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Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature 2020; 588:670-675. [PMID: 33238290 PMCID: PMC8003326 DOI: 10.1038/s41586-020-3014-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [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: 11/08/2017] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate the investigation of pathologies such as interstitial lung disease, cancer and coronavirus disease 2019 (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we describe the development of a long-term feeder-free, chemically defined culture system for distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids were able to differentiate into AT1 cells, and basal cell organoids developed lumens lined with differentiated club and ciliated cells. Single-cell analysis of KRT5+ cells in basal organoids revealed a distinct population of ITGA6+ITGB4+ mitotic cells, whose offspring further segregated into a TNFRSF12Ahi subfraction that comprised about ten per cent of KRT5+ basal cells. This subpopulation formed clusters within terminal bronchioles and exhibited enriched clonogenic organoid growth activity. We created distal lung organoids with apical-out polarity to present ACE2 on the exposed external surface, facilitating infection of AT2 and basal cultures with SARS-CoV-2 and identifying club cells as a target population. This long-term, feeder-free culture of human distal lung organoids, coupled with single-cell analysis, identifies functional heterogeneity among basal cells and establishes a facile in vitro organoid model of human distal lung infections, including COVID-19-associated pneumonia.
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Affiliation(s)
- Ameen A Salahudeen
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Shannon S Choi
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Junjie Zhu
- Stanford University School of Engineering, Department of Electrical Engineering, Stanford, CA, USA
| | - Vincent van Unen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean M de la O
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mar Margalef-Català
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - António J M Santos
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jihang Ju
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arpit Batish
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tatsuya Usui
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent Luca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benedict Anchang
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Monica Nagendran
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Khanh Nguyen
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel J Hart
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Pehr B Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey S Glenn
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chiara Sabatti
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Amieva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Calvin J Kuo
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol 2020; 38:954-961. [PMID: 32231336 PMCID: PMC7416462 DOI: 10.1038/s41587-020-0470-y] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 12/20/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022]
Abstract
Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
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Affiliation(s)
- Joseph M Replogle
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Albert Xu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA.
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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3
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Salahudeen AA, Choi SS, Rustagi A, Zhu J, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, van Unen V, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.27.212076. [PMID: 32743583 PMCID: PMC7386503 DOI: 10.1101/2020.07.27.212076] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange and is affected by disorders including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. Investigations of these localized pathologies have been hindered by a lack of 3D in vitro human distal lung culture systems. Further, human distal lung stem cell identification has been impaired by quiescence, anatomic divergence from mouse and lack of lineage tracing and clonogenic culture. Here, we developed robust feeder-free, chemically-defined culture of distal human lung progenitors as organoids derived clonally from single adult human alveolar epithelial type II (AT2) or KRT5 + basal cells. AT2 organoids exhibited AT1 transdifferentiation potential, while basal cell organoids progressively developed lumens lined by differentiated club and ciliated cells. Organoids consisting solely of club cells were not observed. Upon single cell RNA-sequencing (scRNA-seq), alveolar organoids were composed of proliferative AT2 cells; however, basal organoid KRT5 + cells contained a distinct ITGA6 + ITGB4 + mitotic population whose proliferation segregated to a TNFRSF12A hi subfraction. Clonogenic organoid growth was markedly enriched within the TNFRSF12A hi subset of FACS-purified ITGA6 + ITGB4 + basal cells from human lung or derivative organoids. In vivo, TNFRSF12A + cells comprised ~10% of KRT5 + basal cells and resided in clusters within terminal bronchioles. To model COVID-19 distal lung disease, we everted the polarity of basal and alveolar organoids to rapidly relocate differentiated club and ciliated cells from the organoid lumen to the exterior surface, thus displaying the SARS-CoV-2 receptor ACE2 on the outwardly-facing apical aspect. Accordingly, basal and AT2 apical-out organoids were infected by SARS-CoV-2, identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung alveolar and basal stem cells, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and exemplifies progenitor identification within a slowly proliferating human tissue. Further, our studies establish a facile in vitro organoid model for human distal lung infectious diseases including COVID-19-associated pneumonia.
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Tsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Development 2019; 146:dev174722. [PMID: 31515224 PMCID: PMC6803377 DOI: 10.1242/dev.174722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 12/07/2018] [Accepted: 08/12/2019] [Indexed: 01/23/2023]
Abstract
Maintenance of pluripotency and specification towards a new cell fate are both dependent on precise interactions between extrinsic signals and transcriptional and epigenetic regulators. Directed methylation of cytosines by the de novo methyltransferases DNMT3A and DNMT3B plays an important role in facilitating proper differentiation, whereas DNMT1 is essential for maintaining global methylation levels in all cell types. Here, we generated single-cell mRNA expression data from wild-type, DNMT3A, DNMT3A/3B and DNMT1 knockout human embryonic stem cells and observed a widespread increase in cellular and transcriptional variability, even with limited changes in global methylation levels in the de novo knockouts. Furthermore, we found unexpected transcriptional repression upon either loss of the de novo methyltransferase DNMT3A or the double knockout of DNMT3A/3B that is further propagated upon differentiation to mesoderm and ectoderm. Taken together, our single-cell RNA-sequencing data provide a high-resolution view into the consequences of depleting the three catalytically active DNMTs in human pluripotent stem cells.
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Affiliation(s)
- Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Samuel J Allon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Aleksandra Arczewska
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin E Mead
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Riley S Drake
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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5
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Boutet SC, Walter D, Stubbington MJT, Pfeiffer KA, Lee JY, Taylor SEB, Montesclaros L, Lau JK, Riordan DP, Barrio AM, Brix L, Jacobsen K, Yeung B, Zhao X, Mikkelsen TS. Scalable and comprehensive characterization of antigen-specific CD8 T cells using multi-omics single cell analysis. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.131.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Understanding the antigen binding specificities of lymphocytes is key to the development of effective therapeutics for cancers and infectious diseases. Recent technological advancements have enabled the integration of simultaneous cell-surface protein, transcriptome, immune repertoire and antigen specificity measurements at single cell resolution, providing comprehensive, scalable, high-throughput characterization of immune cells.
Using the 10x Genomics Single Cell Immune Profiling Solution with Feature Barcoding technology with 14 oligo-conjugated antibodies and 50 Immudex peptide-MHC I Dextramer reagents (pMHC) panels spanning different CMV, EBV, Influenza, HIV and Cancer antigens, we performed multi-omic characterization of ~100,000 CD8+ T cells from four MHC-matched donors. The multi-omic combination of gene expression, paired alpha/beta T cell receptor (TCR) repertoire, cell surface proteins and pMHC binding specificity allowed the identification of CD8+ T cell subpopulations with specificity for pMHCs within our panel. We observed multiple TCRs that bound the same pMHC and identified enriched amino acid motifs within TCR sequences that shared specificities. We compared the CDR3 amino acid sequences of the pMHC-specific TCR clonotypes with previously reported sequences with the same binding specificities to show that we could identify new and known CDR3 sequences. This analytical framework provides a systematic and scalable method for deciphering TCR–pMHC specificity combined with cellular phenotype identity which is critical for developing a better understanding of the adaptive immune response to cancer and infectious diseases and will be key in the development of successful immunotherapies.
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Sukovich DJ, Taylor SEB, Pfeiffer KA, Stubbington MJT, Lee JY, Sapida J, Roidan DP, Barrio AM, Walter D, Brix L, Jacobsen K, Yeung B, Zhao X, Mikkelsen TS. An advancement in single cell genomics allows for T cell population analysis at high resolution. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.131.13] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Progress in our understanding of immunology and cancer immunotherapies requires a comprehensive view of immune cell behavior and the interactions of these cells with their environment. Recent technological innovations have facilitated the combination of cell-surface protein, transcriptome, immune repertoire, and antigen specificity measurements from the same single cells, providing thorough and high-throughput lymphocyte characterization.
Using the 10x Genomics Single Cell Immune Profiling Solution with Feature Barcoding technology along with oligo-conjugated antibodies and peptide-MHC (pMHC) Dextramers®, we performed multi-omic characterization of PBMCs from cytomegalovirus (CMV) seronegative and seropositive patients. Next generation sequencing libraries were made following the 10x Genomics workflows, where transcriptome and immune repertoire libraries are generated alongside libraries from DNA barcodes conjugated to antibodies or pMHC.
Full length, paired TCRα/β sequences with specificity to known CMV antigens were identified in the seropositive donor, but not in the seronegative donor. Interestingly, a large Epstein Barr Virus (EBV) pMHC specific T cell expansion was identified in the CMV seronegative donor, suggesting an active EBV response. Moreover, the combination of transcriptomic and cell surface protein information resulted in an increase in resolution of cell type identification. This multi-omic workflow allowed the identification of enriched amino acid motifs within the TCR sequences that contained novel and known CDR3 amino acid sequences specific to CMV.
These technological advancements provide new biological insights that are critical for progress in the field.
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Montesclaros L, Boutet SC, Taylor SEB, Stubbington MJT, Giangarra V, Lau JK, Sapida J, Ziraldo S, Pfeiffer KA, Zheng G, Barrio AM, Lee JY, Marrs S, Wu K, Mikkelsen TS. Deep characterization of tumor microenvironments using single cell multi-omics analysis. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.194.29] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Understanding the complexity of cell interactions in the tumor microenvironment (TME) requires the ability to distinguish each cell type, and is a prerequisite of personalized cancer treatments. Here, we use a fully integrated system for single cell RNA sequencing, to simultaneously profile the transcriptome, cell surface proteins and immune repertoire of cells from primary colorectal cancer (CRC), non-small cell lung cancer (NSCLC), and mucosa-associated lymphoid tissue (MALT) lymphoma. Each tumor varied in type and proportion of its cellular components, and in particular in the proportion of immune cells. The CRC tumor consisted of T (3% CD4+, 3% CD8+), B lymphocytes (5% CD79A+) and plasma B cells (11% IGH high). Repertoire sequencing identified a clonal expansion (>4% of B cell clonotypes) suggesting a strong B cell response in this tumor. The NSCLC tumor displayed a marked immune cell infiltration containing predominantly B cells (30% CD79A+ and 8% IGH high plasma B) with a very limited clonal expansion. The MALT lymphoma consisted of only T and B lymphocytes (31% CD4+, 8% CD8+, 57% CD79A+). In addition to the activated CD4+ and CD8+ T cells, Tfh and Treg cells were clearly identified as well as two distinct large B cell populations showing plasmacytic differentiation. Analysis of the B cell repertoire revealed a large expanded clone bearing an IGHV segment associated with parotid MALT lymphoma. These findings emphasize the importance of combining repertoire and gene expression sequencing data to determine the nature and clonality of an immune response. This method enables full characterization of tumor heterogeneity and the adaptive immune response to the TME and will be key in the development of successful immunotherapies.
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Castaldi PJ, Guo F, Qiao D, Du F, Naing ZZC, Li Y, Pham B, Mikkelsen TS, Cho MH, Silverman EK, Zhou X. Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays. Am J Respir Crit Care Med 2019; 199:52-61. [PMID: 30079747 PMCID: PMC6353020 DOI: 10.1164/rccm.201802-0337oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 02/21/2018] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
RATIONALE The identification of causal variants responsible for disease associations from genome-wide association studies (GWASs) facilitates functional understanding of the biological mechanisms by which those genetic variants influence disease susceptibility. OBJECTIVE We aim to identify causal variants in or near the FAM13A (family with sequence similarity member 13A) GWAS locus associated with chronic obstructive pulmonary disease (COPD). METHODS We used an integrated approach featuring conditional genetic analysis, massively parallel reporter assays (MPRAs), traditional reporter assays, chromatin conformation capture assays, and clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing to characterize COPD-associated regulatory variants in the FAM13A region in human bronchial epithelial cell lines. MEASUREMENTS AND MAIN RESULTS Conditional genetic association suggests the presence of two independent COPD association signals in FAM13A. MPRAs identified 45 regulatory variants within FAM13A, among which six variants were prioritized for further investigation. Three COPD-associated variants demonstrated significant allele-specific activity in reporter assays. One of three variants, rs2013701, was tested in the endogenous genomic context by CRISPR-based genome editing that confirmed its allele-specific effects on FAM13A expression and on cell proliferation, providing functional characterization for this COPD-associated variant. CONCLUSIONS The human GWAS association near FAM13A may contain independent association signals. MPRAs identified multiple functional variants in this region, including rs2013701, a putative COPD-causing variant with allele-specific regulatory activity.
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Affiliation(s)
- Peter J. Castaldi
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Feng Guo
- Channing Division of Network Medicine and
| | - Dandi Qiao
- Channing Division of Network Medicine and
| | - Fei Du
- Channing Division of Network Medicine and
| | | | - Yan Li
- Channing Division of Network Medicine and
| | - Betty Pham
- Channing Division of Network Medicine and
| | | | - Michael H. Cho
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Edwin K. Silverman
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Xiaobo Zhou
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; and
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9
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Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Syst 2018; 7:258-268.e3. [PMID: 30195438 DOI: 10.1016/j.cels.2018.07.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 10/24/2017] [Revised: 04/03/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023]
Abstract
Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy and for revealing principles of gene regulation. However, most reprogramming systems are inefficient, converting only a fraction of cells to the desired state. Here, we analyze MYOD-mediated reprogramming of human fibroblasts to myotubes, a well-characterized model system for direct conversion by defined factors, at pseudotemporal resolution using single-cell RNA-seq. To expose barriers to efficient conversion, we introduce a novel analytic technique, trajectory alignment, which enables quantitative comparison of gene expression kinetics across two biological processes. Reprogrammed cells navigate a trajectory with branch points that correspond to two alternative decision points, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Analysis of these branch points revealed insulin and BMP signaling as crucial molecular determinants of reprogramming. Single-cell trajectory alignment enables rigorous quantitative comparisons between biological trajectories found in diverse processes in development, reprogramming, and other contexts.
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Affiliation(s)
- Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiaojie Qiu
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Eliah Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Shuqiang Li
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Meissner
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tarjei S Mikkelsen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - John L Rinn
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cole Trapnell
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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10
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Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell 2018; 172:1132-1134. [PMID: 29474912 DOI: 10.1016/j.cell.2018.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. Nat Commun 2018; 9:360. [PMID: 29367672 PMCID: PMC5783949 DOI: 10.1038/s41467-017-02107-w] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/27/2017] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have considerably impacted human developmental biology and regenerative medicine, notably because they circumvent the use of cells of embryonic origin and offer the potential to generate patient-specific pluripotent stem cells. However, conventional reprogramming protocols produce developmentally advanced, or primed, human iPSCs (hiPSCs), restricting their use to post-implantation human development modeling. Hence, there is a need for hiPSCs resembling preimplantation naive epiblast. Here, we develop a method to generate naive hiPSCs directly from somatic cells, using OKMS overexpression and specific culture conditions, further enabling parallel generation of their isogenic primed counterparts. We benchmark naive hiPSCs against human preimplantation epiblast and reveal remarkable concordance in their transcriptome, dependency on mitochondrial respiration and X-chromosome status. Collectively, our results are essential for the understanding of pluripotency regulation throughout preimplantation development and generate new opportunities for disease modeling and regenerative medicine.
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Affiliation(s)
- Stéphanie Kilens
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Dimitri Meistermann
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,Laboratoire des Sciences du Numérique de Nantes, LS2N, UMR CNRS 6004, Université de Nantes, Nantes, France
| | - Diego Moreno
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Caroline Chariau
- INSERM UMS 016, SFR Francois Bonamy, iPSC Core Facility, Nantes, France; CNRS, UMS 3556, Nantes, France; Université de Nantes, Nantes, France; CHU Nantes, Nantes, France
| | - Anne Gaignerie
- INSERM UMS 016, SFR Francois Bonamy, iPSC Core Facility, Nantes, France; CNRS, UMS 3556, Nantes, France; Université de Nantes, Nantes, France; CHU Nantes, Nantes, France
| | - Arnaud Reignier
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Service de Biologie de la Reproduction, Nantes, France
| | - Yohann Lelièvre
- Laboratoire des Sciences du Numérique de Nantes, LS2N, UMR CNRS 6004, Université de Nantes, Nantes, France
| | - Miguel Casanova
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France
| | - Céline Vallot
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France
| | - Steven Nedellec
- INSERM UMS 016, SFR Francois Bonamy, MicroPicell Core Facility, Nantes, France; CNRS, UMS 3556, Nantes, France; Université de Nantes, Nantes, France; CHU de Nantes, Nantes, France
| | - Léa Flippe
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Julie Firmin
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Service de Biologie de la Reproduction, Nantes, France
| | - Juan Song
- KU Leuven-University of Leuven, Department of Development and Regeneration, Stem Cell Biology and Embryology Unit, Leuven Stem Cell Institute, Herestraat 49, B-3000, Leuven, Belgium
| | - Eric Charpentier
- INSERM UMR1087, CNRS UMR6291, Université de Nantes l'institut du thorax, Nantes, France
| | - Jenna Lammers
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Service de Biologie de la Reproduction, Nantes, France
| | - Audrey Donnart
- INSERM UMR1087, CNRS UMR6291, Université de Nantes l'institut du thorax, Nantes, France
| | - Nadège Marec
- INSERM, UMS 016, SFR Francois Bonamy, Cytocell Core Facility, Nantes, France; CNRS, UMS 3556, Nantes, France; Université de Nantes, Nantes, France; CHU Nantes, Nantes, France
| | - Wallid Deb
- CHU Nantes, Service de génétique médicale, Nantes, France
| | - Audrey Bihouée
- INSERM UMR1087, CNRS UMR6291, Université de Nantes l'institut du thorax, Nantes, France
| | - Cédric Le Caignec
- CHU Nantes, Service de génétique médicale, Nantes, France.,INSERM, UMR1238, Bone Sarcoma and Remodeling of Calcified Tissue, Nantes, France
| | | | - Richard Redon
- INSERM UMR1087, CNRS UMR6291, Université de Nantes l'institut du thorax, Nantes, France.,CHU Nantes, l'institut du thorax, Nantes, France
| | - Paul Barrière
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Service de Biologie de la Reproduction, Nantes, France
| | - Jérémie Bourdon
- Laboratoire des Sciences du Numérique de Nantes, LS2N, UMR CNRS 6004, Université de Nantes, Nantes, France
| | - Vincent Pasque
- KU Leuven-University of Leuven, Department of Development and Regeneration, Stem Cell Biology and Embryology Unit, Leuven Stem Cell Institute, Herestraat 49, B-3000, Leuven, Belgium
| | - Magali Soumillon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA; Broad Institute, Cambridge, MA 02142, USA.; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA.,Berkeley Lights Inc., 5858 Horton Street, Emeryville, CA, 94608, USA
| | - Tarjei S Mikkelsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA; Broad Institute, Cambridge, MA 02142, USA.; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA.,10x Genomics, 7068 Koll Center Pkwy #401, Pleasanton, CA, 94566, USA
| | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France
| | - Thomas Fréour
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Service de Biologie de la Reproduction, Nantes, France
| | - Laurent David
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France. .,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France. .,INSERM UMS 016, SFR Francois Bonamy, iPSC Core Facility, Nantes, France; CNRS, UMS 3556, Nantes, France; Université de Nantes, Nantes, France; CHU Nantes, Nantes, France.
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12
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Brenan L, Andreev A, Cohen O, Pantel S, Kamburov A, Cacchiarelli D, Persky NS, Zhu C, Bagul M, Goetz EM, Burgin AB, Garraway LA, Getz G, Mikkelsen TS, Piccioni F, Root DE, Johannessen CM. Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants. Cell Rep 2017; 17:1171-1183. [PMID: 27760319 DOI: 10.1016/j.celrep.2016.09.061] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [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: 05/06/2016] [Revised: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022] Open
Abstract
Tumor-specific genomic information has the potential to guide therapeutic strategies and revolutionize patient treatment. Currently, this approach is limited by an abundance of disease-associated mutants whose biological functions and impacts on therapeutic response are uncharacterized. To begin to address this limitation, we functionally characterized nearly all (99.84%) missense mutants of MAPK1/ERK2, an essential effector of oncogenic RAS and RAF. Using this approach, we discovered rare gain- and loss-of-function ERK2 mutants found in human tumors, revealing that, in the context of this assay, mutational frequency alone cannot identify all functionally impactful mutants. Gain-of-function ERK2 mutants induced variable responses to RAF-, MEK-, and ERK-directed therapies, providing a reference for future treatment decisions. Tumor-associated mutations spatially clustered in two ERK2 effector-recruitment domains yet produced mutants with opposite phenotypes. This approach articulates an allele-characterization framework that can be scaled to meet the goals of genome-guided oncology.
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Affiliation(s)
- Lisa Brenan
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ofir Cohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sasha Pantel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Atanas Kamburov
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Davide Cacchiarelli
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicole S Persky
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cong Zhu
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mukta Bagul
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eva M Goetz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alex B Burgin
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - David E Root
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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13
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Kadoki M, Patil A, Thaiss CC, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen TS, Soumillon M, Chevrier N. Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues. Cell 2017; 171:398-413.e21. [PMID: 28942919 DOI: 10.1016/j.cell.2017.08.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [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: 12/09/2016] [Revised: 04/24/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
A fundamental challenge in immunology is to decipher the principles governing immune responses at the whole-organism scale. Here, using a comparative infection model, we observe immune signal propagation within and between organs to obtain a dynamic map of immune processes at the organism level. We uncover two inter-organ mechanisms of protective immunity mediated by soluble and cellular factors. First, analyzing ligand-receptor connectivity across tissues reveals that type I IFNs trigger a whole-body antiviral state, protecting the host within hours after skin vaccination. Second, combining parabiosis, single-cell analyses, and gene knockouts, we uncover a multi-organ web of tissue-resident memory T cells that functionally adapt to their environment to stop viral spread across the organism. These results have implications for manipulating tissue-resident memory T cells through vaccination and open up new lines of inquiry for the analysis of immune responses at the organism level.
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Affiliation(s)
- Motohiko Kadoki
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ashwini Patil
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Cornelius C Thaiss
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Donald J Brooks
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Surya Pandey
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Deeksha Deep
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Alvarez
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ulrich H von Andrian
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tarjei S Mikkelsen
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Magali Soumillon
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Chevrier
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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14
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Pashos EE, Park Y, Wang X, Raghavan A, Yang W, Abbey D, Peters DT, Arbelaez J, Hernandez M, Kuperwasser N, Li W, Lian Z, Liu Y, Lv W, Lytle-Gabbin SL, Marchadier DH, Rogov P, Shi J, Slovik KJ, Stylianou IM, Wang L, Yan R, Zhang X, Kathiresan S, Duncan SA, Mikkelsen TS, Morrisey EE, Rader DJ, Brown CD, Musunuru K. Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. Cell Stem Cell 2017; 20:558-570.e10. [PMID: 28388432 DOI: 10.1016/j.stem.2017.03.017] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [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: 01/13/2017] [Revised: 03/15/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022]
Abstract
Genome-wide association studies have struggled to identify functional genes and variants underlying complex phenotypes. We recruited a multi-ethnic cohort of healthy volunteers (n = 91) and used their tissue to generate induced pluripotent stem cells (iPSCs) and hepatocyte-like cells (HLCs) for genome-wide mapping of expression quantitative trait loci (eQTLs) and allele-specific expression (ASE). We identified many eQTL genes (eGenes) not observed in the comparably sized Genotype-Tissue Expression project's human liver cohort (n = 96). Focusing on blood lipid-associated loci, we performed massively parallel reporter assays to screen candidate functional variants and used genome-edited stem cells, CRISPR interference, and mouse modeling to establish rs2277862-CPNE1, rs10889356-DOCK7, rs10889356-ANGPTL3, and rs10872142-FRK as functional SNP-gene sets. We demonstrated HLC eGenes CPNE1, VKORC1, UBE2L3, and ANGPTL3 and HLC ASE gene ACAA2 to be lipid-functional genes in mouse models. These findings endorse an iPSC-based experimental framework to discover functional variants and genes contributing to complex human traits.
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Affiliation(s)
- Evanthia E Pashos
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - YoSon Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Wenli Yang
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deepti Abbey
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Juan Arbelaez
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mayda Hernandez
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Wenjun Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhaorui Lian
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ying Liu
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenjian Lv
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stacey L Lytle-Gabbin
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dawn H Marchadier
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Jianting Shi
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine J Slovik
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ioannis M Stylianou
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Wang
- Broad Institute, Cambridge, MA 02142, USA
| | - Ruilan Yan
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sekar Kathiresan
- Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | | | - Edward E Morrisey
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kiran Musunuru
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R, Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH, Kuo CJ. Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell 2017; 21:78-90.e6. [PMID: 28686870 PMCID: PMC5642297 DOI: 10.1016/j.stem.2017.06.014] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [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: 09/07/2016] [Revised: 04/17/2017] [Accepted: 06/20/2017] [Indexed: 12/22/2022]
Abstract
Several cell populations have been reported to possess intestinal stem cell (ISC) activity during homeostasis and injury-induced regeneration. Here, we explored inter-relationships between putative mouse ISC populations by comparative RNA-sequencing (RNA-seq). The transcriptomes of multiple cycling ISC populations closely resembled Lgr5+ ISCs, the most well-defined ISC pool, but Bmi1-GFP+ cells were distinct and enriched for enteroendocrine (EE) markers, including Prox1. Prox1-GFP+ cells exhibited sustained clonogenic growth in vitro, and lineage-tracing of Prox1+ cells revealed long-lived clones during homeostasis and after radiation-induced injury in vivo. Single-cell mRNA-seq revealed two subsets of Prox1-GFP+ cells, one of which resembled mature EE cells while the other displayed low-level EE gene expression but co-expressed tuft cell markers, Lgr5 and Ascl2, reminiscent of label-retaining secretory progenitors. Our data suggest that the EE lineage, including mature EE cells, comprises a reservoir of homeostatic and injury-inducible ISCs, extending our understanding of cellular plasticity and stemness.
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Affiliation(s)
- Kelley S Yan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Benedict Anchang
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher S Probert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn A Larkin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paige S Davies
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Zhuan-Fen Cheng
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Arnold Han
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Columbia Center for Translational Immunology, Department of Medicine, Division of Digestive and Liver Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Kelly Roelf
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruben I Calderon
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Esther Cynn
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaoyi Hu
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Komal Mandleywala
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Julie Wilhelmy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sue M Grimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David C Corney
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | | | | - Fengchao Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Nicholas R Smith
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Parthasarathy Chandrakesan
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Randal May
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Mary Ann S Chrissy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajan Jain
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Joyce C Niland
- Department of Diabetes and Cancer Discovery Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Young-Kwon Hong
- Departments of Surgery and of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jill Carrington
- National Institutes of Health, Division of Digestive Diseases and Nutrition, NIDDK, Bethesda, MD 20892, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jonathan Epstein
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Courtney W Houchen
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - John P Lynch
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin G Martin
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children's Hospital and the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvia K Plevritis
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hanlee P Ji
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Susan J Henning
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa H Wong
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Calvin J Kuo
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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16
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Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res 2017; 45:1553-1565. [PMID: 28007941 PMCID: PMC5388403 DOI: 10.1093/nar/gkw1226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 10/13/2016] [Accepted: 11/22/2016] [Indexed: 11/14/2022] Open
Abstract
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.
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Affiliation(s)
- Lauren B A Woodruff
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas E Gorochowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Roehner
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Tarjei S Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - D Benjamin Gordon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Nicol
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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17
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Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A 2017; 114:E1291-E1300. [PMID: 28137873 PMCID: PMC5321001 DOI: 10.1073/pnas.1621150114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [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] [Indexed: 12/21/2022] Open
Abstract
Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.
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Affiliation(s)
- Sharon R Grossman
- Broad Institute, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Health Sciences and Technology, Harvard Medical School, Boston, MA 02215
| | | | - Li Wang
- Broad Institute, Cambridge, MA 02142
| | - Jesse Engreitz
- Broad Institute, Cambridge, MA 02142
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Ryan Tewhey
- Broad Institute, Cambridge, MA 02142
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Alina Isakova
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bradley E Bernstein
- Broad Institute, Cambridge, MA 02142
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tarjei S Mikkelsen
- Broad Institute, Cambridge, MA 02142
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - Eric S Lander
- Broad Institute, Cambridge, MA 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215
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18
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Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res 2017; 45:1567-1568. [PMID: 28100691 PMCID: PMC5388430 DOI: 10.1093/nar/gkx032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 11/12/2022] Open
Affiliation(s)
- Lauren B A Woodruff
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas E Gorochowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Roehner
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Tarjei S Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - D Benjamin Gordon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Nicol
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH. Massively parallel digital transcriptional profiling of single cells. Nat Commun 2017; 8:14049. [PMID: 28091601 PMCID: PMC5241818 DOI: 10.1038/ncomms14049] [Citation(s) in RCA: 3185] [Impact Index Per Article: 455.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023] Open
Abstract
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
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Affiliation(s)
| | | | | | - Paul Ryvkin
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Ryan Wilson
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Junjie Zhu
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Joe Shuga
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Jason G Underwood
- 10x Genomics Inc., Pleasanton, California, 94566, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | - Paul W Wyatt
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Kevin D Ness
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Lan W Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Christopher McFarland
- Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory, Seattle, Washington 98109, USA
| | - Keith R Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emily A Stevens
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | | | | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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20
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Ulirsch JC, Nandakumar SK, Wang L, Giani FC, Zhang X, Rogov P, Melnikov A, McDonel P, Do R, Mikkelsen TS, Sankaran VG. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Cell 2016; 165:1530-1545. [PMID: 27259154 DOI: 10.1016/j.cell.2016.04.048] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/12/2015] [Accepted: 04/12/2016] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Felix C Giani
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Xiaolan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Rogov
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Patrick McDonel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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21
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O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre I, Mikkelsen TS, Xavier RJ. Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing. Cell Syst 2016; 2:323-334. [PMID: 27211859 DOI: 10.1016/j.cels.2016.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/12/2016] [Accepted: 04/15/2016] [Indexed: 12/19/2022]
Abstract
Reporter gene assays are a venerable tool for studying signaling pathways, but they lack the throughput and complexity necessary to contribute to a systems-level understanding of endogenous signaling networks. We present a parallel reporter assay, transcription factor activity sequencing (TF-seq), built on synthetic DNA enhancer elements, which enables parallel measurements in primary cells of the transcriptome and transcription factor activity from more than 40 signaling pathways. Using TF-seq in Myd88(-/-) macrophages, we captured dynamic pathway activity changes underpinning the global transcriptional changes of the innate immune response. We also applied TF-seq to investigate small molecule mechanisms of action and find a role for NF-κB activation and coordination of the STAT1 response in the macrophage reaction to the anti-inflammatory natural product halofuginone. Simultaneous TF-seq and global gene expression profiling represent an integrative approach for gaining mechanistic insight into pathway activity and transcriptional changes that result from genetic and small molecule perturbations.
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Affiliation(s)
- Daniel J O'Connell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Raivo Kolde
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matthew Sooknah
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel B Graham
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Thomas B Sundberg
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142, USA
| | - Isabel Latorre
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | | | - Ramnik J Xavier
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA
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22
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Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell 2015; 162:412-424. [PMID: 26186193 DOI: 10.1016/j.cell.2015.06.016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/18/2015] [Accepted: 06/01/2015] [Indexed: 11/25/2022]
Abstract
Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here, we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered re-activation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. PAPERCLIP.
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Affiliation(s)
- Davide Cacchiarelli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J Ziller
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Magali Soumillon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Marcella Cesana
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Boston Children's Hospital and Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Julie Donaghey
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Sutheera Ratanasirintrawoot
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Boston Children's Hospital and Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | | | - Shannan J Ho Sui
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zhaoting Wu
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Boston Children's Hospital and Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Casey A Gifford
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - George Q Daley
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Boston Children's Hospital and Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Tarjei S Mikkelsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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23
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Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol 2015. [PMID: 25403361 PMCID: PMC4262991 DOI: 10.1186/s13059-014-0519-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.
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24
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Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol 2015; 15:519. [PMID: 25403361 DOI: 10.1186/preaccept-1698056557139770] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Indexed: 12/20/2022] Open
Abstract
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.
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25
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Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA. The regulatory landscape of osteogenic differentiation. Stem Cells 2015; 32:2780-93. [PMID: 24898411 DOI: 10.1002/stem.1759] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [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: 11/18/2013] [Accepted: 04/20/2014] [Indexed: 01/08/2023]
Abstract
Differentiation of osteoblasts from mesenchymal stem cells (MSCs) is an integral part of bone development and homeostasis, and may when improperly regulated cause disease such as bone cancer or osteoporosis. Using unbiased high-throughput methods we here characterize the landscape of global changes in gene expression, histone modifications, and DNA methylation upon differentiation of human MSCs to the osteogenic lineage. Furthermore, we provide a first genome-wide characterization of DNA binding sites of the bone master regulatory transcription factor Runt-related transcription factor 2 (RUNX2) in human osteoblasts, revealing target genes associated with regulation of proliferation, migration, apoptosis, and with a significant overlap with p53 regulated genes. These findings expand on emerging evidence of a role for RUNX2 in cancer, including bone metastases, and the p53 regulatory network. We further demonstrate that RUNX2 binds to distant regulatory elements, promoters, and with high frequency to gene 3' ends. Finally, we identify TEAD2 and GTF2I as novel regulators of osteogenesis.
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Affiliation(s)
- Anne-Mari Håkelien
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital
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26
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Herlofsen SR, Høiby T, Cacchiarelli D, Zhang X, Mikkelsen TS, Brinchmann JE. Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells. Stem Cells 2015; 32:1629-35. [PMID: 24449344 DOI: 10.1002/stem.1642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 10/16/2013] [Accepted: 12/11/2013] [Indexed: 01/05/2023]
Abstract
The transcription factor SOX9 is believed to be the master regulator of chondrogenesis. SOX8 is another SOX group E transcription factor with a high degree of homology to SOX9. Here, we demonstrate that SOX8 mRNA levels decrease during in vitro dedifferentiation of human articular chondrocytes and increase during chondrogenic differentiation of mesenchymal stromal cells. Knockdown of SOX9 reduced the expression of SOX8, COL2A1, and a range of other chondrogenic molecules. SOX8 knockdown reduced the expression of a large number of overlapping chondrogenic molecules, but not SOX9. Neither siSOX9 nor siSOX8 altered expression of the hypertrophic marker gene COL10A1. siSOX9, but not siSOX8 led to upregulation of hypertrophy associated genes MMP13 and ALPL. Transfection of synthetic SOX5, 6, and 9 mRNA trio upregulated SOX8, COL2A1, and ACAN, but not COL10A1 mRNA. Replacement of synthetic SOX9 by SOX8 in the SOX trio showed similar but lower chondrogenic effect. We conclude that SOX8 expression is regulated by SOX9, and that both together with SOX5 and SOX6 are required as a SOX quartet for transcription of COL2A1 and a large number of other chondrogenic molecules. Neither SOX8 nor SOX9 affect COL10A1 expression, but SOX9 inhibits chondrocyte hypertrophy through inhibition of MMP13 and ALPL expression.
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Affiliation(s)
- Sarah R Herlofsen
- Norwegian Center for Stem Cell Research and Institute of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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27
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Ulirsch JC, Lacy JN, An X, Mohandas N, Mikkelsen TS, Sankaran VG. Altered chromatin occupancy of master regulators underlies evolutionary divergence in the transcriptional landscape of erythroid differentiation. PLoS Genet 2014; 10:e1004890. [PMID: 25521328 PMCID: PMC4270484 DOI: 10.1371/journal.pgen.1004890] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 08/08/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary proerythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (∼25% for GATA1, TAL1, and NFE2) but were more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression that is sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites associates with changes in the underlying chromatin structure, driving transcriptional divergence. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the β-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis. The process whereby blood progenitor cells differentiate into red blood cells, known as erythropoiesis, is very similar between mice and humans. Yet, while studies of this process in mouse have substantially improved our knowledge of human erythropoiesis, recent work has shown a significant divergence in global gene expression across species, suggesting that extrapolation from mouse models to human is not always straightforward. In order to better understand these differences, we have performed a comparative epigenomic analysis of six histone modifications and four master transcription factors. By globally comparing chromatin structure across primary cells and model cell lines in both species, we discovered that while chromatin structure is well conserved at orthologous promoters, subtle changes are predictive of species-specific gene expression. Furthermore, we discovered that the genomic localizations of master transcription factors are poorly conserved, and species-specific losses or gains are associated with changes to the underlying chromatin structure and concomitant gene expression. By using our comparative epigenomics framework, we identified a putative human-specific cis-regulatory module that drives expression of human, but not mouse, GDF15, a gene implicated in iron homeostasis. Our results provide a resource to aid researchers in interpreting genetic and epigenetic differences between species.
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Affiliation(s)
- Jacob C. Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica N. Lacy
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Xiuli An
- New York Blood Center, New York, New York, United States of America
| | - Narla Mohandas
- New York Blood Center, New York, New York, United States of America
| | - Tarjei S. Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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28
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Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED. Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. Nat Cell Biol 2014; 17:44-56. [PMID: 25503565 PMCID: PMC4281178 DOI: 10.1038/ncb3080] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [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: 08/06/2014] [Accepted: 11/06/2014] [Indexed: 02/06/2023]
Abstract
Insulin resistance is a sine qua non of Type 2 diabetes (T2D) and a frequent complication of multiple clinical conditions, including obesity, aging, and steroid use, among others. How such a panoply of insults can result in a common phenotype is incompletely understood. Furthermore, very little is known about the transcriptional and epigenetic basis of this disorder, despite evidence that such pathways are likely to play a fundamental role. Here, we compare cell autonomous models of insulin resistance induced by the cytokine tumor necrosis factor-α (TNF) or by the steroid dexamethasone (Dex) to construct detailed transcriptional and epigenomic maps associated with cellular insulin resistance. These data predict that the glucocorticoid receptor and vitamin D receptor are common mediators of insulin resistance, which we validate using gain- and loss-of-function studies. These studies define a common transcriptional and epigenomic signature in cellular insulin resistance enabling the identification of pathogenic mechanisms.
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Affiliation(s)
- Sona Kang
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Linus T Tsai
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Yiming Zhou
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Adam Evertts
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Su Xu
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Michael J Griffin
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Robbyn Issner
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | | | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | - Evan D Rosen
- 1] Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA [2] Broad Institute, Cambridge, Massachusetts 02142, USA [3] Harvard Medical School, Boston, Massachusetts 02215, USA
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29
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Abstract
The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. The potential throughput of this assay has, however, been limited by the need to individually clone and assay the activity of each sequence on interest using protein fluorescence or enzymatic activity as a proxy for regulatory activity. Advances in high-throughput DNA synthesis and sequencing technologies have recently made it possible to overcome these limitations by multiplexing the construction and interrogation of large libraries of reporter constructs. This protocol describes implementation of a Massively Parallel Reporter Assay (MPRA) that allows direct comparison of hundreds of thousands of putative regulatory sequences in a single cell culture dish.
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30
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Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. Cell Rep 2014; 8:284-96. [PMID: 24981863 DOI: 10.1016/j.celrep.2014.05.048] [Citation(s) in RCA: 856] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/07/2014] [Accepted: 05/27/2014] [Indexed: 12/31/2022] Open
Abstract
N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing "basal" degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.
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Affiliation(s)
| | | | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tim Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karolina Maciag
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Graduate Program in Immunology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - G Guy Bushkin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Philipp Mertins
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Naomi Habib
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Davide Cacchiarelli
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | - Michael E Pacold
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
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31
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Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS. Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes. Nucleic Acids Res 2014; 42:e112. [PMID: 24914046 PMCID: PMC4132701 DOI: 10.1093/nar/gku511] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [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] [Indexed: 12/24/2022] Open
Abstract
Deep mutational scanning has emerged as a promising tool for mapping sequence-activity relationships in proteins, ribonucleic acid and deoxyribonucleic acid. In this approach, diverse variants of a sequence of interest are first ranked according to their activities in a relevant assay, and this ranking is then used to infer the shape of the fitness landscape around the wild-type sequence. Little is currently known, however, about the degree to which such fitness landscapes are dependent on the specific assay conditions from which they are inferred. To explore this issue, we performed comprehensive single-substitution mutational scanning of APH(3')II, a Tn5 transposon-derived kinase that confers resistance to aminoglycoside antibiotics, in Escherichia coli under selection with each of six structurally diverse antibiotics at a range of inhibitory concentrations. We found that the resulting local fitness landscapes showed significant dependence on both antibiotic structure and concentration, and that this dependence can be exploited to guide protein engineering. Specifically, we found that differential analysis of fitness landscapes allowed us to generate synthetic APH(3')II variants with orthogonal substrate specificities.
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Affiliation(s)
| | - Peter Rogov
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
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32
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Jakobsen RB, Østrup E, Zhang X, Mikkelsen TS, Brinchmann JE. Analysis of the effects of five factors relevant to in vitro chondrogenesis of human mesenchymal stem cells using factorial design and high throughput mRNA-profiling. PLoS One 2014; 9:e96615. [PMID: 24816923 PMCID: PMC4015996 DOI: 10.1371/journal.pone.0096615] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/09/2014] [Indexed: 02/07/2023] Open
Abstract
The in vitro process of chondrogenic differentiation of mesenchymal stem cells for tissue engineering has been shown to require three-dimensional culture along with the addition of differentiation factors to the culture medium. In general, this leads to a phenotype lacking some of the cardinal features of native articular chondrocytes and their extracellular matrix. The factors used vary, but regularly include members of the transforming growth factor β superfamily and dexamethasone, sometimes in conjunction with fibroblast growth factor 2 and insulin-like growth factor 1, however the use of soluble factors to induce chondrogenesis has largely been studied on a single factor basis. In the present study we combined a factorial quality-by-design experiment with high-throughput mRNA profiling of a customized chondrogenesis related gene set as a tool to study in vitro chondrogenesis of human bone marrow derived mesenchymal stem cells in alginate. 48 different conditions of transforming growth factor β 1, 2 and 3, bone morphogenetic protein 2, 4 and 6, dexamethasone, insulin-like growth factor 1, fibroblast growth factor 2 and cell seeding density were included in the experiment. The analysis revealed that the best of the tested differentiation cocktails included transforming growth factor β 1 and dexamethasone. Dexamethasone acted in synergy with transforming growth factor β 1 by increasing many chondrogenic markers while directly downregulating expression of the pro-osteogenic gene osteocalcin. However, all factors beneficial to the expression of desirable hyaline cartilage markers also induced undesirable molecules, indicating that perfect chondrogenic differentiation is not achievable with the current differentiation protocols.
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Affiliation(s)
- Rune B. Jakobsen
- Norwegian Center for Stem Cell Research, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Biochemistry, Institute of Basic Medical Sciences, The Medical Faculty, University of Oslo, Oslo, Norway
| | - Esben Østrup
- Norwegian Center for Stem Cell Research, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Biomaterials, Institute of Clinical Dentistry, University of Oslo, Oslo, Norway
| | - Xiaolan Zhang
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Tarjei S. Mikkelsen
- Broad Institute, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jan E. Brinchmann
- Norwegian Center for Stem Cell Research, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Biochemistry, Institute of Basic Medical Sciences, The Medical Faculty, University of Oslo, Oslo, Norway
- Institute of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- * E-mail:
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33
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Jiang L, Wallerman O, Younis S, Rubin CJ, Gilbert ER, Sundström E, Ghazal A, Zhang X, Wang L, Mikkelsen TS, Andersson G, Andersson L. ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells. PLoS One 2014; 9:e94187. [PMID: 24714595 PMCID: PMC3979763 DOI: 10.1371/journal.pone.0094187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 03/12/2014] [Indexed: 01/22/2023] Open
Abstract
ZBED6 is a recently discovered transcription factor, unique to placental mammals, that has evolved from a domesticated DNA transposon. It acts as a repressor at the IGF2 locus. Here we show that ZBED6 acts as a transcriptional modulator in mouse myoblast cells, where more than 700 genes were differentially expressed after Zbed6-silencing. The most significantly enriched GO term was muscle protein and contractile fiber, which was consistent with increased myotube formation. Twenty small nucleolar RNAs all showed increased expression after Zbed6-silencing. The co-localization of histone marks and ZBED6 binding sites and the effect of Zbed6-silencing on distribution of histone marks was evaluated by ChIP-seq analysis. There was a strong association between ZBED6 binding sites and the H3K4me3, H3K4me2 and H3K27ac modifications, which are usually found at active promoters, but no association with the repressive mark H3K27me3. Zbed6-silencing led to increased enrichment of active marks at myogenic genes, in agreement with the RNA-seq findings. We propose that ZBED6 preferentially binds to active promoters and modulates transcriptional activity without recruiting repressive histone modifications.
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Affiliation(s)
- Lin Jiang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shady Younis
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Production, Ain Shams University, Shoubra El-Kheima, Cairo, Egypt
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elizabeth R. Gilbert
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elisabeth Sundström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Awaisa Ghazal
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xiaolan Zhang
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Li Wang
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Tarjei S. Mikkelsen
- Broad Institute, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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34
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Karlsen TA, Jakobsen RB, Mikkelsen TS, Brinchmann JE. microRNA-140 targets RALA and regulates chondrogenic differentiation of human mesenchymal stem cells by translational enhancement of SOX9 and ACAN. Stem Cells Dev 2014; 23:290-304. [PMID: 24063364 DOI: 10.1089/scd.2013.0209] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lesions of articular cartilage do not heal spontaneously. One treatment strategy would be to make cartilage in the laboratory by directed chondrogenic differentiation of mesenchymal stem cells (MSCs). To promote our understanding of the molecular control of chondrogenesis, we have compared the changes in microRNAs (miRNAs) during in vitro chondrogenesis of MSCs with those observed in uncultured and dedifferentiated articular chondrocytes (ACs). Several miRNAs showed a reciprocal relationship during the differentiation of MSCs and dedifferentiation of ACs. miR-140-5p and miR-140-3p changed the most during in vitro chondrogenesis, they were the miRNAs most highly expressed in tissue-engineered chondrocytes, and they were also among the miRNAs most highly expressed in uncultured ACs. There was a 57% overlap for the 100 most highly expressed miRNAs in differentiated MSCs and uncultured ACs, but for other miRNAs, the expression pattern was quite different. We transiently and stably inhibited and overexpressed miR-140-5p and miR-140-3p in differentiating MSCs and dedifferentiating ACs, respectively, to describe global effects and identify and validate new targets. Surprisingly, SOX9 and aggrecan proteins were found to be downregulated in anti-miR-140 transduced differentiating MSCs despite unchanged mRNA levels. This suggests that miR-140 stimulates in vitro chondrogenesis by the upregulation of these molecules at the protein level. RALA, a small GTPase, was identified as a miR-140 target and knockdown experiments showed that RALA regulated SOX9 at the protein level. These observations shed new light on the effect of miR-140 for chondrogenesis in vitro and in vivo.
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Affiliation(s)
- Tommy A Karlsen
- 1 Norwegian Center for Stem Cell Research, Oslo University Hospital , Rikshospitalet, Oslo, Norway
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35
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Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 2013; 155:1409-21. [PMID: 24269006 DOI: 10.1016/j.cell.2013.10.047] [Citation(s) in RCA: 474] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 01/12/2023]
Abstract
N(6)-methyladenosine (m(6)A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m(6)A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of eight methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time course and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminate a conserved, dynamically regulated methylation program in yeast meiosis and provide an important resource for studying the function of this epitranscriptomic modification.
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36
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Griffin MJ, Zhou Y, Kang S, Zhang X, Mikkelsen TS, Rosen ED. Early B-cell factor-1 (EBF1) is a key regulator of metabolic and inflammatory signaling pathways in mature adipocytes. J Biol Chem 2013; 288:35925-39. [PMID: 24174531 DOI: 10.1074/jbc.m113.491936] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
EBF1 plays a crucial role in early adipogenesis; however, despite high expression in mature adipocytes, its function in these cells is currently unknown. To identify direct and indirect EBF1 targets in fat, we undertook a combination of transcriptional profiling of EBF1-deficient adipocytes and genome-wide EBF1 location analysis. Our results indicate that many components of metabolic and inflammatory pathways are positively and directly regulated by EBF1, including PI3K/AKT, MAPK, and STAT1 signaling. Accordingly, we observed significant reduction of multiple signaling events in EBF1 knockdown cells as well as a reduction in insulin-stimulated glucose uptake and lipogenesis. Inflammatory signaling, gene expression, and secretion of inflammatory cytokines were also significantly affected by loss of EBF1 in adipocytes, although ChIP-sequencing results suggest that these actions are indirect. We also found that EBF1 occupies some 35,000 sites in adipocytes, most of which occur in enhancers. Significantly, comparison with three other published EBF1 ChIP-sequencing data sets in B-cells reveals both gene- and cell type-specific patterns of EBF1 binding. These results advance our understanding of the transcriptional mechanisms regulating signaling pathways in mature fat cells and indicate that EBF1 functions as a key integrator of signal transduction, inflammation, and metabolism.
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Affiliation(s)
- Michael J Griffin
- From the Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215
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37
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Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 2013; 23:800-11. [PMID: 23512712 PMCID: PMC3638136 DOI: 10.1101/gr.144899.112] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [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: 06/26/2012] [Accepted: 03/14/2013] [Indexed: 01/06/2023]
Abstract
Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale. Here, we use a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145-bp DNA segments centered on evolutionarily conserved regulatory motif instances within enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2104 wild-type sequences and 3314 engineered enhancer variants containing targeted motif disruptions, each using 10 barcode tags and two replicates. The resulting data strongly confirm the enhancer activity and cell-type specificity of enhancer chromatin states, the ability of 145-bp segments to recapitulate both, the necessary role of regulatory motifs in enhancer function, and the complementary roles of activator and repressor motifs. We find statistically robust evidence that (1) disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are predictive of enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually inactive. Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression.
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Affiliation(s)
- Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jason Ernst
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | | | - Peter Rogov
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Li Wang
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Xiaolan Zhang
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jessica Alston
- Broad Institute, Cambridge, Massachusetts 02142, USA
- Program in Biological and Biomedical Sciences and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tarjei S. Mikkelsen
- Broad Institute, Cambridge, Massachusetts 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute, Cambridge, Massachusetts 02142, USA
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38
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Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE. Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells. BMC Genomics 2013; 14:105. [PMID: 23414147 PMCID: PMC3620534 DOI: 10.1186/1471-2164-14-105] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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: 12/03/2012] [Accepted: 02/12/2013] [Indexed: 01/01/2023] Open
Abstract
Background For safe clinical application of engineered cartilage made from mesenchymal stem cells (MSCs), molecular mechanisms for chondrogenic differentiation must be known in detail. Changes in gene expression and extracellular matrix synthesis have been extensively studied, but the epigenomic modifications underlying these changes have not been described. To this end we performed whole-genome chromatin immunoprecipitation and deep sequencing to quantify six histone modifications, reduced representation bisulphite sequencing to quantify DNA methylation and mRNA microarrays to quantify gene expression before and after 7 days of chondrogenic differentiation of MSCs in an alginate scaffold. To add to the clinical relevance of our observations, the study is based on primary bone marrow-derived MSCs from four donors, allowing us to investigate inter-individual variations. Results We see two levels of relationship between epigenetic marking and gene expression. First, a large number of genes ontogenetically linked to MSC properties and the musculoskeletal system are epigenetically prepatterned by moderate changes in H3K4me3 and H3K9ac near transcription start sites. Most of these genes remain transcriptionally unaltered. Second, transcriptionally upregulated genes, more closely associated with chondrogenesis, are marked by H3K36me3 in gene bodies, highly increased H3K4me3 and H3K9ac on promoters and 5' end of genes, and increased H3K27ac and H3K4me1 marking in at least one enhancer region per upregulated gene. Within the 7-day time frame, changes in promoter DNA methylation do not correlate significantly with changes in gene expression. Inter-donor variability analysis shows high level of similarity between the donors for this data set. Conclusions Histone modifications, rather than DNA methylation, provide the primary epigenetic control of early differentiation of MSCs towards the chondrogenic lineage.
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Affiliation(s)
- Sarah R Herlofsen
- Institute of Immunology and Norwegian Center for Stem Cell Research, Oslo University Hospital Rikshospitalet, Oslo 0424, Norway.
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Lancaster CS, Bruun GH, Peer CJ, Mikkelsen TS, Corydon TJ, Gibson AA, Hu S, Orwick SJ, Mathijssen RHJ, Figg WD, Baker SD, Sparreboom A. OATP1B1 polymorphism as a determinant of erythromycin disposition. Clin Pharmacol Ther 2012; 92:642-50. [PMID: 22990751 DOI: 10.1038/clpt.2012.106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previous studies have demonstrated that the pharmacokinetic profile of erythromycin, a probe for CYP3A4 activity, is affected by inhibitors or inducers of hepatic solute carriers. We hypothesized that these interactions are mediated by OATP1B1 (gene symbol, SLCO1B1), a polypeptide expressed on the basolateral surface of hepatocytes. Using stably transfected Flp-In T-Rex293 cells, erythromycin was found to be a substrate for OATP1B1*1A (wild type) with a Michaelis-Menten constant of ~13 µmol/l, and that its transport was reduced by ~50% in cells expressing OATP1B1*5 (V174A). Deficiency of the ortholog transporter Oatp1b2 in mice was associated with a 52% decrease in the metabolic rate of erythromycin (P = 0.000043). In line with these observations, in humans the c.521T>C variant in SLCO1B1 (rs4149056), encoding OATP1B1*5, was associated with a decline in erythromycin metabolism (P = 0.0072). These results suggest that impairment of OATP1B1 function can alter erythromycin metabolism, independent of changes in CYP3A4 activity.
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Affiliation(s)
- C S Lancaster
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
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40
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Das R, Anderson N, Koran MI, Weidman JR, Mikkelsen TS, Kamal M, Murphy SK, Linblad-Toh K, Greally JM, Jirtle RL. Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica. BMC Genomics 2012; 13:394. [PMID: 22899817 PMCID: PMC3507640 DOI: 10.1186/1471-2164-13-394] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [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: 04/18/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin specific monoallelic gene expression. It is postulated to have evolved in placental mammals to modulate intrauterine resource allocation to the offspring. In this study, we determined the imprint status of metatherian orthologues of eutherian imprinted genes. RESULTS L3MBTL and HTR2A were shown to be imprinted in Monodelphis domestica (the gray short-tailed opossum). MEST expressed a monoallelic and a biallelic transcript, as in eutherians. In contrast, IMPACT, COPG2, and PLAGL1 were not imprinted in the opossum. Differentially methylated regions (DMRs) involved in regulating imprinting in eutherians were not found at any of the new imprinted loci in the opossum. Interestingly, a novel DMR was identified in intron 11 of the imprinted IGF2R gene, but this was not conserved in eutherians. The promoter regions of the imprinted genes in the opossum were enriched for the activating histone modification H3 Lysine 4 dimethylation. CONCLUSIONS The phenomenon of genomic imprinting is conserved in Therians, but the marked difference in the number and location of imprinted genes and DMRs between metatherians and eutherians indicates that imprinting is not fully conserved between the two Therian infra-classes. The identification of a novel DMR at a non-conserved location as well as the first demonstration of histone modifications at imprinted loci in the opossum suggest that genomic imprinting may have evolved in a common ancestor of these two Therian infra-classes with subsequent divergence of regulatory mechanisms in the two lineages.
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Affiliation(s)
- Radhika Das
- Department of Radiation Oncology, Duke University Medical Center, Box 3433, Durham, NC 27710, USA
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41
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Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, Rosen ED. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010; 143:156-69. [PMID: 20887899 DOI: 10.1016/j.cell.2010.09.006] [Citation(s) in RCA: 406] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 07/13/2010] [Accepted: 08/27/2010] [Indexed: 11/29/2022]
Abstract
We report the generation and comparative analysis of genome-wide chromatin state maps, PPARγ and CTCF localization maps, and gene expression profiles from murine and human models of adipogenesis. The data provide high-resolution views of chromatin remodeling during cellular differentiation and allow identification of thousands of putative preadipocyte- and adipocyte-specific cis-regulatory elements based on dynamic chromatin signatures. We find that the specific locations of most such elements differ between the two models, including at orthologous loci with similar expression patterns. Based on sequence analysis and reporter assays, we show that these differences are determined, in part, by evolutionary turnover of transcription factor motifs in the genome sequences and that this turnover may be facilitated by the presence of multiple distal regulatory elements at adipogenesis-dependent loci. We also utilize the close relationship between open chromatin marks and transcription factor motifs to identify and validate PLZF and SRF as regulators of adipogenesis.
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42
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Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 2010; 7:133-6. [PMID: 20062050 PMCID: PMC2860480 DOI: 10.1038/nmeth.1414] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [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: 11/17/2009] [Accepted: 12/09/2009] [Indexed: 12/25/2022]
Abstract
Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples.
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Affiliation(s)
- Hongcang Gu
- Broad Institute, Cambridge, Massachusetts, USA
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43
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Markljung E, Jiang L, Jaffe JD, Mikkelsen TS, Wallerman O, Larhammar M, Zhang X, Wang L, Saenz-Vash V, Gnirke A, Lindroth AM, Barrés R, Yan J, Strömberg S, De S, Pontén F, Lander ES, Carr SA, Zierath JR, Kullander K, Wadelius C, Lindblad-Toh K, Andersson G, Hjälm G, Andersson L. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 2009; 7:e1000256. [PMID: 20016685 PMCID: PMC2780926 DOI: 10.1371/journal.pbio.1000256] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [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: 06/24/2009] [Accepted: 11/05/2009] [Indexed: 01/09/2023] Open
Abstract
This study identifies a previously uncharacterized protein, encoded by a domesticated DNA transposon, called ZBED6 that regulates the expression of the insulin-like growth factor 2 (IGF2) gene, and possibly numerous others, in all placental mammals including human. A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth. The molecular identification of genes and mutations affecting complex traits and disorders has proven to be very challenging in humans as well as in model organisms. These so-called quantitative traits arise from interactions between two or more genes and their environment, and can be mapped to their underlying genes via closely linked stretches of DNA called quantitative trait loci (QTL). Previously, we identified a single nucleotide substitution in a noncoding region of the insulin-like growth factor 2 gene (IGF2) in pigs that is underlying a major QTL affecting muscle growth, heart size, and fat deposition. The mutation disrupts interaction with an unknown nuclear protein acting as a repressor of IGF2 transcription. In the present study, we have isolated a zinc finger protein of unknown function and show that it regulates the expression of IGF2. The protein, which we named ZBED6, is encoded by a domesticated DNA transposon that was inserted into the genome prior to the radiation of placental mammals. ZBED6 is exclusive to placental mammals and highly conserved among species. Our functional characterization of ZBED6 shows that it has a broad tissue distribution and may affect the expression of thousands of other genes, besides IGF2, that control fundamental biological processes. We postulate that ZBED6 is an important transcription factor affecting development, cell proliferation, and growth in placental mammals.
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Affiliation(s)
- Ellen Markljung
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lin Jiang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jacob D. Jaffe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tarjei S. Mikkelsen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ola Wallerman
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Xiaolan Zhang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Li Wang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Veronica Saenz-Vash
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andreas Gnirke
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anders M. Lindroth
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Romain Barrés
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Jie Yan
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Sara Strömberg
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sachinandan De
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric S. Lander
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Steven A. Carr
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Juleen R. Zierath
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Klas Kullander
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Hjälm
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7. [PMID: 19182780 DOI: 10.1038/nature07672] [Citation(s) in RCA: 3195] [Impact Index Per Article: 213.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 11/25/2008] [Indexed: 12/19/2022]
Abstract
There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified approximately 1,600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation. We also developed a functional genomics approach that assigns putative functions to each lincRNA, demonstrating a diverse range of roles for lincRNAs in processes from embryonic stem cell pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFkappaB, Sox2, Oct4 (also known as Pou5f1) and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.
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Affiliation(s)
- Mitchell Guttman
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 2008; 4:e1000242. [PMID: 18974828 PMCID: PMC2567431 DOI: 10.1371/journal.pgen.1000242] [Citation(s) in RCA: 776] [Impact Index Per Article: 48.5] [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: 07/31/2008] [Accepted: 09/29/2008] [Indexed: 01/04/2023] Open
Abstract
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes—the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells. Polycomb-group (PcG) proteins play essential roles in the epigenetic regulation of gene expression during development. PcG proteins are repressors that catalyze lysine 27 tri-methylation on histone H3. They are antagonized by trithorax-group proteins that catalyze lysine 4 tri-methylation. Recent studies of ES cells revealed a novel chromatin pattern consisting of overlapping lysine 27 and lysine 4 tri-methylation. Genomic regions with these opposing modifications were termed “bivalent domains” and proposed to silence developmental regulators while keeping them “poised” for alternate fates. However, our understanding of PcG regulation and bivalent domains remains limited. For instance, bivalent domains affect over 2,000 promoters with diverse functions, which suggests that they may function in diverse cellular processes. Moreover, the mechanisms that underlie the targeting of PcG complexes to specific genomic regions remain completely unknown. To gain insight into these issues, we used ultra high-throughput sequencing to map PcG complexes and related modifications genomewide in human and mouse ES cells. The data identify two classes of bivalent domains with distinct regulatory properties. They also reveal striking relationships between genome sequence and chromatin state that suggest a prominent role for the DNA sequence in dictating the genomewide localization of PcG complexes and, consequently, bivalent domains in ES cells.
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Affiliation(s)
- Manching Ku
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Richard P. Koche
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, United States of America
| | - Esther Rheinbay
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Bioinformatics Program and Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Eric M. Mendenhall
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Mitsuhiro Endoh
- RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama, Japan
| | - Tarjei S. Mikkelsen
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, United States of America
| | - Aviva Presser
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Chad Nusbaum
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Xiaohui Xie
- Department of Computer Science, University of California Irvine, Irvine, California, United States of America
| | - Andrew S. Chi
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Mazhar Adli
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program and Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Leon M. Ptaszek
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- Stowers Medical Institute, Center for Regenerative Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chad A. Cowan
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- Stowers Medical Institute, Center for Regenerative Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Eric S. Lander
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Whitehead Institute for Biomedical Research, MIT, Cambridge, Massachusetts, United States of America
| | - Haruhiko Koseki
- RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama, Japan
| | - Bradley E. Bernstein
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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46
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Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Erratum: Dissecting direct reprogramming through integrative genomic analysis. Nature 2008. [DOI: 10.1038/nature07196] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:766-70. [PMID: 18600261 DOI: 10.1038/nature07107] [Citation(s) in RCA: 1851] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 05/21/2008] [Indexed: 02/07/2023]
Abstract
DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
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Affiliation(s)
- Alexander Meissner
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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48
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Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553-60. [PMID: 17603471 PMCID: PMC2921165 DOI: 10.1038/nature06008] [Citation(s) in RCA: 3093] [Impact Index Per Article: 181.9] [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: 05/10/2007] [Accepted: 06/13/2007] [Indexed: 12/11/2022]
Abstract
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
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49
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Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JAM, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007; 447:167-77. [PMID: 17495919 DOI: 10.1038/nature05805] [Citation(s) in RCA: 592] [Impact Index Per Article: 34.8] [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: 12/05/2006] [Accepted: 04/03/2007] [Indexed: 12/15/2022]
Abstract
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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Affiliation(s)
- Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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50
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Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A 2007; 104:7145-50. [PMID: 17442748 PMCID: PMC1852749 DOI: 10.1073/pnas.0701811104] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Experimental evidence suggests that many of these elements play regulatory roles, but little is known about regulatory motifs contained within them. Here we describe a systematic approach to discover and characterize regulatory motifs within mammalian CNEs by searching for long motifs (12-22 nt) with significant enrichment in CNEs and studying their biochemical and genomic properties. Our analysis identifies 233 long motifs (LMs), matching a total of approximately 60,000 conserved instances across the human genome. These motifs include 16 previously known regulatory elements, such as the histone 3'-UTR motif and the neuron-restrictive silencer element, as well as striking examples of novel functional elements. The most highly enriched motif (LM1) corresponds to the X-box motif known from yeast and nematode. We show that it is bound by the RFX1 protein and identify thousands of conserved motif instances, suggesting a broad role for the RFX family in gene regulation. A second group of motifs (LM2*) does not match any previously known motif. We demonstrate by biochemical and computational methods that it defines a binding site for the CTCF protein, which is involved in insulator function to limit the spread of gene activation. We identify nearly 15,000 conserved sites that likely serve as insulators, and we show that nearby genes separated by predicted CTCF sites show markedly reduced correlation in gene expression. These sites may thus partition the human genome into domains of expression.
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Affiliation(s)
- Xiaohui Xie
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
| | - Tarjei S. Mikkelsen
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
- Division of Health Sciences and Technology
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
- Computer Science and Artificial Intelligence Laboratory, and
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- To whom correspondence should be addressed. E-mail:
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