1
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Madhukaran S, Hon GC, Mahendroo M. Protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. STAR Protoc 2023; 4:102631. [PMID: 37897730 PMCID: PMC10751548 DOI: 10.1016/j.xpro.2023.102631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/24/2023] [Accepted: 09/20/2023] [Indexed: 10/30/2023] Open
Abstract
A challenge in studying cervical epithelial cell biology at the single-cell level is that differentiated subtypes, in particular mucus-secreting goblet cells, are sensitive to disassociating enzymes making isolation of all epithelial subpopulations difficult. Here we present a protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. We describe steps for harvesting cervices, preparing cervical tissue, dissociation of cervical cells, and viability checks. We then detail library preparation, sequencing, and procedure for data analysis. For complete details on the use and execution of this protocol, please refer to Cooley et al. (2023).1.
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Affiliation(s)
- ShanmugaPriyaa Madhukaran
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mala Mahendroo
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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2
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Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. bioRxiv 2023:2023.11.20.567880. [PMID: 38045327 PMCID: PMC10690208 DOI: 10.1101/2023.11.20.567880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic studies have associated thousands of enhancers with breast cancer. However, the vast majority have not been functionally characterized. Thus, it remains unclear how variant-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3,512 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of >500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of variant-associated enhancers disrupts breast cancer gene programs. We observe variant-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple variant-associated enhancers indirectly regulate TP53. Comparative studies illustrate sub-type specific functions between enhancers in ER+ and ER- cells. Finally, we developed the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.
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Affiliation(s)
- Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | | | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Huan Zhao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Current address: Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
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3
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Yu L, Logsdon D, Pinzon-Arteaga CA, Duan J, Ezashi T, Wei Y, Ribeiro Orsi AE, Oura S, Liu L, Wang L, Liu K, Ding X, Zhan L, Zhang J, Nahar A, Stobbe C, Katz-Jaffe M, Schoolcraft WB, Tan T, Hon GC, Yuan Y, Wu J. Large-scale production of human blastoids amenable to modeling blastocyst development and maternal-fetal cross talk. Cell Stem Cell 2023; 30:1246-1261.e9. [PMID: 37683605 DOI: 10.1016/j.stem.2023.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 08/15/2022] [Revised: 03/07/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023]
Abstract
Recent advances in human blastoids have opened new avenues for modeling early human development and implantation. One limitation of our first protocol for human blastoid generation was relatively low efficiency. We now report an optimized protocol for the efficient generation of large quantities of high-fidelity human blastoids from naive pluripotent stem cells. This enabled proteomics analysis that identified phosphosite-specific signatures potentially involved in the derivation and/or maintenance of the signaling states in human blastoids. Additionally, we uncovered endometrial stromal effects in promoting trophoblast cell survival, proliferation, and syncytialization during co-culture with blastoids and blastocysts. Side-by-side single-cell RNA sequencing revealed similarities and differences in transcriptome profiles between pre-implantation blastoids and blastocysts, as well as post-implantation cultures, and uncovered a population resembling early migratory trophoblasts during co-culture with endometrial stromal cells. Our optimized protocol will facilitate broader use of human blastoids as an accessible, perturbable, scalable, and tractable model for human blastocysts.
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Affiliation(s)
- Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Deirdre Logsdon
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Carlos A Pinzon-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialei Duan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Toshihiko Ezashi
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Yulei Wei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China, Agricultural University, Beijing, 100193, China
| | - Ana Elisa Ribeiro Orsi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Seiya Oura
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kun Liu
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA; Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Xiaoyun Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Linfeng Zhan
- State Key Laboratory of Primate Biomedical Research Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunan Key Laboratory of Primate Biomedical Research, Kunming 650500, Yunnan, China
| | - Junfei Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China, Agricultural University, Beijing, 100193, China
| | - Asrafun Nahar
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Caitlen Stobbe
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Mandy Katz-Jaffe
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | | | - Tao Tan
- State Key Laboratory of Primate Biomedical Research Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China; Yunan Key Laboratory of Primate Biomedical Research, Kunming 650500, Yunnan, China
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ye Yuan
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Liu L, Oura S, Markham Z, Hamilton JN, Skory RM, Li L, Sakurai M, Wang L, Pinzon-Arteaga CA, Plachta N, Hon GC, Wu J. Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids. Cell 2023; 186:3776-3792.e16. [PMID: 37478861 DOI: 10.1016/j.cell.2023.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [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: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
In vitro stem cell models that replicate human gastrulation have been generated, but they lack the essential extraembryonic cells needed for embryonic development, morphogenesis, and patterning. Here, we describe a robust and efficient method that prompts human extended pluripotent stem cells to self-organize into embryo-like structures, termed peri-gastruloids, which encompass both embryonic (epiblast) and extraembryonic (hypoblast) tissues. Although peri-gastruloids are not viable due to the exclusion of trophoblasts, they recapitulate critical stages of human peri-gastrulation development, such as forming amniotic and yolk sac cavities, developing bilaminar and trilaminar embryonic discs, specifying primordial germ cells, initiating gastrulation, and undergoing early neurulation and organogenesis. Single-cell RNA-sequencing unveiled transcriptomic similarities between advanced human peri-gastruloids and primary peri-gastrulation cell types found in humans and non-human primates. This peri-gastruloid platform allows for further exploration beyond gastrulation and may potentially aid in the development of human fetal tissues for use in regenerative medicine.
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Affiliation(s)
- Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Seiya Oura
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zachary Markham
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James N Hamilton
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robin M Skory
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leijie Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carlos A Pinzon-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicolas Plachta
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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5
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Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. eLife 2023; 12:e88187. [PMID: 37497775 PMCID: PMC10374278 DOI: 10.7554/elife.88187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Despite ground-breaking genetic studies that have identified thousands of risk variants for developmental diseases, how these variants lead to molecular and cellular phenotypes remains a gap in knowledge. Many of these variants are non-coding and occur at enhancers, which orchestrate key regulatory programs during development. The prevailing paradigm is that non-coding variants alter the activity of enhancers, impacting gene expression programs, and ultimately contributing to disease risk. A key obstacle to progress is the systematic functional characterization of non-coding variants at scale, especially since enhancer activity is highly specific to cell type and developmental stage. Here, we review the foundational studies of enhancers in developmental disease and current genomic approaches to functionally characterize developmental enhancers and their variants at scale. In the coming decade, we anticipate systematic enhancer perturbation studies to link non-coding variants to molecular mechanisms, changes in cell state, and disease phenotypes.
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Affiliation(s)
- Daniel A Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
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6
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Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC. CHD-associated enhancers shape human cardiomyocyte lineage commitment. eLife 2023; 12:e86206. [PMID: 37096669 PMCID: PMC10156167 DOI: 10.7554/elife.86206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We perform a single-cell CRISPRi screen to assess the endogenous roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHDs). We identify 16 enhancers whose repression leads to deficient differentiation of human cardiomyocytes (CMs). A focused CRISPRi validation screen shows that repression of TBX5 enhancers delays the transcriptional switch from mid- to late-stage CM states. Endogenous genetic deletions of two TBX5 enhancers phenocopy epigenetic perturbations. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients.
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Affiliation(s)
- Daniel A Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sean C Goetsch
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sushama Sivakumar
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nikhil V Munshi
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Cardiology, Department of Molecular Biology, McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
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Cooley A, Madhukaran S, Stroebele E, Colon Caraballo M, Wang L, Akgul Y, Hon GC, Mahendroo M. Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption. iScience 2023; 26:105953. [PMID: 36718364 PMCID: PMC9883190 DOI: 10.1016/j.isci.2023.105953] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/01/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The cervical epithelium undergoes changes in proliferation, differentiation, and function that are critical to ensure fertility and maintain pregnancy. Here, we identify cervical epithelial subtypes in non-pregnant, pregnant, and in labor mice using single-cell transcriptome and spatial analysis. We identify heterogeneous subpopulations of epithelia displaying spatial and temporal specificity. Notably in pregnancy, two goblet cell subtypes are present in the most luminal layers with one goblet population expanding earlier in pregnancy than the other goblet population. The goblet populations express novel protective factors and distinct mucosal networks. Single-cell analysis in a model of cervical epithelial barrier disruption indicates untimely basal cell proliferation precedes the expansion of goblet cells with diminished mucosal integrity. These data demonstrate how the cervical epithelium undergoes continuous remodeling to maintain dynamic states of homeostasis in pregnancy and labor, and provide a framework to understand perturbations in epithelial health that increase the risk of premature birth.
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Affiliation(s)
- Anne Cooley
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - ShanmugaPriyaa Madhukaran
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth Stroebele
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mariano Colon Caraballo
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yucel Akgul
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mala Mahendroo
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Bhattacharyya S, Kollipara RK, Orquera-Tornakian G, Goetsch S, Zhang M, Perry C, Li B, Shelton JM, Bhakta M, Duan J, Xie Y, Xiao G, Evers BM, Hon GC, Kittler R, Munshi NV. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm. J Clin Invest 2023; 133:e153635. [PMID: 36454649 PMCID: PMC9888383 DOI: 10.1172/jci153635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.
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Affiliation(s)
| | | | | | - Sean Goetsch
- Department of Internal Medicine, Division of Cardiology
| | - Minzhe Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Cameron Perry
- Department of Internal Medicine, Division of Cardiology
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | | | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Bret M. Evers
- Department of Internal Medicine, Division of Cardiology
| | - Gary C. Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
- Department of Bioinformatics
- Hamon Center for Regenerative Science and Medicine, and
| | - Ralf Kittler
- McDermott Center for Human Growth and Development
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology
- McDermott Center for Human Growth and Development
- Hamon Center for Regenerative Science and Medicine, and
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
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Bhattacharyya S, Duan J, Vela RJ, Bhakta M, Bajona P, Mammen PP, Hon GC, Munshi NV. Accurate Classification of Cardiomyopathy Diagnosis by Chromatin Accessibility. Circulation 2022; 146:878-881. [PMID: 36095061 PMCID: PMC9475804 DOI: 10.1161/circulationaha.122.059659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Samadrita Bhattacharyya
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas
| | - Jialei Duan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, UT Southwestern Medical Center, Dallas
| | - Ryan J. Vela
- Department of Cardiothoracic Surgery, UT Southwestern Medical Center, Dallas
| | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas
| | - Pietro Bajona
- AHN Cardiovascular Institute, Allegheny Health Network-Drexel University College of Medicine, Pittsburgh
| | - Pradeep P.A. Mammen
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, UT Southwestern Medical Center, Dallas
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, UT Southwestern Medical Center, Dallas
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas
- Department of Molecular Biology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas
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Abstract
BACKGROUND Single-cell CRISPR screens are powerful tools to understand genome function by linking genetic perturbations to transcriptome-wide phenotypes. However, since few cells can be affordably sequenced in these screens, biased sampling of cells could affect data interpretation. One potential source of biased sampling is clonal cell expansion. RESULTS Here, we identify clonal cells in single cell screens using multiplexed sgRNAs as barcodes. We find that the cells in each clone share transcriptional similarities and bear segmental copy number changes. These analyses suggest that clones are genetically distinct. Finally, we show that the transcriptional similarities of clonally expanded cells contribute to false positives in single-cell CRISPR screens. CONCLUSIONS Experimental conditions that reduce clonal expansion or computational filtering of clonal cells will improve the reliability of single-cell CRISPR screens.
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Affiliation(s)
- Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniel Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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11
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Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Front Bioeng Biotechnol 2021; 9:748942. [PMID: 34733831 PMCID: PMC8558416 DOI: 10.3389/fbioe.2021.748942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.
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Affiliation(s)
- Boxun Li
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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12
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Yu L, Wei Y, Duan J, Schmitz DA, Sakurai M, Wang L, Wang K, Zhao S, Hon GC, Wu J. Blastocyst-like structures generated from human pluripotent stem cells. Nature 2021; 591:620-626. [PMID: 33731924 DOI: 10.1038/s41586-021-03356-y] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
Limited access to embryos has hampered the study of human embryogenesis and disorders that occur during early pregnancy. Human pluripotent stem cells provide an alternative means to study human development in a dish1-7. Recent advances in partial embryo models derived from human pluripotent stem cells have enabled human development to be examined at early post-implantation stages8-14. However, models of the pre-implantation human blastocyst are lacking. Starting from naive human pluripotent stem cells, here we developed an effective three-dimensional culture strategy with successive lineage differentiation and self-organization to generate blastocyst-like structures in vitro. These structures-which we term 'human blastoids'-resemble human blastocysts in terms of their morphology, size, cell number, and composition and allocation of different cell lineages. Single-cell RNA-sequencing analyses also reveal the transcriptomic similarity of blastoids to blastocysts. Human blastoids are amenable to embryonic and extra-embryonic stem cell derivation and can further develop into peri-implantation embryo-like structures in vitro. Using chemical perturbations, we show that specific isozymes of protein kinase C have a critical function in the formation of the blastoid cavity. Human blastoids provide a readily accessible, scalable, versatile and perturbable alternative to blastocysts for studying early human development, understanding early pregnancy loss and gaining insights into early developmental defects.
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Affiliation(s)
- Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yulei Wei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.,International Healthcare Innovation Institute, Jiangmen, China
| | - Jialei Duan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Schmitz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kunhua Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Shuhua Zhao
- Department of Reproduction and Genetics, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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England AR, Chaney CP, Das A, Patel M, Malewska A, Armendariz D, Hon GC, Strand DW, Drake KA, Carroll TJ. Identification and characterization of cellular heterogeneity within the developing renal interstitium. Development 2020; 147:dev190108. [PMID: 32586976 PMCID: PMC7438011 DOI: 10.1242/dev.190108] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/08/2020] [Indexed: 12/29/2022]
Abstract
Kidney formation requires the coordinated growth of multiple cell types including the collecting ducts, nephrons, vasculature and interstitium. There is a long-held belief that interactions between progenitors of the collecting ducts and nephrons are primarily responsible for kidney development. However, over the last several years, it has become increasingly clear that multiple aspects of kidney development require signaling from the interstitium. How the interstitium orchestrates these various roles is poorly understood. Here, we show that during development the interstitium is a highly heterogeneous patterned population of cells that occupies distinct positions correlated to the adjacent parenchyma. Our analysis indicates that the heterogeneity is not a mere reflection of different stages in a linear developmental trajectory but instead represents several novel differentiated cell states. Further, we find that β-catenin has a cell autonomous role in the development of a medullary subset of the interstitium and that this non-autonomously affects the development of the adjacent epithelia. These findings suggest the intriguing possibility that the different interstitial subtypes may create microenvironments that play unique roles in development of the adjacent epithelia and endothelia.
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Affiliation(s)
- Alicia R England
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher P Chaney
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amrita Das
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mohita Patel
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alicia Malewska
- Department of Urology, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel Armendariz
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Douglas W Strand
- Department of Urology, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keri A Drake
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas J Carroll
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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14
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Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC. Rational Reprogramming of Cellular States by Combinatorial Perturbation. Cell Rep 2020; 27:3486-3499.e6. [PMID: 31216470 DOI: 10.1016/j.celrep.2019.05.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/23/2018] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Ectopic expression of transcription factors (TFs) can reprogram cell state. However, because of the large combinatorial space of possible TF cocktails, it remains difficult to identify TFs that reprogram specific cell types. Here, we develop Reprogram-Seq to experimentally screen thousands of TF cocktails for reprogramming performance. Reprogram-Seq leverages organ-specific cell-atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Focusing on the cardiac system, we perform Reprogram-Seq on MEFs using an undirected library of 48 cardiac factors and, separately, a directed library of 10 epicardial-related TFs. We identify a combination of three TFs, which efficiently reprogram MEFs to epicardial-like cells that are transcriptionally, molecularly, morphologically, and functionally similar to primary epicardial cells. Reprogram-Seq holds promise to accelerate the generation of specific cell types for regenerative medicine.
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Affiliation(s)
- Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minoti Bhakta
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiqi Xie
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nikhil V Munshi
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
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15
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Bhattacharyya S, Duan J, Wang L, Li B, Bhakta M, Fernandez-Perez A, Hon GC, Munshi NV. Author Correction: Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition. Sci Rep 2020; 10:4069. [PMID: 32107454 PMCID: PMC7046679 DOI: 10.1038/s41598-020-60915-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Samadrita Bhattacharyya
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lin Wang
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Antonio Fernandez-Perez
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Hamon Center for Regenerative Science and Medicine, Dallas, TX, 75390, USA
| | - Nikhil V Munshi
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA. .,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, 75390, USA. .,McDermott Center for Human Growth and Development, UT Southwestern Medical center, Dallas, TX, 75390, USA. .,Hamon Center for Regenerative Science and Medicine, Dallas, TX, 75390, USA.
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16
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Henry GH, Malewska A, Joseph DB, Malladi VS, Lee J, Torrealba J, Mauck RJ, Gahan JC, Raj GV, Roehrborn CG, Hon GC, MacConmara MP, Reese JC, Hutchinson RC, Vezina CM, Strand DW. A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Rep 2019; 25:3530-3542.e5. [PMID: 30566875 PMCID: PMC6411034 DOI: 10.1016/j.celrep.2018.11.086] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/17/2018] [Accepted: 11/20/2018] [Indexed: 11/30/2022] Open
Abstract
A comprehensive cellular anatomy of normal human prostate is essential for solving the cellular origins of benign prostatic hyperplasia and prostate cancer. The tools used to analyze the contribution of individual cell types are not robust. We provide a cellular atlas of the young adult human prostate and prostatic urethra using an iterative process of single-cell RNA sequencing (scRNA-seq) and flow cytometry on ~98,000 cells taken from different anatomical regions. Immunohistochemistry with newly derived cell type-specific markers revealed the distribution of each epithelial and stromal cell type on whole mounts, revising our understanding of zonal anatomy. Based on discovered cell surface markers, flow cytometry antibody panels were designed to improve the purification of each cell type, with each gate confirmed by scRNA-seq. The molecular classification, anatomical distribution, and purification tools for each cell type in the human prostate create a powerful resource for experimental design in human prostate disease. Using single-cell RNA sequencing, immunofluorescence, and flow cytometry, Henry et al. create a cellular anatomy of the normal human prostate and provide the tools to identify, isolate, and localize every cell type. They identify two additional epithelial cell types enriched in the prostatic urethra and proximal prostatic ducts.
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Affiliation(s)
- Gervaise H Henry
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alicia Malewska
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diya B Joseph
- Department of Comparative Biosciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA
| | - Venkat S Malladi
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeon Lee
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jose Torrealba
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan J Mauck
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey C Gahan
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesh V Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Claus G Roehrborn
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | - Ryan C Hutchinson
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA
| | - Douglas W Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Xie S, Armendariz D, Zhou P, Duan J, Hon GC. Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules. Cell Rep 2019; 29:2570-2578.e5. [PMID: 31775028 PMCID: PMC6904118 DOI: 10.1016/j.celrep.2019.10.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/15/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
Single-cell screens enable high-throughput functional assessment of enhancers in their endogenous genomic context. However, the design of current studies limits their application to identifying the primary gene targets of enhancers. Here, we improve the experimental and computational parameters of single-cell enhancer screens to identify the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells reveals an interwoven enhancer-driven gene regulatory network. We find that enhancers from distinct genomic loci converge to modulate the expression of common sub-modules, including the α- and β-globin loci, by directly regulating transcription factors. Our analysis suggests that several genetic variants associated with myeloid blood cell traits alter the activity of a distal enhancer of MYB (~140 kb away), with downstream consequences on hemoglobin genes expression and cell state. These data have implications for the understanding of enhancer-associated traits and emphasize the flexibility of controlling transcriptional systems by modifying enhancer activity. Xie et al. apply improved strategies for single-cell screens to identify an enhancer-driven transcriptional regulatory network in K562 cells. They demonstrate that the same group of genes can be indirectly regulated by enhancers from distinct genomic loci. These data have implications for the understanding of enhancer-associated traits.
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Affiliation(s)
- Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialei Duan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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18
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Zhang Z, Luo D, Zhong X, Choi JH, Ma Y, Wang S, Mahrt E, Guo W, Stawiski EW, Modrusan Z, Seshagiri S, Kapur P, Hon GC, Brugarolas J, Wang T. SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. Genes (Basel) 2019; 10:E531. [PMID: 31336988 PMCID: PMC6678337 DOI: 10.3390/genes10070531] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [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: 05/23/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022] Open
Abstract
Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore prior knowledge of transcriptomes and the probable structures of the data. Moreover, cell identification heavily relies on subjective and possibly inaccurate human inspection afterwards. To address these analytical challenges, we developed SCINA (Semi-supervised Category Identification and Assignment), a semi-supervised model that exploits previously established gene signatures using an expectation-maximization (EM) algorithm. SCINA is applicable to scRNA-Seq and flow cytometry/CyTOF data, as well as other data of similar format. We applied SCINA to a wide range of datasets, and showed its accuracy, stability and efficiency, which exceeded most popular unsupervised approaches. SCINA discovered an intermediate stage of oligodendrocytes from mouse brain scRNA-Seq data. SCINA also detected immune cell population changes in cytometry data in a genetically-engineered mouse model. Furthermore, SCINA performed well with bulk gene expression data. Specifically, we identified a new kidney tumor clade with similarity to FH-deficient tumors (FHD), which we refer to as FHD-like tumors (FHDL). Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods.
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Affiliation(s)
- Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Danni Luo
- Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuanqing Ma
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Stacy Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elena Mahrt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Guo
- BioHPC, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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19
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Bhattacharyya S, Duan J, Wang L, Li B, Bhakta M, Fernandez-Perez A, Hon GC, Munshi NV. Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition. Sci Rep 2019; 9:2106. [PMID: 30765799 PMCID: PMC6375990 DOI: 10.1038/s41598-019-38683-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/04/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
The atrioventricular node (AVN) coordinates the timing of atrial and ventricular contraction to optimize cardiac performance. To study this critical function using mouse genetics, however, new reagents are needed that allow AVN-specific manipulation. Here we describe a novel Gjd3-CreEGFP mouse line that successfully recombines floxed alleles within the AVN beginning at E12.5. These mice have been engineered to express CreEGFP under the control of endogenous Gjd3 regulatory elements without perturbing native protein expression. Detailed histological analysis of Gjd3-CreEGFP mice reveals specific labeling of AVN cardiomyocytes and a subset of cardiac endothelial cells. Importantly, we show that Gjd3-CreEGFP mice have preserved cardiac mechanical and electrical function. In one application of our newly described mouse line, we provide a three-dimensional (3D) view of the AVN using tissue clearing combined with confocal microscopy. With this 3D model as a reference, we identify specific AVN sub-structures based on marker staining characteristics. In addition, we use our Gjd3-CreEGFP mice to guide microdissection of the AVN and construction of a single-cell atlas. Thus, our results establish a new transgenic tool for AVN-specific recombination, provide an updated model of AVN morphology, and describe a roadmap for exploring AVN cellular heterogeneity.
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Affiliation(s)
- Samadrita Bhattacharyya
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lin Wang
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Antonio Fernandez-Perez
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Hamon Center for Regenerative Science and Medicine, Dallas, TX, 75390, USA
| | - Nikhil V Munshi
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA. .,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, 75390, USA. .,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA. .,Hamon Center for Regenerative Science and Medicine, Dallas, TX, 75390, USA.
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20
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Hepler C, Shan B, Zhang Q, Henry GH, Shao M, Vishvanath L, Ghaben AL, Mobley AB, Strand D, Hon GC, Gupta RK. Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. eLife 2018; 7:39636. [PMID: 30265241 PMCID: PMC6167054 DOI: 10.7554/elife.39636] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
White adipose tissue (WAT) remodeling is dictated by coordinated interactions between adipocytes and resident stromal-vascular cells; however, the functional heterogeneity of adipose stromal cells has remained unresolved. We combined single-cell RNA-sequencing and FACS to identify and isolate functionally distinct subpopulations of PDGFRβ+ stromal cells within visceral WAT of adult mice. LY6C- CD9- PDGFRβ+ cells represent highly adipogenic visceral adipocyte precursor cells (‘APCs’), whereas LY6C+ PDGFRβ+ cells represent fibro-inflammatory progenitors (‘FIPs’). FIPs lack adipogenic capacity, display pro-fibrogenic/pro-inflammatory phenotypes, and can exert an anti-adipogenic effect on APCs. The pro-inflammatory phenotype of PDGFRβ+ cells is regulated, at least in part, by NR4A nuclear receptors. These data highlight the functional heterogeneity of visceral WAT perivascular cells, and provide insight into potential cell-cell interactions impacting adipogenesis and inflammation. These improved strategies to isolate FIPs and APCs from visceral WAT will facilitate the study of physiological WAT remodeling and mechanisms leading to metabolic dysfunction. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter). Fat tissue, also known as white adipose tissue, specializes in storing excess calories. Much of this storage happens under the skin, but fat tissue can also build up inside the abdomen and surround organs, where it is known as ‘visceral’ fat. When visceral fat tissue is unhealthy, it may help diseases such as diabetes and heart disease to develop. Unhealthy fat tissue contains enlarged fat cells, which may die from overwork. The stress this places on the surrounding tissue activates the immune system, causing inflammation and the build-up of collagen fibers around the cells (a condition known as fibrosis). Not all people develop this type of unhealthy fat tissue, but we do not yet understand why. In many tissues, blood vessels serve as a home for several types of adult stem cells that help to rejuvenate the tissue following damage. To identify these cells, Hepler et al. analyzed the genes used by more than 3,000 cells living around the blood vessels in the visceral fat of adult mice. Recent work had already revealed that stem cells called adipocyte precursor cells live in this region. Hepler et al. now reveal the presence of a second group of cells, termed fibro-inflammatory progenitor cells (or FIPs for short). To investigate the roles of each cell type in more detail, Hepler et al. developed a new technique to isolate the adipocyte precursor cells from other cell types. When grown in the right conditions in petri dishes, the adipocyte precursor cells were able to form new fat cells. They could also make new fat cells when transplanted into mice that lacked fat tissue. By contrast, the FIPs can suppress the activity of adipocyte precursor cells and activate immune cells. They may also help fibrosis to develop. It is not yet clear whether FIPs are present in human fat tissue. But, if they are, understanding them in greater detail may suggest new ways to treat diabetes and heart disease in obese people.
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Affiliation(s)
- Chelsea Hepler
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bo Shan
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Qianbin Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gervaise H Henry
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Mengle Shao
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lavanya Vishvanath
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alexandra L Ghaben
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Angela B Mobley
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Douglas Strand
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rana K Gupta
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
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21
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Abstract
Simultaneously detecting CRISPR-based perturbations and induced transcriptional changes in the same cell is a powerful approach to unraveling genome function. Several lentiviral approaches have been developed, some of which rely on the detection of distally located genetic barcodes as an indirect proxy of sgRNA identity. Since barcodes are often several kilobases from their corresponding sgRNAs, viral recombination-mediated swapping of barcodes and sgRNAs is feasible. Using a self-circularization-based sgRNA-barcode library preparation protocol, we estimate the recombination rate to be ~50% and we trace this phenomenon to the pooled viral packaging step. Recombination is random, and decreases the signal-to-noise ratio of the assay. Our results suggest that alternative approaches can increase the throughput and sensitivity of single-cell perturbation assays.
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Affiliation(s)
- Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Anne Cooley
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Daniel Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Pei Zhou
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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22
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Abstract
5-Hydroxymethylcytosine (5hmC) is a modified form of cytosine, which has recently been found in mammalian cells and tissues. 5hmC is derived from 5-methylcytosine (5mC) by Ten-eleven translocation (TET) family protein-mediated oxidation and may regulate gene expression. Numerous affinity-based profiling methods have been developed to help understand the exact function of 5hmC in the genome. However, these methods have a relatively low resolution (~100 bp) without quantitative information of the modification percentage on each site. Here we demonstrated the detailed procedure of Tet-Assistant Bisulfite Sequencing (TAB-Seq), which can detect 5hmC at single-base resolution and quantify its abundance at each site. In this protocol, the genomic DNA is first treated with βGT and recombinant mTet1 consecutively to convert 5hmC to 5gmC and 5mC to 5caC, respectively. The treated genomic DNA can be directly applied to bisulfite treatment to detect 5hmC on specific loci or applied to whole-genome bisulfite sequencing as needed.
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Affiliation(s)
- Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Dali Han
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Gary C Hon
- University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chuan He
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA.
- Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA.
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23
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Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, Shao Z, Xu J. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell 2017; 170:1028-1043.e19. [PMID: 28841410 PMCID: PMC6857456 DOI: 10.1016/j.cell.2017.08.003] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/23/2017] [Accepted: 08/01/2017] [Indexed: 11/26/2022]
Abstract
Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here, we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single-copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally regulated super-enhancers reveals spatial features that causally control gene transcription. Thus, comprehensive and unbiased analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.
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Affiliation(s)
- Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yong Chen
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Mushan Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Feng Zhou
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Minister of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Kailong Li
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Cao
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Ni
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuxuan Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhimin Gu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathryn E Dickerson
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA; MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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24
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Xie S, Duan J, Li B, Zhou P, Hon GC. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Mol Cell 2017; 66:285-299.e5. [PMID: 28416141 DOI: 10.1016/j.molcel.2017.03.007] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 01/18/2017] [Accepted: 03/07/2017] [Indexed: 12/25/2022]
Abstract
The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population and their contribution to expression in these cells. Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a manner greatly exceeding repression of individual constituents.
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Affiliation(s)
- Shiqi Xie
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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25
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Villa GR, Hulce JJ, Zanca C, Bi J, Ikegami S, Cahill GL, Gu Y, Lum KM, Masui K, Yang H, Rong X, Hong C, Turner KM, Liu F, Hon GC, Jenkins D, Martini M, Armando AM, Quehenberger O, Cloughesy TF, Furnari FB, Cavenee WK, Tontonoz P, Gahman TC, Shiau AK, Cravatt BF, Mischel PS. An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers. Cancer Cell 2016; 30:683-693. [PMID: 27746144 PMCID: PMC5479636 DOI: 10.1016/j.ccell.2016.09.008] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/19/2016] [Accepted: 09/17/2016] [Indexed: 12/11/2022]
Abstract
Small-molecule inhibitors targeting growth factor receptors have failed to show efficacy for brain cancers, potentially due to their inability to achieve sufficient drug levels in the CNS. Targeting non-oncogene tumor co-dependencies provides an alternative approach, particularly if drugs with high brain penetration can be identified. Here we demonstrate that the highly lethal brain cancer glioblastoma (GBM) is remarkably dependent on cholesterol for survival, rendering these tumors sensitive to Liver X receptor (LXR) agonist-dependent cell death. We show that LXR-623, a clinically viable, highly brain-penetrant LXRα-partial/LXRβ-full agonist selectively kills GBM cells in an LXRβ- and cholesterol-dependent fashion, causing tumor regression and prolonged survival in mouse models. Thus, a metabolic co-dependency provides a pharmacological means to kill growth factor-activated cancers in the CNS.
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Affiliation(s)
- Genaro R Villa
- Department of Molecular and Medical Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, CA 90095, USA; Medical Scientist Training Program, David Geffen UCLA School of Medicine, Los Angeles, CA 90095, USA; Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonathan J Hulce
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ciro Zanca
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Junfeng Bi
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Shiro Ikegami
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabrielle L Cahill
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuchao Gu
- Department of Molecular and Medical Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, CA 90095, USA; Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Kenneth M Lum
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Huijun Yang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Xin Rong
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cynthia Hong
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Feng Liu
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Gary C Hon
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - David Jenkins
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael Martini
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron M Armando
- Department of Pharmacology, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Oswald Quehenberger
- Department of Pharmacology, UCSD School of Medicine, La Jolla, CA 92093, USA; Department of Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA; Department of Pathology, UCSD School of Medicine, La Jolla, CA 92093, USA; Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA; Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA; Department of Pathology, UCSD School of Medicine, La Jolla, CA 92093, USA; Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093, USA.
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26
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Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, Ren B. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell 2014; 56:286-297. [PMID: 25263596 DOI: 10.1016/j.molcel.2014.08.026] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [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: 02/10/2014] [Revised: 05/07/2014] [Accepted: 08/21/2014] [Indexed: 12/23/2022]
Abstract
In mammals, cytosine methylation (5mC) is widely distributed throughout the genome but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this epigenetic mark at enhancers remains unclear. Recent experiments have demonstrated that enhancers are enriched for 5-hydroxymethylcytosine (5hmC), an oxidization product of the Tet family of 5mC dioxygenases and an intermediate of DNA demethylation. These results support the involvement of Tet proteins in the regulation of dynamic DNA methylation at enhancers. By mapping DNA methylation and hydroxymethylation at base resolution, we find that deletion of Tet2 causes extensive loss of 5hmC at enhancers, accompanied by enhancer hypermethylation, reduction of enhancer activity, and delayed gene induction in the early steps of differentiation. Our results reveal that DNA demethylation modulates enhancer activity, and its disruption influences the timing of transcriptome reprogramming during cellular differentiation.
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Affiliation(s)
- Gary C Hon
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Tingting Du
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Fulai Jin
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | | | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Chia-An Yen
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Shi-Qing Mao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bang-An Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Samantha Kuan
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Lee E Edsall
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA
| | - Boxuan Simen Zhao
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92093.
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27
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Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2013; 505:117-20. [PMID: 24284625 PMCID: PMC3877715 DOI: 10.1038/nature12730] [Citation(s) in RCA: 2744] [Impact Index Per Article: 249.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 10/03/2013] [Indexed: 12/20/2022]
Abstract
N(6)-methyladenosine (m(6)A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes. Although essential to cell viability and development, the exact role of m(6)A modification remains to be determined. The recent discovery of two m(6)A demethylases in mammalian cells highlighted the importance of m(6)A in basic biological functions and disease. Here we show that m(6)A is selectively recognized by the human YTH domain family 2 (YTHDF2) 'reader' protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m(6)A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies. The carboxy-terminal domain of YTHDF2 selectively binds to m(6)A-containing mRNA, whereas the amino-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m(6)A modification is recognized by selectively binding proteins to affect the translation status and lifetime of mRNA.
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Affiliation(s)
- Xiao Wang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Adrian Gomez
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gary C Hon
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Yanan Yue
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Dali Han
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Marc Parisien
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Guifang Jia
- 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2] Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet 2013; 45:1198-206. [PMID: 23995138 PMCID: PMC4095776 DOI: 10.1038/ng.2746] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [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: 01/18/2013] [Accepted: 08/06/2013] [Indexed: 12/13/2022]
Abstract
Mammalian development requires cytosine methylation, a heritable epigenetic mark of cellular memory believed to maintain a cell’s unique gene expression pattern. However, it remains unclear how dynamic DNA methylation relates to cell-type specific gene expression and animal development. Here, by mapping base resolution methylomes in 17 adult mouse tissues at shallow coverage, we identify 302,864 tissue-specific differentially methylated regions (tsDMRs) and estimate that >6.7% of the mouse genome is variably methylated. Supporting a prominent role for DNA methylation in gene regulation, most tsDMRs occur at distal cis-regulatory elements. Surprisingly, some tsDMRs mark enhancers dormant in adult tissues but active in embryonic development. These “vestigial” enhancers are hypomethylated and lack active histone modifications in adult tissue, but nevertheless exhibit activity during embryonic development. Our results provide new insights into the role of DNA methylation at tissue-specific enhancers and suggest that epigenetic memory of embryonic development may be retained in adult tissues.
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Affiliation(s)
- Gary C Hon
- Ludwig Institute for Cancer Research, La Jolla, California, USA
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Hon GC, Shen Y, McCleary DF, Edsall L, Kuan S, Ren B. Abstract 1111: Whole genome bisulfite sequencing reveals tissue-specific DNA methylation in a normal mouse. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic alteration is a hallmark of cancer. In particular, compared to normal cells, the DNA methylomes of cancer cells often exhibit two contrasting phenomena: 1) hypomethylation of large regions of the genome, notably at regions of late replicating DNA; and 2) hypermethylation of focal sites, frequently at CpG-island containing promoters. While this epigenetic variation between cancer cells and normal counterparts has been well documented, the variation between different normal cell types is still unknown. In an effort to better understand the epigenetic variation of a normal individual, we profiled DNA methylation using whole genome bisulfite sequencing in 16 tissues isolated from an individual mouse. We observed a unique distribution of CpG methylation for each tissue, which cluster based on cell lineage and type. Most somatic tissues exhibit a small but consistent decrease in methylation at late-replicating regions of the genome, suggesting the beginnings of global hypomethylation. Our global analysis identified only one-eighth of the genome as tissue-specific differentially methylated regions. Remarkably, the vast majority of these regions exhibit hallmarks of cis-regulatory activity, including: small size (<500 bp), DNase I hypersensitivity, enhancer chromatin modifications (H3K4me1/H3K27ac), and evolutionary conservation. Our results reveal that most somatic cells are primed for global hypomethylation in regions of the genome that are typically hypomethylated in cancer cells, supporting previous observations that hypomethylation may be an indicator of cell age. In addition, our results in normal tissue suggest that hypomethylation in cancer cells could alter transcriptional regulation through disruption of cis-regulatory activity.
Citation Format: Gary C. Hon, Yin Shen, David F. McCleary, Lee Edsall, Samantha Kuan, Bing Ren. Whole genome bisulfite sequencing reveals tissue-specific DNA methylation in a normal mouse. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1111. doi:10.1158/1538-7445.AM2013-1111
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Affiliation(s)
- Gary C. Hon
- Ludwig Institute for Cancer Research, La Jolla, CA
| | - Yin Shen
- Ludwig Institute for Cancer Research, La Jolla, CA
| | | | - Lee Edsall
- Ludwig Institute for Cancer Research, La Jolla, CA
| | | | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA
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Abstract
A complete understanding of the potential function of 5-hydroxymethylcytosine (5-hmC), a DNA cytosine modification in mammalian cells, requires an accurate single-base resolution sequencing method. Here we describe a modified bisulfite-sequencing method, Tet-assisted bisulfite sequencing (TAB-seq), which can identify 5-hmC at single-base resolution, as well as determine its abundance at each modification site. This protocol involves β-glucosyltransferase (β-GT)-mediated protection of 5-hmC (glucosylation) and recombinant mouse Tet1(mTet1)-mediated oxidation of 5-methylcytosine (5-mC) to 5-carboxylcytosine (5-caC). After the subsequent bisulfite treatment and PCR amplification, both cytosine and 5-caC (derived from 5-mC) are converted to thymine (T), whereas 5-hmC reads as C. The treated genomic DNA is suitable for both whole-genome and locus-specific sequencing. The entire procedure (which does not include data analysis) can be completed in 14 d for whole-genome sequencing or 7 d for locus-specific sequencing.
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Affiliation(s)
- Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012; 149:1368-80. [PMID: 22608086 PMCID: PMC3589129 DOI: 10.1016/j.cell.2012.04.027] [Citation(s) in RCA: 761] [Impact Index Per Article: 63.4] [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: 03/07/2012] [Revised: 04/02/2012] [Accepted: 04/19/2012] [Indexed: 10/28/2022]
Abstract
The study of 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach, Tet-assisted bisulfite sequencing (TAB-Seq), that when combined with traditional bisulfite sequencing can be used for mapping 5hmC at base resolution and quantifying the relative abundance of 5hmC as well as 5mC. Application of this method to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at 5hmC sites. We observe high levels of 5hmC and reciprocally low levels of 5mC near but not on transcription factor-binding sites. Additionally, the relative abundance of 5hmC varies significantly among distinct functional sequence elements, suggesting different mechanisms for 5hmC deposition and maintenance.
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Affiliation(s)
- Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Gary C. Hon
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Keith E. Szulwach
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Liang Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Audrey Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Xuekun Li
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Beomseok Park
- Department of Chemistry, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
| | - Jung-Hyun Min
- Department of Chemistry, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
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Abstract
CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in human and murine cells. However, the generality of this phenomenon and the role CBX3 may play in this context are unknown. Genome-wide localization analysis reveals CBX3 binding at genic regions, which strongly correlates with gene activity across multiple cell types. Depletion of CBX3 resulted in down-regulation of a subset of target genes. Loss of CBX3 binding leads to a more dramatic accumulation of unspliced nascent transcripts. In addition, we observed defective recruitment of splicing factors, including SNRNP70, to CBX3 target genes. Collectively, our data suggest a role for CBX3 in aiding in efficient cotranscriptional RNA processing.
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Affiliation(s)
- Andrea Smallwood
- Ludwig Institute for Cancer Research, La Jolla, California 92093, USA
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Abstract
Integrating results from diverse experiments is an essential process in our effort to understand the logic of complex systems, such as development, homeostasis and responses to the environment. With the advent of high-throughput methods--including genome-wide association (GWA) studies, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and RNA sequencing (RNA-seq)--acquisition of genome-scale data has never been easier. Epigenomics, transcriptomics, proteomics and genomics each provide an insightful, and yet one-dimensional, view of genome function; integrative analysis promises a unified, global view. However, the large amount of information and diverse technology platforms pose multiple challenges for data access and processing. This Review discusses emerging issues and strategies related to data integration in the era of next-generation genomics.
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Affiliation(s)
- R. David Hawkins
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0653
| | - Gary C. Hon
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0653
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0653
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Abstract
The DNA sequence of an organism is a blueprint of life: it harbors not only the information about proteins and other molecules produced in each cell, but also instructions on when and where such molecules are made. Chromatin, the structure of histone and DNA that has co-evolved with eukaryotic genome, also contains information that indicates the function and activity of the underlying DNA sequences. Such information exists in the form of covalent modifications to the histone proteins that comprise the nucleosome. Thanks to the development of high throughput technologies such as DNA microarrays and next generation DNA sequencing, we have begun to associate the various combinations of chromatin modification patterns with functional sequences in the human genome. Here, we review the rapid progress from descriptive observations of histone modification profiles to highly predictive models enabling use of chromatin signatures to enumerate novel functional sequences in mammalian genomes that have escaped previous detection.
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Affiliation(s)
- Gary C Hon
- Bioinformatics Program, University of California, San Diego School of Medicine, La Jolla, CA 92093-0653, USA
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Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 2006; 5:11. [PMID: 16762047 PMCID: PMC1561585 DOI: 10.1186/jbiol36] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [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: 10/18/2005] [Revised: 03/17/2006] [Accepted: 03/30/2006] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. RESULTS We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases. CONCLUSION Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.
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Affiliation(s)
- Teresa Reguly
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Ashton Breitkreutz
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Lorrie Boucher
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Bobby-Joe Breitkreutz
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Gary C Hon
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Chad L Myers
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, NJ 08544, USA
| | - Ainslie Parsons
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Helena Friesen
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Amy Tong
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Chris Stark
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Yuen Ho
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Brenda Andrews
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Charles Boone
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Olga G Troyanskya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, NJ 08544, USA
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Kara Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Nizar N Batada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Mike Tyers
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
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