1
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Breitenecker K, Heiden D, Demmer T, Weber G, Primorac AM, Hedrich V, Ortmayr G, Gruenberger T, Starlinger P, Herndler-Brandstetter D, Barozzi I, Mikulits W. Tumor-Extrinsic Axl Expression Shapes an Inflammatory Microenvironment Independent of Tumor Cell Promoting Axl Signaling in Hepatocellular Carcinoma. Int J Mol Sci 2024; 25:4202. [PMID: 38673795 DOI: 10.3390/ijms25084202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The activation of the receptor tyrosine kinase Axl by Gas6 is a major driver of tumorigenesis. Despite recent insights, tumor cell-intrinsic and -extrinsic Axl functions are poorly understood in hepatocellular carcinoma (HCC). Thus, we analyzed the cell-specific aspects of Axl in liver cancer cells and in the tumor microenvironment. We show that tumor-intrinsic Axl expression decreased the survival of mice and elevated the number of pulmonary metastases in a model of resection-based tumor recurrence. Axl expression increased the invasion of hepatospheres by the activation of Akt signaling and a partial epithelial-to-mesenchymal transition (EMT). However, the liver tumor burden of Axl+/+ mice induced by diethylnitrosamine plus carbon tetrachloride was reduced compared to systemic Axl-/- mice. Tumors of Axl+/+ mice were highly infiltrated with cytotoxic cells, suggesting a key immune-modulatory role of Axl. Interestingly, hepatocyte-specific Axl deficiency did not alter T cell infiltration, indicating that these changes are independent of tumor cell-intrinsic Axl. In this context, we observed an upregulation of multiple chemokines in Axl+/+ compared to Axl-/- tumors, correlating with HCC patient data. In line with this, Axl is associated with a cytotoxic immune signature in HCC patients. Together these data show that tumor-intrinsic Axl expression fosters progression, while tumor-extrinsic Axl expression shapes an inflammatory microenvironment.
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Affiliation(s)
- Kristina Breitenecker
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Denise Heiden
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Tobias Demmer
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerhard Weber
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Ana-Maria Primorac
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Viola Hedrich
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Ortmayr
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Gruenberger
- Department of Surgery, HPB Center, Viennese Health Network, Clinic Favoriten and Sigmund Freud Private University, 1100 Vienna, Austria
| | - Patrick Starlinger
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
- Centre of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Iros Barozzi
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Mikulits
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
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2
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Di Chiaro P, Nacci L, Arco F, Brandini S, Polletti S, Palamidessi A, Donati B, Soriani C, Gualdrini F, Frigè G, Mazzarella L, Ciarrocchi A, Zerbi A, Spaggiari P, Scita G, Rodighiero S, Barozzi I, Diaferia GR, Natoli G. Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer. Cancer Cell 2024; 42:662-681.e10. [PMID: 38518775 DOI: 10.1016/j.ccell.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
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Affiliation(s)
- Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Lucia Nacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Fabiana Arco
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrea Palamidessi
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Chiara Soriani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy; Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandro Zerbi
- IRCCS Humanitas Research Hospital, Rozzano, Milano, Italy; Humanitas University, Pieve Emanuele - Milano, Italy
| | | | - Giorgio Scita
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Milano, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
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3
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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4
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Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024:OF1-OF24. [PMID: 38527495 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs.
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Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
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5
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Dynamic enhancer landscapes in human craniofacial development. Nat Commun 2024; 15:2030. [PMID: 38448444 PMCID: PMC10917818 DOI: 10.1038/s41467-024-46396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, 3010, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Lucile Packard Children's Hospital, Stanford University, Stanford, CA, 94304, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA, 94110, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Octant Inc., Emeryville, CA, 94608, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, CA, USA.
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6
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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7
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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8
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D'Artista L, Moschopoulou AA, Barozzi I, Craig AJ, Seehawer M, Herrmann L, Minnich M, Kang TW, Rist E, Henning M, Klotz S, Heinzmann F, Harbig J, Sipos B, Longerich T, Eilers M, Dauch D, Zuber J, Wang XW, Zender L. MYC determines lineage commitment in KRAS-driven primary liver cancer development. J Hepatol 2023; 79:141-149. [PMID: 36906109 PMCID: PMC10330789 DOI: 10.1016/j.jhep.2023.02.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND & AIMS Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), two frequent and lethal tumour types that differ regarding their tumour biology and responses to cancer therapies. Liver cells harbour a high degree of cellular plasticity and can give rise to either HCC or iCCA. However, little is known about the cell-intrinsic mechanisms directing an oncogenically transformed liver cell to either HCC or iCCA. The scope of this study was to identify cell-intrinsic factors determining lineage commitment in PLC. METHODS Cross-species transcriptomic and epigenetic profiling was applied to murine HCCs and iCCAs and to two human PLC cohorts. Integrative data analysis comprised epigenetic Landscape In Silico deletion Analysis (LISA) of transcriptomic data and Hypergeometric Optimization of Motif EnRichment (HOMER) analysis of chromatin accessibility data. Identified candidate genes were subjected to functional genetic testing in non-germline genetically engineered PLC mouse models (shRNAmir knockdown or overexpression of full-length cDNAs). RESULTS Integrative bioinformatic analyses of transcriptomic and epigenetic data pinpointed the Forkhead-family transcription factors FOXA1 and FOXA2 as MYC-dependent determination factors of the HCC lineage. Conversely, the ETS family transcription factor ETS1 was identified as a determinant of the iCCA lineage, which was found to be suppressed by MYC during HCC development. Strikingly, shRNA-mediated suppression of FOXA1 and FOXA2 with concomitant ETS1 expression fully switched HCC to iCCA development in PLC mouse models. CONCLUSIONS The herein reported data establish MYC as a key determinant of lineage commitment in PLC and provide a molecular explanation why common liver-damaging risk factors such as alcoholic or non-alcoholic steatohepatitis can lead to either HCC or iCCA. IMPACT AND IMPLICATIONS Liver cancer is a major health problem and comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), two frequent and lethal tumour types that differ regarding their morphology, tumour biology, and responses to cancer therapies. We identified the transcription factor and oncogenic master regulator MYC as a switch between HCC and iCCA development. When MYC levels are high at the time point when a hepatocyte becomes a tumour cell, an HCC is growing out. Conversely, if MYC levels are low at this time point, the result is the outgrowth of an iCCA. Our study provides a molecular explanation why common liver-damaging risk factors such as alcoholic or non-alcoholic steatohepatitis can lead to either HCC or iCCA. Furthermore, our data harbour potential for the development of better PLC therapies.
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Affiliation(s)
- Luana D'Artista
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Athina Anastasia Moschopoulou
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Iros Barozzi
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria; Department of Surgery and Cancer, Imperial College London, London, UK
| | - Amanda J Craig
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marco Seehawer
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Lea Herrmann
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Martina Minnich
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tae-Won Kang
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Elke Rist
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Melanie Henning
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Sabrina Klotz
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Florian Heinzmann
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Jule Harbig
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Bence Sipos
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Daniel Dauch
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany; iFIT Cluster of Excellence EXC 2180 'Image Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany; German Cancer Research Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Cell Type- and Tissue-specific Enhancers in Craniofacial Development. bioRxiv 2023:2023.06.26.546603. [PMID: 37425964 PMCID: PMC10327103 DOI: 10.1101/2023.06.26.546603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development1-3. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined histone modification and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. We used transgenic mouse reporter assays to determine the in vivo activity patterns of human face enhancers predicted from these data. Across 16 in vivo validated human enhancers, we observed a rich diversity of craniofacial subregions in which these enhancers are active in vivo. To annotate the cell type specificities of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating these data across species, we find that the majority (56%) of human craniofacial enhancers are functionally conserved in mice, providing cell type- and embryonic stage-resolved predictions of their in vivo activity profiles. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we demonstrate the utility of these data for predicting the in vivo cell type specificity of enhancers. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Laura E. Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Cailyn H. Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Lucile Packard Children’s Hospital, Stanford University, Stanford, CA 94304
| | - Matthew J. Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA 94110
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E. Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Octant Inc., Emeryville, CA 94608, USA
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, California, USA
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10
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Rajderkar S, Barozzi I, Zhu Y, Hu R, Zhang Y, Li B, Alcaina Caro A, Fukuda-Yuzawa Y, Kelman G, Akeza A, Blow MJ, Pham Q, Harrington AN, Godoy J, Meky EM, von Maydell K, Hunter RD, Akiyama JA, Novak CS, Plajzer-Frick I, Afzal V, Tran S, Lopez-Rios J, Talkowski ME, Lloyd KCK, Ren B, Dickel DE, Visel A, Pennacchio LA. Topologically associating domain boundaries are required for normal genome function. Commun Biol 2023; 6:435. [PMID: 37081156 PMCID: PMC10119121 DOI: 10.1038/s42003-023-04819-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1-3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.
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Affiliation(s)
- Sudha Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ana Alcaina Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adyam Akeza
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Quan Pham
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Anne N Harrington
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Janeth Godoy
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eman M Meky
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA.
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11
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Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. The co-evolution of the genome and epigenome in colorectal cancer. Nature 2022; 611:733-743. [PMID: 36289335 PMCID: PMC9684080 DOI: 10.1038/s41586-022-05202-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
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Affiliation(s)
- Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Ketevan Chkhaidze
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helena Costa
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marnix Jansen
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Triest, Triest, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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12
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Osterwalder M, Abassah-Oppong S, Mannion B, Rouco R, Zoia M, Roland V, Barozzi I, Lopez-Rios J, Andrey G, Visel A, Pennacchio L, Cobb J. Cis-regulatory architecture and functions of a gene desert controlling pleiotropic expression and cardiac pacemaker development. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Gene deserts are extensive genomic regions spanning more than 500 kilobases and enriched near developmental genes. Despite their proposed critical roles in development, the enhancer architecture, and biological functions of most gene deserts in mammalian genomes remain unknown. The Shox2 transcription factor is a key regulator of cardiac pacemaker differentiation and at the genomic level is flanked by a centromeric gene desert harboring a multitude of predicted cis-regulatory modules (CRMs). Using CRISPR-Cas9 we demonstrate a requirement of this gene desert for pleiotropic expression and embryonic survival through full control of Shox2 in the sinoatrial node (SAN). To decode the underlying chromatin architecture and CRM logic, we performed region-specific chromatin conformation capture, epigenomic analysis and transgenic in vivo reporter assays. While the Shox2 regulatory landscape was found partitioned into largely tissue-invariant chromatin loops, we identified a surprising cardiac-specific contact domain within the gene desert. Subsequent transgenic analysis revealed clustering of non-cardiac enhancers with activities in limb, craniofacial or neuronal populations in this domain, pointing to a potential tissue-specific 3D-mechanism for enhancer attenuation. In addition, SAN-chromatin assessment and H3K27ac profiling from human fetal cardiac compartments enabled the identification of a unique cardiac enhancer located outside of the contact domain and essential for robust Shox2 levels during cardiac pacemaker development. In summary, our results serve as a blueprint to investigate gene desert function in context to cardiac defects and identify the Shox2 gene desert as a robust cis-regulatory hub indispensable for pleiotropic patterning, cardiac pacemaker differentiation and embryonic survival.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science Foundation (SNSF),National Institutes of Health (NIH)
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Affiliation(s)
- M Osterwalder
- Department for BioMedical Research of University of Bern , Bern , Switzerland
| | - S Abassah-Oppong
- University of Calgary, Department of Biological Sciences , Calgary , Canada
| | - B Mannion
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley , CA , United States of America
| | - R Rouco
- University of Geneva, Department of Genetic Medicine and Development , Geneva , Switzerland
| | - M Zoia
- Department for BioMedical Research of University of Bern , Bern , Switzerland
| | - V Roland
- Department for BioMedical Research of University of Bern , Bern , Switzerland
| | - I Barozzi
- Medical University of Vienna, Center for Cancer Research , Vienna , Austria
| | - J Lopez-Rios
- University Pablo de Olavide, Centro Andaluz de Biología del Desarrollo (CABD) , Seville , Spain
| | - G Andrey
- University of Geneva, Department of Genetic Medicine and Development , Geneva , Switzerland
| | - A Visel
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley , CA , United States of America
| | - L Pennacchio
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley , CA , United States of America
| | - J Cobb
- University of Calgary, Department of Biological Sciences , Calgary , Canada
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13
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Spurrell CH, Barozzi I, Kosicki M, Mannion BJ, Blow MJ, Fukuda-Yuzawa Y, Slaven N, Afzal SY, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Lee EA, Garvin TH, Pham QT, Kronshage AN, Lisgo S, Bristow J, Cappola TP, Morley MP, Margulies KB, Pennacchio LA, Dickel DE, Visel A. Genome-wide fetalization of enhancer architecture in heart disease. Cell Rep 2022; 40:111400. [PMID: 36130500 PMCID: PMC9534044 DOI: 10.1016/j.celrep.2022.111400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.
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Affiliation(s)
- Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Neil Slaven
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Y Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Kronshage
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - James Bristow
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas P Cappola
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA.
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14
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Platanitis E, Gruener S, Ravi Sundar Jose Geetha A, Boccuni L, Vogt A, Novatchkova M, Sommer A, Barozzi I, Müller M, Decker T. Interferons reshape the 3D conformation and accessibility of macrophage chromatin. iScience 2022; 25:103840. [PMID: 35243225 PMCID: PMC8857492 DOI: 10.1016/j.isci.2022.103840] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022] Open
Abstract
Engagement of macrophages in innate immune responses is directed by type I and type II interferons (IFN-I and IFN-γ, respectively). IFN triggers drastic changes in cellular transcriptomes, executed by JAK-STAT signal transduction and the transcriptional control of interferon-stimulated genes (ISG) by STAT transcription factors. Here, we study the immediate-early nuclear response to IFN-I and IFN-γ in murine macrophages. We show that the mechanism of gene control by both cytokines includes a rapid increase of DNA accessibility and rearrangement of the 3D chromatin contacts particularly between open chromatin of ISG loci. IFN-stimulated gene factor 3 (ISGF3), the major transcriptional regulator of ISG, controlled homeostatic and, most notably, induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.
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Affiliation(s)
| | - Stephan Gruener
- Max Perutz Labs, University of Vienna, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | | | - Laura Boccuni
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Andreas Sommer
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Iros Barozzi
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Decker
- Max Perutz Labs, University of Vienna, Vienna, Austria
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15
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Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. Proc Natl Acad Sci U S A 2021; 118:e2024795118. [PMID: 34921112 PMCID: PMC8713794 DOI: 10.1073/pnas.2024795118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.
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Affiliation(s)
- Athéna R Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
| | - Kartik Pattabiraman
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - Olga Golonzhka
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- School of Natural Sciences, University of California, Merced, CA 95343
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
| | - Len A Pennachio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Iros Barozzi
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, United Kingdom
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - John L Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
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16
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Gamart J, Barozzi I, Laurent F, Reinhardt R, Martins LR, Oberholzer T, Visel A, Zeller R, Zuniga A. SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning. Development 2021; 148:273522. [PMID: 34822715 PMCID: PMC8714076 DOI: 10.1242/dev.200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022]
Abstract
SMAD4 regulates gene expression in response to BMP and TGFβ signal transduction, and is required for diverse morphogenetic processes, but its target genes have remained largely elusive. Here, we identify the SMAD4 target genes in mouse limb buds using an epitope-tagged Smad4 allele for ChIP-seq analysis in combination with transcription profiling. This analysis shows that SMAD4 predominantly mediates BMP signal transduction during early limb bud development. Unexpectedly, the expression of cholesterol biosynthesis enzymes is precociously downregulated and intracellular cholesterol levels are reduced in Smad4-deficient limb bud mesenchymal progenitors. Most importantly, our analysis reveals a predominant function of SMAD4 in upregulating target genes in the anterior limb bud mesenchyme. Analysis of differentially expressed genes shared between Smad4- and Shh-deficient limb buds corroborates this function of SMAD4 and also reveals the repressive effect of SMAD4 on posterior genes that are upregulated in response to SHH signaling. This analysis uncovers opposing trans-regulatory inputs from SHH- and SMAD4-mediated BMP signal transduction on anterior and posterior gene expression during the digit patterning and outgrowth in early limb buds. Summary: The transcriptional targets of SMAD4 in early limb buds are identified and the largely opposing impact of BMP and SHH signaling on early digit patterning and outgrowth is revealed.
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Affiliation(s)
- Julie Gamart
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Iros Barozzi
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Frédéric Laurent
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Robert Reinhardt
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Laurène Ramos Martins
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Thomas Oberholzer
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Axel Visel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.,School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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17
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Melixetian M, Bossi D, Mihailovich M, Punzi S, Barozzi I, Marocchi F, Cuomo A, Bonaldi T, Testa G, Marine JC, Leucci E, Minucci S, Pelicci PG, Lanfrancone L. Long non-coding RNA TINCR suppresses metastatic melanoma dissemination by preventing ATF4 translation. EMBO Rep 2021; 22:e50852. [PMID: 33586907 PMCID: PMC7926219 DOI: 10.15252/embr.202050852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
Transition from proliferative‐to‐invasive phenotypes promotes metastasis and therapy resistance in melanoma. Reversion of the invasive phenotype, however, is challenged by the poor understanding of mechanisms underlying its maintenance. Here, we report that the lncRNA TINCR is down‐regulated in metastatic melanoma and its silencing increases the expression levels of invasive markers, in vitro migration, in vivo tumor growth, and resistance to BRAF and MEK inhibitors. The critical mediator is ATF4, a central player of the integrated stress response (ISR), which is activated in TINCR‐depleted cells in the absence of starvation and eIF2α phosphorylation. TINCR depletion increases global protein synthesis and induces translational reprogramming, leading to increased translation of mRNAs encoding ATF4 and other ISR proteins. Strikingly, re‐expression of TINCR in metastatic melanoma suppresses the invasive phenotype, reduces numbers of tumor‐initiating cells and metastasis formation, and increases drug sensitivity. Mechanistically, TINCR interacts with mRNAs associated with the invasive phenotype, including ATF4, preventing their binding to ribosomes. Thus, TINCR is a suppressor of the melanoma invasive phenotype, which functions in nutrient‐rich conditions by repressing translation of selected ISR RNAs.
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Affiliation(s)
- Marine Melixetian
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Daniela Bossi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Simona Punzi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Federica Marocchi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Saverio Minucci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Biosciences, University of Milan, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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18
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Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 2021; 589:E4. [PMID: 33398137 PMCID: PMC8064906 DOI: 10.1038/s41586-020-03089-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03089-4.
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Affiliation(s)
- David U Gorkin
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yuan Zhao
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Andre Wildberg
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bo Ding
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Mengchi Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - J Seth Strattan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Jean M Davidson
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anne N Harrington
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yupeng He
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Jee Yun Han
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry Amrhein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - J Michael Cherry
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Kyle Gaulton
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yin Shen
- Institute for Human Genetics and University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA. .,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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19
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Schmitt MJ, Company C, Dramaretska Y, Barozzi I, Göhrig A, Kertalli S, Großmann M, Naumann H, Sanchez-Bailon MP, Hulsman D, Glass R, Squatrito M, Serresi M, Gargiulo G. Phenotypic Mapping of Pathologic Cross-Talk between Glioblastoma and Innate Immune Cells by Synthetic Genetic Tracing. Cancer Discov 2020; 11:754-777. [PMID: 33361384 DOI: 10.1158/2159-8290.cd-20-0219] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/27/2022]
Abstract
Glioblastoma is a lethal brain tumor that exhibits heterogeneity and resistance to therapy. Our understanding of tumor homeostasis is limited by a lack of genetic tools to selectively identify tumor states and fate transitions. Here, we use glioblastoma subtype signatures to construct synthetic genetic tracing cassettes and investigate tumor heterogeneity at cellular and molecular levels, in vitro and in vivo. Through synthetic locus control regions, we demonstrate that proneural glioblastoma is a hardwired identity, whereas mesenchymal glioblastoma is an adaptive and metastable cell state driven by proinflammatory and differentiation cues and DNA damage, but not hypoxia. Importantly, we discovered that innate immune cells divert glioblastoma cells to a proneural-to-mesenchymal transition that confers therapeutic resistance. Our synthetic genetic tracing methodology is simple, scalable, and widely applicable to study homeostasis in development and diseases. In glioblastoma, the method causally links distinct (micro)environmental, genetic, and pharmacologic perturbations and mesenchymal commitment. SIGNIFICANCE: Glioblastoma is heterogeneous and incurable. Here, we designed synthetic reporters to reflect the transcriptional output of tumor cell states and signaling pathways' activity. This method is generally applicable to study homeostasis in normal tissues and diseases. In glioblastoma, synthetic genetic tracing causally connects cellular and molecular heterogeneity to therapeutic responses.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
| | - Carlos Company
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | | | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Andreas Göhrig
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Melanie Großmann
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Heike Naumann
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | | | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rainer Glass
- Neurosurgical Research, Department of Neurosurgery, University Hospital, Munich, Germany
| | - Massimo Squatrito
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, Madrid, Spain
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany.
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20
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Ostasov P, Robertson H, Piazza P, Datta A, Apperley J, Houdova L, Lysak D, Holubova M, Tesarova K, Caputo VS, Barozzi I. Evolution of Advanced Chronic Lymphoid Leukemia Unveiled by Single-Cell Transcriptomics: A Case Report. Front Oncol 2020; 10:584607. [PMID: 33194728 PMCID: PMC7664833 DOI: 10.3389/fonc.2020.584607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic and transcriptional heterogeneity of Chronic lymphocytic leukaemia (CLL) limits prevention of disease progression. Longitudinal single-cell transcriptomics represents the state-of-the-art method to profile the disease heterogeneity at diagnosis and to inform about disease evolution. Here, we apply single-cell RNA-seq to a CLL case, sampled at diagnosis and relapse, that was treated with FCR (Fludarabine, Cyclophosphamide, Rituximab) and underwent a dramatic decrease in CD19 expression during disease progression. Computational analyses revealed a major switch in clones’ dominance during treatment. The clone that expanded at relapse showed 17p and 3p chromosomal deletions, and up-regulation of pathways related to motility, cytokine signaling and antigen presentation. Single-cell RNA-seq uniquely revealed that this clone was already present at low frequency at diagnosis, and it displays feature of plasma cell differentiation, consistent with a more aggressive phenotype. This study shows the benefit of single-cell profiling of CLL heterogeneity at diagnosis, to identify clones that might otherwise not be recognized and to determine the best treatment options.
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Affiliation(s)
- Pavel Ostasov
- Laboratory of Tumor Biology and Immunotherapy, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia.,Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Robertson
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Paolo Piazza
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Avik Datta
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Jane Apperley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Lucie Houdova
- NTIS, Faculty of Applied Science, University of West Bohemia, Pilsen, Czechia
| | - Daniel Lysak
- Department of Haematology and Oncology, University Hospital Pilsen, Pilsen, Czechia
| | - Monika Holubova
- Laboratory of Tumor Biology and Immunotherapy, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia.,Department of Haematology and Oncology, University Hospital Pilsen, Pilsen, Czechia
| | - Katerina Tesarova
- Faculty of Medicine in Pilsen, Institute of Medical Genetics, Charles University in Prague and Faculty Hospital, Pilsen, Czechia
| | - Valentina S Caputo
- Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
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21
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Schmitt MJ, Company C, Dramaretska Y, Barozzi I, Göhrig A, Kertalli S, Großmann M, Naumann H, Wierikx J, Hulsman D, Glass R, Squatrito M, Serresi M, Gargiulo G. Abstract PO-104: Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Glioblastoma is a lethal brain tumor with a high degree of heterogeneity and resistance to therapy. The lack of genetic tracing approaches to selectively identify tumor states and fate transitions limited our understanding of tumor homeostasis. By translating glioblastoma subtype signatures into synthetic genetic tracing cassettes, we investigated tumor heterogeneity at cellular and molecular level, in vitro and in vivo. Synthetic genetic tracing demonstrated that proneural glioblastoma is a hardwired identity, whereas the mesenchymal glioblastoma is an adaptive and metastable state downstream pro-inflammatory and differentiation cues, similarly wired in breast and lung tumors. Importantly, we discovered that innate immune cells divert glioblastoma cells into a proneural-to-mesenchymal transition causal to therapeutic resistance. Systematic phenotypic mapping using synthetic locus control regions (sLCRs) is a simple, automated, and scalable strategy for genetic tracing, generally applicable to study developmental and disease homeostasis. In glioblastoma, it uncovered causality between various (micro)environmental, genetic and pharmacological perturbations and mesenchymal commitment.
Citation Format: Matthias Jürgen Schmitt, Carlos Company, Yuliia Dramaretska, Iros Barozzi, Andreas Göhrig, Sonia Kertalli, Melanie Großmann, Heike Naumann, Jikke Wierikx, Danielle Hulsman, Rainer Glass, Massimo Squatrito, Michela Serresi, Gaetano Gargiulo. Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-104.
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Affiliation(s)
| | - Carlos Company
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | | | | | - Andreas Göhrig
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | - Sonia Kertalli
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | - Melanie Großmann
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | - Heike Naumann
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | - Jikke Wierikx
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | | | - Rainer Glass
- 4Ludwig-Maximilians-University, Munich, Germany,
| | | | - Michela Serresi
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
| | - Gaetano Gargiulo
- 1Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany,
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22
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Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 2020; 586:E31. [PMID: 33037424 PMCID: PMC7962567 DOI: 10.1038/s41586-020-2841-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David U Gorkin
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yuan Zhao
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Andre Wildberg
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bo Ding
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Mengchi Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - J Seth Strattan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Jean M Davidson
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anne N Harrington
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yupeng He
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Jee Yun Han
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry Amrhein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - J Michael Cherry
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Kyle Gaulton
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yin Shen
- Institute for Human Genetics and University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA. .,Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. .,Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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23
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Acar A, Nichol D, Fernandez-Mateos J, Cresswell GD, Barozzi I, Hong SP, Trahearn N, Spiteri I, Stubbs M, Burke R, Stewart A, Caravagna G, Werner B, Vlachogiannis G, Maley CC, Magnani L, Valeri N, Banerji U, Sottoriva A. Exploiting evolutionary steering to induce collateral drug sensitivity in cancer. Nat Commun 2020; 11:1923. [PMID: 32317663 PMCID: PMC7174377 DOI: 10.1038/s41467-020-15596-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance.
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Affiliation(s)
- Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Javier Fernandez-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sung Pil Hong
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mark Stubbs
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rosemary Burke
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Stewart
- Clinical Pharmacology-Adaptive Therapy Group, Division of Cancer Therapeutics and Clinical Studies, The Institute of Cancer Research, London, UK
| | - Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Georgios Vlachogiannis
- Gastrointestinal Cancer Biology and Genomics Team, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicola Valeri
- Gastrointestinal Cancer Biology and Genomics Team, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Udai Banerji
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
- Clinical Pharmacology-Adaptive Therapy Group, Division of Cancer Therapeutics and Clinical Studies, The Institute of Cancer Research, London, UK.
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden Hospital NHS Foundation Trust, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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24
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Ravasio R, Ceccacci E, Nicosia L, Hosseini A, Rossi PL, Barozzi I, Fornasari L, Zuffo RD, Valente S, Fioravanti R, Mercurio C, Varasi M, Mattevi A, Mai A, Pavesi G, Bonaldi T, Minucci S. Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation. Sci Adv 2020; 6:eaax2746. [PMID: 32284990 PMCID: PMC7141832 DOI: 10.1126/sciadv.aax2746] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 01/15/2020] [Indexed: 05/08/2023]
Abstract
The histone demethylase LSD1 is deregulated in several tumors, including leukemias, providing the rationale for the clinical use of LSD1 inhibitors. In acute promyelocytic leukemia (APL), pharmacological doses of retinoic acid (RA) induce differentiation of APL cells, triggering degradation of the PML-RAR oncogene. APL cells are resistant to LSD1 inhibition or knockout, but targeting LSD1 sensitizes them to physiological doses of RA without altering of PML-RAR levels, and extends survival of leukemic mice upon RA treatment. The combination of RA with LSD1 inhibition (or knockout) is also effective in other non-APL, acute myeloid leukemia (AML) cells. Nonenzymatic activities of LSD1 are essential to block differentiation, while RA with targeting of LSD1 releases a differentiation gene expression program, not strictly dependent on changes in histone H3K4 methylation. Integration of proteomic/epigenomic/mutational studies showed that LSD1 inhibitors alter the recruitment of LSD1-containing complexes to chromatin, inhibiting the interaction between LSD1 and the transcription factor GFI1.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Catalysis
- Cell Differentiation/drug effects
- Cell Differentiation/genetics
- Cell Line, Tumor
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm
- Histone Demethylases/antagonists & inhibitors
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Promyelocytic, Acute
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Tretinoin/pharmacology
- Tumor Cells, Cultured
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Affiliation(s)
- Roberto Ravasio
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Elena Ceccacci
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Amir Hosseini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Pier Luigi Rossi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, Hammersmith, London W12, UK
| | - Lorenzo Fornasari
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
- EryDel SpA, Via Meucci 3, 20091 Bresso (MI), Italy
| | - Roberto Dal Zuffo
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, Milan 20139, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, Milan 20139, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, Milan 20139, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Via Adamello 16, Milan 20139, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
- New Drugs Program, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
- Corresponding author.
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25
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Abstract
Abstract
Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. During this talk, I will briefly introduce a series of molecular tools that can be used to study transcriptional changes at the single cell level in relevant models. I will then show how used these tools to dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we could disentangle the transcriptional variability of plastic cells and define a rare subpopulation of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. We find evidence for sub-clonal expression of a PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. I will then update the audience on how it is possible to integrate these technologies directly into clinical studies and what developments are happening in the field of single cell technologies. I will finally propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
Citation Format: L Magnani, I Barozzi, S Hong. Single cell transcriptomics reveals multi-step adaptations to endocrine therapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr ES4-2.
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Affiliation(s)
- L Magnani
- Imperial College London, London, United Kingdom
| | - I Barozzi
- Imperial College London, London, United Kingdom
| | - S Hong
- Imperial College London, London, United Kingdom
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26
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Rocca A, Ravaioli S, Fonzi E, Barozzi I, Perone Y, Magnani L, Pirini F, Martinelli G, Bravaccini S. Abstract P4-07-06: Breast cancer subtype classification using NanoString and RNAseq technologies. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-07-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Immunohistochemistry (IHC) is conventionally used in clinical practice to define Breast Cancer (BC) subtypes, while PAM50 is useful in specific cases. The former is partly subjective and semi-quantitative, the latter is based on gene expression profile. We compared gene expression data obtained by NanoString BC 360™ panel with those obtained by RNAseq on 12 Formalin-Fixed Paraffin-Embedded (FFPE) BC samples.
Methods: RNA was isolated from FFPE tumors and the quality was checked before performing NanoString BC 360™ assay and preparing RNAseq library (NEBNext Ultra II RNA Library Prep Kit, Illumina) following the manufacturers’ instructions. Libraries were sequenced on NextSeq500 (Illumina). Reads were aligned using Kallisto and raw read counts were normalized as Transcripts Per Million (TPM). PAM50 and Tumor Inflammation Signature (TIS) were determined on NanoString data. Two-sided t-test on TPM and on normalized NanoString counts was used to compare luminal and Triple Negative (TN) BCs (p <0.05 statistically significant), considering the 734 genes shared by the 2 assays. Deseq2 (1.22.1) was used to perform a differential gene expression analysis on raw RNAseq counts. Enrichment tests were performed on KEGG pathways (FDR < 0.05). Python and R softwares were used for statistical analyses.
Results: Of the 12 BC samples, 3 were luminal A-like, 3 luminal B (HER2+)-like and 6 TN by IHC (Table 1). Pearson’s correlation coefficient between NanoString counts and RNAseq TPM was 0.72.
Out of the 734 genes shared by both methods, those differentially expressed between luminal and TN BCs, defined based on IHC, were 135 according to RNAseq TPM, 155 according to NanoString counts and 88 according to both methods. These 88 genes belonged to “cell cycle”, “pathways in cancer”, “HIF-1 signaling”, “progesterone-mediated oocyte maturation”, “prostate cancer” and “basal cell carcinoma” KEGG pathways.
When considering the whole transcriptome analyzed by RNAseq, the differential gene expression analysis between luminal and TN/basal BCs was performed according to both IHC and PAM50 classifications. Considering the former, there were 1143 differentially expressed genes out of a total of 20936 (5.5%) and the pathways involved were “fatty acid elongation”, “cell cycle”, “oocyte meiosis”, “p53 signaling” and “alcoholism”. The analysis on the latter classification showed 1608 differentially expressed genes out of 21048 (7.6%), and the enriched pathways were “cell cycle”, “p53 signaling”, “DNA replication”, “alcoholism” and “systemic lupus erythematosus”.
Regarding the TIS, no significant differences were found between TN/basal and luminal BCs, comparing both IHC and the PAM50 subtypes. An expected heterogeneity was found among TNBCs, that showed 3 distinct signatures: basal-like immune activated, basal-like immune-suppressed and luminal androgen receptor.
Conclusions: This preliminary analysis shows a good concordance between NanoString and RNAseq data. The choice of the method must take into account important factors such as the costs, the number of genes analyzed, the requirement of bioinformatic support, the working time. Further analyses on pathway enrichment will be presented.
Table 1. Breast cancer samples characteristics.Sample ID Age Grade T N IHC subtype PAM50 Subtype TIS scoreTNBC signature 0172222aLumALumB7,0NA026031c2aTNBasal7,2BLIA037221cxTNLumA7,4LAR045231c0LumALumA7,5NA053531c1aTNBasal5,5BLIS0675320TNBasal6,2BLIS077931cxLumB HER2+LumB6,7NA0878220LumALumB7,7NA097431a2aTNBasal8,5BLIA106031c1LumB HER2+LumA8,2NA116621b0LumB HER2+LumA6,1NA1241321aTNBasal7,5BLIATIS: Tumor Inflammation Signature; BLIA: Basal-like Immune Activated; BLIS: Basal-like Immune-Suppressed; LAR: Luminal Androgen Receptor.
Citation Format: Andrea Rocca, Sara Ravaioli, Eugenio Fonzi, Iros Barozzi, Ylenia Perone, Luca Magnani, Francesca Pirini, Giovanni Martinelli, Sara Bravaccini. Breast cancer subtype classification using NanoString and RNAseq technologies [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-06.
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Affiliation(s)
- Andrea Rocca
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Ravaioli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Eugenio Fonzi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Iros Barozzi
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Ylenia Perone
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Luca Magnani
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Francesca Pirini
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Bravaccini
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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27
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Zhang Y, Takahashi Y, Hong SP, Liu F, Bednarska J, Goff PS, Novak P, Shevchuk A, Gopal S, Barozzi I, Magnani L, Sakai H, Suguru Y, Fujii T, Erofeev A, Gorelkin P, Majouga A, Weiss DJ, Edwards C, Ivanov AP, Klenerman D, Sviderskaya EV, Edel JB, Korchev Y. High-resolution label-free 3D mapping of extracellular pH of single living cells. Nat Commun 2019; 10:5610. [PMID: 31811139 PMCID: PMC6898398 DOI: 10.1038/s41467-019-13535-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023] Open
Abstract
Dynamic mapping of extracellular pH (pHe) at the single-cell level is critical for understanding the role of H+ in cellular and subcellular processes, with particular importance in cancer. While several pHe sensing techniques have been developed, accessing this information at the single-cell level requires improvement in sensitivity, spatial and temporal resolution. We report on a zwitterionic label-free pH nanoprobe that addresses these long-standing challenges. The probe has a sensitivity > 0.01 units, 2 ms response time, and 50 nm spatial resolution. The platform was integrated into a double-barrel nanoprobe combining pH sensing with feedback-controlled distance dependance via Scanning Ion Conductance Microscopy. This allows for the simultaneous 3D topographical imaging and pHe monitoring of living cancer cells. These classes of nanoprobes were used for real-time high spatiotemporal resolution pHe mapping at the subcellular level and revealed tumour heterogeneity of the peri-cellular environments of melanoma and breast cancer cells.
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Affiliation(s)
- Yanjun Zhang
- Department of Medicine, Imperial College London, London, W12 0NN, UK.
- Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Yasufumi Takahashi
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Sung Pil Hong
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Fengjie Liu
- Department of Earth Science & Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Joanna Bednarska
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Philip S Goff
- Cell Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Pavel Novak
- Department of Medicine, Imperial College London, London, W12 0NN, UK
- National University of Science and Technology "MISIS", Leninskiy prospect 4, 119991, Moscow, Russian Federation
| | - Andrew Shevchuk
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Sahana Gopal
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Hideki Sakai
- Department of Pharmaceutical Physiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
| | - Yoshimoto Suguru
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Takuto Fujii
- Department of Pharmaceutical Physiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
| | - Alexander Erofeev
- National University of Science and Technology "MISIS", Leninskiy prospect 4, 119991, Moscow, Russian Federation
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye gory 1-3, GSP-1, 119991, Moscow, Russian Federation
| | - Peter Gorelkin
- National University of Science and Technology "MISIS", Leninskiy prospect 4, 119991, Moscow, Russian Federation
| | - Alexander Majouga
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye gory 1-3, GSP-1, 119991, Moscow, Russian Federation
| | - Dominik J Weiss
- Department of Earth Science & Engineering, Imperial College London, London, SW7 2AZ, UK
| | | | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, London, CB2 1EW, UK
| | - Elena V Sviderskaya
- Cell Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's, University of London, London, SW17 0RE, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
| | - Yuri Korchev
- Department of Medicine, Imperial College London, London, W12 0NN, UK.
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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28
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Hong SP, Chan TE, Lombardo Y, Corleone G, Rotmensz N, Bravaccini S, Rocca A, Pruneri G, McEwen KR, Coombes RC, Barozzi I, Magnani L. Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. Nat Commun 2019; 10:3840. [PMID: 31477698 PMCID: PMC6718416 DOI: 10.1038/s41467-019-11721-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. Here, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare subpopulation of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. We find evidence for sub-clonal expression of a PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
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Affiliation(s)
- Sung Pil Hong
- Department of Surgery and Cancer, Imperial College London, London, UK.
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Thalia E Chan
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Ylenia Lombardo
- Department of Surgery and Cancer, Imperial College London, London, UK
- Nature Communications, The Macmillan Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Giacomo Corleone
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicole Rotmensz
- Division of Pathology, European Institute of Oncology and University of Milan, School of Medicine, Milan, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Andrea Rocca
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giancarlo Pruneri
- Division of Pathology, European Institute of Oncology and University of Milan, School of Medicine, Milan, Italy
| | - Kirsten R McEwen
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK.
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK.
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29
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Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. Genes Dev 2019; 33:1159-1174. [PMID: 31371436 PMCID: PMC6719622 DOI: 10.1101/gad.326348.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.
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Affiliation(s)
- Federico Comoglio
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
- Department of Hematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Marta Simonatto
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Sara Polletti
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London W12 00N, United Kingdom
| | - Gioacchino Natoli
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
- Humanitas Istituto di Ricovero e Cura a Carattere Scientifico, Rozzano, Milano 20089, Italy
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30
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Nguyen VTM, Barozzi I, Faronato M, Lombardo Y, Steel JH, Patel N, Darbre P, Castellano L, Győrffy B, Woodley L, Rodriguez-Meira A, Patten DK, Vircillo V, Periyasamy M, Ali S, Frige G, Minucci S, Coombes RC, Magnani L. Author Correction: Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion. Nat Commun 2019; 10:3505. [PMID: 31388012 PMCID: PMC6684632 DOI: 10.1038/s41467-019-11569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Van T M Nguyen
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Iros Barozzi
- IFOM-IEO Campus, European Institute of Oncology, Milan, 20139, Italy
| | - Monica Faronato
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Ylenia Lombardo
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Jennifer H Steel
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Naina Patel
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Philippa Darbre
- School of Biological Science, University of Reading, Reading, RG6 6LA, UK
| | - Leandro Castellano
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Balázs Győrffy
- MTATTK Lendület Cancer Biomarker Research Group, 2nd Department of Pediatrics, Semmelweis University, Budapest, H-1117, Hungary
- MTA-SE Pediatrics and Nephrology Research Group, 2nd Department of Pediatrics, Semmelweis University, Budapest, H-1117, Hungary
| | | | | | - Darren K Patten
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Valentina Vircillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende (CS), 87036, Italy
| | | | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Gianmaria Frige
- IFOM-IEO Campus, European Institute of Oncology, Milan, 20139, Italy
| | - Saverio Minucci
- IFOM-IEO Campus, European Institute of Oncology, Milan, 20139, Italy
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK.
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31
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Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat Immunol 2018; 19:932-941. [PMID: 30127433 PMCID: PMC6195188 DOI: 10.1038/s41590-018-0184-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023]
Abstract
Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.
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Affiliation(s)
- Sergi Cuartero
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Elizabeth Ing-Simmons
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Silvia Masella
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Irene Robles-Rebollo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Xiaolin Xiao
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Department of Surgery and Cancer, Department of Medicine, Imperial College London, London, UK
| | - Dounia Djeghloul
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Mariane T Amano
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Robin D Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Kikuë Tachibana
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gioacchino Natoli
- Humanitas Clinical and Research Center, Milan, Italy
- Humanitas University, Milan, Italy
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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Patten DK, Corleone G, Győrffy B, Perone Y, Slaven N, Barozzi I, Erdős E, Saiakhova A, Goddard K, Vingiani A, Shousha S, Pongor LS, Hadjiminas DJ, Schiavon G, Barry P, Palmieri C, Coombes RC, Scacheri P, Pruneri G, Magnani L. Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Nat Med 2018; 24:1469-1480. [PMID: 30038216 PMCID: PMC6130800 DOI: 10.1038/s41591-018-0091-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/14/2018] [Indexed: 12/31/2022]
Abstract
The degree of intrinsic and interpatient phenotypic heterogeneity and its role in tumor evolution is poorly understood. Phenotypic drifts can be transmitted via inheritable transcriptional programs. Cell-type specific transcription is maintained through the activation of epigenetically defined regulatory regions including promoters and enhancers. Here we have annotated the epigenome of 47 primary and metastatic estrogen-receptor (ERα)-positive breast cancer clinical specimens and inferred phenotypic heterogeneity from the regulatory landscape, identifying key regulatory elements commonly shared across patients. Shared regions contain a unique set of regulatory information including the motif for transcription factor YY1. We identify YY1 as a critical determinant of ERα transcriptional activity promoting tumor growth in most luminal patients. YY1 also contributes to the expression of genes mediating resistance to endocrine treatment. Finally, we used H3K27ac levels at active enhancer elements as a surrogate of intra-tumor phenotypic heterogeneity to track the expansion and contraction of phenotypic subpopulations throughout breast cancer progression. By tracking the clonality of SLC9A3R1-positive cells, a bona fide YY1-ERα-regulated gene, we show that endocrine therapies select for phenotypic clones under-represented at diagnosis. Collectively, our data show that epigenetic mechanisms significantly contribute to phenotypic heterogeneity and evolution in systemically treated breast cancer patients.
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Affiliation(s)
- Darren K Patten
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- Semmelweis University, 2nd Deptartment of Pediatrics, Budapest, Hungary
| | - Ylenia Perone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Neil Slaven
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Edina Erdős
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kate Goddard
- Department of Breast and General Surgery, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Andrea Vingiani
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Sami Shousha
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | - Lőrinc Sándor Pongor
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dimitri J Hadjiminas
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | | | - Peter Barry
- Department of Breast Surgery, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Carlo Palmieri
- Institute of Translational Medicine University of Liverpool, Clatterbridge Cancer Centre, NHS Foundation Trust, and Royal Liverpool University Hospital, Liverpool, Merseyside, UK
| | - Raul C Coombes
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Giancarlo Pruneri
- Pathology Department, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.
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33
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Comoglio F, Park HJ, Schoenfelder S, Barozzi I, Bode D, Fraser P, Green AR. Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures. Genome Res 2018; 28:gr.227272.117. [PMID: 29429976 PMCID: PMC5848609 DOI: 10.1101/gr.227272.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022]
Abstract
Thrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relation between cis- regulatory activity and chromatin architecture. We show that TPO profoundly alters the transcriptome of HSPCs, with key hematopoietic regulators being transcriptionally repressed within 30 minutes of TPO. By examining cis-regulatory dynamics and chromatin architectures, we demonstrate that these changes are accompanied by rapid and extensive epigenome remodeling of cis-regulatory landscapes that is spatially coordinated within topologically associating domains (TADs). Moreover, TPO-responsive enhancers are spatially clustered and engage in preferential homotypic intra- and inter-TAD interactions that are largely refractory to TPO signaling. By further examining the link between cis-regulatory dynamics and chromatin looping, we show that rapid modulation of cis-regulatory activity is largely independent of chromatin looping dynamics. Finally, we show that, although activated and repressed cis-regulatory elements share remarkably similar DNA sequence compositions, transcription factor binding patterns accurately predict rapid cis-regulatory responses to TPO.
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34
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Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A. Ultraconserved Enhancers Are Required for Normal Development. Cell 2018; 172:491-499.e15. [PMID: 29358049 DOI: 10.1016/j.cell.2017.12.017] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/27/2017] [Accepted: 12/11/2017] [Indexed: 01/26/2023]
Abstract
Non-coding "ultraconserved" regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. Here, we show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.
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Affiliation(s)
- Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Athena R Ypsilanti
- Department of Psychiatry, Neuroscience Program, UCSF Weill Institute for Neurosciences and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ramón Pla
- Department of Psychiatry, Neuroscience Program, UCSF Weill Institute for Neurosciences and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yiwen Zhu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Yupar S Khin
- Department of Psychiatry, Neuroscience Program, UCSF Weill Institute for Neurosciences and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S Pickle
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Anne N Harrington
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program, UCSF Weill Institute for Neurosciences and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California Merced, Merced, CA 95343, USA.
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35
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Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson HL, Stadler HS, Visel A, Drouin J, Kmita M. Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep 2017; 17:2913-2926. [PMID: 27974206 PMCID: PMC5697718 DOI: 10.1016/j.celrep.2016.11.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 01/12/2023] Open
Abstract
The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13−/−; Hoxd13−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
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Affiliation(s)
- Rushikesh Sheth
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada.
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Langlais
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, H3G0B1 QC, Canada
| | | | - Stephen Nemec
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada
| | - Hanqian L Carlson
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95340, USA
| | - Jacques Drouin
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada
| | - Marie Kmita
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada.
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36
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Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput Biol 2017; 13:e1005720. [PMID: 28827824 PMCID: PMC5578682 DOI: 10.1371/journal.pcbi.1005720] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/31/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisticated, integrative methods have been described, but commonly suffer from limited accessibility to the resulting predictions and reduced biological interpretability. Here we present the Limb-Enhancer Genie (LEG), a collection of highly accurate, genome-wide predictions of enhancers in the developing limb, available through a user-friendly online interface. We predict limb enhancers using a combination of >50 published limb-specific datasets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage of the patterns observed at previously in vivo validated elements. By combining different statistical models, our approach outperforms current state-of-the-art methods and provides interpretable measures of feature importance. Our results indicate that including a previously unappreciated score that quantifies tissue-specific nuclease accessibility significantly improves prediction performance. We demonstrate the utility of our approach through in vivo validation of newly predicted elements. Moreover, we describe general features that can guide the type of datasets to include when predicting tissue-specific enhancers genome-wide, while providing an accessible resource to the general biological community and facilitating the functional interpretation of genetic studies of limb malformations.
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Affiliation(s)
- Remo Monti
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint Genome Institute, U.S. Department of Energy, Walnut Creek, California, United States of America
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Marco Osterwalder
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Elizabeth Lee
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Momoe Kato
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Tyler H. Garvin
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ingrid Plajzer-Frick
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Catherine S. Pickle
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jennifer A. Akiyama
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Veena Afzal
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Diane E. Dickel
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint Genome Institute, U.S. Department of Energy, Walnut Creek, California, United States of America
- School of Natural Sciences, University of California, Merced, California, United States of America
| | - Len A. Pennacchio
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint Genome Institute, U.S. Department of Energy, Walnut Creek, California, United States of America
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37
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Montagner S, Leoni C, Emming S, Della Chiara G, Balestrieri C, Barozzi I, Piccolo V, Togher S, Ko M, Rao A, Natoli G, Monticelli S. TET2 Regulates Mast Cell Differentiation and Proliferation through Catalytic and Non-catalytic Activities. Cell Rep 2017; 20:1744. [PMID: 28813683 DOI: 10.1016/j.celrep.2017.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Curina A, Termanini A, Barozzi I, Prosperini E, Simonatto M, Polletti S, Silvola A, Soldi M, Austenaa L, Bonaldi T, Ghisletti S, Natoli G. High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins. Genes Dev 2017; 31:399-412. [PMID: 28275002 PMCID: PMC5358759 DOI: 10.1101/gad.293134.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/03/2017] [Indexed: 11/24/2022]
Abstract
Here, Curina et al. found that a subgroup of ETS family transcription factors (the ELF proteins) shows a strong bias in its genomic distribution by binding in very close proximity (<60 nt) to the transcription start sites of housekeeping genes. They show that a limited number of highly active transcription factors can equip cis-regulatory elements with disparate functional roles and cell type specificity with the ability to efficiently promote transcription. Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised, macrophage-specific enhancers and promoters. The role of ELFs in promoting high-level constitutive transcription was suggested by multiple evidence: ELF sites enabled robust transcriptional activation by endogenous and minimal synthetic promoters, ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data suggest that the co-optation of a limited number of highly active transcription factors represents a broadly adopted strategy to equip both cell type-specific and housekeeping cis-regulatory elements with the ability to efficiently promote transcription.
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Affiliation(s)
- Alessia Curina
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | | | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Marta Simonatto
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Alessio Silvola
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Liv Austenaa
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Serena Ghisletti
- Humanitas Clinical and Research Center, 20089 Rozzano-Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy.,Humanitas University, 20089 Rozzano-Milan, Italy
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39
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Magnani L, Frige G, Gadaleta RM, Corleone G, Fabris S, Kempe MH, Vershure PJ, Barozzi I, Vircillo V, Hong SP, Perone Y, Saini M, Trumpp A, Viale G, Neri A, Ali S, Colleoni MA, Pruneri G, Minucci S. Acquired CYP19A1 amplification is an early specific mechanism of aromatase inhibitor resistance in ERα metastatic breast cancer. Nat Genet 2017; 49:444-450. [PMID: 28112739 PMCID: PMC5326683 DOI: 10.1038/ng.3773] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/21/2016] [Indexed: 12/25/2022]
Abstract
Tumor evolution is shaped by many variables, potentially involving external selective pressures induced by therapies. After surgery, patients with estrogen receptor (ERα)-positive breast cancer are treated with adjuvant endocrine therapy, including selective estrogen receptor modulators (SERMs) and/or aromatase inhibitors (AIs). However, more than 20% of patients relapse within 10 years and eventually progress to incurable metastatic disease. Here we demonstrate that the choice of therapy has a fundamental influence on the genetic landscape of relapsed diseases. We found that 21.5% of AI-treated, relapsed patients had acquired CYP19A1 (encoding aromatase) amplification (CYP19A1amp). Relapsed patients also developed numerous mutations targeting key breast cancer-associated genes, including ESR1 and CYP19A1. Notably, CYP19A1amp cells also emerged in vitro, but only in AI-resistant models. CYP19A1 amplification caused increased aromatase activity and estrogen-independent ERα binding to target genes, resulting in CYP19A1amp cells showing decreased sensitivity to AI treatment. These data suggest that AI treatment itself selects for acquired CYP19A1amp and promotes local autocrine estrogen signaling in AI-resistant metastatic patients.
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Affiliation(s)
- Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London,
UK
| | - Gianmaria Frige
- Department of Experimental Oncology, European Institute of Oncology
Milan, Italy
| | | | - Giacomo Corleone
- Department of Surgery and Cancer, Imperial College London, London,
UK
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca’ Granda, Ospedale
Maggiore Policlinico, Milan, IT
| | - Mannus H. Kempe
- Swammerdam Institute for Life Sciences, University of
Amsterdam
| | | | - Iros Barozzi
- Genomics Division, Lawrence Berkeley National Laboratory, 1
Cyclotron Road, Berkeley, CA, USA
| | - Valentina Vircillo
- Department of Pharmacy, Health and Nutritional Sciences, University
of Calabria, Arcavacata di Rende (CS), Italy
| | - Sung-Pil Hong
- Department of Surgery and Cancer, Imperial College London, London,
UK
| | - Ylenia Perone
- Department of Surgery and Cancer, Imperial College London, London,
UK
| | - Massimo Saini
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum
(DKFZ), and Institute for Stem Cell Technology and Experimental Medicine GmbH,
Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum
(DKFZ), and Institute for Stem Cell Technology and Experimental Medicine GmbH,
Heidelberg, Germany
| | - Giuseppe Viale
- Division of Pathology, European Institute of Oncology and University
of Milan, School of Medicine, Milan, Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Ca’ Granda, Ospedale
Maggiore Policlinico, Milan, IT
- Department of Oncology and Hemato-oncology, University of Milano,
Milan, IT
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London,
UK
| | | | - Giancarlo Pruneri
- Division of Pathology, European Institute of Oncology and University
of Milan, School of Medicine, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology
Milan, Italy
- Department of Biosciences, University of Milano, Milan, IT
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40
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Zhan Y, Mariani L, Barozzi I, Schulz EG, Blüthgen N, Stadler M, Tiana G, Giorgetti L. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res 2017; 27:479-490. [PMID: 28057745 PMCID: PMC5340975 DOI: 10.1101/gr.212803.116] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/04/2017] [Indexed: 12/02/2022]
Abstract
Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here, we present a novel algorithm named CaTCH that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation, which is a single and biologically relevant parameter. By applying CaTCH to published Hi-C data sets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal boundary enrichment in CTCF and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that the likelihood that genes in a domain are coregulated during differentiation is also maximized at the scale of TADs. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the same scale. Our analysis suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the specific genomic position of regulatory sequences.
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Affiliation(s)
- Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, CH-4058, Switzerland.,University of Basel, CH-4003 Basel, Switzerland
| | - Luca Mariani
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Iros Barozzi
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Edda G Schulz
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Nils Blüthgen
- Institute of Pathology, Charité -Universitätsmedizin Berlin, 10117 Berlin, Germany.,Interdisciplinary Research Institute for the Life Sciences, Humboldt University, 10115 Berlin, Germany
| | - Michael Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, CH-4058, Switzerland.,Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, University of Milano and Istituto Nazionale di Fisica Nucleare, 20133, Milano, Italy
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, CH-4058, Switzerland
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41
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Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 2016; 167:633-642.e11. [PMID: 27768887 DOI: 10.1016/j.cell.2016.09.028] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/07/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.
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Affiliation(s)
- Evgeny Z Kvon
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Olga K Kamneva
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Uirá S Melo
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Catherine S Pickle
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Elizabeth A Lee
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Lopez-Rios
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Edward M Rubin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Diane E Dickel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Len A Pennacchio
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Axel Visel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
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42
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Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nat Commun 2016; 7:12923. [PMID: 27703156 PMCID: PMC5059478 DOI: 10.1038/ncomms12923] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/16/2016] [Indexed: 12/04/2022] Open
Abstract
Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations prevents their interpretation. We describe the genome-wide landscape of distant-acting enhancers active in the developing and adult human heart, an organ whose impairment is a predominant cause of mortality and morbidity. Using integrative analysis of >35 epigenomic data sets from mouse and human pre- and postnatal hearts we created a comprehensive reference of >80,000 putative human heart enhancers. To illustrate the importance of enhancers in the regulation of genes involved in heart disease, we deleted the mouse orthologs of two human enhancers near cardiac myosin genes. In both cases, we observe in vivo expression changes and cardiac phenotypes consistent with human heart disease. Our study provides a comprehensive catalogue of human heart enhancers for use in clinical whole-genome sequencing studies and highlights the importance of enhancers for cardiac function. Identification of non-coding variants has outstripped our ability to annotate and interpret them. Dickel et al. present a compendium of over 80,000 putative human heart enhancers and demonstrate that two conserved enhancers are required for proper cardiac function in mice.
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Affiliation(s)
- Diane E Dickel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Iros Barozzi
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Yiwen Zhu
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Yoko Fukuda-Yuzawa
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Marco Osterwalder
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Brandon J Mannion
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Dalit May
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Cailyn H Spurrell
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Ingrid Plajzer-Frick
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Catherine S Pickle
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Elizabeth Lee
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Tyler H Garvin
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Momoe Kato
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Jennifer A Akiyama
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Veena Afzal
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Edward M Rubin
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Axel Visel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,School of Natural Sciences, University of California, Merced, Merced, California 95343, USA
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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43
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Barozzi I, Visel A, Dickel DE. Fishing for Function in the Human Gene Pool. Trends Genet 2016; 32:392-394. [PMID: 27220646 DOI: 10.1016/j.tig.2016.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 11/28/2022]
Abstract
Identification and characterization of causal non-coding variants in human genomes is challenging and requires substantial experimental resources. A new study by Tehranchi et al. describes a cost-effective approach for accurate mapping of molecular quantitative trait loci (QTLs) from pooled samples, a powerful way to link disease-associated changes to molecular functions.
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Affiliation(s)
- Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, California, USA.
| | - Diane E Dickel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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44
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Montagner S, Leoni C, Emming S, Della Chiara G, Balestrieri C, Barozzi I, Piccolo V, Togher S, Ko M, Rao A, Natoli G, Monticelli S. TET2 Regulates Mast Cell Differentiation and Proliferation through Catalytic and Non-catalytic Activities. Cell Rep 2016; 15:1566-1579. [PMID: 27160912 DOI: 10.1016/j.celrep.2016.04.044] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/08/2016] [Accepted: 04/07/2016] [Indexed: 12/13/2022] Open
Abstract
Dioxygenases of the TET family impact genome functions by converting 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC). Here, we identified TET2 as a crucial regulator of mast cell differentiation and proliferation. In the absence of TET2, mast cells showed disrupted gene expression and altered genome-wide 5hmC deposition, especially at enhancers and in the proximity of downregulated genes. Impaired differentiation of Tet2-ablated cells could be relieved or further exacerbated by modulating the activity of other TET family members, and mechanistically it could be linked to the dysregulated expression of C/EBP family transcription factors. Conversely, the marked increase in proliferation induced by the loss of TET2 could be rescued exclusively by re-expression of wild-type or catalytically inactive TET2. Our data indicate that, in the absence of TET2, mast cell differentiation is under the control of compensatory mechanisms mediated by other TET family members, while proliferation is strictly dependent on TET2 expression.
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Affiliation(s)
- Sara Montagner
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Stefan Emming
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Giulia Della Chiara
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Chiara Balestrieri
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Susan Togher
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Myunggon Ko
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; School of Life Sciences, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland.
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45
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Nguyen VTM, Barozzi I, Faronato M, Lombardo Y, Steel JH, Patel N, Darbre P, Castellano L, Győrffy B, Woodley L, Meira A, Patten DK, Vircillo V, Periyasamy M, Ali S, Frige G, Minucci S, Coombes RC, Magnani L. Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion. Nat Commun 2015; 6:10044. [PMID: 26610607 PMCID: PMC4674692 DOI: 10.1038/ncomms10044] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 10/28/2015] [Indexed: 12/24/2022] Open
Abstract
Endocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients.
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Affiliation(s)
- Van T. M. Nguyen
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Iros Barozzi
- IFOM-IEO Campus, European Institute of Oncology, Milan 20139, Italy
| | - Monica Faronato
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Ylenia Lombardo
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Jennifer H. Steel
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Naina Patel
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Philippa Darbre
- School of Biological Science, University of Reading, Reading RG6 6LA, UK
| | - Leandro Castellano
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, 2nd Department of Pediatrics, Semmelweis University, Budapest H-1117, Hungary
- MTA-SE Pediatrics and Nephrology Research Group, 2nd Department of Pediatrics, Semmelweis University, Budapest H-1117, Hungary
| | | | - Alba Meira
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Darren K. Patten
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Valentina Vircillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende (CS) 87036, Italy
| | | | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Gianmaria Frige
- IFOM-IEO Campus, European Institute of Oncology, Milan 20139, Italy
| | - Saverio Minucci
- IFOM-IEO Campus, European Institute of Oncology, Milan 20139, Italy
| | - R. Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
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46
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Austenaa L, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman B, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination. Mol Cell 2015; 60:460-74. [DOI: 10.1016/j.molcel.2015.09.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/13/2015] [Accepted: 09/17/2015] [Indexed: 12/12/2022]
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47
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Chiaradonna F, Barozzi I, Miccolo C, Bucci G, Palorini R, Fornasari L, Botrugno OA, Pruneri G, Masullo M, Passafaro A, Galimberti VE, Fantin VR, Richon VM, Pece S, Viale G, Di Fiore PP, Draetta G, Pelicci PG, Minucci S, Chiocca S. Redox-Mediated Suberoylanilide Hydroxamic Acid Sensitivity in Breast Cancer. Antioxid Redox Signal 2015; 23:15-29. [PMID: 25897982 PMCID: PMC4492673 DOI: 10.1089/ars.2014.6189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AIMS Vorinostat (suberoylanilide hydroxamic acid; SAHA) is a histone deacetylase inhibitor (HDACi) approved in the clinics for the treatment of T-cell lymphoma and with the potential to be effective also in breast cancer. We investigated the responsiveness to SAHA in human breast primary tumors and cancer cell lines. RESULTS We observed a differential response to drug treatment in both human breast primary tumors and cancer cell lines. Gene expression analysis of the breast cancer cell lines revealed that genes involved in cell adhesion and redox pathways, especially glutathione metabolism, were differentially expressed in the cell lines resistant to SAHA compared with the sensitive ones, indicating their possible association with drug resistance mechanisms. Notably, such an association was also observed in breast primary tumors. Indeed, addition of buthionine sulfoximine (BSO), a compound capable of depleting cellular glutathione, significantly enhanced the cytotoxicity of SAHA in both breast cancer cell lines and primary breast tumors. INNOVATION We identify and validate transcriptional differences in genes involved in redox pathways, which include potential predictive markers of sensitivity to SAHA. CONCLUSION In breast cancer, it could be relevant to evaluate the expression of antioxidant genes that may favor tumor resistance as a factor to consider for potential clinical application and treatment with epigenetic drugs (HDACis).
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Affiliation(s)
- Ferdinando Chiaradonna
- 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca , Milan, Italy .,2 SYSBIO Centre of Systems Biology , Milan, Italy
| | - Iros Barozzi
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Claudia Miccolo
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Gabriele Bucci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Roberta Palorini
- 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca , Milan, Italy .,2 SYSBIO Centre of Systems Biology , Milan, Italy
| | - Lorenzo Fornasari
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Oronza A Botrugno
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giancarlo Pruneri
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Michele Masullo
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Alfonso Passafaro
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | | | - Valeria R Fantin
- 6 Oncology Research Unit, Pfizer Global Research and Development , La Jolla, California
| | | | - Salvatore Pece
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giuseppe Viale
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Pier Paolo Di Fiore
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giulio Draetta
- 8 Institute for Applied Cancer, The University of Texas MD Anderson Cancer Center Science , Houston, Texas
| | - Pier Giuseppe Pelicci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Saverio Minucci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy .,9 Department of Biosciences, University of Milan , Milan, Italy
| | - Susanna Chiocca
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
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48
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Mancino A, Termanini A, Barozzi I, Ghisletti S, Ostuni R, Prosperini E, Ozato K, Natoli G. A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages. Genes Dev 2015; 29:394-408. [PMID: 25637355 PMCID: PMC4335295 DOI: 10.1101/gad.257592.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The transcription factor IRF8 controls both developmental and inflammatory stimulus-inducible genes in macrophages. Mancino et al. found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. Overall, these data show at the genome scale how the same TF can be linked to constitutive and inducible gene regulation via distinct combinations of alternative DNA-binding sites.
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Affiliation(s)
- Alessandra Mancino
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Alberto Termanini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Renato Ostuni
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Keiko Ozato
- Laboratory of Molecular Growth Regulation, Genomics of Differentiation Program, National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy;
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Barozzi I, Bora P, Morelli MJ. Corrigendum: Comparative evaluation of DNase-seq footprint identification strategies. Front Genet 2014. [PMCID: PMC4168722 DOI: 10.3389/fgene.2014.00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Iros Barozzi
- Department of Experimental Oncology, European Institute of OncologyMilan, Italy
| | - Pranami Bora
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT)Milan, Italy
| | - Marco J. Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT)Milan, Italy
- *Correspondence:
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Abstract
DNase I is an enzyme preferentially cleaving DNA in highly accessible regions. Recently, Next-Generation Sequencing has been applied to DNase I assays (DNase-seq) to obtain genome-wide maps of these accessible chromatin regions. With high-depth sequencing, DNase I cleavage sites can be identified with base-pair resolution, revealing the presence of protected regions ("footprints"), corresponding to bound molecules on the DNA. Integrating footprint positions close to transcription start sites with motif analysis can reveal the presence of regulatory interactions between specific transcription factors (TFs) and genes. However, this inference heavily relies on the accuracy of the footprint call and on the sequencing depth of the DNase-seq experiment. Using ENCODE data, we comprehensively evaluate the performances of two recent footprint callers (Wellington and DNaseR) and one metric (the Footprint Occupancy Score, or FOS), and assess the consequences of different footprint calls on the reconstruction of TF-TF regulatory networks. We rate Wellington as the method of choice among those tested: not only its predictions are the best in terms of accuracy, but also the properties of the inferred networks are robust against sequencing depth.
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Affiliation(s)
- Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology Milan, Italy
| | - Pranami Bora
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) Milan, Italy
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