
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Bhakti Dwivedi
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Manali Rupji
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Niveda Sundararaman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chaojie Zhong
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Benjamin G Barwick
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeanne Kowalski
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Adam I Marcus
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Paula M Vertino
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
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130
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Khaliq M, Fallahi-Sichani M. Epigenetic Mechanisms of Escape from BRAF Oncogene Dependency. Cancers (Basel) 2019; 11:cancers11101480. [PMID: 31581557 PMCID: PMC6826668 DOI: 10.3390/cancers11101480] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 12/14/2022] Open
Abstract
About eight percent of all human tumors (including 50% of melanomas) carry gain-of-function mutations in the BRAF oncogene. Mutated BRAF and subsequent hyperactivation of the MAPK signaling pathway has motivated the use of MAPK-targeted therapies for these tumors. Despite great promise, however, MAPK-targeted therapies in BRAF-mutant tumors are limited by the emergence of drug resistance. Mechanisms of resistance include genetic, non-genetic and epigenetic alterations. Epigenetic plasticity, often modulated by histone-modifying enzymes and gene regulation, can influence a tumor cell's BRAF dependency and therefore, response to therapy. In this review, focusing primarily on class 1 BRAF-mutant cells, we will highlight recent work on the contribution of epigenetic mechanisms to inter- and intratumor cell heterogeneity in MAPK-targeted therapy response.
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Affiliation(s)
- Mehwish Khaliq
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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131
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Ding L, Su Y, Fassl A, Hinohara K, Qiu X, Harper NW, Huh SJ, Bloushtain-Qimron N, Jovanović B, Ekram M, Zi X, Hines WC, Alečković M, Gil Del Alcazar C, Caulfield RJ, Bonal DM, Nguyen QD, Merino VF, Choudhury S, Ethington G, Panos L, Grant M, Herlihy W, Au A, Rosson GD, Argani P, Richardson AL, Dillon D, Allred DC, Babski K, Kim EMH, McDonnell CH, Wagner J, Rowberry R, Bobolis K, Kleer CG, Hwang ES, Blum JL, Cristea S, Sicinski P, Fan R, Long HW, Sukumar S, Park SY, Garber JE, Bissell M, Yao J, Polyak K. Perturbed myoepithelial cell differentiation in BRCA mutation carriers and in ductal carcinoma in situ. Nat Commun 2019; 10:4182. [PMID: 31519911 PMCID: PMC6744561 DOI: 10.1038/s41467-019-12125-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 08/21/2019] [Indexed: 12/24/2022] Open
Abstract
Myoepithelial cells play key roles in normal mammary gland development and in limiting pre-invasive to invasive breast tumor progression, yet their differentiation and perturbation in ductal carcinoma in situ (DCIS) are poorly understood. Here, we investigated myoepithelial cells in normal breast tissues of BRCA1 and BRCA2 germline mutation carriers and in non-carrier controls, and in sporadic DCIS. We found that in the normal breast of non-carriers, myoepithelial cells frequently co-express the p63 and TCF7 transcription factors and that p63 and TCF7 show overlapping chromatin peaks associated with differentiated myoepithelium-specific genes. In contrast, in normal breast tissues of BRCA1 mutation carriers the frequency of p63+TCF7+ myoepithelial cells is significantly decreased and p63 and TCF7 chromatin peaks do not overlap. These myoepithelial perturbations in normal breast tissues of BRCA1 germline mutation carriers may play a role in their higher risk of breast cancer. The fraction of p63+TCF7+ myoepithelial cells is also significantly decreased in DCIS, which may be associated with invasive progression.
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Affiliation(s)
- Lina Ding
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Ying Su
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Deciphera Pharmaceuticals, Waltham, MA, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
| | - Sung Jin Huh
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- ImmunoGen, Inc, Waltham, MA, USA
| | - Noga Bloushtain-Qimron
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- EMEA Site Intelligence and Activation, Tel Aviv, Israel
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Muhammad Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- WuXi NextCODE, Cambridge, MA, USA
| | - Xiaoyuan Zi
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Second Military Medical University, Shanghai, 200433, P.R. China
| | - William C Hines
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Carlos Gil Del Alcazar
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Ryan J Caulfield
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
| | - Vanessa F Merino
- Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Sibgat Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Metamark Genetics Inc, Worcester, MA, USA
| | | | - Laura Panos
- Baylor-Charles A. Sammons Cancer Center, Dallas, TX, 75246, USA
| | - Michael Grant
- Baylor-Charles A. Sammons Cancer Center, Dallas, TX, 75246, USA
| | - William Herlihy
- Baylor-Charles A. Sammons Cancer Center, Dallas, TX, 75246, USA
| | - Alfred Au
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94143, USA
| | - Gedge D Rosson
- Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Pedram Argani
- Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
- Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - D Craig Allred
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kirsten Babski
- Sutter Roseville Medical Center, Roseville, CA, 95661, USA
| | - Elizabeth Min Hui Kim
- Sutter Roseville Medical Center, Roseville, CA, 95661, USA
- Cancer Treatment Centers of America, Atlanta, GA, USA
| | | | - Jon Wagner
- Sutter Roseville Medical Center, Roseville, CA, 95661, USA
| | - Ron Rowberry
- Sutter Roseville Medical Center, Roseville, CA, 95661, USA
| | | | - Celina G Kleer
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - E Shelley Hwang
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94143, USA
- Duke University, Durham, NC, USA
| | - Joanne L Blum
- Baylor-Charles A. Sammons Cancer Center, Dallas, TX, 75246, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health Boston, Boston, MA, 02215, USA
- Department of Stem Cell and Regenerative Biology, Harvard University Cambridge, Cambridge, MA, 02138, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Saraswati Sukumar
- Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - So Yeon Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mina Bissell
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jun Yao
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Boston, MA, 02215, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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132
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Hong SP, Chan TE, Lombardo Y, Corleone G, Rotmensz N, Bravaccini S, Rocca A, Pruneri G, McEwen KR, Coombes RC, Barozzi I, Magnani L. Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. Nat Commun 2019; 10:3840. [PMID: 31477698 PMCID: PMC6718416 DOI: 10.1038/s41467-019-11721-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. Here, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare subpopulation of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. We find evidence for sub-clonal expression of a PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
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Affiliation(s)
- Sung Pil Hong
- Department of Surgery and Cancer, Imperial College London, London, UK.
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Thalia E Chan
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Ylenia Lombardo
- Department of Surgery and Cancer, Imperial College London, London, UK
- Nature Communications, The Macmillan Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Giacomo Corleone
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicole Rotmensz
- Division of Pathology, European Institute of Oncology and University of Milan, School of Medicine, Milan, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Andrea Rocca
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giancarlo Pruneri
- Division of Pathology, European Institute of Oncology and University of Milan, School of Medicine, Milan, Italy
| | - Kirsten R McEwen
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK.
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK.
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133
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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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134
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De Angelis ML, Francescangeli F, La Torre F, Zeuner A. Stem Cell Plasticity and Dormancy in the Development of Cancer Therapy Resistance. Front Oncol 2019; 9:626. [PMID: 31355143 PMCID: PMC6636659 DOI: 10.3389/fonc.2019.00626] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Cancer treatment with either standard chemotherapy or targeted agents often results in the emergence of drug-refractory cell populations, ultimately leading to therapy failure. The biological features of drug resistant cells are largely overlapping with those of cancer stem cells and include heterogeneity, plasticity, self-renewal ability, and tumor-initiating capacity. Moreover, drug resistance is usually characterized by a suppression of proliferation that can manifest as quiescence, dormancy, senescence, or proliferative slowdown. Alterations in key cellular pathways such as autophagy, unfolded protein response or redox signaling, as well as metabolic adaptations also contribute to the establishment of drug resistance, thus representing attractive therapeutic targets. Moreover, a complex interplay of drug resistant cells with the micro/macroenvironment and with the immune system plays a key role in dictating and maintaining the resistant phenotype. Recent studies have challenged traditional views of cancer drug resistance providing innovative perspectives, establishing new connections between drug resistant cells and their environment and indicating unexpected therapeutic strategies. In this review we discuss recent advancements in understanding the mechanisms underlying drug resistance and we report novel targeting agents able to overcome the drug resistant status, with particular focus on strategies directed against dormant cells. Research on drug resistant cancer cells will take us one step forward toward the development of novel treatment approaches and the improvement of relapse-free survival in solid and hematological cancer patients.
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Affiliation(s)
- Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Filippo La Torre
- Department of Surgical Sciences Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Ann Zeuner
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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135
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Bell CC, Fennell KA, Chan YC, Rambow F, Yeung MM, Vassiliadis D, Lara L, Yeh P, Martelotto LG, Rogiers A, Kremer BE, Barbash O, Mohammad HP, Johanson TM, Burr ML, Dhar A, Karpinich N, Tian L, Tyler DS, MacPherson L, Shi J, Pinnawala N, Yew Fong C, Papenfuss AT, Grimmond SM, Dawson SJ, Allan RS, Kruger RG, Vakoc CR, Goode DL, Naik SH, Gilan O, Lam EYN, Marine JC, Prinjha RK, Dawson MA. Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun 2019; 10:2723. [PMID: 31222014 PMCID: PMC6586637 DOI: 10.1038/s41467-019-10652-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/21/2019] [Indexed: 12/16/2022] Open
Abstract
Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Bone Marrow/pathology
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Epigenesis, Genetic/drug effects
- Female
- Gene Expression Regulation, Leukemic/drug effects
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Sequence Analysis, RNA
- Single-Cell Analysis
- Trans-Activators/antagonists & inhibitors
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic/drug effects
- Treatment Outcome
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Katie A Fennell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
| | - Miriam M Yeung
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Dane Vassiliadis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Luis Lara
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Paul Yeh
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Brandon E Kremer
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Helai P Mohammad
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Arindam Dhar
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Luyi Tian
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Dean S Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan Pinnawala
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sean M Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Ryan G Kruger
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - David L Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Rab K Prinjha
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.
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136
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Zhou W, Lin J, Zhao K, Jin K, He Q, Hu Y, Feng G, Cai Y, Xia C, Liu H, Shen W, Hu X, Ouyang H. Single-Cell Profiles and Clinically Useful Properties of Human Mesenchymal Stem Cells of Adipose and Bone Marrow Origin. Am J Sports Med 2019; 47:1722-1733. [PMID: 31100005 DOI: 10.1177/0363546519848678] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) can be isolated from various tissues and can present themselves as a promising cell source for cell-based therapies. Although adipose- and bone marrow-derived mesenchymal stem cells have already been used in a considerable number of clinical trials for osteoarthritis treatment, systematic analyses from single- to bulk-cell resolution as well as clinical outcomes of these 2 MSCs are still insufficient. PURPOSE To explore the characteristics and differences of adipose-derived stem cells (ADSCs) and bone marrow MSCs (BMSCs) at single- and bulk-cell levels, to study the clinical outcomes of these 2 cells on the treatment of osteoarthritis, and to provide potential guidance on the more precise clinical application of these MSCs. STUDY DESIGN Controlled laboratory study and meta-analysis. METHODS Same donor-derived ADSCs and BMSCs were isolated and cultured. Single- and bulk-cell assays were used to identify the characteristics of these 2 cells. Meta-analysis of clinical trials was done to compare the clinical therapeutic effects in osteoarthritis treatment with ADSCs and BMSCs. RESULTS Single-cell RNA sequencing analysis showed that the population of ADSCs showed lower transcriptomic heterogeneity when compared with BMSCs. Additionally, as compared with BMSCs, ADSCs were less dependent on mitochondrial respiration for energy production. Furthermore, ADSCs had a lower expression level of human leukocyte antigen class I antigen and higher immunosuppression capacity when compared with the BMSC population. Meta-analysis of current clinical trials of osteoarthritis treatment with MSCs consistently showed that ADSCs are more stable than BMSCs in their therapeutic effect. CONCLUSION These results provide basic biological insights into human ADSCs and BMSCs at the single-cell resolution. Findings indicated that ADSCs may be a more controllable stem cell source, may be more adaptable to surviving in the hypoxic articular cavity niche, and may exhibit superiority in regulating inflammation. Based on the meta-analysis results of the different characteristics of ADSCs and BMSCs, ADSCs were implicated as being a better cell source for osteoarthritis treatment. CLINICAL RELEVANCE These results guide a more precise clinical application of adipose and bone marrow mesenchymal stem cells.
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Affiliation(s)
- Wenyan Zhou
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Junxin Lin
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Kun Zhao
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Kaixiu Jin
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiulin He
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Yejun Hu
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Gang Feng
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Youzhi Cai
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Xia
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Liu
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Weiliang Shen
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Xueqing Hu
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
| | - Hongwei Ouyang
- Investigation performed at the School of Medicine, Zhejiang University, Hangzhou, China
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137
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Hinohara K, Polyak K. Intratumoral Heterogeneity: More Than Just Mutations. Trends Cell Biol 2019; 29:569-579. [PMID: 30987806 DOI: 10.1016/j.tcb.2019.03.003] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 12/19/2022]
Abstract
Most human tumors are composed of genetically and phenotypically heterogeneous cancer cell populations, which poses a major challenge for the clinical management of cancer patients. Advances of single-cell technologies have allowed the profiling of tumors at unprecedented depth, which, in combination with newly developed computational tools, enable the dissection of tumor evolution with increasing precision. However, our understanding of mechanisms that regulate intratumoral heterogeneity and our ability to modulate it has been lagging behind. Recent data demonstrate that epigenetic regulators, including histone demethylases, may control the cell-to-cell variability of transcriptomes and chromatin profiles and they may modulate therapeutic responses via this function. Thus, the therapeutic targeting of epigenetic enzymes may be used to decrease intratumoral cellular heterogeneity and treatment resistance, when used in combination with other types of agents.
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Affiliation(s)
- Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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138
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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Shang W, Chen G, Li Y, Zhuo Y, Wang Y, Fang Z, Yu Y, Ren H. Static Magnetic Field Accelerates Diabetic Wound Healing by Facilitating Resolution of Inflammation. J Diabetes Res 2019; 2019:5641271. [PMID: 31886281 PMCID: PMC6915019 DOI: 10.1155/2019/5641271] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/22/2019] [Indexed: 12/15/2022] Open
Abstract
Impaired wound healing is commonly encountered in patients with diabetes mellitus, which may lead to severe outcomes such as amputation, if untreated timely. Macrophage plays a critical role in the healing process including the resolution phase. Although magnetic therapy is known to improve microcirculation, its effect on wound healing remains uncertain. In the present study, we found that 0.6 T static magnetic field (SMF) significantly accelerated wound closure and elevated reepithelialization and revascularization in diabetic mice. Notably, SMF promoted the wound healing by skewing the macrophage polarization towards M2 phenotype, thus facilitating the resolution of inflammation. In addition, SMF upregulated anti-inflammatory gene expression via activating STAT6 and suppressing STAT1 in macrophage. Taken together, our results indicate that SMF may be a promising adjuvant therapeutic tool for treating diabetic wounds.
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Affiliation(s)
- Wenlong Shang
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Guilin Chen
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yinxiu Li
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yujuan Zhuo
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuhong Wang
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhicai Fang
- Heye Health Industrial Research Institute of Zhejiang Heye Health Technology, Anji, Zhejiang 313300, China
| | - Ying Yu
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Huiwen Ren
- Department of Pharmacology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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