201
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Korenfeld N, Toft NI, Dam TV, Charni-Natan M, Grøntved L, Goldstein I. Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue. STAR Protoc 2023; 4:102462. [PMID: 37590150 PMCID: PMC10440357 DOI: 10.1016/j.xpro.2023.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 08/19/2023] Open
Abstract
The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.
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Affiliation(s)
- Noga Korenfeld
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Nicolaj I Toft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Trine V Dam
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel.
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202
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Feng W, Liu S, Deng Q, Fu S, Yang Y, Dai X, Wang S, Wang Y, Liu Y, Lin X, Pan X, Hao S, Yuan Y, Gu Y, Zhang X, Li H, Liu L, Liu C, Fei JF, Wei X. A scATAC-seq atlas of chromatin accessibility in axolotl brain regions. Sci Data 2023; 10:627. [PMID: 37709774 PMCID: PMC10502032 DOI: 10.1038/s41597-023-02533-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is an excellent model for investigating regeneration, the interaction between regenerative and developmental processes, comparative genomics, and evolution. The brain, which serves as the material basis of consciousness, learning, memory, and behavior, is the most complex and advanced organ in axolotl. The modulation of transcription factors is a crucial aspect in determining the function of diverse regions within the brain. There is, however, no comprehensive understanding of the gene regulatory network of axolotl brain regions. Here, we utilized single-cell ATAC sequencing to generate the chromatin accessibility landscapes of 81,199 cells from the olfactory bulb, telencephalon, diencephalon and mesencephalon, hypothalamus and pituitary, and the rhombencephalon. Based on these data, we identified key transcription factors specific to distinct cell types and compared cell type functions across brain regions. Our results provide a foundation for comprehensive analysis of gene regulatory programs, which are valuable for future studies of axolotl brain development, regeneration, and evolution, as well as on the mechanisms underlying cell-type diversity in vertebrate brains.
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Affiliation(s)
- Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Sulei Fu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Yunzhi Yang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Dai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yijin Wang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiangyu Pan
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- Guangdong Cardiovsacular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yue Yuan
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Hanbo Li
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI-Qingdao, Qingdao, 266555, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Xiaoyu Wei
- BGI-Hangzhou, Hangzhou, 310012, China.
- BGI-Shenzhen, Shenzhen, 518103, China.
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203
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.531029. [PMID: 36945441 PMCID: PMC10028846 DOI: 10.1101/2023.03.03.531029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Statistics, University of Chicago, Chicago, IL, USA
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204
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Lewis SA, Doratt BM, Qiao Q, Blanton M, Grant KA, Messaoudi I. Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow. Stem Cell Reports 2023; 18:1884-1897. [PMID: 37657446 PMCID: PMC10545484 DOI: 10.1016/j.stemcr.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023] Open
Abstract
Chronic heavy alcohol drinking (CHD) rewires monocytes and macrophages toward heightened inflammatory states with compromised antimicrobial defenses that persist after 1-month abstinence. To determine whether these changes are mediated through alterations in the bone marrow niche, we profiled monocytes and hematopoietic stem cell progenitors (HSCPs) from CHD rhesus macaques using a combination of functional assays and single cell genomics. CHD resulted in transcriptional profiles consistent with increased activation and inflammation within bone marrow resident monocytes and macrophages. Furthermore, CHD resulted in transcriptional signatures associated with increased oxidative and cellular stress in HSCP. Differentiation of HSCP in vitro revealed skewing toward monocytes expressing "neutrophil-like" markers with greater inflammatory responses to bacterial agonists. Further analyses of HSCPs showed broad epigenetic changes that were in line with exacerbated inflammatory responses within monocytes and their progenitors. In summary, CHD alters HSCPs in the bone marrow leading to the production of monocytes poised to generate dysregulated hyper-inflammatory responses.
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Affiliation(s)
- Sloan A Lewis
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Qi Qiao
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Madison Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Kathleen A Grant
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.
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205
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Tan L, Shi J, Moghadami S, Parasar B, Wright CP, Seo Y, Vallejo K, Cobos I, Duncan L, Chen R, Deisseroth K. Lifelong restructuring of 3D genome architecture in cerebellar granule cells. Science 2023; 381:1112-1119. [PMID: 37676945 PMCID: PMC11059189 DOI: 10.1126/science.adh3253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
The cerebellum contains most of the neurons in the human brain and exhibits distinctive modes of development and aging. In this work, by developing our single-cell three-dimensional (3D) genome assay-diploid chromosome conformation capture, or Dip-C-into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we resolved the first 3D genome structures of single cerebellar cells, created life-spanning 3D genome atlases for both humans and mice, and jointly measured transcriptome and chromatin accessibility during development. We found that although the transcriptome and chromatin accessibility of cerebellar granule neurons mature in early postnatal life, 3D genome architecture gradually remodels throughout life, establishing ultra-long-range intrachromosomal contacts and specific interchromosomal contacts that are rarely seen in neurons. These results reveal unexpected evolutionarily conserved molecular processes that underlie distinctive features of neural development and aging across the mammalian life span.
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Affiliation(s)
- Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - Jenny Shi
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Siavash Moghadami
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305
| | - Bibudha Parasar
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
| | - Cydney P. Wright
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Biology, Stanford University, Stanford, CA, 94305
| | - Yunji Seo
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
| | - Kristen Vallejo
- Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Inma Cobos
- Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305
- Howard Hughes Medical Institute, Stanford, CA, 94305
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206
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Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Integration of spatial and single-cell data across modalities with weakly linked features. Nat Biotechnol 2023:10.1038/s41587-023-01935-0. [PMID: 37679544 DOI: 10.1038/s41587-023-01935-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori 'linked' features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked. MaxFuse is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving 20~70% relative improvement over existing methods under key evaluation metrics on benchmarking datasets. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, MaxFuse enabled the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
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Affiliation(s)
- Shuxiao Chen
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sijia Huang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - John W Hickey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Nancy R Zhang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
| | - Zongming Ma
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA.
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207
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Ma Z, Zhang X, Zhong W, Yi H, Chen X, Zhao Y, Ma Y, Song E, Xu T. Deciphering early human pancreas development at the single-cell level. Nat Commun 2023; 14:5354. [PMID: 37660175 PMCID: PMC10475098 DOI: 10.1038/s41467-023-40893-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Understanding pancreas development can provide clues for better treatments of pancreatic diseases. However, the molecular heterogeneity and developmental trajectory of the early human pancreas are poorly explored. Here, we performed large-scale single-cell RNA sequencing and single-cell assay for transposase accessible chromatin sequencing of human embryonic pancreas tissue obtained from first-trimester embryos. We unraveled the molecular heterogeneity, developmental trajectories and regulatory networks of the major cell types. The results reveal that dorsal pancreatic multipotent cells in humans exhibit different gene expression patterns than ventral multipotent cells. Pancreato-biliary progenitors that generate ventral multipotent cells in humans were identified. Notch and MAPK signals from mesenchymal cells regulate the differentiation of multipotent cells into trunk and duct cells. Notably, we identified endocrine progenitor subclusters with different differentiation potentials. Although the developmental trajectories are largely conserved between humans and mice, some distinct gene expression patterns have also been identified. Overall, we provide a comprehensive landscape of early human pancreas development to understand its lineage transitions and molecular complexity.
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Affiliation(s)
- Zhuo Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Wen Zhong
- Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, 581 83, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Xiaowei Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinsuo Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China.
| | - Eli Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Guangzhou Laboratory, Guangzhou, 510005, China.
- Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
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208
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Engel JL, Zhang X, Lu DR, Vila OF, Arias V, Lee J, Hale C, Hsu YH, Li CM, Wu RS, Vedantham V, Ang YS. Single Cell Multi-Omics of an iPSC Model of Human Sinoatrial Node Development Reveals Genetic Determinants of Heart Rate and Arrhythmia Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.01.547335. [PMID: 37425707 PMCID: PMC10327193 DOI: 10.1101/2023.07.01.547335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cellular heterogeneity within the sinoatrial node (SAN) is functionally important but has been difficult to model in vitro , presenting a major obstacle to studies of heart rate regulation and arrhythmias. Here we describe a scalable method to derive sinoatrial node pacemaker cardiomyocytes (PCs) from human induced pluripotent stem cells that recapitulates differentiation into distinct PC subtypes, including SAN Head, SAN Tail, transitional zone cells, and sinus venosus myocardium. Single cell (sc) RNA-sequencing, sc-ATAC-sequencing, and trajectory analyses were used to define epigenetic and transcriptomic signatures of each cell type, and to identify novel transcriptional pathways important for PC subtype differentiation. Integration of our multi-omics datasets with genome wide association studies uncovered cell type-specific regulatory elements that associated with heart rate regulation and susceptibility to atrial fibrillation. Taken together, these datasets validate a novel, robust, and realistic in vitro platform that will enable deeper mechanistic exploration of human cardiac automaticity and arrhythmia.
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209
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Zhong J, Qiu M, Meng Y, Wang P, Chen S, Wang L. Single-cell multi-omics sequencing reveals the immunological disturbance underlying STAT3-V637M Hyper-IgE syndrome. Int Immunopharmacol 2023; 122:110624. [PMID: 37480751 DOI: 10.1016/j.intimp.2023.110624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
Hyper-IgE syndrome (HIES) is a primary immunodeficiency characterized by, among others, the excessive production of IgE and repetitive bacterial/fungal infections. Mutations in STAT3, a transcription factor that orchestrates immune responses, may cause HIES, but the underlying mechanisms are not fully understood. Here, we used multi-omic approaches to comprehensively decipher the immune disturbance in a male HIES patient harboring STAT3-V637M. In his peripheral blood mononuclear cell (PBMC) we found significant clonal expansion of CD8 T cells (with increased CD8 subunits expression, potentially enhancing responsiveness to MHC I molecules), but not in his CD4 T cells and B cells. Although his B cells exhibited a higher potential in producing immunoglobulin, elevated SPIC binding might bias the products toward IgE isotype. Immune checkpoint inhibitors, including CTLA4, LAG3, were overexpressed in his PBMC-CD4 T cells, accompanied by reduced CD28 and IL6ST (gp130) expression. In his CD4 T cells, integrative analyses predicted upstream transcription factors (including ETV6, KLF13, and RORA) for LAG3, IL6ST, and CD28, respectively. The down-regulation of phagocytosis and nitric oxide synthesis-related genes in his PBMC-monocytes seem to be the culprit of his disseminated bacterial/fungal infection. Counterintuitively, in his PBMC we predicted increased STAT3 binding in both naïve and mature CD4 compartments, although this was not observed in most of his PBMC. In his bronchoalveolar lavage fluid (BALF), we found two macrophage subtypes with anti-bacterial properties, which were identified by CXCL8/S100A8/S100A9, or SOD2, respectively. Together, we described how the immune cell landscape was disturbed in STAT3-V637M HIES, providing a resource for further studies.
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Affiliation(s)
- Jiacheng Zhong
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China
| | - Minzhi Qiu
- Health Management Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Yu Meng
- Department of Quality Control, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China
| | - Peizhong Wang
- Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shanze Chen
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
| | - Lingwei Wang
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
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210
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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211
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Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023; 20:1368-1378. [PMID: 37537351 DOI: 10.1038/s41592-023-01971-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.
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Affiliation(s)
- Lingfei Wang
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Trasanidis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Ting Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Guanlan Dong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA
| | - Michael Hu
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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212
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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213
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Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM. Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. Alzheimers Dement 2023; 19:3902-3915. [PMID: 37037656 PMCID: PMC10529851 DOI: 10.1002/alz.13075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in AD brains from APOE ε4/ε4 carriers. Chromatin accessibility differences could contribute to these expression changes. METHODS We performed single nuclei assays for transposase accessible chromatin sequencing from the frontal cortex of six ALA and six ELA AD brains, homozygous for local ancestry and APOE ε4. RESULTS Our results showed an increased chromatin accessibility at the APOE ε4 promoter area in ELA versus ALA astrocytes. This increased accessibility in ELA astrocytes extended genome wide. Genes with increased accessibility in ELA in astrocytes were enriched for synapsis, cholesterol processing, and astrocyte reactivity. DISCUSSION Our results suggest that increased chromatin accessibility of APOE ε4 in ELA astrocytes contributes to the observed elevated APOE ε4 expression, corresponding to the increased AD risk in ELA versus ALA APOE ε4/ε4 carriers.
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Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Maria DM. Muniz Moreno
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Margaret Flanagan
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Sandra Weintraub
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Changiz Geula
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Marla Gearing
- Goizueta Alzheimer’s Disease Research Center, Emory University, Atlanta, GA, USA, 15213
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA, 20814
- Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, MD, USA, 20817
- Department of Anatomy Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA, 20814
| | - Fulai Jin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA, 44106
| | - David A. Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA, 60612
| | - Theresa Schuck
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,19104
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Juan I. Young
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
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214
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Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023; 186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
Abstract
Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.
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Affiliation(s)
- Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Siddhartha Sharma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Simon A Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paoline Laurent
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Lucinda Paddock
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Emin Onur Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinay K Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Jim K Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Minh Y Mays
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexia Martinez de Paz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dughan Ahimovic
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Victor Ramos
- The Rockefeller University, New York, NY 10065, USA
| | | | - Erik Nielsen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ling Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Alisha Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lexi Robbins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Karissa L Weidman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sabrina Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - He S Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David R Price
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Louise Leyre
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junbum Kim
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Northwell Health, Greenvale, NY 11548, USA
| | | | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Virginia Pascual
- Department of Pediatrics, Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Rachel E Niec
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; The Rockefeller University, New York, NY 10065, USA
| | - Franck J Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA; HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lindsay Lief
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
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215
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Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
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Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
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216
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Liu X, Liu X, Du Y, Zou D, Tian C, Li Y, Lan X, David CJ, Sun Q, Chen M. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression. Cell Rep 2023; 42:112979. [PMID: 37572321 DOI: 10.1016/j.celrep.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023] Open
Abstract
KRAS is the most commonly mutated oncogene in human cancer, and mutant KRAS is responsible for over 90% of pancreatic ductal adenocarcinoma (PDAC), the most lethal cancer. Here, we show that RNA polymerase II-associated factor 1 complex (PAF1C) is specifically required for survival of PDAC but not normal adult pancreatic cells. We show that PAF1C maintains cancer cell genomic stability by restraining overaccumulation of enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of pervasive transcripts on chromatin and concomitant aberrant R-loop formation and DNA damage, which, in turn, trigger cell death. We go on to demonstrate that the global transcriptional hyperactivation driven by Kras signaling during tumorigenesis underlies the specific demand for PAF1C by cancer cells. Our work provides insights into how enhancer transcription hyperactivation causes general transcription factor addiction during tumorigenesis.
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Affiliation(s)
- Xinhong Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangzheng Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yingxue Du
- Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Di Zou
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chen Tian
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yong Li
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Charles J David
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua University School of Life Sciences, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China.
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217
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Leon J, Chowdhary K, Zhang W, Ramirez RN, André I, Hur S, Mathis D, Benoist C. Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction. Cell Rep 2023; 42:113018. [PMID: 37605532 PMCID: PMC10565790 DOI: 10.1016/j.celrep.2023.113018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
Mutations of the transcription factor FoxP3 in patients with "IPEX" (immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome) disrupt regulatory T cells (Treg), causing an array of multiorgan autoimmunity. To understand the functional impact of mutations across FoxP3 domains, without genetic and environmental confounders, six human FOXP3 missense mutations are engineered into mice. Two classes of mutations emerge from combined immunologic and genomic analyses. A mutation in the DNA-binding domain shows the same lymphoproliferation and multiorgan infiltration as complete FoxP3 knockouts but delayed by months. Tregs expressing this mutant FoxP3 are destabilized by normal Tregs in heterozygous females compared with hemizygous males. Mutations in other domains affect chromatin opening differently, involving different cofactors and provoking more specific autoimmune pathology (dermatitis, colitis, diabetes), unmasked by immunological challenges or incrossing NOD autoimmune-susceptibility alleles. This work establishes that IPEX disease heterogeneity results from the actual mutations, combined with genetic and environmental perturbations, explaining then the intra-familial variation in IPEX.
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Affiliation(s)
- Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA, USA; INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | | | - Wenxiang Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Isabelle André
- INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | - Sun Hur
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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218
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Gunawan I, Vafaee F, Meijering E, Lock JG. An introduction to representation learning for single-cell data analysis. CELL REPORTS METHODS 2023; 3:100547. [PMID: 37671013 PMCID: PMC10475795 DOI: 10.1016/j.crmeth.2023.100547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Single-cell-resolved systems biology methods, including omics- and imaging-based measurement modalities, generate a wealth of high-dimensional data characterizing the heterogeneity of cell populations. Representation learning methods are routinely used to analyze these complex, high-dimensional data by projecting them into lower-dimensional embeddings. This facilitates the interpretation and interrogation of the structures, dynamics, and regulation of cell heterogeneity. Reflecting their central role in analyzing diverse single-cell data types, a myriad of representation learning methods exist, with new approaches continually emerging. Here, we contrast general features of representation learning methods spanning statistical, manifold learning, and neural network approaches. We consider key steps involved in representation learning with single-cell data, including data pre-processing, hyperparameter optimization, downstream analysis, and biological validation. Interdependencies and contingencies linking these steps are also highlighted. This overview is intended to guide researchers in the selection, application, and optimization of representation learning strategies for current and future single-cell research applications.
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Affiliation(s)
- Ihuan Gunawan
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
| | - Erik Meijering
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | - John George Lock
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
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219
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Kim H, Wisniewska K, Regner MJ, Thennavan A, Spanheimer PM, Franco HL. Single-Cell Transcriptional and Epigenetic Profiles of Male Breast Cancer Nominate Salient Cancer-Specific Enhancers. Int J Mol Sci 2023; 24:13053. [PMID: 37685859 PMCID: PMC10487538 DOI: 10.3390/ijms241713053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Male breast cancer represents about 1% of all breast cancer diagnoses and, although there are some similarities between male and female breast cancer, the paucity of data available on male breast cancer makes it difficult to establish targeted therapies. To date, most male breast cancers (MBCs) are treated according to protocols established for female breast cancer (FBC). Thus, defining the transcriptional and epigenetic landscape of MBC with improved resolution is critical for developing better avenues for therapeutic intervention. In this study, we present matched transcriptional (scRNA-seq) and epigenetic (scATAC-seq) profiles at single-cell resolution of two treatment naïve MBC tumors processed immediately after surgical resection. These data enable the detection of differentially expressed genes between male and female breast tumors across immune, stromal, and malignant cell types, to highlight several genes that may have therapeutic implications. Notably, MYC target genes and mTORC1 signaling genes were significantly upregulated in the malignant cells of MBC compared to the female counterparts. To understand how the regulatory landscape of MBC gives rise to these male-specific gene expression patterns, we leveraged the scATAC-seq data to systematically link changes in chromatin accessibility to changes in gene expression within each cell type. We observed cancer-specific rewiring of several salient enhancers and posit that these enhancers have a higher regulatory load than lineage-specific enhancers. We highlight two examples of previously unannotated cancer-cell-specific enhancers of ANXA2 and PRDX4 gene expression and show evidence for super-enhancer regulation of LAMB3 and CD47 in male breast cancer cells. Overall, this dataset annotates clinically relevant regulatory networks in male breast tumors, providing a useful resource that expands our current understanding of the gene expression programs that underlie the biology of MBC.
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Affiliation(s)
- Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Aatish Thennavan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Oral and Craniofacial Biomedicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Surgical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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220
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John L, Poos AM, Brobeil A, Schinke C, Huhn S, Prokoph N, Lutz R, Wagner B, Zangari M, Tirier SM, Mallm JP, Schumacher S, Vonficht D, Solé-Boldo L, Quick S, Steiger S, Przybilla MJ, Bauer K, Baumann A, Hemmer S, Rehnitz C, Lückerath C, Sachpekidis C, Mechtersheimer G, Haberkorn U, Dimitrakopoulou-Strauss A, Reichert P, Barlogie B, Müller-Tidow C, Goldschmidt H, Hillengass J, Rasche L, Haas SF, van Rhee F, Rippe K, Raab MS, Sauer S, Weinhold N. Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level. Nat Commun 2023; 14:5011. [PMID: 37591845 PMCID: PMC10435504 DOI: 10.1038/s41467-023-40584-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
In multiple myeloma spatial differences in the subclonal architecture, molecular signatures and composition of the microenvironment remain poorly characterized. To address this shortcoming, we perform multi-region sequencing on paired random bone marrow and focal lesion samples from 17 newly diagnosed patients. Using single-cell RNA- and ATAC-seq we find a median of 6 tumor subclones per patient and unique subclones in focal lesions. Genetically identical subclones display different levels of spatial transcriptional plasticity, including nearly identical profiles and pronounced heterogeneity at different sites, which can include differential expression of immunotherapy targets, such as CD20 and CD38. Macrophages are significantly depleted in the microenvironment of focal lesions. We observe proportional changes in the T-cell repertoire but no site-specific expansion of T-cell clones in intramedullary lesions. In conclusion, our results demonstrate the relevance of considering spatial heterogeneity in multiple myeloma with potential implications for models of cell-cell interactions and disease progression.
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Affiliation(s)
- Lukas John
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M Poos
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Brobeil
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stefanie Huhn
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Nina Prokoph
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Lutz
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Barbara Wagner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephan M Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Sabine Quick
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Moritz J Przybilla
- Division Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Anja Baumann
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Hemmer
- Department of Orthopedic Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Rehnitz
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Lückerath
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christos Sachpekidis
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Antonia Dimitrakopoulou-Strauss
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Reichert
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jens Hillengass
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Simon F Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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221
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Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023; 14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.
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Affiliation(s)
- Alan Selewa
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Wasney
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Linsin Smith
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chenwei Tang
- The College, The University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ivan P Moskowitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anindita Basu
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Sebastian Pott
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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222
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Berson E, Sreenivas A, Phongpreecha T, Perna A, Grandi FC, Xue L, Ravindra NG, Payrovnaziri N, Mataraso S, Kim Y, Espinosa C, Chang AL, Becker M, Montine KS, Fox EJ, Chang HY, Corces MR, Aghaeepour N, Montine TJ. Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature. Nat Commun 2023; 14:4947. [PMID: 37587197 PMCID: PMC10432546 DOI: 10.1038/s41467-023-40611-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. To address this, we developed Cellformer, a deep learning method that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enables cost-effective cell type-specific open chromatin profiling in large cohorts. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms involved in resilience to Alzheimer's disease, an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer's disease. Cell type-resolved chromatin profiling unveils cell type-specific pathways and nominates potential epigenetic mediators underlying resilience that may illuminate therapeutic opportunities to limit the cognitive impact of the disease. Cellformer is freely available to facilitate future investigations using high-throughput bulk ATAC-seq data.
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Affiliation(s)
- Eloise Berson
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Anjali Sreenivas
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Amalia Perna
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lei Xue
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Neal G Ravindra
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Neelufar Payrovnaziri
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yeasul Kim
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Edward J Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
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223
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Abstract
Organismal aging exhibits wide-ranging hallmarks in divergent cell types across tissues, organs, and systems. The advancement of single-cell technologies and generation of rich datasets have afforded the scientific community the opportunity to decode these hallmarks of aging at an unprecedented scope and resolution. In this review, we describe the technological advancements and bioinformatic methodologies enabling data interpretation at the cellular level. Then, we outline the application of such technologies for decoding aging hallmarks and potential intervention targets and summarize common themes and context-specific molecular features in representative organ systems across the body. Finally, we provide a brief summary of available databases relevant for aging research and present an outlook on the opportunities in this emerging field.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xu Chi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zhejun Ji
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jie Ren
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
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224
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Flynn E, Almonte-Loya A, Fragiadakis GK. Single-Cell Multiomics. Annu Rev Biomed Data Sci 2023; 6:313-337. [PMID: 37159875 PMCID: PMC11146013 DOI: 10.1146/annurev-biodatasci-020422-050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Single-cell RNA sequencing methods have led to improved understanding of the heterogeneity and transcriptomic states present in complex biological systems. Recently, the development of novel single-cell technologies for assaying additional modalities, specifically genomic, epigenomic, proteomic, and spatial data, allows for unprecedented insight into cellular biology. While certain technologies collect multiple measurements from the same cells simultaneously, even when modalities are separately assayed in different cells, we can apply novel computational methods to integrate these data. The application of computational integration methods to multimodal paired and unpaired data results in rich information about the identities of the cells present and the interactions between different levels of biology, such as between genetic variation and transcription. In this review, we both discuss the single-cell technologies for measuring these modalities and describe and characterize a variety of computational integration methods for combining the resulting data to leverage multimodal information toward greater biological insight.
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Affiliation(s)
- Emily Flynn
- CoLabs, University of California, San Francisco, California, USA;
| | - Ana Almonte-Loya
- CoLabs, University of California, San Francisco, California, USA;
- Biomedical Informatics Program, University of California, San Francisco, California, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, California, USA;
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
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225
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Miyata K, Zhou X, Nishio M, Hanyu A, Chiba M, Kawasaki H, Osako T, Takeuchi K, Ohno S, Ueno T, Maruyama R, Takahashi A. Chromatin conformational changes at human satellite II contribute to the senescence phenotype in the tumor microenvironment. Proc Natl Acad Sci U S A 2023; 120:e2305046120. [PMID: 37523559 PMCID: PMC10410700 DOI: 10.1073/pnas.2305046120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
Cellular senescence and senescence-associated secretory phenotype (SASP) in stromal cells within the tumor microenvironment promote cancer progression. Although cellular senescence has been shown to induce changes in the higher-order chromatin structure and abnormal transcription of repetitive elements in the genome, the functional significance of these changes is unclear. In this study, we examined the human satellite II (hSATII) loci in the pericentromere to understand these changes and their functional significance. Our results indicated that the hSATII loci decompact during senescence induction, resulting in new DNA-DNA interactions in distinct genomic regions, which we refer to as DRISR (Distinctive Regions Interacted with Satellite II in Replicative senescent Fibroblasts). Interestingly, decompaction occurs before the expression of hSATII RNA. The DRISR with altered chromatin accessibility was enriched for motifs associated with cellular senescence and inflammatory SASP genes. Moreover, DNA-fluorescence in situ hybridization analysis of the breast cancer tissues revealed hSATII decompaction in cancer and stromal cells. Furthermore, we reanalyzed the single-cell assay for transposase-accessible chromatin with sequencing data and found increased SASP-related gene expression in fibroblasts exhibiting hSATII decompaction in breast cancer tissues. These findings suggest that changes in the higher-order chromatin structure of the pericentromeric repetitive sequences during cellular senescence might directly contribute to the cellular senescence phenotype and cancer progression via inflammatory gene expression.
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Affiliation(s)
- Kenichi Miyata
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Xiangyu Zhou
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Mika Nishio
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Aki Hanyu
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Masatomo Chiba
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Hiroko Kawasaki
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Tomo Osako
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Shinji Ohno
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Takayuki Ueno
- Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Akiko Takahashi
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Advanced Research and Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development, Tokyo100-0004, Japan
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226
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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, HItchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552451. [PMID: 37609307 PMCID: PMC10441373 DOI: 10.1101/2023.08.08.552451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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227
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Okafor AE, Lin X, Situ C, Wei X, Xiang Y, Wei X, Wu Z, Diao Y. Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state. J Cell Biol 2023; 222:e202211073. [PMID: 37382627 PMCID: PMC10309185 DOI: 10.1083/jcb.202211073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/30/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023] Open
Abstract
A balance between self-renewal and differentiation is critical for the regenerative capacity of tissue-resident stem cells. In skeletal muscle, successful regeneration requires the orchestrated activation, proliferation, and differentiation of muscle satellite cells (MuSCs) that are normally quiescent. A subset of MuSCs undergoes self-renewal to replenish the stem cell pool, but the features that identify and define self-renewing MuSCs remain to be elucidated. Here, through single-cell chromatin accessibility analysis, we reveal the self-renewal versus differentiation trajectories of MuSCs over the course of regeneration in vivo. We identify Betaglycan as a unique marker of self-renewing MuSCs that can be purified and efficiently contributes to regeneration after transplantation. We also show that SMAD4 and downstream genes are genetically required for self-renewal in vivo by restricting differentiation. Our study unveils the identity and mechanisms of self-renewing MuSCs, while providing a key resource for comprehensive analysis of muscle regeneration.
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Affiliation(s)
- Arinze E. Okafor
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Chenghao Situ
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xiaolin Wei
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Xiuqing Wei
- Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Zhenguo Wu
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
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228
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Vandereyken K, Sifrim A, Thienpont B, Voet T. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet 2023; 24:494-515. [PMID: 36864178 PMCID: PMC9979144 DOI: 10.1038/s41576-023-00580-2] [Citation(s) in RCA: 188] [Impact Index Per Article: 188.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 03/04/2023]
Abstract
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.
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Affiliation(s)
- Katy Vandereyken
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Alejandro Sifrim
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Bernard Thienpont
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium.
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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229
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Li C, Chen X, Chen S, Jiang R, Zhang X. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinformatics 2023; 39:btad453. [PMID: 37494428 PMCID: PMC10394124 DOI: 10.1093/bioinformatics/btad453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
MOTIVATION Single-cell chromatin accessibility sequencing (scCAS) technology provides an epigenomic perspective to characterize gene regulatory mechanisms at single-cell resolution. With an increasing number of computational methods proposed for analyzing scCAS data, a powerful simulation framework is desirable for evaluation and validation of these methods. However, existing simulators generate synthetic data by sampling reads from real data or mimicking existing cell states, which is inadequate to provide credible ground-truth labels for method evaluation. RESULTS We present simCAS, an embedding-based simulator, for generating high-fidelity scCAS data from both cell- and peak-wise embeddings. We demonstrate simCAS outperforms existing simulators in resembling real data and show that simCAS can generate cells of different states with user-defined cell populations and differentiation trajectories. Additionally, simCAS can simulate data from different batches and encode user-specified interactions of chromatin regions in the synthetic data, which provides ground-truth labels more than cell states. We systematically demonstrate that simCAS facilitates the benchmarking of four core tasks in downstream analysis: cell clustering, trajectory inference, data integration, and cis-regulatory interaction inference. We anticipate simCAS will be a reliable and flexible simulator for evaluating the ongoing computational methods applied on scCAS data. AVAILABILITY AND IMPLEMENTATION simCAS is freely available at https://github.com/Chen-Li-17/simCAS.
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Affiliation(s)
- Chen Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaoyang Chen
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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230
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Llorens-Bobadilla E, Zamboni M, Marklund M, Bhalla N, Chen X, Hartman J, Frisén J, Ståhl PL. Solid-phase capture and profiling of open chromatin by spatial ATAC. Nat Biotechnol 2023; 41:1085-1088. [PMID: 36604544 PMCID: PMC10421738 DOI: 10.1038/s41587-022-01603-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
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Affiliation(s)
| | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maja Marklund
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nayanika Bhalla
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xinsong Chen
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Patrik L Ståhl
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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231
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Zhang W, Xu Y, Wang X, Oikawa T, Su G, Wauthier E, Wu G, Sethupathy P, He Z, Liu J, Reid LM. Fibrolamellar carcinomas-growth arrested by paracrine signals complexed with synthesized 3-O sulfated heparan sulfate oligosaccharides. Matrix Biol 2023; 121:194-216. [PMID: 37402431 DOI: 10.1016/j.matbio.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/30/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Fibrolamellar carcinomas (FLCs), lethal tumors occurring in children to young adults, have genetic signatures implicating derivation from biliary tree stem cell (BTSC) subpopulations, co-hepato/pancreatic stem cells, involved in hepatic and pancreatic regeneration. FLCs and BTSCs express pluripotency genes, endodermal transcription factors, and stem cell surface, cytoplasmic and proliferation biomarkers. The FLC-PDX model, FLC-TD-2010, is driven ex vivo to express pancreatic acinar traits, hypothesized responsible for this model's propensity for enzymatic degradation of cultures. A stable ex vivo model of FLC-TD-2010 was achieved using organoids in serum-free Kubota's Medium (KM) supplemented with 0.1% hyaluronans (KM/HA). Heparins (10 ng/ml) caused slow expansion of organoids with doubling times of ∼7-9 days. Spheroids, organoids depleted of mesenchymal cells, survived indefinitely in KM/HA in a state of growth arrest for more than 2 months. Expansion was restored with FLCs co-cultured with mesenchymal cell precursors in a ratio of 3:7, implicating paracrine signaling. Signals identified included FGFs, VEGFs, EGFs, Wnts, and others, produced by associated stellate and endothelial cell precursors. Fifty-three, unique heparan sulfate (HS) oligosaccharides were synthesized, assessed for formation of high affinity complexes with paracrine signals, and each complex screened for biological activity(ies) on organoids. Ten distinct HS-oligosaccharides, all 10-12 mers or larger, and in specific paracrine signal complexes elicited particular biological responses. Of note, complexes of paracrine signals and 3-O sulfated HS-oligosaccharides elicited slowed growth, and with Wnt3a, elicited growth arrest of organoids for months. If future efforts are used to prepare HS-oligosaccharides resistant to breakdown in vivo, then [paracrine signal-HS-oligosaccharide] complexes are potential therapeutic agents for clinical treatments of FLCs, an exciting prospect for a deadly disease.
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Affiliation(s)
- Wencheng Zhang
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States; Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China; Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai 200335, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, United States; Glycan Therapeutics Corporation, 617 Hutton Street, Raleigh, NC 27606, United States
| | - Xicheng Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China; Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai 200335, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Tsunekazu Oikawa
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Guowei Su
- Glycan Therapeutics Corporation, 617 Hutton Street, Raleigh, NC 27606, United States
| | - Eliane Wauthier
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Guoxiu Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China; Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai 200335, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Praveen Sethupathy
- Division of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China; Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai 200335, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, United States; Glycan Therapeutics Corporation, 617 Hutton Street, Raleigh, NC 27606, United States
| | - Lola M Reid
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States; Program in Molecular Biology and Biotechnology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, United States.
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232
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Ashuach T, Gabitto MI, Koodli RV, Saldi GA, Jordan MI, Yosef N. MultiVI: deep generative model for the integration of multimodal data. Nat Methods 2023; 20:1222-1231. [PMID: 37386189 PMCID: PMC10406609 DOI: 10.1038/s41592-023-01909-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/10/2023] [Indexed: 07/01/2023]
Abstract
Jointly profiling the transcriptome, chromatin accessibility and other molecular properties of single cells offers a powerful way to study cellular diversity. Here we present MultiVI, a probabilistic model to analyze such multiomic data and leverage it to enhance single-modality datasets. MultiVI creates a joint representation that allows an analysis of all modalities included in the multiomic input data, even for cells for which one or more modalities are missing. It is available at scvi-tools.org .
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Affiliation(s)
- Tal Ashuach
- Center for Computational Biology, University of California, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Mariano I Gabitto
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Rohan V Koodli
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | | | - Michael I Jordan
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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233
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Gaulton KJ, Preissl S, Ren B. Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nat Rev Genet 2023; 24:516-534. [PMID: 37161089 PMCID: PMC10629587 DOI: 10.1038/s41576-023-00598-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence variants in the human genome to common traits and diseases. However, translating this knowledge into a mechanistic understanding of disease-relevant biology remains challenging, largely because such variants are predominantly in non-protein-coding sequences that still lack functional annotation at cell-type resolution. Recent advances in single-cell epigenomics assays have enabled the generation of cell type-, subtype- and state-resolved maps of the epigenome in heterogeneous human tissues. These maps have facilitated cell type-specific annotation of candidate cis-regulatory elements and their gene targets in the human genome, enhancing our ability to interpret the genetic basis of common traits and diseases.
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Affiliation(s)
- Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
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234
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Ober-Reynolds B, Wang C, Ko JM, Rios EJ, Aasi SZ, Davis MM, Oro AE, Greenleaf WJ. Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. Nat Genet 2023; 55:1288-1300. [PMID: 37500727 PMCID: PMC11190942 DOI: 10.1038/s41588-023-01445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/17/2023] [Indexed: 07/29/2023]
Abstract
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. We generated matched single-cell chromatin profiles and transcriptomes from scalp tissue from healthy controls and patients with alopecia areata, identifying diverse cell types of the hair follicle niche. By interrogating these datasets at multiple levels of cellular resolution, we infer 50-100% more enhancer-gene links than previous approaches and show that aggregate enhancer accessibility for highly regulated genes predicts expression. We use these gene-regulatory maps to prioritize cell types, genes and causal variants implicated in the pathobiology of androgenetic alopecia (AGA), eczema and other complex traits. AGA genome-wide association studies signals are enriched in dermal papilla regulatory regions, supporting the role of these cells as drivers of AGA pathogenesis. Finally, we train machine learning models to nominate single-nucleotide polymorphisms that affect gene expression through disruption of transcription factor binding, predicting candidate functional single-nucleotide polymorphism for AGA and eczema.
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Affiliation(s)
| | - Chen Wang
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Justin M Ko
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Eon J Rios
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - Sumaira Z Aasi
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anthony E Oro
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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235
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Barnett J, Sotudeh N, Rao P, Silverman J, Jafar T, Wang L. AtlasXplore: a web platform for visualizing and sharing spatial epigenome data. Bioinformatics 2023; 39:btad447. [PMID: 37478350 PMCID: PMC10394123 DOI: 10.1093/bioinformatics/btad447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023] Open
Abstract
MOTIVATION In recent years, a growing number of spatial epigenome datasets have been generated, presenting rich opportunities for studying the regulation mechanisms in solid tissue sections. However, visual exploration of these datasets requires extensive computational processing of raw data, presenting a challenge for researchers without advanced computational skills to fully explore and analyze such datasets. RESULTS Here, we introduce AtlasXplore, a web-based platform that enables scientists to interactively navigate a growing collection of spatial epigenome data using an expanding set of tools. AVAILABILITY AND IMPLEMENTATION https://web.atlasxomics.com.
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Affiliation(s)
- Joshua Barnett
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
| | - Noori Sotudeh
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
| | - Poorvi Rao
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
| | - Jonah Silverman
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
| | - Tamara Jafar
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
| | - Liya Wang
- Bioinformatics and Software Engineering, AtlasXomics Inc, New Haven, CT 06519, United States
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236
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Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F, Schiller HB, Theis FJ. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023; 24:550-572. [PMID: 37002403 PMCID: PMC10066026 DOI: 10.1038/s41576-023-00586-w] [Citation(s) in RCA: 137] [Impact Index Per Article: 137.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 04/03/2023]
Abstract
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
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Affiliation(s)
- Lukas Heumos
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Anna C Schaar
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany
| | - Christopher Lance
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Paediatrics, Dr von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anastasia Litinetskaya
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Felix Drost
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Luke Zappia
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Malte D Lücken
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity, Helmholtz Munich, Munich, Germany
| | - Daniel C Strobl
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Juan Henao
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
| | - Fabiola Curion
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Herbert B Schiller
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany.
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237
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Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550836. [PMID: 37546906 PMCID: PMC10402156 DOI: 10.1101/2023.07.27.550836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The identification of cell-type-specific 3D chromatin interactions between regulatory elements can help to decipher gene regulation and to interpret the function of disease-associated non-coding variants. However, current chromosome conformation capture (3C) technologies are unable to resolve interactions at this resolution when only small numbers of cells are available as input. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps and regulatory interactions from single-cell ATAC sequencing (scATAC-seq) data alone. ChromaFold uses pseudobulk chromatin accessibility, co-accessibility profiles across metacells, and predicted CTCF motif tracks as input features and employs a lightweight architecture to enable training on standard GPUs. Once trained on paired scATAC-seq and Hi-C data in human cell lines and tissues, ChromaFold can accurately predict both the 3D contact map and peak-level interactions across diverse human and mouse test cell types. In benchmarking against a recent deep learning method that uses bulk ATAC-seq, DNA sequence, and CTCF ChIP-seq to make cell-type-specific predictions, ChromaFold yields superior prediction performance when including CTCF ChIP-seq data as an input and comparable performance without. Finally, fine-tuning ChromaFold on paired scATAC-seq and Hi-C in a complex tissue enables deconvolution of chromatin interactions across cell subpopulations. ChromaFold thus achieves state-of-the-art prediction of 3D contact maps and regulatory interactions using scATAC-seq alone as input data, enabling accurate inference of cell-type-specific interactions in settings where 3C-based assays are infeasible.
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Affiliation(s)
- Vianne R. Gao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Rui Yang
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Arnav Das
- University of Washington, Seattle, WA, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dylan R. McNally
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioannis Karagiannidis
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darko Barisic
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Yingqian A. Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Effie Apostolou
- Sanford I Weill department of Medicine, Sandra and Edward Meyer Cancer center, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Alexander Y. Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christina S. Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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238
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The Impact of Genomic Variation on Function (IGVF) Consortium. ARXIV 2023:arXiv:2307.13708v1. [PMID: 37547663 PMCID: PMC10402186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could reveal novel mechanisms of human biology and uncover the basis of genetic predispositions to diseases, thereby guiding the development of new diagnostics and therapeutics. Yet, understanding how genomic variation alters genome function to influence phenotype has proven challenging. To unlock these insights, we need a systematic and comprehensive catalog of genome function and the molecular and cellular effects of genomic variants. Toward this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations, and predictive modeling to investigate the relationships among genomic variation, genome function, and phenotypes. Through systematic comparisons and benchmarking of experimental and computational methods, we aim to create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how both coding and noncoding variants may connect through gene regulatory and protein interaction networks. These experimental data, computational predictions, and accompanying standards and pipelines will be integrated into an open resource that will catalyze community efforts to explore genome function and the impact of genetic variation on human biology and disease across populations.
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239
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Wang D, Li H, Chandel NS, Dou Y, Yi R. MOF-mediated histone H4 Lysine 16 acetylation governs mitochondrial and ciliary functions by controlling gene promoters. Nat Commun 2023; 14:4404. [PMID: 37479688 PMCID: PMC10362062 DOI: 10.1038/s41467-023-40108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
Histone H4 lysine 16 acetylation (H4K16ac), governed by the histone acetyltransferase MOF, orchestrates gene expression regulation and chromatin interaction. However, the roles of MOF and H4K16ac in controlling cellular function and regulating mammalian tissue development remain unclear. Here we show that conditional deletion of Mof in the skin, but not Kansl1, causes severe defects in the self-renewal of basal epithelial progenitors, epidermal differentiation, and hair follicle growth, resulting in barrier defects and perinatal lethality. MOF-regulated genes are highly enriched for essential functions in the mitochondria and cilia. Genetic deletion of Uqcrq, an essential subunit for the electron transport chain (ETC) Complex III, in the skin, recapitulates the defects in epidermal differentiation and hair follicle growth observed in MOF knockout mouse. Together, this study reveals the requirement of MOF-mediated epigenetic mechanism for regulating mitochondrial and ciliary gene expression and underscores the important function of the MOF/ETC axis for mammalian skin development.
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Affiliation(s)
- Dongmei Wang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Haimin Li
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Navdeep S Chandel
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Yali Dou
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Rui Yi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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240
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Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
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Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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241
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Lei Y, Meng Q, Hong F, Zhao M, Gao X. Pan-cancer survey of lncRNA rewiring and functional alternation in tumor-infiltrating T cell by scLNC. Cancer Lett 2023:216319. [PMID: 37468058 DOI: 10.1016/j.canlet.2023.216319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been reported to involve in diverse biological processes, including tumor immunity. Since lncRNAs are expressed with high cell-type specificity, investigation of lncRNAs at the single-cell level will unveil the cell-type-specific functions of lncRNAs. However, at the single-cell level, a systematic pan-cancer analysis of lncRNA functions in tumor immune microenvironments (TIMEs) remains lacking. Here, we performed pan-cancer single-cell profiling of lncRNA functions in TIMEs and developed a tool, scLNC, tailored for lncRNA functional characterization at the single-cell level. scLNC enabled the comparison of lncRNA function from the levels of lncRNA-mRNA pairs, lncRNA regulatory unit activity and unit function in a cell-type-specific manner. Applying scLNC, our analysis depicted the cross-tumor and tumor-specific lncRNA regulatory profiles in the T cell subtypes and revealed the new regulatory units that lncRNAs established in tumor-infiltrating T cells, particularly in the tumor-enriched T cells. We further characterized the activity and functional alternations of lncRNAs through their regulatory units. Overall, our findings suggested that lncRNAs played an important role in the regulation of cytokine production, cell activation and migration in tumor-enriched T cells and further in immunotherapy.
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Affiliation(s)
- Yang Lei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qianqian Meng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Mengyu Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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242
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Otto D, Jordan C, Dury B, Dien C, Setty M. Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548272. [PMID: 37502954 PMCID: PMC10369887 DOI: 10.1101/2023.07.09.548272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cell-state density characterizes the distribution of cells along phenotypic landscapes and is crucial for unraveling the mechanisms that drive cellular differentiation, regeneration, and disease. Here, we present Mellon, a novel computational algorithm for high-resolution estimation of cell-state densities from single-cell data. We demonstrate Mellon's efficacy by dissecting the density landscape of various differentiating systems, revealing a consistent pattern of high-density regions corresponding to major cell types intertwined with low-density, rare transitory states. Utilizing hematopoietic stem cell fate specification to B-cells as a case study, we present evidence implicating enhancer priming and the activation of master regulators in the emergence of these transitory states. Mellon offers the flexibility to perform temporal interpolation of time-series data, providing a detailed view of cell-state dynamics during the inherently continuous developmental processes. Scalable and adaptable, Mellon facilitates density estimation across various single-cell data modalities, scaling linearly with the number of cells. Our work underscores the importance of cell-state density in understanding the differentiation processes, and the potential of Mellon to provide new insights into the regulatory mechanisms guiding cellular fate decisions.
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Affiliation(s)
- Dominik Otto
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Cailin Jordan
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
- Molecular and Cellular Biology Program, University of Washington, Seattle WA
| | - Brennan Dury
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Christine Dien
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
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243
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a Novel Long Noncoding RNA Promoting Vascular Smooth Muscle Inflammation via Scaffolding MKL1 and USP10. Circulation 2023; 148:47-67. [PMID: 37199168 PMCID: PMC10330325 DOI: 10.1161/circulationaha.123.063760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Activation of vascular smooth muscle cell (VSMC) inflammation is vital to initiate vascular disease. The role of human-specific long noncoding RNAs in VSMC inflammation is poorly understood. METHODS Bulk RNA sequencing in differentiated human VSMCs revealed a novel human-specific long noncoding RNA called inflammatory MKL1 (megakaryoblastic leukemia 1) interacting long noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation as well as human atherosclerosis and abdominal aortic aneurysm. The transcriptional regulation of INKILN was verified through luciferase reporter and chromatin immunoprecipitation assays. Loss-of-function and gain-of-function studies and multiple RNA-protein and protein-protein interaction assays were used to uncover a mechanistic role of INKILN in the VSMC proinflammatory gene program. Bacterial artificial chromosome transgenic mice were used to study INKILN expression and function in ligation injury-induced neointimal formation. RESULTS INKILN expression is downregulated in contractile VSMCs and induced in human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB (nuclear factor kappa B) site within its proximal promoter. INKILN activates proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks interleukin-1β-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1 and the luciferase activity of an NF-κB reporter. Furthermore, INKILN knockdown enhances MKL1 ubiquitination through reduced physical interaction with the deubiquitinating enzyme USP10 (ubiquitin-specific peptidase 10). INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in bacterial artificial chromosome transgenic mice. CONCLUSIONS These findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human bacterial artificial chromosome transgenic mice offer a novel and physiologically relevant approach for investigating human-specific long noncoding RNAs under vascular disease conditions.
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Affiliation(s)
- Wei Zhang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jinjing Zhao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Lin Deng
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
| | - Wen Wu
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Shengshuai Shan
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Wolfgang Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
| | | | - David Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Matthew Bennett
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Julie Rodor
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Yao Wei Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Ping Gao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Mihyun Choi
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Margarida M Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - William B. Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
- German Center for Cardiovascular Research (DZHK, partner site Munich), Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Joseph M. Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
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244
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Gao L, Mathur V, Tam SKM, Zhou X, Cheung MF, Chan LY, Estrada-Gutiérrez G, Leung BW, Moungmaithong S, Wang CC, Poon LC, Leung D. Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal-fetal interface following SARS-CoV-2 infection. Nat Cell Biol 2023:10.1038/s41556-023-01169-x. [PMID: 37400500 PMCID: PMC10344786 DOI: 10.1038/s41556-023-01169-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 05/22/2023] [Indexed: 07/05/2023]
Abstract
During pregnancy the maternal-fetal interface plays vital roles in fetal development. Its disruption is frequently found in pregnancy complications. Recent studies show increased incidences of adverse pregnancy outcomes in patients with COVID-19; however, the mechanism remains unclear. Here we analysed the molecular impacts of SARS-CoV-2 infection on the maternal-fetal interface. Generating bulk and single-nucleus transcriptomic and epigenomic profiles from patients with COVID-19 and control samples, we discovered aberrant immune activation and angiogenesis patterns in distinct cells from patients. Surprisingly, retrotransposons were also dysregulated in specific cell types. Notably, reduced enhancer activities of LTR8B elements were functionally linked to the downregulation of pregnancy-specific glycoprotein genes in syncytiotrophoblasts. Our findings revealed that SARS-CoV-2 infection induced substantial changes to the epigenome and transcriptome at the maternal-fetal interface, which may be associated with pregnancy complications.
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Grants
- GRF16103721 Research Grants Council, University Grants Committee (RGC, UGC)
- GRF16103721 Research Grants Council, University Grants Committee (RGC, UGC)
- GRF16103721 Research Grants Council, University Grants Committee (RGC, UGC)
- CRF C5045-20EF Research Grants Council, University Grants Committee (RGC, UGC)
- CRF C5045-20EF Research Grants Council, University Grants Committee (RGC, UGC)
- CRF C5045-20EF Research Grants Council, University Grants Committee (RGC, UGC)
- CRF C5045-20EF Research Grants Council, University Grants Committee (RGC, UGC)
- CUHK 2020.053 Chinese University of Hong Kong (CUHK)
- CUHK 2020.053 Chinese University of Hong Kong (CUHK)
- CUHK 2020.053 Chinese University of Hong Kong (CUHK)
- CUHK 2020.053 Chinese University of Hong Kong (CUHK)
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Affiliation(s)
- Lin Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Vrinda Mathur
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Sabrina Ka Man Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xuemeng Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ming Fung Cheung
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lu Yan Chan
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Bo Wah Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Sakita Moungmaithong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Sciences; School of Biomedical Sciences and The Chinese University of Hong Kong-Sichuan University Joint Laboratory in Reproductive Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liona C Poon
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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245
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Smith MH, Gao VR, Periyakoil PK, Kochen A, DiCarlo EF, Goodman SM, Norman TM, Donlin LT, Leslie CS, Rudensky AY. Drivers of heterogeneity in synovial fibroblasts in rheumatoid arthritis. Nat Immunol 2023; 24:1200-1210. [PMID: 37277655 PMCID: PMC10307631 DOI: 10.1038/s41590-023-01527-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Inflammation of non-barrier immunologically quiescent tissues is associated with a massive influx of blood-borne innate and adaptive immune cells. Cues from the latter are likely to alter and expand activated states of the resident cells. However, local communications between immigrant and resident cell types in human inflammatory disease remain poorly understood. Here, we explored drivers of fibroblast-like synoviocyte (FLS) heterogeneity in inflamed joints of patients with rheumatoid arthritis using paired single-cell RNA and ATAC sequencing, multiplexed imaging and spatial transcriptomics along with in vitro modeling of cell-extrinsic factor signaling. These analyses suggest that local exposures to myeloid and T cell-derived cytokines, TNF, IFN-γ, IL-1β or lack thereof, drive four distinct FLS states some of which closely resemble fibroblast states in other disease-affected tissues including skin and colon. Our results highlight a role for concurrent, spatially distributed cytokine signaling within the inflamed synovium.
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Affiliation(s)
- Melanie H Smith
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA.
- Howard Hughes Medical Institute and Immunology Program at Sloan Kettering Institute, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Vianne R Gao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College and Graduate School, New York, NY, USA
| | - Preethi K Periyakoil
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alejandro Kochen
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Edward F DiCarlo
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, NY, USA
| | - Susan M Goodman
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medical College and Graduate School, New York, NY, USA
| | - Thomas M Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura T Donlin
- Weill Cornell Medical College and Graduate School, New York, NY, USA
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program at Sloan Kettering Institute, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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246
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Kanemaru K, Cranley J, Muraro D, Miranda AMA, Ho SY, Wilbrey-Clark A, Patrick Pett J, Polanski K, Richardson L, Litvinukova M, Kumasaka N, Qin Y, Jablonska Z, Semprich CI, Mach L, Dabrowska M, Richoz N, Bolt L, Mamanova L, Kapuge R, Barnett SN, Perera S, Talavera-López C, Mulas I, Mahbubani KT, Tuck L, Wang L, Huang MM, Prete M, Pritchard S, Dark J, Saeb-Parsy K, Patel M, Clatworthy MR, Hübner N, Chowdhury RA, Noseda M, Teichmann SA. Spatially resolved multiomics of human cardiac niches. Nature 2023; 619:801-810. [PMID: 37438528 PMCID: PMC10371870 DOI: 10.1038/s41586-023-06311-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.
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Affiliation(s)
- Kazumasa Kanemaru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - James Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Siew Yen Ho
- Cardiac Morphology Unit, Royal Brompton Hospital and Imperial College London, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Litvinukova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yue Qin
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Zuzanna Jablonska
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia I Semprich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rakeshlal Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carlos Talavera-López
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Würzburg Institute for Systems Immunology, Max Planck Research Group, Julius-Maximilian-Universität, Würzburg, Germany
| | - Ilaria Mulas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lu Wang
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret M Huang
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John Dark
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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247
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Sun X, Zhou L, Wang Y, Deng G, Cao X, Ke B, Wu X, Gu Y, Cheng H, Xu Q, Du Q, Chen H, Sun Y. Single-cell analyses reveal cannabidiol rewires tumor microenvironment via inhibiting alternative activation of macrophage and synergizes with anti-PD-1 in colon cancer. J Pharm Anal 2023; 13:726-744. [PMID: 37577382 PMCID: PMC10422166 DOI: 10.1016/j.jpha.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 08/15/2023] Open
Abstract
Colorectal tumors often create an immunosuppressive microenvironment that prevents them from responding to immunotherapy. Cannabidiol (CBD) is a non-psychoactive natural active ingredient from the cannabis plant that has various pharmacological effects, including neuroprotective, antiemetic, anti-inflammatory, and antineoplastic activities. This study aimed to elucidate the specific anticancer mechanism of CBD by single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) technologies. Here, we report that CBD inhibits colorectal cancer progression by modulating the suppressive tumor microenvironment (TME). Our single-cell transcriptome and ATAC sequencing results showed that CBD suppressed M2-like macrophages and promoted M1-like macrophages in tumors both in strength and quantity. Furthermore, CBD significantly enhanced the interaction between M1-like macrophages and tumor cells and restored the intrinsic anti-tumor properties of macrophages, thereby preventing tumor progression. Mechanistically, CBD altered the metabolic pattern of macrophages and related anti-tumor signaling pathways. We found that CBD inhibited the alternative activation of macrophages and shifted the metabolic process from oxidative phosphorylation and fatty acid oxidation to glycolysis by inhibiting the phosphatidylinositol 3-kinase-protein kinase B signaling pathway and related downstream target genes. Furthermore, CBD-mediated macrophage plasticity enhanced the response to anti-programmed cell death protein-1 (PD-1) immunotherapy in xenografted mice. Taken together, we provide new insights into the anti-tumor effects of CBD.
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Affiliation(s)
- Xiaofan Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, 210008, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Lisha Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi Wang
- Colon and Rectal Surgery, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210001, China
| | - Guoliang Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xinran Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Bowen Ke
- Laboratory of Anesthesia and Critical Care Medicine, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610044, China
| | - Xiaoqi Wu
- Genergy Bio-technology (Shanghai) Co., Ltd, Shanghai, 200241, China
| | - Yanhong Gu
- The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Haibo Cheng
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, The First Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianming Du
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
- School of Basic Medicine & Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hongqi Chen
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200030, China
| | - Yang Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, 210008, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
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248
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Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. NATURE COMPUTATIONAL SCIENCE 2023; 3:644-657. [PMID: 37974651 PMCID: PMC10653299 DOI: 10.1038/s43588-023-00476-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/06/2023] [Indexed: 11/19/2023]
Abstract
Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping), a hierarchical Bayesian approach that leverages paired single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from subjects with bloodstream infection and uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant and methicillin-susceptible S. aureus infections. Although differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished methicillin-resistant from methicillin-susceptible S. aureus infections.
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Affiliation(s)
- Xi Chen
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wan-Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandria Vornholt
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Michael Dagher
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Daniel G. Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W. Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
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249
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Bouzid H, Belk JA, Jan M, Qi Y, Sarnowski C, Wirth S, Ma L, Chrostek MR, Ahmad H, Nachun D, Yao W, Beiser A, Bick AG, Bis JC, Fornage M, Longstreth WT, Lopez OL, Natarajan P, Psaty BM, Satizabal CL, Weinstock J, Larson EB, Crane PK, Keene CD, Seshadri S, Satpathy AT, Montine TJ, Jaiswal S. Clonal hematopoiesis is associated with protection from Alzheimer's disease. Nat Med 2023; 29:1662-1670. [PMID: 37322115 PMCID: PMC10353941 DOI: 10.1038/s41591-023-02397-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a premalignant expansion of mutated hematopoietic stem cells. As CHIP-associated mutations are known to alter the development and function of myeloid cells, we hypothesized that CHIP may also be associated with the risk of Alzheimer's disease (AD), a disease in which brain-resident myeloid cells are thought to have a major role. To perform association tests between CHIP and AD dementia, we analyzed blood DNA sequencing data from 1,362 individuals with AD and 4,368 individuals without AD. Individuals with CHIP had a lower risk of AD dementia (meta-analysis odds ratio (OR) = 0.64, P = 3.8 × 10-5), and Mendelian randomization analyses supported a potential causal association. We observed that the same mutations found in blood were also detected in microglia-enriched fraction of the brain in seven of eight CHIP carriers. Single-nucleus chromatin accessibility profiling of brain-derived nuclei in six CHIP carriers revealed that the mutated cells comprised a large proportion of the microglial pool in the samples examined. While additional studies are required to validate the mechanistic findings, these results suggest that CHIP may have a role in attenuating the risk of AD.
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Affiliation(s)
- Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Max Jan
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA
| | - Sara Wirth
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Ma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R Chrostek
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Herra Ahmad
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Cardiology, Charité Universitätsmedizin, Berlin, Germany
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Winnie Yao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexa Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alexander G Bick
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - William T Longstreth
- Departments of Neurology and Epidemiology, University of Washington, Seattle, WA, USA
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Joshua Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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250
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Ton MLN, Keitley D, Theeuwes B, Guibentif C, Ahnfelt-Rønne J, Andreassen TK, Calero-Nieto FJ, Imaz-Rosshandler I, Pijuan-Sala B, Nichols J, Benito-Gutiérrez È, Marioni JC, Göttgens B. An atlas of rabbit development as a model for single-cell comparative genomics. Nat Cell Biol 2023; 25:1061-1072. [PMID: 37322291 DOI: 10.1038/s41556-023-01174-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg-cylinder gastrulation and method of implantation, diverge from other mammals, thus complicating inferences about human development. Like the human embryo, rabbits develop as a flat-bilaminar disc. Here we constructed a morphological and molecular atlas of rabbit development. We report transcriptional and chromatin accessibility profiles for over 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis and early organogenesis. Using a neighbourhood comparison pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism. We characterize the gene regulatory programmes underlying trophoblast differentiation and identify signalling interactions involving the yolk sac mesothelium during haematopoiesis. We demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and computational pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single-cell comparative genomics more broadly across biomedical research.
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Affiliation(s)
- Mai-Linh Nu Ton
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Bart Theeuwes
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carolina Guibentif
- Inst. Biomedicine, Dept. Microbiology and Immunology, Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Fernando J Calero-Nieto
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Blanca Pijuan-Sala
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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