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Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, Mason CE, de Stanchina E, Abida W, Lujambio A, Li S, Lowe SW, Mendell JT, Malladi VS, Sawyers CL, Mu P. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Cancer Cell 2020; 37:584-598.e11. [PMID: 32220301 PMCID: PMC7292228 DOI: 10.1016/j.ccell.2020.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/04/2019] [Accepted: 02/28/2020] [Indexed: 12/25/2022]
Abstract
Metastatic prostate cancer is characterized by recurrent genomic copy number alterations that are presumed to contribute to resistance to hormone therapy. We identified CHD1 loss as a cause of antiandrogen resistance in an in vivo small hairpin RNA (shRNA) screen of 730 genes deleted in prostate cancer. ATAC-seq and RNA-seq analyses showed that CHD1 loss resulted in global changes in open and closed chromatin with associated transcriptomic changes. Integrative analysis of this data, together with CRISPR-based functional screening, identified four transcription factors (NR3C1, POU3F2, NR2F1, and TBX2) that contribute to antiandrogen resistance, with associated activation of non-luminal lineage programs. Thus, CHD1 loss results in chromatin dysregulation, thereby establishing a state of transcriptional plasticity that enables the emergence of antiandrogen resistance through heterogeneous mechanisms.
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MESH Headings
- Androgen Antagonists/pharmacology
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Chromatin/genetics
- Chromatin/metabolism
- DNA Helicases/antagonists & inhibitors
- DNA Helicases/genetics
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Neoplastic
- High-Throughput Screening Assays
- Humans
- Male
- Mice
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- RNA, Small Interfering/genetics
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Transcription Factors/metabolism
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Zeda Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chuanli Zhou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D Barnes
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth Hoover
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Young Sun Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Wongvipat
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Danielle Choi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Eliot Linton
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoping Chen
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yupu Liang
- Center for Clinical and Translational Science, Rockefeller University, New York, NY 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Elisa de Stanchina
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Venkat S Malladi
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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153
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Poirier JT, George J, Owonikoko TK, Berns A, Brambilla E, Byers LA, Carbone D, Chen HJ, Christensen CL, Dive C, Farago AF, Govindan R, Hann C, Hellmann MD, Horn L, Johnson JE, Ju YS, Kang S, Krasnow M, Lee J, Lee SH, Lehman J, Lok B, Lovly C, MacPherson D, McFadden D, Minna J, Oser M, Park K, Park KS, Pommier Y, Quaranta V, Ready N, Sage J, Scagliotti G, Sos ML, Sutherland KD, Travis WD, Vakoc CR, Wait SJ, Wistuba I, Wong KK, Zhang H, Daigneault J, Wiens J, Rudin CM, Oliver TG. New Approaches to SCLC Therapy: From the Laboratory to the Clinic. J Thorac Oncol 2020; 15:520-540. [PMID: 32018053 PMCID: PMC7263769 DOI: 10.1016/j.jtho.2020.01.016] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/12/2022]
Abstract
The outcomes of patients with SCLC have not yet been substantially impacted by the revolution in precision oncology, primarily owing to a paucity of genetic alterations in actionable driver oncogenes. Nevertheless, systemic therapies that include immunotherapy are beginning to show promise in the clinic. Although, these results are encouraging, many patients do not respond to, or rapidly recur after, current regimens, necessitating alternative or complementary therapeutic strategies. In this review, we discuss ongoing investigations into the pathobiology of this recalcitrant cancer and the therapeutic vulnerabilities that are exposed by the disease state. Included within this discussion, is a snapshot of the current biomarker and clinical trial landscapes for SCLC. Finally, we identify key knowledge gaps that should be addressed to advance the field in pursuit of reduced SCLC mortality. This review largely summarizes work presented at the Third Biennial International Association for the Study of Lung Cancer SCLC Meeting.
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Affiliation(s)
- John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne Germany
| | | | - Anton Berns
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | | | | | - Caroline Dive
- Cancer Research United Kingdom, Manchester Institute, Manchester, United Kingdom
| | - Anna F Farago
- Massachusetts General Hospital, Boston, Massachusetts
| | | | - Christine Hann
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Leora Horn
- Vanderbilt University, Nashville, Tennessee
| | | | | | - Sumin Kang
- Emory University, Winship Cancer Institute, Atlanta, Georgia
| | - Mark Krasnow
- Stanford University School of Medicine, Stanford, California
| | - James Lee
- The Ohio State University, Columbus, Ohio
| | - Se-Hoon Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Benjamin Lok
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | | | - John Minna
- UT Southwestern Medical Center, Dallas, Texas
| | - Matthew Oser
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keunchil Park
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Yves Pommier
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | - Julien Sage
- Stanford University School of Medicine, Stanford, California
| | | | - Martin L Sos
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne Germany; Molecular Pathology, Institute of Pathology, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Kate D Sutherland
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | | | - Sarah J Wait
- Huntsman Cancer Institute and University of Utah, Salt Lake City, Utah
| | | | - Kwok Kin Wong
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Hua Zhang
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Jillian Daigneault
- International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Jacinta Wiens
- International Association for the Study of Lung Cancer, Aurora, Colorado
| | | | - Trudy G Oliver
- Huntsman Cancer Institute and University of Utah, Salt Lake City, Utah.
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154
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Cristea S, Coles GL, Hornburg D, Gershkovitz M, Arand J, Cao S, Sen T, Williamson SC, Kim JW, Drainas AP, He A, Cam LL, Byers LA, Snyder MP, Contrepois K, Sage J. The MEK5-ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer. Cancer Res 2020; 80:1293-1303. [PMID: 31969375 PMCID: PMC7073279 DOI: 10.1158/0008-5472.can-19-1027] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 12/31/2022]
Abstract
Small-cell lung cancer (SCLC) is an aggressive form of lung cancer with dismal survival rates. While kinases often play key roles driving tumorigenesis, there are strikingly few kinases known to promote the development of SCLC. Here, we investigated the contribution of the MAPK module MEK5-ERK5 to SCLC growth. MEK5 and ERK5 were required for optimal survival and expansion of SCLC cell lines in vitro and in vivo. Transcriptomics analyses identified a role for the MEK5-ERK5 axis in the metabolism of SCLC cells, including lipid metabolism. In-depth lipidomics analyses showed that loss of MEK5/ERK5 perturbs several lipid metabolism pathways, including the mevalonate pathway that controls cholesterol synthesis. Notably, depletion of MEK5/ERK5 sensitized SCLC cells to pharmacologic inhibition of the mevalonate pathway by statins. These data identify a new MEK5-ERK5-lipid metabolism axis that promotes the growth of SCLC. SIGNIFICANCE: This study is the first to investigate MEK5 and ERK5 in SCLC, linking the activity of these two kinases to the control of cell survival and lipid metabolism.
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Affiliation(s)
- Sandra Cristea
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Garry L Coles
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Daniel Hornburg
- Department of Genetics, Stanford University, Stanford, California
| | - Maya Gershkovitz
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Julia Arand
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Siqi Cao
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Triparna Sen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stuart C Williamson
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Jun W Kim
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Andrew He
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Laurent Le Cam
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Lauren Averett Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, California
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, California.
- Department of Genetics, Stanford University, Stanford, California
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155
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Cai WL, Greer CB, Chen JF, Arnal-Estapé A, Cao J, Yan Q, Nguyen DX. Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain. BMC Med Genomics 2020; 13:33. [PMID: 32143622 PMCID: PMC7060551 DOI: 10.1186/s12920-020-0695-0] [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: 10/08/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background Few somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, the epigenomic alterations and transcription factors (TFs) which underlie these alterations remain unclear. Methods To identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and its brain (BrM2) and lung (LM2) metastatic sub-populations. We incorporated ATAC-seq data from TCGA to assess metastatic open chromatin signatures, and gene expression data from human metastatic datasets to nominate transcription factor biomarkers. Results Our integrated epigenomic analyses found that lung and brain metastatic cells exhibit both shared and distinctive signatures of active chromatin. Notably, metastatic sub-populations exhibit increased activation of both promoters and enhancers. We also integrated these data with chromosome conformation capture coupled with ChIP-seq (HiChIP) derived enhancer-promoter interactions to predict enhancer-controlled pathway alterations. We found that enhancer changes are associated with endothelial cell migration in LM2, and negative regulation of epithelial cell proliferation in BrM2. Promoter changes are associated with vasculature development in LM2 and homophilic cell adhesion in BrM2. Using ATAC-seq, we identified a metastasis open-chromatin signature that is elevated in basal-like and HER2-enriched breast cancer subtypes and associates with worse prognosis in human samples. We further uncovered TFs associated with the open chromatin landscapes of metastatic cells and whose expression correlates with risk for metastasis. While some of these TFs are associated with primary breast tumor subtypes, others more specifically correlate with lung or brain metastasis. Conclusions We identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain. We also demonstrate that signatures of active chromatin sites are partially linked to human breast cancer subtypes with poor prognosis, and that specific TFs can independently distinguish lung and brain relapse.
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Affiliation(s)
- Wesley L Cai
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Celeste B Greer
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Department of Pharmacology, Vanderbilt University School of Medicine, 2209 Garland Ave, Nashville, TN, 37240-0002, USA
| | - Jocelyn F Chen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Anna Arnal-Estapé
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Rutgers Cancer Institute of New Jersey, Rutgers, 195 Little Albany St, New Brunswick, NJ, 08903-2681, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA. .,Department of Medicine (Medical Oncology), Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.
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156
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Sui JSY, Martin P, Gray SG. Pre-clinical models of small cell lung cancer and the validation of therapeutic targets. Expert Opin Ther Targets 2020; 24:187-204. [PMID: 32068452 DOI: 10.1080/14728222.2020.1732353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Small-cell lung cancer (SCLC) is an aggressive form of lung cancer that has a dismal prognosis. One of the factors hindering therapeutic developments for SCLC is that most SCLC is not surgically resected resulting in a paucity of material for analysis. To address this, significant efforts have been made by investigators to develop pre-clinical models of SCLC allowing for downstream target identification in this difficult to treat cancer.Areas covered: In this review, we describe the current pre-clinical models that have been developed to interrogate SCLC, and outline the benefits and limitations associated with each. Using examples we show how each has been used to (i) improve our knowledge of this intractable cancer, and (ii) identify and validate potential therapeutic targets that (iii) are currently under development and testing within the clinic.Expert opinion: The large numbers of preclinical models that have been developed have dramatically improved the ways in which we can examine SCLC and test therapeutic targets/interventions. The newer models are rapidly providing novel avenues for the design and testing of new therapeutics. Despite this many of these models have inherent flaws that limit the possibility of their use for individualized therapy decision-making for SCLC.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland.,Department of Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Petra Martin
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland.,Labmed Directorate, St. James's Hospital, Dublin, Ireland.,School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland
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157
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Expression of NFIA and NFIB within the murine spinal cord. Gene Expr Patterns 2020; 35:119098. [PMID: 32068188 DOI: 10.1016/j.gep.2020.119098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/17/2022]
Abstract
The Nuclear factor I proteins comprise a family of transcription factors that are expressed in many developing and mature cell populations, including within the central nervous system. Within the embryonic mouse spinal cord, NFIA and NFIB are expressed by neural progenitor cells lining the central canal, where they act to promote astrocytic and oligodendrocytic lineage specification. Cells lining the mature spinal cord central canal retain characteristics of neural progenitor cells, but the expression of NFIA and NFIB within the mature spinal cord at a cell-type-specific level remains undefined. Here, we investigated where these two transcription factors are expressed within the adult mouse spinal cord. We reveal that both factors are expressed in similar cohorts of mature cells, including ependymal cells, interneurons and motor neurons. We also show robust and widespread expression of NFIA and NFIB within nestin-expressing cells following injury to the spinal cord. Collectively, these data provide a basis to further define what functional role(s) NFIA and NFIB play within the adult spinal cord.
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158
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Fraser J, Essebier A, Brown AS, Davila RA, Harkins D, Zalucki O, Shapiro LP, Penzes P, Wainwright BJ, Scott MP, Gronostajski RM, Bodén M, Piper M, Harvey TJ. Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development. CEREBELLUM (LONDON, ENGLAND) 2020; 19:89-101. [PMID: 31838646 PMCID: PMC7815246 DOI: 10.1007/s12311-019-01089-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcriptional regulation plays a central role in controlling neural stem and progenitor cell proliferation and differentiation during neurogenesis. For instance, transcription factors from the nuclear factor I (NFI) family have been shown to co-ordinate neural stem and progenitor cell differentiation within multiple regions of the embryonic nervous system, including the neocortex, hippocampus, spinal cord and cerebellum. Knockout of individual Nfi genes culminates in similar phenotypes, suggestive of common target genes for these transcription factors. However, whether or not the NFI family regulates common suites of genes remains poorly defined. Here, we use granule neuron precursors (GNPs) of the postnatal murine cerebellum as a model system to analyse regulatory targets of three members of the NFI family: NFIA, NFIB and NFIX. By integrating transcriptomic profiling (RNA-seq) of Nfia- and Nfix-deficient GNPs with epigenomic profiling (ChIP-seq against NFIA, NFIB and NFIX, and DNase I hypersensitivity assays), we reveal that these transcription factors share a large set of potential transcriptional targets, suggestive of complementary roles for these NFI family members in promoting neural development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Lauren P Shapiro
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peter Penzes
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Matthew P Scott
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Mikael Bodén
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
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159
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Shan Y, Zhang Y, Zhao Y, Wang T, Zhang J, Yao J, Ma N, Liang Z, Huang W, Huang K, Zhang T, Su Z, Chen Q, Zhu Y, Wu C, Zhou T, Sun W, Wei Y, Zhang C, Li C, Su S, Liao B, Zhong M, Zhong X, Nie J, Pei D, Pan G. JMJD3 and UTX determine fidelity and lineage specification of human neural progenitor cells. Nat Commun 2020; 11:382. [PMID: 31959746 PMCID: PMC6971254 DOI: 10.1038/s41467-019-14028-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/13/2019] [Indexed: 02/08/2023] Open
Abstract
Neurogenesis, a highly orchestrated process, entails the transition from a pluripotent to neural state and involves neural progenitor cells (NPCs) and neuronal/glial subtypes. However, the precise epigenetic mechanisms underlying fate decision remain poorly understood. Here, we delete KDM6s (JMJD3 and/or UTX), the H3K27me3 demethylases, in human embryonic stem cells (hESCs) and show that their deletion does not impede NPC generation from hESCs. However, KDM6-deficient NPCs exhibit poor proliferation and a failure to differentiate into neurons and glia. Mechanistically, both JMJD3 and UTX are found to be enriched in gene loci essential for neural development in hNPCs, and KDM6 impairment leads to H3K27me3 accumulation and blockade of DNA accessibility at these genes. Interestingly, forced expression of neuron-specific chromatin remodelling BAF (nBAF) rescues the neuron/glia defect in KDM6-deficient NPCs despite H3K27me3 accumulation. Our findings uncover the differential requirement of KDM6s in specifying NPCs and neurons/glia and highlight the contribution of individual epigenetic regulators in fate decisions in a human development model. Neurogenesis is an ordered transition from pluriptotent cells to neural precursor cells (NPCs) to neurons. Here the authors show that loss of the lysine demethylases JMJD3 and UTX leads reduced DNA accessibility at neurogenesis loci in human NPCs, and that the chromatin remodeller BAF can rescue differentiation defects.
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Affiliation(s)
- Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jiao Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ning Ma
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Zechuan Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wenhao Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ke Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tian Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Zhenghui Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chuman Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wei Sun
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chenxu Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shuquan Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Baojian Liao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Mei Zhong
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China. .,Shandong Medicinal Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250012, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, China.
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160
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Ganesh K, Basnet H, Kaygusuz Y, Laughney AM, He L, Sharma R, O'Rourke KP, Reuter VP, Huang YH, Turkekul M, Emrah E, Masilionis I, Manova-Todorova K, Weiser MR, Saltz LB, Garcia-Aguilar J, Koche R, Lowe SW, Pe'er D, Shia J, Massagué J. L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer. ACTA ACUST UNITED AC 2020; 1:28-45. [PMID: 32656539 DOI: 10.1038/s43018-019-0006-x] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastasis-initiating cells with stem-like properties drive cancer lethality, yet their origins and relationship to primary-tumor-initiating stem cells are not known. We show that L1CAM+ cells in human colorectal cancer (CRC) have metastasis-initiating capacity, and we define their relationship to tissue regeneration. L1CAM is not expressed in the homeostatic intestinal epithelium, but is induced and required for epithelial regeneration following colitis and in CRC organoid growth. By using human tissues and mouse models, we show that L1CAM is dispensable for adenoma initiation but required for orthotopic carcinoma propagation, liver metastatic colonization and chemoresistance. L1CAMhigh cells partially overlap with LGR5high stem-like cells in human CRC organoids. Disruption of intercellular epithelial contacts causes E-cadherin-REST transcriptional derepression of L1CAM, switching chemoresistant CRC progenitors from an L1CAMlow to an L1CAMhigh state. Thus, L1CAM dependency emerges in regenerative intestinal cells when epithelial integrity is lost, a phenotype of wound healing deployed in metastasis-initiating cells.
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Affiliation(s)
- Karuna Ganesh
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Yasemin Kaygusuz
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Ashley M Laughney
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Present address: Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Lan He
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Applied Physics and Applied Math, Columbia University, New York, NY, USA.,Present address: New York Genome Center, New York, NY, USA
| | - Kevin P O'Rourke
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Vincent P Reuter
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Han Huang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Mesruh Turkekul
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ekrem Emrah
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Present address: Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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161
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Ng SR, Rideout WM, Akama-Garren EH, Bhutkar A, Mercer KL, Schenkel JM, Bronson RT, Jacks T. CRISPR-mediated modeling and functional validation of candidate tumor suppressor genes in small cell lung cancer. Proc Natl Acad Sci U S A 2020; 117:513-521. [PMID: 31871154 PMCID: PMC6955235 DOI: 10.1073/pnas.1821893117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer that remains among the most lethal of solid tumor malignancies. Recent genomic sequencing studies have identified many recurrently mutated genes in human SCLC tumors. However, the functional roles of most of these genes remain to be validated. Here, we have adapted the CRISPR-Cas9 system to a well-established murine model of SCLC to rapidly model loss-of-function mutations in candidate genes identified from SCLC sequencing studies. We show that loss of the gene p107 significantly accelerates tumor progression. Notably, compared with loss of the closely related gene p130, loss of p107 results in fewer but larger tumors as well as earlier metastatic spread. In addition, we observe differences in proliferation and apoptosis as well as altered distribution of initiated tumors in the lung, resulting from loss of p107 or p130 Collectively, these data demonstrate the feasibility of using the CRISPR-Cas9 system to model loss of candidate tumor suppressor genes in SCLC, and we anticipate that this approach will facilitate efforts to investigate mechanisms driving tumor progression in this deadly disease.
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Affiliation(s)
- Sheng Rong Ng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Elliot H Akama-Garren
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kim L Mercer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Roderick T Bronson
- Department of Pathology, Tufts University School of Veterinary Medicine, North Grafton, MA 01536
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
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162
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Yang D, Qu F, Cai H, Chuang CH, Lim JS, Jahchan N, Grüner BM, S Kuo C, Kong C, Oudin MJ, Winslow MM, Sage J. Axon-like protrusions promote small cell lung cancer migration and metastasis. eLife 2019; 8:50616. [PMID: 31833833 PMCID: PMC6940020 DOI: 10.7554/elife.50616] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Metastasis is the main cause of death in cancer patients but remains a poorly understood process. Small cell lung cancer (SCLC) is one of the most lethal and most metastatic cancer types. SCLC cells normally express neuroendocrine and neuronal gene programs but accumulating evidence indicates that these cancer cells become relatively more neuronal and less neuroendocrine as they gain the ability to metastasize. Here we show that mouse and human SCLC cells in culture and in vivo can grow cellular protrusions that resemble axons. The formation of these protrusions is controlled by multiple neuronal factors implicated in axonogenesis, axon guidance, and neuroblast migration. Disruption of these axon-like protrusions impairs cell migration in culture and inhibits metastatic ability in vivo. The co-option of developmental neuronal programs is a novel molecular and cellular mechanism that contributes to the high metastatic ability of SCLC.
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Affiliation(s)
- Dian Yang
- Cancer Biology Program, Stanford University School of Medicine, Stanford, United States.,Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Fangfei Qu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Chen-Hua Chuang
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Jing Shan Lim
- Cancer Biology Program, Stanford University School of Medicine, Stanford, United States.,Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Nadine Jahchan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Barbara M Grüner
- Department of Genetics, Stanford University School of Medicine, Stanford, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK) partner site Essen, Essen, Germany
| | - Christin S Kuo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Christina Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
| | - Madeleine J Oudin
- Department of Biomedical Engineering, Tufts University, Medford, United States
| | - Monte M Winslow
- Cancer Biology Program, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, United States
| | - Julien Sage
- Cancer Biology Program, Stanford University School of Medicine, Stanford, United States.,Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
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163
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Le-Bel G, Cortez Ghio S, Guérin LP, Bisson F, Germain L, Guérin SL. Irradiated Human Fibroblasts as a Substitute Feeder Layer to Irradiated Mouse 3T3 for the Culture of Human Corneal Epithelial Cells: Impact on the Stability of the Transcription Factors Sp1 and NFI. Int J Mol Sci 2019; 20:ijms20246296. [PMID: 31847118 PMCID: PMC6940969 DOI: 10.3390/ijms20246296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022] Open
Abstract
Because of the worldwide shortage of graftable corneas, alternatives to restore visual impairments, such as the production of a functional human cornea by tissue engineering, have emerged. Self-renewal of the corneal epithelium through the maintenance of a sub-population of corneal stem cells is required to maintain the functionality of such a reconstructed cornea. We previously reported an association between stem cell differentiation and the level to which they express the transcription factors Sp1 and NFI. In this study, we investigated the impact of replacing irradiated 3T3 (i3T3) murine fibroblast feeder cells by irradiated human corneal fibroblasts (iHFL) on the expression of Sp1 and NFI and evaluated their contribution to the proliferative properties of human corneal epithelial cells (hCECs) in both monolayer cultures and human tissue engineered corneas (hTECs). hCECs co-cultured with iHFL could be maintained for up to two more passages than when they were grown with i3T3. Western Blot and electrophoretic mobility shift assays (EMSAs) revealed no significant difference in the feeder-layer dependent increase in Sp1 at both the protein and DNA binding level, respectively, between HCECs grown with either i3T3 or iHFL. On the other hand, a significant increase in the expression and DNA binding of NFI was observed at each subsequent passage when hCECs were co-cultured along with i3T3. These changes were found to result from an increased expression of the NFIA and NFIB isoforms in hCECs grown with i3T3. Exposure of hCECs to cycloheximide revealed an increased stability of NFIB that likely resulted from post-translational glycosylation of this protein when these cells were co-cultured with i3T3. In addition, iHFL were as efficient as i3T3 at preserving corneal, slow-cycling, epithelial stem cells in the basal epithelium of the reconstructed hTECs. Furthermore, we observed an increased expression of genes whose encoded products promote hCECs differentiation along several passages in hCECs co-cultured with either type of feeder layer. Therefore, the iHFL feeder layer appears to be the most effective at maintaining the proliferative properties of hCECs in culture most likely by preserving high levels of Sp1 and low levels of NFIB, which is known for its gene repressor and cell differentiation properties.
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Affiliation(s)
- Gaëtan Le-Bel
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Centre Universitaire d’Ophtalmologie (CUO)-Recherche, Centre de recherche FRQS du CHU de Québec, Axe Médecine Régénératrice, Québec, QC G1J 1Z4, Canada
- Département de Chirurgie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sergio Cortez Ghio
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Département de Chirurgie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Louis-Philippe Guérin
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Département d’Ophtalmologie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Francis Bisson
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Département de Chirurgie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Lucie Germain
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Département de Chirurgie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Département d’Ophtalmologie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain L. Guérin
- Centre LOEX de l’Université Laval, Génie Tissulaire et Régénération, Centre de Recherche du CHU de Québec -Université Laval, Axe Médecine Régénératrice, Québec, QC G1V 0A6, Canada; (G.L.-B.); (S.C.G.); (L.-P.G.); (F.B.); (L.G.)
- Centre Universitaire d’Ophtalmologie (CUO)-Recherche, Centre de recherche FRQS du CHU de Québec, Axe Médecine Régénératrice, Québec, QC G1J 1Z4, Canada
- Département d’Ophtalmologie, Faculté de médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-682-7565
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164
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Tarbell ED, Liu T. HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. Nucleic Acids Res 2019; 47:e91. [PMID: 31199868 PMCID: PMC6895260 DOI: 10.1093/nar/gkz533] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/23/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human ATAC-seq datasets. We find that single-end sequenced or size-selected ATAC-seq datasets result in a loss of sensitivity compared to paired-end datasets without size-selection.
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Affiliation(s)
- Evan D Tarbell
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14203, USA.,Enhanced Pharmacodynamics LLC, Buffalo, NY 14203, USA
| | - Tao Liu
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14203, USA.,Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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165
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Epithelial tumor suppressor ELF3 is a lineage-specific amplified oncogene in lung adenocarcinoma. Nat Commun 2019; 10:5438. [PMID: 31780666 PMCID: PMC6882813 DOI: 10.1038/s41467-019-13295-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/24/2019] [Indexed: 01/22/2023] Open
Abstract
Gene function in cancer is often cell type-specific. The epithelial cell-specific transcription factor ELF3 is a documented tumor suppressor in many epithelial tumors yet displays oncogenic properties in others. Here, we show that ELF3 is an oncogene in the adenocarcinoma subtype of lung cancer (LUAD), providing genetic, functional, and clinical evidence of subtype specificity. We discover a region of focal amplification at chromosome 1q32.1 encompassing the ELF3 locus in LUAD which is absent in the squamous subtype. Gene dosage and promoter hypomethylation affect the locus in up to 80% of LUAD analyzed. ELF3 expression was required for tumor growth and a pan-cancer expression network analysis supports its subtype and tissue specificity. We further show that ELF3 displays strong prognostic value in LUAD but not LUSC. We conclude that, contrary to many other tumors of epithelial origin, ELF3 is an oncogene and putative therapeutic target in LUAD. Tissue context can dictate why a gene can have seemingly opposing functions in different settings. ELF3 is tumor suppressive in many cancers of epithelial origin but in lung cancer, the authors describe an oncogenic role in the adenocarcinoma histology of non-small cell lung cancer.
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166
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Zenker M, Bunt J, Schanze I, Schanze D, Piper M, Priolo M, Gerkes EH, Gronostajski RM, Richards LJ, Vogt J, Wessels MW, Hennekam RC. Variants in nuclear factor I genes influence growth and development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:611-626. [DOI: 10.1002/ajmg.c.31747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Martin Zenker
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Jens Bunt
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
| | - Ina Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Denny Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Michael Piper
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Manuela Priolo
- Operative Unit of Medical GeneticsGreat Metropolitan Hospital Bianchi‐Melacrino‐Morelli Reggio Calabria Italy
| | - Erica H. Gerkes
- Department of Genetics, University of GroningenUniversity Medical Center Groningen Groningen the Netherlands
| | - Richard M. Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life SciencesState University of New York Buffalo NY
| | - Linda J. Richards
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health PartnersWomen's and Children's Hospitals NHS Foundation Trust Birmingham UK
| | - Marja W. Wessels
- Department of Clinical Genetics, Erasmus MCUniversity Medical Center Rotterdam Rotterdam The Netherlands
| | - Raoul C. Hennekam
- Department of PediatricsUniversity of Amsterdam Amsterdam The Netherlands
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167
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Abstract
Cancer arises from a single cell through a series of acquired mutations and epigenetic alterations. Tumors gradually develop into a complex tissue comprised of phenotypically heterogeneous cancer cell populations, as well as noncancer cells that make up the tumor microenvironment. The phenotype, or state, of each cancer and stromal cell is influenced by a plethora of cell-intrinsic and cell-extrinsic factors. The diversity of these cellular states promotes tumor progression, enables metastasis, and poses a challenge for effective cancer treatments. Thus, the identification of strategies for the therapeutic manipulation of tumor heterogeneity would have significant clinical implications. A major barrier in the field is the difficulty in functionally investigating heterogeneity in tumors in cancer patients. Here we review how mouse models of human cancer can be leveraged to interrogate tumor heterogeneity and to help design better therapeutic strategies.
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Affiliation(s)
- Tuomas Tammela
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julien Sage
- Department of Pediatrics and Department of Genetics, Stanford University, Stanford, California 94305, USA
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168
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Sun L, Fang Y, Wang X, Han Y, Du F, Li C, Hu H, Liu H, Liu Q, Wang J, Liang J, Chen P, Yang H, Nie Y, Wu K, Fan D, Coffey RJ, Lu Y, Zhao X, Wang X. miR-302a Inhibits Metastasis and Cetuximab Resistance in Colorectal Cancer by Targeting NFIB and CD44. Am J Cancer Res 2019; 9:8409-8425. [PMID: 31754405 PMCID: PMC6857048 DOI: 10.7150/thno.36605] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/10/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction: Metastasis and drug resistance contribute substantially to the poor prognosis of colorectal cancer (CRC) patients. However, the epigenetic regulatory mechanisms by which CRC develops metastatic and drug-resistant characteristics remain unclear. This study aimed to investigate the role of miR-302a in the metastasis and molecular-targeted drug resistance of CRC and elucidate the underlying molecular mechanisms. Methods: miR-302a expression in CRC cell lines and patient tissue microarrays was analyzed by qPCR and fluorescence in situ hybridization. The roles of miR-302a in metastasis and cetuximab (CTX) resistance were evaluated both in vitro and in vivo. Bioinformatic prediction algorithms and luciferase reporter assays were performed to identify the miR-302a binding regions in the NFIB and CD44 3'-UTRs. A chromatin immunoprecipitation assay was performed to examine NFIB occupancy in the ITGA6 promoter region. Immunoblotting was performed to identify the EGFR-mediated pathways altered by miR-302a. Results: miR-302a expression was frequently reduced in CRC cells and tissues, especially in CTX-resistant cells and patient-derived xenografts. The decreased miR-302a levels correlated with poor overall CRC patient survival. miR-302a overexpression inhibited metastasis and restored CTX responsiveness in CRC cells, whereas miR-302a silencing exerted the opposite effects. NFIB and CD44 were identified as novel targets of miR-302a. miR-302a inhibited the metastasis-promoting effect of NFIB that physiologically activates ITGA6 transcription. miR-302a restored CTX responsiveness by suppressing CD44-induced cancer stem cell-like properties and EGFR-mediated MAPK and AKT signaling. These results are consistent with clinical observations indicating that miR-302a expression is inversely correlated with the expression of its targets in CRC specimens. Conclusions: Our findings show that miR-302a acts as a multifaceted regulator of CRC metastasis and CTX resistance by targeting NFIB and CD44, respectively. Our study implicates miR-302a as a candidate prognostic predictor and a therapeutic agent in CRC.
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169
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Wooten DJ, Groves SM, Tyson DR, Liu Q, Lim JS, Albert R, Lopez CF, Sage J, Quaranta V. Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers. PLoS Comput Biol 2019; 15:e1007343. [PMID: 31671086 PMCID: PMC6860456 DOI: 10.1371/journal.pcbi.1007343] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/18/2019] [Accepted: 08/19/2019] [Indexed: 01/15/2023] Open
Abstract
Adopting a systems approach, we devise a general workflow to define actionable subtypes in human cancers. Applied to small cell lung cancer (SCLC), the workflow identifies four subtypes based on global gene expression patterns and ontologies. Three correspond to known subtypes (SCLC-A, SCLC-N, and SCLC-Y), while the fourth is a previously undescribed ASCL1+ neuroendocrine variant (NEv2, or SCLC-A2). Tumor deconvolution with subtype gene signatures shows that all of the subtypes are detectable in varying proportions in human and mouse tumors. To understand how multiple stable subtypes can arise within a tumor, we infer a network of transcription factors and develop BooleaBayes, a minimally-constrained Boolean rule-fitting approach. In silico perturbations of the network identify master regulators and destabilizers of its attractors. Specific to NEv2, BooleaBayes predicts ELF3 and NR0B1 as master regulators of the subtype, and TCF3 as a master destabilizer. Since the four subtypes exhibit differential drug sensitivity, with NEv2 consistently least sensitive, these findings may lead to actionable therapeutic strategies that consider SCLC intratumoral heterogeneity. Our systems-level approach should generalize to other cancer types.
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Affiliation(s)
- David J. Wooten
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Sarah M. Groves
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Qi Liu
- Departments of Biomedical Informatics and Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jing S. Lim
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, United States of America
| | - Réka Albert
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Carlos F. Lopez
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, United States of America
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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170
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Pozo K, Kelenis DP, Minna JD, Johnson JE. Different Originating Cells Underlie Intertumoral Heterogeneity in Lung Neuroendocrine Tumors. Cancer Discov 2019; 8:1216-1218. [PMID: 30279195 DOI: 10.1158/2159-8290.cd-18-0979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studies in genetically engineered mouse models of neuroendocrine lung cancer suggest that differences in cells of origin underlie subtype variations in this class of cancers. These findings highlight the concept that the same driver mutations introduced into different cells of origin lead to tumors with the same histology but dramatically different metastatic programs and potentially different therapeutic responses. Cancer Discov; 8(10); 1216-8. ©2018 AACR See related article by Yang et al., p. 1316.
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Affiliation(s)
- Karine Pozo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas.,Department of Surgery, UT Southwestern Medical Center, Dallas, Texas
| | - Demetra P Kelenis
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas
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171
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Quintanal-Villalonga Á, Molina-Pinelo S. Epigenetics of lung cancer: a translational perspective. Cell Oncol (Dordr) 2019; 42:739-756. [PMID: 31396859 DOI: 10.1007/s13402-019-00465-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lung cancer remains the most common cause of cancer-related death, with a 5-year survival rate of only 18%. In recent years, the development of targeted pharmacological agents and immunotherapies has substantially increased the survival of a subset of patients. However, most patients lack such efficacious therapy and are, thus, treated with classical chemotherapy with poor clinical outcomes. Therefore, novel therapeutic strategies are urgently needed. In recent years, the development of epigenetic assays and their application to cancer research have highlighted the relevance of epigenetic regulation in the initiation, development, progression and treatment of lung cancer. CONCLUSIONS A variety of epigenetic modifications do occur at different steps of lung cancer development, some of which are key to tumor progression. The rise of cutting-edge technologies such as single cell epigenomics is, and will continue to be, crucial for uncovering epigenetic events at a single cell resolution, leading to a better understanding of the biology underlying lung cancer development and to the design of novel therapeutic options. This approach has already led to the development of strategies involving single agents or combined agents targeting epigenetic modifiers, currently in clinical trials. Here, we will discuss the epigenetics of every step of lung cancer development, as well as the translation of these findings into clinical applications.
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Affiliation(s)
| | - Sonia Molina-Pinelo
- Unidad Clínica de Oncología Médica, Radioterapia y Radiofísica, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Avda. Manuel Siurot s/n, 41013, Seville, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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172
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Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 2019; 37:925-936. [PMID: 31375813 PMCID: PMC7299161 DOI: 10.1038/s41587-019-0206-z] [Citation(s) in RCA: 512] [Impact Index Per Article: 102.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023]
Abstract
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | | | - Jean Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Li Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | | | | | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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173
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Zhang T, Huang K, Zhu Y, Wang T, Shan Y, Long B, Li Y, Chen Q, Wang P, Zhao S, Li D, Wu C, Kang B, Gu J, Mai Y, Wang Q, Li J, Zhang Y, Liang Z, Guo L, Wu F, Su S, Wang J, Gao M, Zhong X, Liao B, Chen J, Zhang X, Shu X, Pei D, Nie J, Pan G. Vitamin C-dependent lysine demethylase 6 (KDM6)-mediated demethylation promotes a chromatin state that supports the endothelial-to-hematopoietic transition. J Biol Chem 2019; 294:13657-13670. [PMID: 31341023 DOI: 10.1074/jbc.ra119.009757] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/14/2019] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic stem cells (HSCs)/progenitor cells (HPCs) are generated from hemogenic endothelial cells (HECs) during the endothelial-to-hematopoietic transition (EHT); however, the underlying mechanism remains poorly understood. Here, using an array of approaches, including CRSPR/Cas9 gene knockouts, RNA-Seq, ChIP-Seq, ATAC-Seq etc., we report that vitamin C (Vc) is essential in HPC generation during human pluripotent stem cell (hPSC) differentiation in defined culture conditions. Mechanistically, we found that the endothelial cells generated in the absence of Vc fail to undergo the EHT because of an apparent failure in opening up genomic loci essential for hematopoiesis. Under Vc deficiency, these loci exhibited abnormal accumulation of histone H3 trimethylation at Lys-27 (H3K27me3), a repressive histone modification that arose because of lower activities of demethylases that target H3K27me3. Consistently, deletion of the two H3K27me3 demethylases, Jumonji domain-containing 3 (JMJD3 or KDM6B) and histone demethylase UTX (UTX or KDM6A), impaired HPC generation even in the presence of Vc. Furthermore, we noted that Vc and jmjd3 are also important for HSC generation during zebrafish development. Together, our findings reveal an essential role for Vc in the EHT for hematopoiesis, and identify KDM6-mediated chromatin demethylation as an important regulatory mechanism in hematopoietic cell differentiation.
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Affiliation(s)
- Tian Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005 China
| | - Ke Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005 China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Bing Long
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Yuhang Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Pengtao Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shaoyang Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Dongwei Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chuman Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Baoqiang Kang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiaming Gu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuchan Mai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qing Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinbing Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zechuan Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lin Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Fang Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shuquan Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Junwei Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Minghui Gao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Baojian Liao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiao Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaodong Shu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005 China.,Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250012, China
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174
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Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT. Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions. Nat Commun 2019; 10:3221. [PMID: 31324780 PMCID: PMC6642133 DOI: 10.1038/s41467-019-11118-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/20/2019] [Indexed: 01/12/2023] Open
Abstract
The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. Here we have used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We have found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple, regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix) characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high affinity binding but is essential for specificity. Finally, we find that Satb1-DNA interactions are mechanosensitive. Increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.
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Affiliation(s)
- Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Linfeng Yang
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Michael P Reddick
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Polly Fordyce
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and the Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, United States
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
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175
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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176
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Vo TM, Jain S, Burchett R, Monckton EA, Godbout R. A positive feedback loop involving nuclear factor IB and calpain 1 suppresses glioblastoma cell migration. J Biol Chem 2019; 294:12638-12654. [PMID: 31262726 DOI: 10.1074/jbc.ra119.008291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma (GBM) is a brain tumor that remains largely incurable because of its highly-infiltrative properties. Nuclear factor I (NFI)-type transcription factors regulate genes associated with GBM cell migration and infiltration. We have previously shown that NFI activity depends on the NFI phosphorylation state and that calcineurin phosphatase dephosphorylates and activates NFI. Calcineurin is cleaved and activated by calpain proteases whose activity is, in turn, regulated by an endogenous inhibitor, calpastatin (CAST). The CAST gene is a target of NFI in GBM cells, with differentially phosphorylated NFIs regulating the levels of CAST transcript variants. Here, we uncovered an NFIB-calpain 1-positive feedback loop mediated through CAST and calcineurin. In NFI-hyperphosphorylated GBM cells, NFIB expression decreased the CAST-to-calpain 1 ratio in the cytoplasm. This reduced ratio increased autolysis and activity of cytoplasmic calpain 1. Conversely, in NFI-hypophosphorylated cells, NFIB expression induced differential subcellular compartmentalization of CAST and calpain 1, with CAST localizing primarily to the cytoplasm and calpain 1 to the nucleus. Overall, this altered compartmentalization increased nuclear calpain 1 activity. We also show that nuclear calpain 1, by cleaving and activating calcineurin, induces NFIB dephosphorylation. Of note, knockdown of calpain 1, NFIB, or both increased GBM cell migration and up-regulated the pro-migratory factors fatty acid-binding protein 7 (FABP7) and Ras homolog family member A (RHOA). In summary, our findings reveal bidirectional cross-talk between NFIB and calpain 1 in GBM cells. A physiological consequence of this positive feedback loop appears to be decreased GBM cell migration.
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Affiliation(s)
- The Minh Vo
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Saket Jain
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Rebecca Burchett
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Elizabeth A Monckton
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Roseline Godbout
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
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177
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Jin Y, Ma D, Gramyk T, Guo C, Fang R, Ji H, Shi YG. Kdm1a promotes SCLC progression by transcriptionally silencing the tumor suppressor Rest. Biochem Biophys Res Commun 2019; 515:214-221. [DOI: 10.1016/j.bbrc.2019.05.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 05/18/2019] [Indexed: 01/22/2023]
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178
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Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron 2019; 102:1111-1126.e5. [PMID: 31128945 PMCID: PMC6768831 DOI: 10.1016/j.neuron.2019.04.010] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
Precise temporal control of gene expression in neuronal progenitors is necessary for correct regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of the developing CNS has posed a major obstacle to identifying the gene regulatory networks that control these processes. To address this, we used single-cell RNA sequencing to profile ten developmental stages encompassing the full course of retinal neurogenesis. This allowed us to comprehensively characterize changes in gene expression that occur during initiation of neurogenesis, changes in developmental competence, and specification and differentiation of each major retinal cell type. We identify the NFI transcription factors (Nfia, Nfib, and Nfix) as selectively expressed in late retinal progenitor cells and show that they control bipolar interneuron and Müller glia cell fate specification and promote proliferative quiescence.
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Affiliation(s)
- Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Stein-O'Brien
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fion Shiau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gabrielle H Cannon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis-Marcisak
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh V Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fatemeh Rajaii
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rebecca E James-Esposito
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Computational Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Mathematical Institute for Data Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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179
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Böttger F, Semenova EA, Song JY, Ferone G, van der Vliet J, Cozijnsen M, Bhaskaran R, Bombardelli L, Piersma SR, Pham TV, Jimenez CR, Berns A. Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer. Cell Rep 2019; 27:3345-3358.e4. [PMID: 31189116 PMCID: PMC6581744 DOI: 10.1016/j.celrep.2019.05.057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/26/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022] Open
Abstract
Small-cell lung cancer is the most aggressive type of lung cancer, characterized by a remarkable response to chemotherapy followed by development of resistance. Here, we describe SCLC subtypes in Mycl- and Nfib-driven GEMM that include CDH1-high peripheral primary tumor lesions and CDH1-negative, aggressive intrapulmonary metastases. Cisplatin treatment preferentially eliminates the latter, thus revealing a striking differential response. Using a combined transcriptomic and proteomic approach, we find a marked reduction in proliferation and metabolic rewiring following cisplatin treatment and present evidence for a distinctive metabolic and structural profile defining intrinsically resistant populations. This offers perspectives for effective combination therapies that might also hold promise for treating human SCLC, given the very similar response of both mouse and human SCLC to cisplatin.
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Affiliation(s)
- Franziska Böttger
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Ekaterina A Semenova
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Ji-Ying Song
- Department of Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Giustina Ferone
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Jan van der Vliet
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Miranda Cozijnsen
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rajith Bhaskaran
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lorenzo Bombardelli
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Sander R Piersma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Thang V Pham
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Anton Berns
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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180
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Wang X, Sterr M, Ansarullah, Burtscher I, Böttcher A, Beckenbauer J, Siehler J, Meitinger T, Häring HU, Staiger H, Cernilogar FM, Schotta G, Irmler M, Beckers J, Wright CVE, Bakhti M, Lickert H. Point mutations in the PDX1 transactivation domain impair human β-cell development and function. Mol Metab 2019; 24:80-97. [PMID: 30930126 PMCID: PMC6531841 DOI: 10.1016/j.molmet.2019.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Hundreds of missense mutations in the coding region of PDX1 exist; however, if these mutations predispose to diabetes mellitus is unknown. METHODS In this study, we screened a large cohort of subjects with increased risk for diabetes and identified two subjects with impaired glucose tolerance carrying common, heterozygous, missense mutations in the PDX1 coding region leading to single amino acid exchanges (P33T, C18R) in its transactivation domain. We generated iPSCs from patients with heterozygous PDX1P33T/+, PDX1C18R/+ mutations and engineered isogenic cell lines carrying homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations and a heterozygous PDX1 loss-of-function mutation (PDX1+/-). RESULTS Using an in vitro β-cell differentiation protocol, we demonstrated that both, heterozygous PDX1P33T/+, PDX1C18R/+ and homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations impair β-cell differentiation and function. Furthermore, PDX1+/- and PDX1P33T/P33T mutations reduced differentiation efficiency of pancreatic progenitors (PPs), due to downregulation of PDX1-bound genes, including transcription factors MNX1 and PDX1 as well as insulin resistance gene CES1. Additionally, both PDX1P33T/+ and PDX1P33T/P33T mutations in PPs reduced the expression of PDX1-bound genes including the long-noncoding RNA, MEG3 and the imprinted gene NNAT, both involved in insulin synthesis and secretion. CONCLUSIONS Our results reveal mechanistic details of how common coding mutations in PDX1 impair human pancreatic endocrine lineage formation and β-cell function and contribute to the predisposition for diabetes.
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Affiliation(s)
- Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Ansarullah
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julia Beckenbauer
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hans-Ulrich Häring
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Harald Staiger
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Filippo M Cernilogar
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Beckers
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Christopher V E Wright
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
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181
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Zibetti C, Liu S, Wan J, Qian J, Blackshaw S. Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin. Commun Biol 2019; 2:142. [PMID: 31044167 PMCID: PMC6484012 DOI: 10.1038/s42003-019-0375-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 03/11/2019] [Indexed: 11/14/2022] Open
Abstract
Retinal neurogenesis occurs through partially overlapping temporal windows, driven by concerted actions of transcription factors which, in turn, may contribute to the establishment of divergent genetic programs in the developing retina by coordinating variations in chromatin landscapes. Here we comprehensively profile murine retinal progenitors by integrating next generation sequencing methods and interrogate changes in chromatin accessibility at embryonic and post-natal stages. An unbiased search for motifs in open chromatin regions identifies putative factors involved in the developmental progression of the epigenome in retinal progenitor cells. Among these factors, the transcription factor LHX2 exhibits a developmentally regulated cis-regulatory repertoire and stage-dependent motif instances. Using loss-of-function assays, we determine LHX2 coordinates variations in chromatin accessibility, by competition for nucleosome occupancy and secondary regulation of candidate pioneer factors.
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Affiliation(s)
- Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sheng Liu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Jun Wan
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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182
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Metze K, Adam R, Florindo JB. The fractal dimension of chromatin - a potential molecular marker for carcinogenesis, tumor progression and prognosis. Expert Rev Mol Diagn 2019; 19:299-312. [DOI: 10.1080/14737159.2019.1597707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall Adam
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - João Batista Florindo
- Department of Applied Mathematics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas, Campinas, Brazil
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183
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Rogerson C, Britton E, Withey S, Hanley N, Ang YS, Sharrocks AD. Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state. Genome Res 2019; 29:723-736. [PMID: 30962179 PMCID: PMC6499311 DOI: 10.1101/gr.243345.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcriptome. We show that this network is activated in Barrett's esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett's-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorize EAC at a genome scale and implicate HNF4A activation as a potential pivotal event in its malignant transition from healthy cells.
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Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Withey
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Neil Hanley
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, United Kingdom
| | - Yeng S Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,GI Science Centre, Salford Royal NHS FT, University of Manchester, Salford M6 8HD, United Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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184
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The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting. Nat Genet 2019; 51:618-626. [PMID: 30858614 PMCID: PMC6755913 DOI: 10.1038/s41588-019-0363-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 12/02/2022]
Abstract
Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events in cancer1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2–5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. However, the consequences of dual ATPase subunit loss on mSWI/SNF complex subunit composition, chromatin targeting, DNA accessibility and gene expression remain unknown. Here we identify an ATPase module of subunits that is required for functional specification of BAF and PBAF subcomplexes. Using SMARCA4/2 ATPase mutant variants, we define the catalytic activity -dependent and -independent contributions of the ATPase module to the targeting of BAF and PBAF complexes on chromatin genome-wide. Finally, by linking distinct mSWI/SNF complex target sites to tumor-suppressive gene expression programs, we clarify the transcriptional consequences of SMARCA4/2 dual loss in SCCOHT.
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185
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Monroe TO, Hill MC, Morikawa Y, Leach JP, Heallen T, Cao S, Krijger PHL, de Laat W, Wehrens XHT, Rodney GG, Martin JF. YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo. Dev Cell 2019; 48:765-779.e7. [PMID: 30773489 DOI: 10.1016/j.devcel.2019.01.017] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/10/2018] [Accepted: 01/17/2019] [Indexed: 01/22/2023]
Abstract
Specialized adult somatic cells, such as cardiomyocytes (CMs), are highly differentiated with poor renewal capacity, an integral reason underlying organ failure in disease and aging. Among the least renewable cells in the human body, CMs renew approximately 1% annually. Consistent with poor CM turnover, heart failure is the leading cause of death. Here, we show that an active version of the Hippo pathway effector YAP, termed YAP5SA, partially reprograms adult mouse CMs to a more fetal and proliferative state. One week after induction, 19% of CMs that enter S-phase do so twice, CM number increases by 40%, and YAP5SA lineage CMs couple to pre-existing CMs. Genomic studies showed that YAP5SA increases chromatin accessibility and expression of fetal genes, partially reprogramming long-lived somatic cells in vivo to a primitive, fetal-like, and proliferative state.
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Affiliation(s)
- Tanner O Monroe
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yuka Morikawa
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, 6770 Bertner Avenue, Houston, TX 77030, USA
| | - John P Leach
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Todd Heallen
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, 6770 Bertner Avenue, Houston, TX 77030, USA
| | - Shuyi Cao
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands; University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands; University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xander H T Wehrens
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - George G Rodney
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiomyocyte Renewal Laboratory, Texas Heart Institute, 6770 Bertner Avenue, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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186
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Bertolini I, Terrasi A, Martelli C, Gaudioso G, Di Cristofori A, Storaci AM, Formica M, Braidotti P, Todoerti K, Ferrero S, Caroli M, Ottobrini L, Vaccari T, Vaira V. A GBM-like V-ATPase signature directs cell-cell tumor signaling and reprogramming via large oncosomes. EBioMedicine 2019; 41:225-235. [PMID: 30737083 PMCID: PMC6441844 DOI: 10.1016/j.ebiom.2019.01.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/17/2022] Open
Abstract
Background The V-ATPase proton pump controls acidification of intra and extra-cellular milieu in both physiological and pathological conditions. We previously showed that some V-ATPase subunits are enriched in glioma stem cells and in patients with poor survival. In this study, we investigated how expression of a GBM-like V-ATPase pump influences the non-neoplastic brain microenvironment. Methods Large oncosome (LO) vesicles were isolated from primary glioblastoma (GBM) neurospheres, or from patient sera, and co-cultured with primary neoplastic or non-neoplastic brain cells. LO transcript and protein contents were analyzed by qPCR, immunoblotting and immunogold staining. Activation of pathways in recipient cells was determined at gene and protein expression levels. V-ATPase activity was impaired by Bafilomycin A1 or gene silencing. Findings GBM neurospheres influence their non-neoplastic microenvironment by delivering the V-ATPase subunit V1G1 and the homeobox genes HOXA7, HOXA10, and POU3F2 to recipient cells via LO. LOs reprogram recipient cells to proliferate, grow as spheres and to migrate. Moreover, LOs are particularly abundant in the circulation of GBM patients with short survival time. Finally, impairment of V-ATPase reduces LOs activity. Interpretation We identified a novel mechanism adopted by glioma stem cells to promote disease progression via LO-mediated reprogramming of their microenvironment. Our data provide preliminary evidence for future development of LO-based liquid biopsies and suggest a novel potential strategy to contrast glioma progression. Fund This work was supported by Fondazione Cariplo (2014-1148 to VV) and by the Italian Minister of Health-Ricerca Corrente program 2017 (to SF).
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Affiliation(s)
- Irene Bertolini
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Terrasi
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Martelli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Gabriella Gaudioso
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Di Cristofori
- Division of Neurosurgery, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Maria Storaci
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Miriam Formica
- Department of Biosciences, Universita' degli Studi di Milano, Milan, Italy
| | | | - Katia Todoerti
- Department of Oncology and Hemato-oncology, University of Milan, Hematology Division, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Biosciences, University of Milan, Milan, Italy
| | - Manuela Caroli
- Division of Neurosurgery, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisa Ottobrini
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Thomas Vaccari
- Department of Biosciences, University of Milan, Milan, Italy.
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; Fondazione Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
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187
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News Feature: Targeting metastasis to halt cancer's spread. Proc Natl Acad Sci U S A 2019; 115:12539-12543. [PMID: 30538210 DOI: 10.1073/pnas.1818892115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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188
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Zhou ZH, Wang QL, Mao LH, Li XQ, Liu P, Song JW, Liu X, Xu F, Lei J, He S. Chromatin accessibility changes are associated with enhanced growth and liver metastasis capacity of acid-adapted colorectal cancer cells. Cell Cycle 2019; 18:511-522. [PMID: 30712429 PMCID: PMC6422493 DOI: 10.1080/15384101.2019.1578145] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/19/2018] [Accepted: 12/27/2018] [Indexed: 02/08/2023] Open
Abstract
The acidic extracellular microenvironment, namely acidosis, is a biochemical hallmark of solid tumors. However, the tumorigenicity, metastatic potential, gene expression profile and chromatin accessibility of acidosis-adapted colorectal cancer cells remain unknown. The colorectal cancer cell SW620 was cultured in acidic medium (pH 6.5) for more than 3 months to be acidosis-adapted (SW620-AA). In comparison to parental cells, SW620-AA cells exhibit enhanced tumorigenicity and liver metastatic potential in vivo. Following mRNA and lncRNA expression profiling, we validated that OLMF1, NFIB, SMAD9, DGKB are upregulated, while SESN2, MAP1B, UTRN, PCDH19, IL18, LMO2, CNKSR3, GXYLT2 are downregulated in SW620-AA cells. The differentially expressed mRNAs were significantly enriched in DNA remodeling-associated pathways including HDACs deacetylate histones, SIRT1 pathway, DNA methylation, DNA bending complex, and RNA polymerase 1 chain elongation. Finally, chromatin accessibility evaluation by ATAC-sequencing revealed that the differentially opened peaks were enriched in pathways such as small cell lung cancer, pathways in cancer, ErbB signaling, endometrial cancer, and chronic myeloid leukemia, which were mainly distributed in intergenic regions and introns. These results suggest that the chromatin accessibility changes are correlated with enhanced growth and liver metastasis capacity of acid-adapted colorectal cancer cells.
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Affiliation(s)
- Zhi-Hang Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathology, the 309 hospital of PLA, Beijing, China
| | - Qing-Liang Wang
- Department of Pathology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin-Hong Mao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiao-Qin Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Liu
- Department of Emergency, Chest Pain Center, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Jin-Wen Song
- Treatment and Research Center for Infectious Diseases, The 302nd hosptital of PLA, Beijing, China
| | - Xue Liu
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong, China
| | - Feng Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Lei
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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189
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Zhao G, Gong L, Su D, Jin Y, Guo C, Yue M, Yao S, Qin Z, Ye Y, Tang Y, Wu Q, Zhang J, Cui B, Ding Q, Huang H, Hu L, Chen Y, Zhang P, Hu G, Chen L, Wong KK, Gao D, Ji H. Cullin5 deficiency promotes small-cell lung cancer metastasis by stabilizing integrin β1. J Clin Invest 2019; 129:972-987. [PMID: 30688657 DOI: 10.1172/jci122779] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/30/2018] [Indexed: 12/21/2022] Open
Abstract
Metastasis is the dominant cause of patient death in small-cell lung cancer (SCLC), and a better understanding of the molecular mechanisms underlying SCLC metastasis may potentially improve clinical treatment. Through genome-scale screening for key regulators of mouse Rb1-/- Trp53-/- SCLC metastasis using the pooled CRISPR/Cas9 library, we identified Cullin5 (CUL5) and suppressor of cytokine signaling 3 (SOCS3), two components of the Cullin-RING E3 ubiquitin ligase complex, as top candidates. Mechanistically, the deficiency of CUL5 or SOCS3 disrupted the functional formation of the E3 ligase complex and prevented the degradation of integrin β1, which stabilized integrin β1 and activated downstream focal adhesion kinase/SRC (FAK/SRC) signaling and eventually drove SCLC metastasis. Low expression levels of CUL5 and SOCS3 were significantly associated with high integrin β1 levels and poor prognosis in a large cohort of 128 clinical patients with SCLC. Moreover, the CUL5-deficient SCLCs were vulnerable to the treatment of the FDA-approved SRC inhibitor dasatinib. Collectively, this work identifies the essential role of CUL5- and SOCS3-mediated integrin β1 turnover in controlling SCLC metastasis, which might have therapeutic implications.
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Affiliation(s)
- Gaoxiang Zhao
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Liyan Gong
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Yujuan Jin
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Meiting Yue
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Shun Yao
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhen Qin
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Ye
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Ying Tang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Qibiao Wu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Jian Zhang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Binghai Cui
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hsinyi Huang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yuting Chen
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Peiyuan Zhang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guohong Hu
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York, USA
| | - Daming Gao
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
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190
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Saito S, Lin YC, Nakamura Y, Eckner R, Wuputra K, Kuo KK, Lin CS, Yokoyama KK. Potential application of cell reprogramming techniques for cancer research. Cell Mol Life Sci 2019; 76:45-65. [PMID: 30283976 PMCID: PMC6326983 DOI: 10.1007/s00018-018-2924-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/15/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Abstract
The ability to control the transition from an undifferentiated stem cell to a specific cell fate is one of the key techniques that are required for the application of interventional technologies to regenerative medicine and the treatment of tumors and metastases and of neurodegenerative diseases. Reprogramming technologies, which include somatic cell nuclear transfer, induced pluripotent stem cells, and the direct reprogramming of specific cell lineages, have the potential to alter cell plasticity in translational medicine for cancer treatment. The characterization of cancer stem cells (CSCs), the identification of oncogene and tumor suppressor genes for CSCs, and the epigenetic study of CSCs and their microenvironments are important topics. This review summarizes the application of cell reprogramming technologies to cancer modeling and treatment and discusses possible obstacles, such as genetic and epigenetic alterations in cancer cells, as well as the strategies that can be used to overcome these obstacles to cancer research.
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Affiliation(s)
- Shigeo Saito
- Saito Laboratory of Cell Technology, Yaita, Tochigi, 329-1571, Japan
- College of Engineering, Nihon University, Koriyama, Fukushima, 963-8642, Japan
| | - Ying-Chu Lin
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Richard Eckner
- Department of Biochemistry and Molecular Biology, Rutgers, New Jersey Medical School-Rutgers, The State University of New Jersey, Newark, NJ, 07101, USA
| | - Kenly Wuputra
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Kung-Kai Kuo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Faculty of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
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191
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Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 2018; 362:362/6413/eaav1898. [PMID: 30361341 DOI: 10.1126/science.aav1898] [Citation(s) in RCA: 648] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
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192
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Liu RZ, Vo TM, Jain S, Choi WS, Garcia E, Monckton EA, Mackey JR, Godbout R. NFIB promotes cell survival by directly suppressing p21 transcription in TP53-mutated triple-negative breast cancer. J Pathol 2018; 247:186-198. [PMID: 30350349 DOI: 10.1002/path.5182] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 12/27/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited treatment options and poor prognosis. There is an urgent need to identify and understand the key factors and signalling pathways driving TNBC tumour progression, relapse, and treatment resistance. In this study, we report that gene copy numbers and expression levels of nuclear factor IB (NFIB), a recently identified oncogene in small cell lung cancer, are preferentially increased in TNBC compared to other breast cancer subtypes. Furthermore, increased levels of NFIB are significantly associated with high tumour grade, poor prognosis, and reduced chemotherapy response. Concurrent TP53 mutations and NFIB overexpression (z-scores > 0) were observed in 77.9% of TNBCs, in contrast to 28.5% in non-TNBCs. Depletion of NFIB in TP53-mutated TNBC cell lines promotes cell death, cell cycle arrest, and enhances sensitivity to docetaxel, a first-line chemotherapeutic drug in breast cancer treatment. Importantly, these alterations in growth properties were accompanied by induction of CDKN1A, the gene encoding p21, a downstream effector of p53. We show that NFIB directly interacts with the CDKN1A promoter in TNBC cells. Furthermore, knockdown of combined p21 and NFIB reverses the docetaxel-induced cell growth inhibition observed upon NFIB knockdown, indicating that NFIB's effect on chemotherapeutic drug response is mediated through p21. Our results indicate that NFIB is an important TNBC factor that drives tumour cell growth and drug resistance, leading to poor clinical outcomes. Thus, targeting NFIB in TP53-mutated TNBC may reverse oncogenic properties associated with mutant p53 by restoring p21 activity. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Rong-Zong Liu
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - The M Vo
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Saket Jain
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Won-Shik Choi
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Elizabeth Garcia
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
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193
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Fraser J, Essebier A, Brown AS, Davila RA, Sengar AS, Tu Y, Ensbey KS, Day BW, Scott MP, Gronostajski RM, Wainwright BJ, Boden M, Harvey TJ, Piper M. Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development. Brain Struct Funct 2018; 224:811-827. [PMID: 30511336 DOI: 10.1007/s00429-018-1801-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/24/2018] [Indexed: 01/06/2023]
Abstract
Cerebellar granule neurons are the most numerous neuronal subtype in the central nervous system. Within the developing cerebellum, these neurons are derived from a population of progenitor cells found within the external granule layer of the cerebellar anlage, namely the cerebellar granule neuron precursors (GNPs). The timely proliferation and differentiation of these precursor cells, which, in rodents occurs predominantly in the postnatal period, is tightly controlled to ensure the normal morphogenesis of the cerebellum. Despite this, our understanding of the factors mediating how GNP differentiation is controlled remains limited. Here, we reveal that the transcription factor nuclear factor I X (NFIX) plays an important role in this process. Mice lacking Nfix exhibit reduced numbers of GNPs during early postnatal development, but elevated numbers of these cells at postnatal day 15. Moreover, Nfix-/- GNPs exhibit increased proliferation when cultured in vitro, suggestive of a role for NFIX in promoting GNP differentiation. At a mechanistic level, profiling analyses using both ChIP-seq and RNA-seq identified the actin-associated factor intersectin 1 as a downstream target of NFIX during cerebellar development. In support of this, mice lacking intersectin 1 also displayed delayed GNP differentiation. Collectively, these findings highlight a key role for NFIX and intersectin 1 in the regulation of cerebellar development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - YuShan Tu
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - Kathleen S Ensbey
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Bryan W Day
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Mikael Boden
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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194
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Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018; 563:501-507. [PMID: 30429615 PMCID: PMC6421076 DOI: 10.1038/s41586-018-0692-z] [Citation(s) in RCA: 315] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/05/2018] [Indexed: 11/10/2022]
Abstract
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.
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Affiliation(s)
- Benjamin J Matthews
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA. .,Kavli Neural Systems Institute, New York, NY, USA.
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - William J Glassford
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
| | - Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Gareth D Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK.,Liverpool John Moores University, Liverpool, UK
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.,Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Sanjit S Batra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Carlos A Brito-Sierra
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Steven D Buckingham
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Corey L Campbell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Saki Chan
- Bionano Genomics, San Diego, CA, USA
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin R Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thanyalak Fansiri
- Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France.,Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), IHU - Méditerranée Infection, Marseille, France
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | | | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Raissa G G Kay
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Gareth J Lycett
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | | | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Vidya Ramasamy
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sourav Roy
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Karla Saavedra-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Shruti Sharan
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Atashi Sharma
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA
| | | | - Joe Turner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Zhilei Zhao
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Omar S Akbari
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA, USA
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alexander S Raikhel
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | | | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria V Sharakhova
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | | | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
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195
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Zalucki O, Harris L, Harvey TJ, Harkins D, Widagdo J, Oishi S, Matuzelski E, Yong XLH, Schmidt H, Anggono V, Burne THJ, Gronostajski RM, Piper M. NFIX-Mediated Inhibition of Neuroblast Branching Regulates Migration Within the Adult Mouse Ventricular–Subventricular Zone. Cereb Cortex 2018; 29:3590-3604. [DOI: 10.1093/cercor/bhy233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Abstract
Understanding the migration of newborn neurons within the brain presents a major challenge in contemporary biology. Neuronal migration is widespread within the developing brain but is also important within the adult brain. For instance, stem cells within the ventricular–subventricular zone (V-SVZ) and the subgranular zone of dentate gyrus of the adult rodent brain produce neuroblasts that migrate to the olfactory bulb and granule cell layer of the dentate gyrus, respectively, where they regulate key brain functions including innate olfactory responses, learning, and memory. Critically, our understanding of the factors mediating neuroblast migration remains limited. The transcription factor nuclear factor I X (NFIX) has previously been implicated in embryonic cortical development. Here, we employed conditional ablation of Nfix from the adult mouse brain and demonstrated that the removal of this gene from either neural stem and progenitor cells, or neuroblasts, within the V-SVZ culminated in neuroblast migration defects. Mechanistically, we identified aberrant neuroblast branching, due in part to increased expression of the guanylyl cyclase natriuretic peptide receptor 2 (Npr2), as a factor contributing to abnormal migration in Nfix-deficient adult mice. Collectively, these data provide new insights into how neuroblast migration is regulated at a transcriptional level within the adult brain.
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Affiliation(s)
- Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jocelyn Widagdo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elise Matuzelski
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Xuan Ling Hilary Yong
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Hannes Schmidt
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Victor Anggono
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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196
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Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM. Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. Cancer Discov 2018; 8:1316-1331. [PMID: 30228179 DOI: 10.1158/2159-8290.cd-17-0987] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 05/14/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse models of small cell lung cancer (SCLC), we uncovered distinct metastatic programs attributable to the cell type of origin. In one model, tumors gain metastatic ability through amplification of the transcription factor NFIB and a widespread increase in chromatin accessibility, whereas in the other model, tumors become metastatic in the absence of NFIB-driven chromatin alterations. Gene-expression and chromatin accessibility analyses identify distinct mechanisms as well as markers predictive of metastatic progression in both groups. Underlying the difference between the two programs was the cell type of origin of the tumors, with NFIB-independent metastases arising from mature neuroendocrine cells. Our findings underscore the importance of the identity of cell type of origin in influencing tumor evolution and metastatic mechanisms.Significance: We show that SCLC can arise from different cell types of origin, which profoundly influences the eventual genetic and epigenetic changes that enable metastatic progression. Understanding intertumoral heterogeneity in SCLC, and across cancer types, may illuminate mechanisms of tumor progression and uncover how the cell type of origin affects tumor evolution. Cancer Discov; 8(10); 1316-31. ©2018 AACR. See related commentary by Pozo et al., p. 1216 This article is highlighted in the In This Issue feature, p. 1195.
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Affiliation(s)
- Dian Yang
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Sarah K Denny
- Department of Genetics, Stanford University, Stanford, California.,Biophysics Program, Stanford University, Stanford, California
| | - Peyton G Greenside
- Program in Biomedical Informatics, Stanford University, Stanford, California
| | - Andrea C Chaikovsky
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Jennifer J Brady
- Department of Genetics, Stanford University, Stanford, California
| | - Youcef Ouadah
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Biochemistry, Stanford University, Stanford, California
| | - Jeffrey M Granja
- Department of Genetics, Stanford University, Stanford, California.,Biophysics Program, Stanford University, Stanford, California
| | - Nadine S Jahchan
- Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Jing Shan Lim
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Shirley Kwok
- Department of Pathology, Stanford University, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University, Stanford, California
| | - Anna S Berghoff
- Institute of Neurology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center CNS Tumors Unit, Medical University of Vienna, Vienna, Austria
| | - Anna Schmitt
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany
| | - H Christian Reinhardt
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Matthias Preusser
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center CNS Tumors Unit, Medical University of Vienna, Vienna, Austria
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California.,Department of Computer Science, Stanford University, Stanford, California
| | | | - Julien Sage
- Cancer Biology Program, Stanford University, Stanford, California. .,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Monte M Winslow
- Cancer Biology Program, Stanford University, Stanford, California. .,Department of Genetics, Stanford University, Stanford, California.,Department of Pathology, Stanford University, Stanford, California
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197
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Strub T, Ghiraldini FG, Carcamo S, Li M, Wroblewska A, Singh R, Goldberg MS, Hasson D, Wang Z, Gallagher SJ, Hersey P, Ma'ayan A, Long GV, Scolyer RA, Brown B, Zheng B, Bernstein E. SIRT6 haploinsufficiency induces BRAF V600E melanoma cell resistance to MAPK inhibitors via IGF signalling. Nat Commun 2018; 9:3440. [PMID: 30143629 PMCID: PMC6109055 DOI: 10.1038/s41467-018-05966-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022] Open
Abstract
While multiple mechanisms of BRAFV600-mutant melanoma resistance to targeted MAPK signaling inhibitors (MAPKi) have been reported, the epigenetic regulation of this process remains undetermined. Here, using a CRISPR–Cas9 screen targeting chromatin regulators, we discover that haploinsufficiency of the histone deacetylase SIRT6 allows melanoma cell persistence in the presence of MAPKi. Haploinsufficiency, but not complete loss of SIRT6 promotes IGFBP2 expression via increased chromatin accessibility, H3K56 acetylation at the IGFBP2 locus, and consequent activation of the IGF-1 receptor (IGF-1R) and downstream AKT signaling. Combining a clinically applicable IGF-1Ri with BRAFi overcomes resistance of SIRT6 haploinsufficient melanoma cells in vitro and in vivo. Using matched melanoma samples derived from patients receiving dabrafenib + trametinib, we identify IGFBP2 as a potential biomarker for MAPKi resistance. Our study has not only identified an epigenetic mechanism of drug resistance, but also provides insights into a combinatorial therapy that may overcome resistance to standard-of-care therapy for BRAFV600-mutant melanoma patients. The epigenetic mechanisms of melanoma drug resistance are poorly understood. Here, the authors develop a CRISPR-Cas9 screen targeting epigenetic regulators and discover that SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling.
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Affiliation(s)
- Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Flavia G Ghiraldini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Man Li
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Aleksandra Wroblewska
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Matthew S Goldberg
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Stuart J Gallagher
- Centenary Institute, Camperdown NSW 2050, The University of Sydney, Sydney, Australia.,Melanoma Institute Australia, Wollstonecraft NSW 2065, The University of Sydney, Sydney, Australia
| | - Peter Hersey
- Centenary Institute, Camperdown NSW 2050, The University of Sydney, Sydney, Australia.,Melanoma Institute Australia, Wollstonecraft NSW 2065, The University of Sydney, Sydney, Australia
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Georgina V Long
- Melanoma Institute Australia, Wollstonecraft NSW 2065, The University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2050, Australia.,Royal North Shore Hospital, Sydney, NSW, 2065, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, Wollstonecraft NSW 2065, The University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2050, Australia.,Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia
| | - Brian Brown
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bin Zheng
- Centenary Institute, Camperdown NSW 2050, The University of Sydney, Sydney, Australia
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
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198
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da Silva-Diz V, Lorenzo-Sanz L, Bernat-Peguera A, Lopez-Cerda M, Muñoz P. Cancer cell plasticity: Impact on tumor progression and therapy response. Semin Cancer Biol 2018; 53:48-58. [PMID: 30130663 DOI: 10.1016/j.semcancer.2018.08.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/12/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023]
Abstract
Most tumors exhibit intra-tumor heterogeneity, which is associated with disease progression and an impaired response to therapy. Cancer cell plasticity has been proposed as being an important mechanism that, along with genetic and epigenetic alterations, promotes cancer cell diversity and contributes to intra-tumor heterogeneity. Plasticity endows cancer cells with the capacity to shift dynamically between a differentiated state, with limited tumorigenic potential, and an undifferentiated or cancer stem-like cell (CSC) state, which is responsible for long-term tumor growth. In addition, it confers the ability to transit into distinct CSC states with different competence to invade, disseminate and seed metastasis. Cancer cell plasticity has been linked to the epithelial-to-mesenchymal transition program and relies not only on cell-autonomous mechanisms, but also on signals provided by the tumor microenvironment and/or induced in response to therapy. We provide an overview of the dynamic transition for cancer cell states, the mechanisms governing cell plasticity and their impact on tumor progression, metastasis and therapy response. Understanding the mechanisms involved in cancer cell plasticity will provide insights for establishing new therapeutic interventions.
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Affiliation(s)
| | - Laura Lorenzo-Sanz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Adrià Bernat-Peguera
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Marta Lopez-Cerda
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Purificación Muñoz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.
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199
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An integrative transcriptome analysis reveals a functional role for thyroid transcription factor-1 in small cell lung cancer. J Pathol 2018; 246:154-165. [DOI: 10.1002/path.5109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/28/2018] [Accepted: 06/01/2018] [Indexed: 12/31/2022]
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200
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Testa U, Castelli G, Pelosi E. Lung Cancers: Molecular Characterization, Clonal Heterogeneity and Evolution, and Cancer Stem Cells. Cancers (Basel) 2018; 10:E248. [PMID: 30060526 PMCID: PMC6116004 DOI: 10.3390/cancers10080248] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022] Open
Abstract
Lung cancer causes the largest number of cancer-related deaths in the world. Most (85%) of lung cancers are classified as non-small-cell lung cancer (NSCLC) and small-cell lung cancer (15%) (SCLC). The 5-year survival rate for NSCLC patients remains very low (about 16% at 5 years). The two predominant NSCLC histological phenotypes are adenocarcinoma (ADC) and squamous cell carcinoma (LSQCC). ADCs display several recurrent genetic alterations, including: KRAS, BRAF and EGFR mutations; recurrent mutations and amplifications of several oncogenes, including ERBB2, MET, FGFR1 and FGFR2; fusion oncogenes involving ALK, ROS1, Neuregulin1 (NRG1) and RET. In LSQCC recurrent mutations of TP53, FGFR1, FGFR2, FGFR3, DDR2 and genes of the PI3K pathway have been detected, quantitative gene abnormalities of PTEN and CDKN2A. Developments in the characterization of lung cancer molecular abnormalities provided a strong rationale for new therapeutic options and for understanding the mechanisms of drug resistance. However, the complexity of lung cancer genomes is particularly high, as shown by deep-sequencing studies supporting the heterogeneity of lung tumors at cellular level, with sub-clones exhibiting different combinations of mutations. Molecular studies performed on lung tumors during treatment have shown the phenomenon of clonal evolution, thus supporting the occurrence of a temporal tumor heterogeneity.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
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