1
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Yu J, Shang C, Deng X, Jia J, Shang X, Wang Z, Zheng Y, Zhang R, Wang Y, Zhang H, Liu H, Liu WJ, Li H, Cao B. Time-resolved scRNA-seq reveals transcription dynamics of polarized macrophages with influenza A virus infection and antigen presentation to T cells. Emerg Microbes Infect 2024; 13:2387450. [PMID: 39129565 PMCID: PMC11370681 DOI: 10.1080/22221751.2024.2387450] [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: 03/25/2024] [Revised: 07/02/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
Throughout history, the influenza A virus has caused numerous devastating global pandemics. Macrophages, as pivotal innate immune cells, exhibit a wide range of immune functions characterized by distinct polarization states, reflecting their intricate heterogeneity. In this study, we employed the time-resolved single-cell sequencing technique coupled with metabolic RNA labelling to elucidate the dynamic transcriptional changes in distinct polarized states of bone marrow-derived macrophages (BMDMs) upon infection with the influenza A virus. Our approach not only captures the temporal dimension of transcriptional activity, which is lacking in conventional scRNA-seq methods, but also reveals that M2-polarized Arg1_macrophage cluster is the sole state supporting successful replication of influenza A virus. Furthermore, we identified distinct antigen presentation capabilities to CD4+ T and CD8+ T cells across diverse polarized states of macrophages. Notably, the M1 phenotype, exhibited by (BMDMs) and murine alveolar macrophages (AMs), demonstrated superior conventional and cross-presentation abilities for exogenous antigens, with a particular emphasis on cross-presentation capacity. Additionally, as CD8+ T cell differentiation progressed, M1 polarization exhibited an enhanced capacity for cross-presentation. All three phenotypes of BMDMs, including M1, demonstrated robust presentation to CD4+ regulatory T cells, while displaying limited ability to present to naive CD4+ T cells. These findings offer novel insights into the immunological regulatory mechanisms governing distinct polarized states of macrophages, particularly their roles in restricting the replication of influenza A virus and modulating antigen-specific T cell responses through innate immunity.
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Affiliation(s)
- Jiapei Yu
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Congcong Shang
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaoyan Deng
- THU-PKU Joint Center for Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Ju Jia
- Department of Infectious Disease, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Xiao Shang
- THU-PKU Joint Center for Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Zeyi Wang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People’s Republic of China
| | - Ying Zheng
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, People’s Republic of China
| | - Rongling Zhang
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People’s Republic of China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Hui Zhang
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, People’s Republic of China
| | - Hongyu Liu
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, People’s Republic of China
| | - William J. Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention,Beijing, People’s Republic of China
| | - Hui Li
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People’s Republic of China
- Department of Infectious Disease, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, People’s Republic of China
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2
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Ramsköld D, Hendriks GJ, Larsson AJM, Mayr JV, Ziegenhain C, Hagemann-Jensen M, Hartmanis L, Sandberg R. Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts. Nat Cell Biol 2024:10.1038/s41556-024-01486-9. [PMID: 39198695 DOI: 10.1038/s41556-024-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/15/2024] [Indexed: 09/01/2024]
Abstract
Analyses of transcriptional bursting from single-cell RNA-sequencing data have revealed patterns of variation and regulation in the kinetic parameters that could be inferred. Here we profiled newly transcribed (4-thiouridine-labelled) RNA across 10,000 individual primary mouse fibroblasts to more broadly infer bursting kinetics and coordination. We demonstrate that inference from new RNA profiles could separate the kinetic parameters that together specify the burst size, and that the synthesis rate (and not the transcriptional off rate) controls the burst size. Importantly, transcriptome-wide inference of transcriptional on and off rates provided conclusive evidence that RNA polymerase II transcribes genes in bursts. Recent reports identified examples of transcriptional co-bursting, yet no global analyses have been performed. The deep new RNA profiles we generated with allelic resolution demonstrated that co-bursting rarely appears more frequently than expected by chance, except for certain gene pairs, notably paralogues located in close genomic proximity. Altogether, new RNA single-cell profiling critically improves the inference of transcriptional bursting and provides strong evidence for independent transcriptional bursting of mammalian genes.
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Affiliation(s)
- Daniel Ramsköld
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Juliane V Mayr
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
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3
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Schofield JA, Hahn S. Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq. Cell Rep 2024; 43:114593. [PMID: 39102335 DOI: 10.1016/j.celrep.2024.114593] [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: 02/26/2024] [Revised: 06/29/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
We describe a time-resolved nascent single-cell RNA sequencing (RNA-seq) approach that measures gene-specific transcriptional noise and the fraction of active genes in S. cerevisiae. Most genes are expressed with near-constitutive behavior, while a subset of genes show high mRNA variance suggestive of transcription bursting. Transcriptional noise is highest in the cofactor/coactivator-redundant (CR) gene class (dependent on both SAGA and TFIID) and strongest in TATA-containing CR genes. Using this approach, we also find that histone gene transcription switches from a low-level, low-noise constitutive mode during M and M/G1 to an activated state in S phase that shows both an increase in the fraction of active promoters and a switch to a noisy and bursty transcription mode. Rapid depletion of cofactors SAGA and MED Tail indicates that both factors play an important role in stimulating the fraction of active promoters at CR genes, with a more modest role in transcriptional noise.
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Affiliation(s)
| | - Steven Hahn
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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4
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Tang X, Zhang Y, Zhang H, Zhang N, Dai Z, Cheng Q, Li Y. Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases. Clin Rev Allergy Immunol 2024:10.1007/s12016-024-09001-6. [PMID: 39186216 DOI: 10.1007/s12016-024-09001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2024] [Indexed: 08/27/2024]
Abstract
Autoimmune diseases (AIDs) are complex in etiology and diverse in classification but clinically show similar symptoms such as joint pain and skin problems. As a result, the diagnosis is challenging, and usually, only broad treatments can be available. Consequently, the clinical responses in patients with different types of AIDs are unsatisfactory. Therefore, it is necessary to conduct more research to figure out the pathogenesis and therapeutic targets of AIDs. This requires research technologies with strong extraction and prediction capabilities. Single-cell sequencing technology analyses the genomic, epigenomic, or transcriptomic information at the single-cell level. It can define different cell types and states in greater detail, further revealing the molecular mechanisms that drive disease progression. These advantages enable cell biology research to achieve an unprecedented resolution and scale, bringing a whole new vision to life science research. In recent years, single-cell technology especially single-cell RNA sequencing (scRNA-seq) has been widely used in various disease research. In this paper, we present the innovations and applications of single-cell sequencing in the medical field and focus on the application contributing to the differential diagnosis and precise treatment of AIDs. Despite some limitations, single-cell sequencing has a wide range of applications in AIDs. We finally present a prospect for the development of single-cell sequencing. These ideas may provide some inspiration for subsequent research.
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Affiliation(s)
- Xuening Tang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yudi Zhang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongzhen Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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5
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Volteras D, Shahrezaei V, Thomas P. Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing. Cell Syst 2024; 15:694-708.e12. [PMID: 39121860 DOI: 10.1016/j.cels.2024.07.002] [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: 10/24/2023] [Revised: 02/29/2024] [Accepted: 07/11/2024] [Indexed: 08/12/2024]
Abstract
Single-cell transcriptomics reveals significant variations in transcriptional activity across cells. Yet, it remains challenging to identify mechanisms of transcription dynamics from static snapshots. It is thus still unknown what drives global transcription dynamics in single cells. We present a stochastic model of gene expression with cell size- and cell cycle-dependent rates in growing and dividing cells that harnesses temporal dimensions of single-cell RNA sequencing through metabolic labeling protocols and cel lcycle reporters. We develop a parallel and highly scalable approximate Bayesian computation method that corrects for technical variation and accurately quantifies absolute burst frequency, burst size, and degradation rate along the cell cycle at a transcriptome-wide scale. Using Bayesian model selection, we reveal scaling between transcription rates and cell size and unveil waves of gene regulation across the cell cycle-dependent transcriptome. Our study shows that stochastic modeling of dynamical correlations identifies global mechanisms of transcription regulation. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Dimitris Volteras
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Philipp Thomas
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
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6
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Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
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Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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7
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He L, Xiang Y. Interrogating the Presence of RNA Phosphorothioate in Nature by a Highly Selective and Sensitive Fluorescence Method. Anal Chem 2024. [PMID: 39138966 DOI: 10.1021/acs.analchem.4c01597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In nature, DNA phosphorothioate (PT) is found in the genomic materials of some prokaryotes. In contrast, whether there is natural RNA PT is still a question under debate. A groundbreaking study reported the discovery of RNA PT in cellular RNA samples from both prokaryotes and eukaryotes at contents of >100 PT per million nucleotides (PPM-nt) according to liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis. However, this finding was challenged by a later work showing that other RNA modifications, such as 2'-O-methylation, could give almost the same LC-MS/MS signal patterns as RNA PT. As the LC-MS/MS technique led to contradicting conclusions, another independent method is thus needed to interrogate the presence of RNA PT in nature. In this work, we have developed a highly selective and sensitive fluorescence method for RNA PT quantification based on a new RNA PT-specific conversion reaction. It can detect as low as 2.8 PPM-nt in RNA without interference from RNA thiobases or protein cysteines. We measured the total RNA samples from some bacteria and human cells using this method. None of these samples gave any RNA PT signal above the detection limit (2.8 PPM-nt), suggesting that the widespread presence of natural RNA PT at the 100 PPM-nt level or above is highly unlikely. Nevertheless, due to the limited number of cell species tested in this work, the possible existence of natural RNA PT cannot be excluded. The fluorescence method reported here is simple and low-cost; therefore, it should be an ideal assay for broadly screening various types of cells to search for the clue of RNA PT in nature.
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Affiliation(s)
- Luo He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
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8
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Nat Biotechnol 2024; 42:1218-1223. [PMID: 37749268 PMCID: PMC10961254 DOI: 10.1038/s41587-023-01948-9] [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: 12/05/2022] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
We present a combinatorial indexing method, PerturbSci-Kinetics, for capturing whole transcriptomes, nascent transcriptomes and single guide RNA (sgRNA) identities across hundreds of genetic perturbations at the single-cell level. Profiling a pooled CRISPR screen targeting various biological processes, we show the gene expression regulation during RNA synthesis, processing and degradation, miRNA biogenesis and mitochondrial mRNA processing, systematically decoding the genome-wide regulatory network that underlies RNA temporal dynamics at scale.
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Affiliation(s)
- Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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9
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024; 84:2765-2784.e16. [PMID: 38964322 PMCID: PMC11315470 DOI: 10.1016/j.molcel.2024.06.008] [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: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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10
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Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing unveils coordinated global transcription. Nature 2024; 631:216-223. [PMID: 38839954 PMCID: PMC11222150 DOI: 10.1038/s41586-024-07517-7] [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: 09/15/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1,2. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations3. However, fundamental questions about the temporal regulation of transcription and enhancer-gene coordination remain unanswered, primarily because of the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq-a new single-cell nascent RNA sequencing assay that uses click chemistry-and unveil coordinated transcription throughout the genome. We demonstrate the episodic nature of transcription and the co-transcription of functionally related genes. scGRO-seq can estimate burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells and can leverage replication-dependent non-polyadenylated histone gene transcription to elucidate cell cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq enables the identification of networks of enhancers and genes. Our results suggest that the bursting of transcription at super-enhancers precedes bursting from associated genes. By imparting insights into the dynamic nature of global transcription and the origin and propagation of transcription signals, we demonstrate the ability of scGRO-seq to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
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Affiliation(s)
- Dig B Mahat
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathaniel D Tippens
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Sean K Waterton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiayu Fu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Sarah E Blatt
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Exact Sciences, Madison, WI, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Weiler P, Lange M, Klein M, Pe'er D, Theis F. CellRank 2: unified fate mapping in multiview single-cell data. Nat Methods 2024; 21:1196-1205. [PMID: 38871986 PMCID: PMC11239496 DOI: 10.1038/s41592-024-02303-9] [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: 07/18/2023] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.
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Affiliation(s)
- Philipp Weiler
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Marius Lange
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michal Klein
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Machine Learning Research, Apple, Paris, France
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fabian Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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12
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Gerke C, Bauersfeld L, Schirmeister I, Mireisz CNM, Oberhardt V, Mery L, Wu D, Jürges CS, Spaapen RM, Mussolino C, Le-Trilling VTK, Trilling M, Dölken L, Paster W, Erhard F, Hofmann M, Schlosser A, Hengel H, Momburg F, Halenius A. Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning. eLife 2024; 13:e85560. [PMID: 38900146 PMCID: PMC11189632 DOI: 10.7554/elife.85560] [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: 12/13/2022] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Human leucocyte antigen class I (HLA-I) molecules play a central role for both NK and T-cell responses that prevent serious human cytomegalovirus (HCMV) disease. To create opportunities for viral spread, several HCMV-encoded immunoevasins employ diverse strategies to target HLA-I. Among these, the glycoprotein US10 is so far insufficiently studied. While it was reported that US10 interferes with HLA-G expression, its ability to manipulate classical HLA-I antigen presentation remains unknown. In this study, we demonstrate that US10 recognizes and binds to all HLA-I (HLA-A, -B, -C, -E, -G) heavy chains. Additionally, impaired recruitment of HLA-I to the peptide loading complex was observed. Notably, the associated effects varied significantly dependending on HLA-I genotype and allotype: (i) HLA-A molecules evaded downregulation by US10, (ii) tapasin-dependent HLA-B molecules showed impaired maturation and cell surface expression, and (iii) β2m-assembled HLA-C, in particular HLA-C*05:01 and -C*12:03, and HLA-G were strongly retained in complex with US10 in the endoplasmic reticulum. These genotype-specific effects on HLA-I were confirmed through unbiased HLA-I ligandome analyses. Furthermore, in HCMV-infected fibroblasts inhibition of overlapping US10 and US11 transcription had little effect on HLA-A, but induced HLA-B antigen presentation. Thus, the US10-mediated impact on HLA-I results in multiple geno- and allotypic effects in a so far unparalleled and multimodal manner.
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Affiliation(s)
- Carolin Gerke
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Spemann Graduate School of Biology and Medicine (SGBM), University of FreiburgFreiburgGermany
- Faculty of Biology, University of FreiburgFreiburgGermany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Ivo Schirmeister
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Chiara Noemi-Marie Mireisz
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Valerie Oberhardt
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Lea Mery
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Di Wu
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | | | - Robbert M Spaapen
- Department of Immunopathology, Sanquin ResearchAmsterdamNetherlands
- Landsteiner Laboratory, Amsterdam UMC, University of AmsterdamAmsterdamNetherlands
| | - Claudio Mussolino
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center University of FreiburgFreiburgGermany
- Center for Chronic Immunodeficiency, Medical Center University of FreiburgFreiburgGermany
| | | | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-EssenEssenGermany
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital EssenEssenGermany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Wolfgang Paster
- St. Anna Children’s Cancer Research Institute (CCRI)ViennaAustria
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
| | - Maike Hofmann
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Hartmut Hengel
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Frank Momburg
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, National Center for Tumor Diseases (NCT), Heidelberg University HospitalHeidelbergGermany
| | - Anne Halenius
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
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13
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Cui Y, Li Y, Ji J, Hu N, Min K, Ying W, Fan L, Hong M, Li J, Sun Z, Qu X. Dynamic Single-Cell RNA-Seq reveals mechanism of Selinexor-Resistance in Chronic myeloid leukemia. Int Immunopharmacol 2024; 134:112212. [PMID: 38728882 DOI: 10.1016/j.intimp.2024.112212] [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: 03/24/2024] [Revised: 04/23/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
Chronic myeloid leukemia (CML) is a type of hematologic malignancies caused by BCR-ABL chimeric oncogene. Resistance to tyrosine kinase inhibitors (TKIs) leads to the progression of CML into advanced stages. Selinexor is a small molecule inhibitor that targets a nuclear transporter called Exportin 1. Combined with imatinib, selinexor has been shown to disrupt nuclear-cytoplasmic transport signal of leukemia stem cells, resulting in cell death. The objective of this study was to investigate the mechanism of drug resistance to selinexor in CML. We established K562 cell line resistant to selinexor and conducted single cell dynamic transcriptome sequencing to analyze the heterogeneity within the parental and selinexor resistant cell populations. We identified specific gene expression changes associated with resistance to selinexor. Our results revealed differential expression patterns in genes such as MT2A, TFPI, MTND3, and HMGCS1 in the total RNA, as well as MT-TW, DNAJB1, and HSPB1 in the newly synthesized RNA, between the parental and drug-resistant groups. By applying pseudo-time analysis, we discovered that a specific cluster of cells exhibited characteristics of tumor stem cells. Furthermore, we observed a gradual decrease in the expression of ferroptosis-related molecules as drug resistance developed. In vitro experiments confirmed that the combination of a ferroptosis inducer called RSL3 effectively overcame drug resistance. In conclusion, this study revealed the resistance mechanism of selinexor in CML. In conclusion, we identified a subgroup of CML cells with tumor stem cell properties and demonstrated that ferroptosis inducer improved the efficacy of selinexor in overcoming drug resistance.
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Affiliation(s)
- Yunqi Cui
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Yating Li
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Jiamei Ji
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Na Hu
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China; Department of Hematology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, 120 Suzhi Road, Suqian 223812, Jiangsu, China
| | - Ke Min
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Wanting Ying
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Lei Fan
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China
| | - Ming Hong
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China.
| | - Jianyong Li
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China.
| | - Zhengxu Sun
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China.
| | - Xiaoyan Qu
- Department of Hematology, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu, China.
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14
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Zhou P, Bocci F, Li T, Nie Q. Spatial transition tensor of single cells. Nat Methods 2024; 21:1053-1062. [PMID: 38755322 PMCID: PMC11166574 DOI: 10.1038/s41592-024-02266-x] [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: 07/03/2023] [Accepted: 04/02/2024] [Indexed: 05/18/2024]
Abstract
Spatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states and transitions. The current lineage-inference methods either lack spatial dynamics for state transition or cannot capture different dynamics associated with multiple cell states and transition paths. Here we present spatial transition tensor (STT), a method that uses messenger RNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multistability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-state-specific dynamics and spatial state transitions via both short-time local tensor streamlines between cells and long-time transition paths among attractors. Benchmarking and applications of STT on several transcriptome datasets via multiple technologies on epithelial-mesenchymal transitions, blood development, spatially resolved mouse brain and chicken heart development, indicate STT's capability in recovering cell-state-specific dynamics and their associated genes not seen using existing methods. Overall, STT provides a consistent multiscale description of single-cell transcriptome data across multiple spatiotemporal scales.
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Affiliation(s)
- Peijie Zhou
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- Center for Machine Learning Research, Peking University, Beijing, China
- AI for Science Institute, Beijing, China
- National Engineering Laboratory for Big Data Analysis and Applications, Beijing, China
| | - Federico Bocci
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Tiejun Li
- LMAM and School of Mathematical Sciences, Peking University, Beijing, China
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- Department of Cell and Developmental Biology, University of California, Irvine, Irvine, CA, USA.
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15
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Maizels RJ, Snell DM, Briscoe J. Reconstructing developmental trajectories using latent dynamical systems and time-resolved transcriptomics. Cell Syst 2024; 15:411-424.e9. [PMID: 38754365 DOI: 10.1016/j.cels.2024.04.004] [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: 09/19/2023] [Revised: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
The snapshot nature of single-cell transcriptomics presents a challenge for studying the dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal information at single-cell level, but current methods have limitations. Here, we present a framework that overcomes these limitations: experimentally, we developed sci-FATE2, an optimized method for metabolic labeling with increased data quality, which we used to profile 45,000 embryonic stem (ES) cells differentiating into neural tube identities. Computationally, we developed a two-stage framework for dynamical modeling: VelvetVAE, a variational autoencoder (VAE) for velocity inference that outperforms all other tools tested, and VelvetSDE, a neural stochastic differential equation (nSDE) framework for simulating trajectory distributions. These recapitulate underlying dataset distributions and capture features such as decision boundaries between alternative fates and fate-specific gene expression. These methods recast single-cell analyses from descriptions of observed data to models of the dynamics that generated them, providing a framework for investigating developmental fate decisions.
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Affiliation(s)
- Rory J Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College, London, UK
| | - Daniel M Snell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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16
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Berg K, Lodha M, Delazer I, Bartosik K, Garcia YC, Hennig T, Wolf E, Dölken L, Lusser A, Prusty B, Erhard F. Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data. Nucleic Acids Res 2024; 52:e35. [PMID: 38381903 PMCID: PMC11039982 DOI: 10.1093/nar/gkae120] [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: 04/23/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA expression profiles from a single sequencing library. Cytotoxicity due to extended periods of labelling or high 4sU concentrations has been described, but the effects of extensive 4sU labelling on expression estimates from nucleotide conversion RNA-seq have not been studied. Here, we performed nucleotide conversion RNA-seq with escalating doses of 4sU with short-term labelling (1h) and over a progressive time course (up to 2h) in different cell lines. With high concentrations or at later time points, expression estimates were biased in an RNA half-life dependent manner. We show that bias arose by a combination of reduced mappability of reads carrying multiple conversions, and a global, unspecific underrepresentation of labelled RNA emerging during library preparation and potentially global reduction of RNA synthesis. We developed a computational tool to rescue unmappable reads, which performed favourably compared to previous read mappers, and a statistical method, which could fully remove remaining bias. All methods developed here are freely available as part of our GRAND-SLAM pipeline and grandR package.
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Affiliation(s)
- Kevin Berg
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Manivel Lodha
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Isabel Delazer
- Medical University of Innsbruck, Biocenter, Institute of Molecular Biology, Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Yilliam Cruz Garcia
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Thomas Hennig
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Alexandra Lusser
- Medical University of Innsbruck, Biocenter, Institute of Molecular Biology, Innsbruck, Austria
| | - Bhupesh K Prusty
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Florian Erhard
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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17
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Maizels RJ. A dynamical perspective: moving towards mechanism in single-cell transcriptomics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230049. [PMID: 38432314 PMCID: PMC10909508 DOI: 10.1098/rstb.2023.0049] [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: 07/10/2023] [Accepted: 10/31/2023] [Indexed: 03/05/2024] Open
Abstract
As the field of single-cell transcriptomics matures, research is shifting focus from phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the gene regulation underneath. This perspective considers the value of capturing dynamical information at single-cell resolution for gaining mechanistic insight; reviews the available technologies for recording and inferring temporal information in single cells; and explores whether better dynamical resolution is sufficient to adequately capture the causal relationships driving complex biological systems. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Rory J. Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- University College London, London WC1E 6BT, UK
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18
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Fishman L, Modak A, Nechooshtan G, Razin T, Erhard F, Regev A, Farrell JA, Rabani M. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nat Commun 2024; 15:3104. [PMID: 38600066 PMCID: PMC11006943 DOI: 10.1038/s41467-024-47290-9] [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: 04/12/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Avani Modak
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Talya Razin
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA, 02139, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, 02142, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA.
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
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19
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Nadal-Ribelles M, Solé C, de Nadal E, Posas F. The rise of single-cell transcriptomics in yeast. Yeast 2024; 41:158-170. [PMID: 38403881 DOI: 10.1002/yea.3934] [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: 09/29/2023] [Revised: 01/24/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
The field of single-cell omics has transformed our understanding of biological processes and is constantly advancing both experimentally and computationally. One of the most significant developments is the ability to measure the transcriptome of individual cells by single-cell RNA-seq (scRNA-seq), which was pioneered in higher eukaryotes. While yeast has served as a powerful model organism in which to test and develop transcriptomic technologies, the implementation of scRNA-seq has been significantly delayed in this organism, mainly because of technical constraints associated with its intrinsic characteristics, namely the presence of a cell wall, a small cell size and little amounts of RNA. In this review, we examine the current technologies for scRNA-seq in yeast and highlight their strengths and weaknesses. Additionally, we explore opportunities for developing novel technologies and the potential outcomes of implementing single-cell transcriptomics and extension to other modalities. Undoubtedly, scRNA-seq will be invaluable for both basic and applied yeast research, providing unique insights into fundamental biological processes.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carme Solé
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulalia de Nadal
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Posas
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
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20
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Mitic N, Neuschulz A, Spanjaard B, Schneider J, Fresmann N, Novoselc KT, Strunk T, Münster L, Olivares-Chauvet P, Ninkovic J, Junker JP. Dissecting the spatiotemporal diversity of adult neural stem cells. Mol Syst Biol 2024; 20:321-337. [PMID: 38365956 PMCID: PMC10987636 DOI: 10.1038/s44320-024-00022-z] [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: 05/04/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze the regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells, with some subtypes being restricted to a single brain region, while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation, with different states being involved in proliferative and non-proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for the functional manipulation of neural stem cell subtypes.
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Affiliation(s)
- Nina Mitic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Anika Neuschulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Julia Schneider
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Nora Fresmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klara Tereza Novoselc
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Taraneh Strunk
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lisa Münster
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jovica Ninkovic
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany.
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21
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Yang G, Xin Q, Dean J. Degradation and translation of maternal mRNA for embryogenesis. Trends Genet 2024; 40:238-249. [PMID: 38262796 DOI: 10.1016/j.tig.2023.12.008] [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: 09/25/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Maternal mRNAs accumulate during egg growth and must be judiciously degraded or translated to ensure successful development of mammalian embryos. In this review we integrate recent investigations into pathways controlling rapid degradation of maternal mRNAs during the maternal-to-zygotic transition. Degradation is not indiscriminate, and some mRNAs are selectively protected and rapidly translated after fertilization for reprogramming the zygotic genome during early embryogenesis. Oocyte specific cofactors and pathways have been illustrated to control different futures of maternal mRNAs. We discuss mechanisms that control the fate of maternal mRNAs during late oogenesis and after fertilization. Issues to be resolved in current maternal mRNA research are described, and future research directions are proposed.
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Affiliation(s)
- Guanghui Yang
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Qiliang Xin
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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22
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Lu X, Wang S, Hua X, Chen X, Zhan M, Hu Q, Cao L, Wu Z, Zhang W, Zuo X, Gui R, Fan L, Li J, Shi W, Jin H. Targeting the cGAS-STING Pathway Inhibits Peripheral T-cell Lymphoma Progression and Enhances the Chemotherapeutic Efficacy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306092. [PMID: 38145335 PMCID: PMC10933671 DOI: 10.1002/advs.202306092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Peripheral T-cell lymphoma (PTCL) is a highly heterogeneous group of mature T-cell malignancies. The efficacy of current first-line treatment is dismal, and novel agents are urgently needed to improve patient outcomes. A close association between the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway and tumor promotion exists, revealing prospective therapeutic targets. This study, investigates the role of the cGAS-STING pathway and its underlying mechanisms in PTCL progression. Single-cell RNA sequencing showes that the cGAS-STING pathway is highly expressed and closely associated with PTCL proliferation. cGAS inhibition suppresses tumor growth and impaires DNA damage repair. Moreover, Cdc2-like kinase 1 (CLK1) is critical for residual tumor cell survival after treatment with cGAS inhibitors, and CLK1 suppression enhances sensitivity to cGAS inhibitors. Single-cell dynamic transcriptomic analysis indicates reduced proliferation-associated nascent RNAs as the underlying mechanism. In first-line therapy, chemotherapy-triggered DNA damage activates the cGAS-STING pathway, and cGAS inhibitors can synergize with chemotherapeutic agents to kill tumors. The cGAS-STING pathway is oncogenic in PTCL, whereas targeting cGAS suppresses tumor growth, and CLK1 may be a sensitivity indicator for cGAS inhibitors. These findings provide a theoretical foundation for optimizing therapeutic strategies for PTCL, especially in patients with relapsed/refractory disease.
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Affiliation(s)
- Xueying Lu
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Shunan Wang
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Xin Hua
- Department of OncologyAffiliated Hospital of Nantong UniversityNantong226001China
| | - Xiao Chen
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Mengtao Zhan
- Nanjing Aoyin Biotechnology Company LimitedNanjing210043China
| | - Qiaoyun Hu
- Singleron BiotechnologiesNanjing211899China
| | - Lei Cao
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
- Nanjing Pukou Central HospitalPuKou Branch Hospital of Jiangsu Province HospitalNanjing211800China
| | - Zijuan Wu
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Wei Zhang
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Xiaoling Zuo
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Renfu Gui
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Lei Fan
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
| | - Jianyong Li
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
- National Clinical Research Center for Hematologic DiseasesThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Wenyu Shi
- Department of OncologyAffiliated Hospital of Nantong UniversityNantong226001China
| | - Hui Jin
- Lymphoma Center, Department of HematologyJiangsu Province HospitalThe First Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Key Laboratory of Hematology of Nanjing Medical UniversityNanjing210029China
- Jiangsu Key Lab of Cancer BiomarkersPrevention, and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing210029China
- National Clinical Research Center for Hematologic DiseasesThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
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23
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Jogi HR, Smaraki N, Nayak SS, Rajawat D, Kamothi DJ, Panigrahi M. Single cell RNA-seq: a novel tool to unravel virus-host interplay. Virusdisease 2024; 35:41-54. [PMID: 38817399 PMCID: PMC11133279 DOI: 10.1007/s13337-024-00859-w] [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: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 06/01/2024] Open
Abstract
Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.
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Affiliation(s)
- Harsh Rajeshbhai Jogi
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Nabaneeta Smaraki
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Dhaval J. Kamothi
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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24
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Costa B, Becker J, Krammer T, Mulenge F, Durán V, Pavlou A, Gern OL, Chu X, Li Y, Čičin-Šain L, Eiz-Vesper B, Messerle M, Dölken L, Saliba AE, Erhard F, Kalinke U. Human cytomegalovirus exploits STING signaling and counteracts IFN/ISG induction to facilitate infection of dendritic cells. Nat Commun 2024; 15:1745. [PMID: 38409141 PMCID: PMC10897438 DOI: 10.1038/s41467-024-45614-3] [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: 10/01/2021] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Human cytomegalovirus (HCMV) is a widespread pathogen that in immunocompromised hosts can cause life-threatening disease. Studying HCMV-exposed monocyte-derived dendritic cells by single-cell RNA sequencing, we observe that most cells are entered by the virus, whereas less than 30% of them initiate viral gene expression. Increased viral gene expression is associated with activation of the stimulator of interferon genes (STING) that usually induces anti-viral interferon responses, and with the induction of several pro- (RHOB, HSP1A1, DNAJB1) and anti-viral (RNF213, TNFSF10, IFI16) genes. Upon progression of infection, interferon-beta but not interferon-lambda transcription is inhibited. Similarly, interferon-stimulated gene expression is initially induced and then shut off, thus further promoting productive infection. Monocyte-derived dendritic cells are composed of 3 subsets, with one being especially susceptible to HCMV. In conclusion, HCMV permissiveness of monocyte-derived dendritic cells depends on complex interactions between virus sensing, regulation of the interferon response, and viral gene expression.
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Grants
- 158989968 - SFB 900-B2 Deutsche Forschungsgemeinschaft (German Research Foundation)
- 398367752 - FOR 2830 Deutsche Forschungsgemeinschaft (German Research Foundation)
- EXC 2155 "RESIST" - Project ID 39087428 Deutsche Forschungsgemeinschaft (German Research Foundation)
- DO 1275/7-1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- ER 927/2-1 - FOR2830 Deutsche Forschungsgemeinschaft (German Research Foundation)
- COALITION Niedersächsisches Ministerium für Wissenschaft und Kultur (Ministry for Science and Culture of Lower Saxony)
- Marie Skłodowska-Curie Actions Innovative Training Network (VIROINF: 955974) European Commission (EC)
- Marie Skłodowska-Curie Actions Innovative Training Network (VIROINF: 955974) European Commission (EC)
- 0703/68674/5/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
- 0703/89374/3/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
- 0703/68674/5/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
- 0703/89374/3/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
- 0703/68674/5/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
- 0703/89374/3/2017 Bayerisches Staatsministerium für Wirtschaft und Medien, Energie und Technologie (Bavarian Ministry of Economic Affairs and Media, Energy and Technology)
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Affiliation(s)
- Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Jennifer Becker
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Felix Mulenge
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Verónica Durán
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Olivia Luise Gern
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Xiaojing Chu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Yang Li
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Luka Čičin-Šain
- Institute for Immune Aging and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Britta Eiz-Vesper
- Institute for Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany.
- Faculty for Informatics and Data Science, University of Regensburg, Regensburg, Germany.
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany.
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25
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Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O, Odom DT. The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nat Commun 2024; 15:1272. [PMID: 38341412 PMCID: PMC10858866 DOI: 10.1038/s41467-024-45133-1] [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: 02/07/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.
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Affiliation(s)
- Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Christina Ernst
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Nils Eling
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland
- ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093, Switzerland
| | - Rebecca E Wagner
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Maja Satorius
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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26
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Liu Y, Huang K, Chen W. Resolving cellular dynamics using single-cell temporal transcriptomics. Curr Opin Biotechnol 2024; 85:103060. [PMID: 38194753 DOI: 10.1016/j.copbio.2023.103060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/11/2024]
Abstract
Cellular dynamics, the transition of a cell from one state to another, is central to understanding developmental processes and disease progression. Single-cell transcriptomics has been pushing the frontiers of cellular dynamics studies into a genome-wide and single-cell level. While most single-cell RNA sequencing approaches are disruptive and only provide a snapshot of cell states, the dynamics of a cell could be reconstructed by either exploiting temporal information hiding in the transcriptomics data or integrating additional information. In this review, we describe these approaches, highlighting their underlying principles, key assumptions, and the rationality to interpret the results as models. We also discuss the recently emerging nondisruptive live-cell transcriptomics methods, which are highly complementary to the computational models for their assumption-free nature.
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Affiliation(s)
- Yifei Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kai Huang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wanze Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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27
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Wyler E. Single-Cell RNA-Sequencing of RVFV Infection. Methods Mol Biol 2024; 2824:361-372. [PMID: 39039423 DOI: 10.1007/978-1-0716-3926-9_22] [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] [Indexed: 07/24/2024]
Abstract
On the RNA level, viral infections are characterized by perturbations in the host cell transcriptome as well as the development of viral genetic information. Investigating the abundance and dynamic of RNA molecules can provide ample information to understand many aspects of the infection, from viral replication to pathogenesis. A key aspect therein is the resolution of the data, as infections are generally highly heterogeneous. Even in simple model systems such as cell lines, viral infections happen in a very asynchronous way. Quantifying RNAs at single-cell resolution can therefore substantially increase our understanding of these processes.Whereas measuring the RNA in bulk, that is, in samples containing thousands to hundreds of thousands of cells, is established and widely used since many years, methods for studying not only just a few different RNAs in individual cells became widely available only recently. Here, I outline and compare current concepts and methodologies for using single-cell RNA-sequencing to study virus infections. This covers sample preparation, cell preservation, biosafety considerations, and various experimental methods, with a special focus on the aspects that are important for studying virus infections. Since there is not "the one" method for doing single-cell RNA-sequencing, I will not provide a detailed protocol. Rather, this chapter should serve as a primer for getting started with single-cell RNA-sequencing experiments of virus infections and discusses the criteria that allow readers to choose the best procedures for their specific research question.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany.
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28
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Zhang C, Fang Y, Chen W, Chen Z, Zhang Y, Xie Y, Chen W, Xie Z, Guo M, Wang J, Tan C, Wang H, Tang C. Improving the RNA velocity approach with single-cell RNA lifecycle (nascent, mature and degrading RNAs) sequencing technologies. Nucleic Acids Res 2023; 51:e112. [PMID: 37941145 PMCID: PMC10711548 DOI: 10.1093/nar/gkad969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/27/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023] Open
Abstract
We presented an experimental method called FLOUR-seq, which combines BD Rhapsody and nanopore sequencing to detect the RNA lifecycle (including nascent, mature, and degrading RNAs) in cells. Additionally, we updated our HIT-scISOseq V2 to discover a more accurate RNA lifecycle using 10x Chromium and Pacbio sequencing. Most importantly, to explore how single-cell full-length RNA sequencing technologies could help improve the RNA velocity approach, we introduced a new algorithm called 'Region Velocity' to more accurately configure cellular RNA velocity. We applied this algorithm to study spermiogenesis and compared the performance of FLOUR-seq with Pacbio-based HIT-scISOseq V2. Our findings demonstrated that 'Region Velocity' is more suitable for analyzing single-cell full-length RNA data than traditional RNA velocity approaches. These novel methods could be useful for researchers looking to discover full-length RNAs in single cells and comprehensively monitor RNA lifecycle in cells.
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Affiliation(s)
| | | | - Weitian Chen
- BGI, Shenzhen 518000, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | | | - Ying Zhang
- Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China; NHC Key Laboratory of Male Reproduction and Genetics, Guangzhou, China
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29
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Sha Y, Qiu Y, Zhou P, Nie Q. Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. NAT MACH INTELL 2023; 6:25-39. [PMID: 38274364 PMCID: PMC10805654 DOI: 10.1038/s42256-023-00763-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/25/2023] [Indexed: 01/27/2024]
Abstract
Time-series single-cell RNA sequencing (scRNA-seq) datasets provide unprecedented opportunities to learn dynamic processes of cellular systems. Due to the destructive nature of sequencing, it remains challenging to link the scRNA-seq snapshots sampled at different time points. Here we present TIGON, a dynamic, unbalanced optimal transport algorithm that reconstructs dynamic trajectories and population growth simultaneously as well as the underlying gene regulatory network from multiple snapshots. To tackle the high-dimensional optimal transport problem, we introduce a deep learning method using a dimensionless formulation based on the Wasserstein-Fisher-Rao (WFR) distance. TIGON is evaluated on simulated data and compared with existing methods for its robustness and accuracy in predicting cell state transition and cell population growth. Using three scRNA-seq datasets, we show the importance of growth in the temporal inference, TIGON's capability in reconstructing gene expression at unmeasured time points and its applications to temporal gene regulatory networks and cell-cell communication inference.
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Affiliation(s)
- Yutong Sha
- Department of Mathematics, University of California, Irvine, Irvine, CA USA
| | - Yuchi Qiu
- Department of Mathematics, Michigan State University, East Lansing, MI USA
| | - Peijie Zhou
- Department of Mathematics, University of California, Irvine, Irvine, CA USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA USA
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30
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Martin B, Suter DM. Gene expression flux analysis reveals specific regulatory modalities of gene expression. iScience 2023; 26:107758. [PMID: 37701574 PMCID: PMC10493597 DOI: 10.1016/j.isci.2023.107758] [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: 01/17/2023] [Revised: 06/02/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
The level of a given protein is determined by the synthesis and degradation rates of its mRNA and protein. While several studies have quantified the contribution of different gene expression steps in regulating protein levels, these are limited by using equilibrium approximations in out-of-equilibrium biological systems. Here, we introduce gene expression flux analysis to quantitatively dissect the dynamics of the expression level for specific proteins and use it to analyze published transcriptomics and proteomics datasets. Our analysis reveals distinct regulatory modalities shared by sets of genes with clear functional signatures. We also find that protein degradation plays a stronger role than expected in the adaptation of protein levels. These findings suggest that shared regulatory strategies can lead to versatile responses at the protein level and highlight the importance of going beyond equilibrium approximations to dissect the quantitative contribution of different steps of gene expression to protein dynamics.
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Affiliation(s)
- Benjamin Martin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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31
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Heindel AJ, Brulet JW, Wang X, Founds MW, Libby AH, Bai DL, Lemke MC, Leace DM, Harris TE, Hafner M, Hsu KL. Chemoproteomic capture of RNA binding activity in living cells. Nat Commun 2023; 14:6282. [PMID: 37805600 PMCID: PMC10560261 DOI: 10.1038/s41467-023-41844-z] [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: 03/13/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
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Affiliation(s)
- Andrew J Heindel
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Xiantao Wang
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Michael W Founds
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David M Leace
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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32
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Liu H, Arsiè R, Schwabe D, Schilling M, Minia I, Alles J, Boltengagen A, Kocks C, Falcke M, Friedman N, Landthaler M, Rajewsky N. SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle. Mol Syst Biol 2023; 19:1-23. [PMID: 38778223 PMCID: PMC10568207 DOI: 10.15252/msb.202211427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 05/25/2024] Open
Abstract
RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes.
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Affiliation(s)
- Haiyue Liu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Roberto Arsiè
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Daniel Schwabe
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marcel Schilling
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Igor Minia
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christine Kocks
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Physics, Humboldt University Berlin, Berlin, Germany
| | - Nir Friedman
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Center for Computational Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Berlin, Germany.
- NeuroCure Cluster of Excellence, Berlin, Germany.
- German Cancer Consortium (DKTK), Berlin, Germany.
- National Center for Tumor Diseases (NCT), Berlin, Germany.
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33
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Landon-Brace N, Li NT, McGuigan AP. Exploring New Dimensions of Tumor Heterogeneity: The Application of Single Cell Analysis to Organoid-Based 3D In Vitro Models. Adv Healthc Mater 2023; 12:e2300903. [PMID: 37589373 DOI: 10.1002/adhm.202300903] [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: 03/21/2023] [Revised: 06/28/2023] [Indexed: 08/18/2023]
Abstract
Modeling the heterogeneity of the tumor microenvironment (TME) in vitro is essential to investigating fundamental cancer biology and developing novel treatment strategies that holistically address the factors affecting tumor progression and therapeutic response. Thus, the development of new tools for both in vitro modeling, such as patient-derived organoids (PDOs) and complex 3D in vitro models, and single cell omics analysis, such as single-cell RNA-sequencing, represents a new frontier for investigating tumor heterogeneity. Specifically, the integration of PDO-based 3D in vitro models and single cell analysis offers a unique opportunity to explore the intersecting effects of interpatient, microenvironmental, and tumor cell heterogeneity on cell phenotypes in the TME. In this review, the current use of PDOs in complex 3D in vitro models of the TME is discussed and the emerging directions in the development of these models are highlighted. Next, work that has successfully applied single cell analysis to PDO-based models is examined and important experimental considerations are identified for this approach. Finally, open questions are highlighted that may be amenable to exploration using the integration of PDO-based models and single cell analysis. Ultimately, such investigations may facilitate the identification of novel therapeutic targets for cancer that address the significant influence of tumor-TME interactions.
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Affiliation(s)
- Natalie Landon-Brace
- Institute of Biomedical Engineering, University of Toronto, 200 College Street, Toronto, M5S3E5, Canada
| | - Nancy T Li
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, M5S3E5, Canada
| | - Alison P McGuigan
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomedical Engineering, University of Toronto, 200 College St, Toronto, M5S3E5, Canada
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34
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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35
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Zheng Z, Chang L, Li Y, Liu K, Mu J, Zhang S, Li J, Wu Y, Zou L, Ni Q, Wan Y. Screening single-cell trajectories via continuity assessments for cell transition potential. Brief Bioinform 2023; 24:bbad356. [PMID: 37864296 PMCID: PMC10589400 DOI: 10.1093/bib/bbad356] [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: 02/16/2023] [Revised: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 10/22/2023] Open
Abstract
Advances in single-cell sequencing and data analysis have made it possible to infer biological trajectories spanning heterogeneous cell populations based on transcriptome variation. These trajectories yield a wealth of novel insights into dynamic processes such as development and differentiation. However, trajectory analysis relies on an assumption of trajectory continuity, and experimental limitations preclude some real-world scenarios from meeting this condition. The current lack of assessment metrics makes it difficult to ascertain if/when a given trajectory deviates from continuity, and what impact such a divergence would have on inference accuracy is unclear. By analyzing simulated breaks introduced into in silico and real single-cell data, we found that discontinuity caused precipitous drops in the accuracy of trajectory inference. We then generate a simple scoring algorithm for assessing trajectory continuity, and found that continuity assessments in real-world cases of intestinal stem cell development and CD8 + T cells differentiation efficiently identifies trajectories consistent with empirical knowledge. This assessment approach can also be used in cases where a priori knowledge is lacking to screen a pool of inferred lineages for their adherence to presumed continuity, and serve as a means for weighing higher likelihood trajectories for validation via empirical studies, as exemplified by our case studies in psoriatic arthritis and acute kidney injury. This tool is freely available through github at qingshanni/scEGRET.
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Affiliation(s)
- Zihan Zheng
- Institute of Immunology PLA, Army Medical University, Chongqing, China
- Biomedical Analysis Center, Army Medical University, Chongqing, China
- Department of Autoimmune Disease, Chongqing International Institute for Immunology, Chongqing, Chongqing, China
| | - Ling Chang
- Institute of Immunology PLA, Army Medical University, Chongqing, China
| | - Yinong Li
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Kun Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Jie Mu
- School of Big Data and Software Engineering, Chongqing University, Chongqing, China
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Song Zhang
- College of Life Sciences, Institute for Immunology, Nankai University, Tianjin, China
| | - Jingyi Li
- Department of Autoimmune Disease, Chongqing International Institute for Immunology, Chongqing, Chongqing, China
- Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, Chongqing, China
| | - Yuzhang Wu
- Institute of Immunology PLA, Army Medical University, Chongqing, China
| | - Liyun Zou
- Institute of Immunology PLA, Army Medical University, Chongqing, China
| | - Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China
- School of Big Data and Software Engineering, Chongqing University, Chongqing, China
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36
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Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558015. [PMID: 37745427 PMCID: PMC10516050 DOI: 10.1101/2023.09.15.558015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1-5. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations6-9. However, fundamental questions in the temporal regulation of transcription and enhancer-gene synchrony remain unanswered primarily due to the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq - a novel single-cell nascent RNA sequencing assay using click-chemistry - and unveil the coordinated transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription, and estimates burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells. It reveals the co-transcription of functionally related genes and leverages the replication-dependent non-polyadenylated histone genes transcription to elucidate cell-cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq identifies networks of enhancers and genes and indicates that the bursting of transcription at super-enhancers precedes the burst from associated genes. By imparting insights into the dynamic nature of transcription and the origin and propagation of transcription signals, scGRO-seq demonstrates its unique ability to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
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Affiliation(s)
- Dig B. Mahat
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nathaniel D. Tippens
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sean K. Waterton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Department of Biology, Stanford University, Stanford, CA 94305
| | - Jiayu Fu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208
| | - Sarah E. Blatt
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Exact Sciences Corporation, Madison, WI 53719
| | - Phillip A. Sharp
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Lead Contact
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37
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Erbe R, Stein-O’Brien G, Fertig EJ. Transcriptomic forecasting with neural ordinary differential equations. PATTERNS (NEW YORK, N.Y.) 2023; 4:100793. [PMID: 37602211 PMCID: PMC10435954 DOI: 10.1016/j.patter.2023.100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 08/22/2023]
Abstract
Single-cell transcriptomics technologies can uncover changes in the molecular states that underlie cellular phenotypes. However, understanding the dynamic cellular processes requires extending from inferring trajectories from snapshots of cellular states to estimating temporal changes in cellular gene expression. To address this challenge, we have developed a neural ordinary differential-equation-based method, RNAForecaster, for predicting gene expression states in single cells for multiple future time steps in an embedding-independent manner. We demonstrate that RNAForecaster can accurately predict future expression states in simulated single-cell transcriptomic data with cellular tracking over time. We then show that by using metabolic labeling single-cell RNA sequencing (scRNA-seq) data from constitutively dividing cells, RNAForecaster accurately recapitulates many of the expected changes in gene expression during progression through the cell cycle over a 3-day period. Thus, RNAForecaster enables short-term estimation of future expression states in biological systems from high-throughput datasets with temporal information.
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Affiliation(s)
- Rossin Erbe
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Genevieve Stein-O’Brien
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neurodiscovery Institute, Baltimore, MD, USA
- Single Cell Training and Analysis Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elana J. Fertig
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA
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38
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Jiao C, Reckstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL. RNA recording in single bacterial cells using reprogrammed tracrRNAs. Nat Biotechnol 2023; 41:1107-1116. [PMID: 36604543 PMCID: PMC7614944 DOI: 10.1038/s41587-022-01604-8] [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: 04/19/2022] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Capturing an individual cell's transcriptional history is a challenge exacerbated by the functional heterogeneity of cellular communities. Here, we leverage reprogrammed tracrRNAs (Rptrs) to record selected cellular transcripts as stored DNA edits in single living bacterial cells. Rptrs are designed to base pair with sensed transcripts, converting them into guide RNAs. The guide RNAs then direct a Cas9 base editor to target an introduced DNA target. The extent of base editing can then be read in the future by sequencing. We use this approach, called TIGER (transcribed RNAs inferred by genetically encoded records), to record heterologous and endogenous transcripts in individual bacterial cells. TIGER can quantify relative expression, distinguish single-nucleotide differences, record multiple transcripts simultaneously and read out single-cell phenomena. We further apply TIGER to record metabolic bet hedging and antibiotic resistance mobilization in Escherichia coli as well as host cell invasion by Salmonella. Through RNA recording, TIGER connects current cellular states with past transcriptional states to decipher complex cellular responses in single cells.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Claas Reckstadt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Fabian König
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Christina Homberger
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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39
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Vock IW, Simon MD. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA (NEW YORK, N.Y.) 2023; 29:958-976. [PMID: 37028916 DOI: 10.1261/rna.079451.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortcoming and are widely used approaches to identify changes in RNA synthesis and degradation kinetics. While advanced statistical models implemented in user-friendly software (e.g., DESeq2) have ensured the statistical rigor of differential expression analyses, no such tools that facilitate differential kinetic analysis with NR-seq exist. Here, we report the development of Bayesian analysis of the kinetics of RNA (bakR; https:// github.com/simonlabcode/bakR), an R package to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Analyses of simulated data confirmed that bakR implementations of the hierarchical model outperform attempts to analyze differential kinetics with existing models. bakR also uncovers biological signals in real NR-seq data sets and provides improved analyses of existing data sets. This work establishes bakR as an important tool for identifying differential RNA synthesis and degradation kinetics.
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Affiliation(s)
- Isaac W Vock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
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40
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Li Q. scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics. Genome Biol 2023; 24:149. [PMID: 37353848 PMCID: PMC10290357 DOI: 10.1186/s13059-023-02988-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of cellular dynamics with minimal influence from batch effects. For inference, scTour simultaneously estimates the developmental pseudotime, delineates the vector field, and maps the transcriptomic latent space under a single, integrated framework. For prediction, scTour precisely reconstructs the underlying dynamics of unseen cellular states or a new independent dataset. scTour's functionalities are demonstrated in a variety of biological processes from 19 datasets.
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Affiliation(s)
- Qian Li
- Department of Pathology, University of Cambridge, Cambridge, UK.
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41
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Zeng Q, Mousa M, Nadukkandy AS, Franssens L, Alnaqbi H, Alshamsi FY, Safar HA, Carmeliet P. Understanding tumour endothelial cell heterogeneity and function from single-cell omics. Nat Rev Cancer 2023:10.1038/s41568-023-00591-5. [PMID: 37349410 DOI: 10.1038/s41568-023-00591-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Anti-angiogenic therapies (AATs) are used to treat different types of cancers. However, their success is limited owing to insufficient efficacy and resistance. Recently, single-cell omics studies of tumour endothelial cells (TECs) have provided new mechanistic insight. Here, we overview the heterogeneity of human TECs of all tumour types studied to date, at the single-cell level. Notably, most human tumour types contain varying numbers but only a small population of angiogenic TECs, the presumed targets of AATs, possibly contributing to the limited efficacy of and resistance to AATs. In general, TECs are heterogeneous within and across all tumour types, but comparing TEC phenotypes across tumours is currently challenging, owing to the lack of a uniform nomenclature for endothelial cells and consistent single-cell analysis protocols, urgently raising the need for a more consistent approach. Nonetheless, across most tumour types, universal TEC markers (ACKR1, PLVAP and IGFBP3) can be identified. Besides angiogenesis, biological processes such as immunomodulation and extracellular matrix organization are among the most commonly predicted enriched signatures of TECs across different tumour types. Although angiogenesis and extracellular matrix targets have been considered for AAT (without the hoped success), the immunomodulatory properties of TECs have not been fully considered as a novel anticancer therapeutic approach. Therefore, we also discuss progress, limitations, solutions and novel targets for AAT development.
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Affiliation(s)
- Qun Zeng
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Aisha Shigna Nadukkandy
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lies Franssens
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Fatima Yousif Alshamsi
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Habiba Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, UAE.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE.
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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42
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Edwards DM, Davies P, Hebenstreit D. Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting. Genome Biol 2023; 24:138. [PMID: 37328900 PMCID: PMC10276402 DOI: 10.1186/s13059-023-02977-y] [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: 09/06/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical model and Bayesian inference implementation to facilitate genome-wide joint parameter estimation and confidence quantification (R package: burstMCMC). We demonstrate that, unlike conventional scRNA-seq, 4sU scRNA-seq resolves temporal parameters and furthermore boosts inference of dimensionless parameters via a synergy between single-cell resolution and 4sU labelling. We apply our method to published 4sU scRNA-seq data and linked with ChIP-seq data, we uncover previously obscured associations between different parameters and histone modifications.
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Affiliation(s)
| | - Philip Davies
- School of Life Sciences, University of Warwick, Coventry, UK
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43
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Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun 2023; 14:3559. [PMID: 37321987 PMCID: PMC10272207 DOI: 10.1038/s41467-023-39163-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
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Affiliation(s)
- Teresa Rummel
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany.
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstr. 4, 93053, Regensburg, Germany.
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44
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Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
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Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
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45
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526143. [PMID: 36778497 PMCID: PMC9915486 DOI: 10.1101/2023.01.29.526143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., whole transcriptomes, nascent transcriptomes, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens targeting a variety of biological processes, we were able to decipher the complexity of RNA regulations at multiple levels (e.g., synthesis, processing, degradation), and revealed key regulators involved in miRNA and mitochondrial RNA processing pathways. Our technique opens the possibility of systematically decoding the genome-wide regulatory network underlying RNA temporal dynamics at scale and cost-effectively.
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46
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Ren J, Zhou H, Zeng H, Wang CK, Huang J, Qiu X, Sui X, Li Q, Wu X, Lin Z, Lo JA, Maher K, He Y, Tang X, Lam J, Chen H, Li B, Fisher DE, Liu J, Wang X. Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape. Nat Methods 2023; 20:695-705. [PMID: 37038000 PMCID: PMC10172111 DOI: 10.1038/s41592-023-01829-8] [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] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/22/2023] [Indexed: 04/12/2023]
Abstract
Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap-a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed 'kinetic gene clusters' whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles.
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Affiliation(s)
- Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Haowen Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hu Zeng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jiahao Huang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research Cambridge, Cambridge, MA, USA
| | - Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qiang Li
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Xunwei Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Zuwan Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jennifer A Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kamal Maher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yichun He
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Xin Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Judson Lam
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hongyu Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Jia Liu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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47
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Li L, Su H, Ji Y, Zhu F, Deng J, Bai X, Li H, Liu X, Luo Y, Lin B, Liu T, Lu Y. Deciphering Cell-Cell Interactions with Integrative Single-Cell Secretion Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2301018. [PMID: 37186381 DOI: 10.1002/advs.202301018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/05/2023] [Indexed: 05/17/2023]
Abstract
Cell-cell interactions are the fundamental behaviors to regulate cellular activities. A comprehensive evaluation of intercellular interactions requires direct profiling of various signaling behaviors simultaneously at the single-cell level, which remains lacking. Herein, an integrative single-cell secretion analysis platform is presented to profile different secreted factors (four proteins, three extracellular vesicles (EV) phenotypes), spatial distances, and migration information (distances and direction) simultaneously from high-throughput paired single cells using an antibody-barcode microchip. Applying the platform to analyze the tumor-stromal and tumor-immune interactions with the human oral squamous cell carcinoma (OSCC) cell lines and primary OSCC cells reveals that the initial distances between cells would determine their migratory distances and direction to approach stable organization. The cell-cell in close proximity enhances protein secretions while attenuating EV secretions. Migration has a more profound correlation with protein secretions than EV secretions, in which absolute migration distance affects protein secretions significantly but not the direction. These findings highlight the significance of spatial organization in regulating cell signaling behaviors and demonstrate that the integrative single-cell secretion profiling platform is well-suited for a comprehensive dissection of intercellular communication and interactions, providing new avenues for understanding cell-cell interaction biology and how different signaling behaviors coordinate within the tumor microenvironment.
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Affiliation(s)
- Linmei Li
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, 321004, China
| | - Haoran Su
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
- College of Stomatology, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Yahui Ji
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Fengjiao Zhu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Jiu Deng
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Xue Bai
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Huibing Li
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Xianming Liu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Yong Luo
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Bingcheng Lin
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Tingjiao Liu
- Department of Oral Pathology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Tianjin Road No.2, Huangpu District, Shanghai, 200001, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Tianjin Road No.2, Huangpu District, Shanghai, 200001, China
| | - Yao Lu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
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48
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Fishman L, Nechooshtan G, Erhard F, Regev A, Farrell JA, Rabani M. Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537620. [PMID: 37131717 PMCID: PMC10153228 DOI: 10.1101/2023.04.20.537620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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49
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Papež M, Jiménez Lancho V, Eisenhut P, Motheramgari K, Borth N. SLAM-seq reveals early transcriptomic response mechanisms upon glutamine deprivation in Chinese hamster ovary cells. Biotechnol Bioeng 2023; 120:970-986. [PMID: 36575109 DOI: 10.1002/bit.28320] [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: 09/14/2022] [Revised: 11/30/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Mammalian cells frequently encounter subtle perturbations during recombinant protein production. Identifying the genetic factors that govern the cellular stress response can facilitate targeted genetic engineering to obtain production cell lines that demonstrate a higher stress tolerance. To simulate nutrient stress, Chinese hamster ovary (CHO) cells were transferred into a glutamine(Q)-free medium and transcriptional dynamics using thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) along with standard RNA-seq of stressed and unstressed cells were investigated. The SLAM-seq method allows differentiation between actively transcribed, nascent mRNA, and total (previously present) mRNA in the sample, adding an additional, time-resolved layer to classic RNA-sequencing. The cells tackle amino acid (AA) limitation by inducing the integrated stress response (ISR) signaling pathway, reflected in Atf4 overexpression in the early hours post Q deprivation, leading to subsequent activation of its targets, Asns, Atf3, Ddit3, Eif4ebp1, Gpt2, Herpud1, Slc7a1, Slc7a11, Slc38a2, Trib3, and Vegfa. The GCN2-eIF2α-ATF4 pathway is confirmed by a significant halt in transcription of translation-related genes at 24 h post Q deprivation. The downregulation of lipid synthesis indicates the inhibition of the mTOR pathway, further confirmed by overexpression of Sesn2. Furthermore, SLAM-seq detects short-lived transcription factors, such as Egr1, that would have been missed in standard experimental designs with RNA-seq. Our results describe the successful establishment of SLAM-seq in CHO cells and therefore facilitate its future use in other scenarios where dynamic transcriptome profiling in CHO cells is essential.
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Affiliation(s)
- Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | | | - Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | | | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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50
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Well-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics. Nat Commun 2023; 14:1272. [PMID: 36882403 PMCID: PMC9992361 DOI: 10.1038/s41467-023-36902-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) reveals the transcriptional heterogeneity of cells, but the static snapshots fail to reveal the time-resolved dynamics of transcription. Herein, we develop Well-TEMP-seq, a high-throughput, cost-effective, accurate, and efficient method for massively parallel profiling the temporal dynamics of single-cell gene expression. Well-TEMP-seq combines metabolic RNA labeling with scRNA-seq method Well-paired-seq to distinguish newly transcribed RNAs marked by T-to-C substitutions from pre-existing RNAs in each of thousands of single cells. The Well-paired-seq chip ensures a high single cell/barcoded bead pairing rate (~80%) and the improved alkylation chemistry on beads greatly alleviates chemical conversion-induced cell loss (~67.5% recovery). We further apply Well-TEMP-seq to profile the transcriptional dynamics of colorectal cancer cells exposed to 5-AZA-CdR, a DNA-demethylating drug. Well-TEMP-seq unbiasedly captures the RNA dynamics and outperforms the splicing-based RNA velocity method. We anticipate that Well-TEMP-seq will be broadly applicable to unveil the dynamics of single-cell gene expression in diverse biological processes.
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