1
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Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
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Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
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2
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Liu Y, Fan M, Yang J, Mihaljević L, Chen KH, Ye Y, Sun S, Qiu Z. KAT6A deficiency impairs cognitive functions through suppressing RSPO2/Wnt signaling in hippocampal CA3. SCIENCE ADVANCES 2024; 10:eadm9326. [PMID: 38758792 PMCID: PMC11100567 DOI: 10.1126/sciadv.adm9326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Intellectual disability (ID) affects ~2% of the population and ID-associated genes are enriched for epigenetic factors, including those encoding the largest family of histone lysine acetyltransferases (KAT5-KAT8). Among them is KAT6A, whose mutations cause KAT6A syndrome, with ID as a common clinical feature. However, the underlying molecular mechanism remains unknown. Here, we find that KAT6A deficiency impairs synaptic structure and plasticity in hippocampal CA3, but not in CA1 region, resulting in memory deficits in mice. We further identify a CA3-enriched gene Rspo2, encoding Wnt activator R-spondin 2, as a key transcriptional target of KAT6A. Deletion of Rspo2 in excitatory neurons impairs memory formation, and restoring RSPO2 expression in CA3 neurons rescues the deficits in Wnt signaling and learning-associated behaviors in Kat6a mutant mice. Collectively, our results demonstrate that KAT6A-RSPO2-Wnt signaling plays a critical role in regulating hippocampal CA3 synaptic plasticity and cognitive function, providing potential therapeutic targets for KAT6A syndrome and related neurodevelopmental diseases.
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Affiliation(s)
- Yongqing Liu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Minghua Fan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junhua Yang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ljubica Mihaljević
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kevin Hong Chen
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Fansler MM, Mitschka S, Mayr C. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 2024; 15:4050. [PMID: 38744866 PMCID: PMC11094166 DOI: 10.1038/s41467-024-48254-9] [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: 08/30/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
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Affiliation(s)
- Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine Mayr
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA.
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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4
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Gorin G, Carilli M, Chari T, Pachter L. Spectral neural approximations for models of transcriptional dynamics. Biophys J 2024:S0006-3495(24)00314-X. [PMID: 38715358 DOI: 10.1016/j.bpj.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The advent of high-throughput transcriptomics provides an opportunity to advance mechanistic understanding of transcriptional processes and their connections to cellular function at an unprecedented, genome-wide scale. These transcriptional systems, which involve discrete stochastic events, are naturally modeled using chemical master equations (CMEs), which can be solved for probability distributions to fit biophysical rates that govern system dynamics. While CME models have been used as standards in fluorescence transcriptomics for decades to analyze single-species RNA distributions, there are often no closed-form solutions to CMEs that model multiple species, such as nascent and mature RNA transcript counts. This has prevented the application of standard likelihood-based statistical methods for analyzing high-throughput, multi-species transcriptomic datasets using biophysical models. Inspired by recent work in machine learning to learn solutions to complex dynamical systems, we leverage neural networks and statistical understanding of system distributions to produce accurate approximations to a steady-state bivariate distribution for a model of the RNA life cycle that includes nascent and mature molecules. The steady-state distribution to this simple model has no closed-form solution and requires intensive numerical solving techniques: our approach reduces likelihood evaluation time by several orders of magnitude. We demonstrate two approaches, whereby solutions are approximated by 1) learning the weights of kernel distributions with constrained parameters or 2) learning both weights and scaling factors for parameters of kernel distributions. We show that our strategies, denoted by kernel weight regression and parameter-scaled kernel weight regression, respectively, enable broad exploration of parameter space and can be used in existing likelihood frameworks to infer transcriptional burst sizes, RNA splicing rates, and mRNA degradation rates from experimental transcriptomic data.
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Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Maria Carilli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California.
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5
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Luebbert L, Sullivan DK, Carilli M, Hjörleifsson KE, Winnett AV, Chari T, Pachter L. Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.11.571168. [PMID: 38168363 PMCID: PMC10760059 DOI: 10.1101/2023.12.11.571168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infection is vital to understanding its impact on human health and to make accurate predictions to limit adverse effects, such as future epidemics. The increasing use of high-throughput sequencing methods in research, agriculture, and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus-disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on highly conserved amino acid domains, which enables the detection of RNA viruses covering up to 1012 virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We applied our method to identify putative novel viruses in rhesus macaque PBMC data that display cell type specificity and whose presence correlates with altered host gene expression.
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Affiliation(s)
- Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Delaney K. Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Maria Carilli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | | | - Alexander Viloria Winnett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California
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6
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Castro Dopico X, Guryleva M, Mandolesi M, Corcoran M, Coquet JM, Murrell B, Karlsson Hedestam GB. Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque. Clin Transl Immunology 2024; 13:e1508. [PMID: 38707998 PMCID: PMC11063928 DOI: 10.1002/cti2.1508] [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: 01/06/2024] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Objectives The caecum bridges the small and large intestine and plays a front-line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically. Methods To address this issue, we applied single-cell transcriptomic-V(D)J sequencing to FACS-isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5-year-old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues. Results We found caecal NK cells and ILC3s to co-exist with a spectrum of effector T cells partially derived from SOX4 + recent thymic emigrants. Tolerogenic Vγ8Vδ1-T cells, plastic CD4+ T helper cells and GZMK + EOMES + and TMIGD2 + tissue-resident memory CD8+ T cells were present and differed metabolically. An IL13 + GATA3 + Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1 + GATA3 + regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen-presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1 + PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies. Conclusions The data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Mariia Guryleva
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Immunology and MicrobiologyUniversity of CopenhagenCopenhagenDKDenmark
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
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7
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Köhnke T, Nuno KA, Alder CC, Gars EJ, Phan P, Fan AC, Majeti R. Human ASXL1-Mutant Hematopoiesis Is Driven by a Truncated Protein Associated with Aberrant Deubiquitination of H2AK119. Blood Cancer Discov 2024; 5:202-223. [PMID: 38359087 PMCID: PMC11061584 DOI: 10.1158/2643-3230.bcd-23-0235] [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: 11/13/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024] Open
Abstract
Mutations in additional sex combs like 1 (ASXL1) confer poor prognosis both in myeloid malignancies and in premalignant clonal hematopoiesis (CH). However, the mechanisms by which these mutations contribute to disease initiation remain unresolved, and mutation-specific targeting has remained elusive. To address this, we developed a human disease model that recapitulates the disease trajectory from ASXL1-mutant CH to lethal myeloid malignancy. We demonstrate that mutations in ASXL1 lead to the expression of a functional, truncated protein and determine that truncated ASXL1 leads to global redistribution of the repressive chromatin mark H2AK119Ub, increased transposase-accessible chromatin, and activation of both myeloid and stem cell gene-expression programs. Finally, we demonstrate that H2AK119Ub levels are tied to truncated ASXL1 expression levels and leverage this observation to demonstrate that inhibition of the PRC1 complex might be an ASXL1-mutant-specific therapeutic vulnerability in both premalignant CH and myeloid malignancy. SIGNIFICANCE Mutant ASXL1 is a common driver of CH and myeloid malignancy. Using primary human HSPCs, we determine that truncated ASXL1 leads to redistribution of H2AK119Ub and may affect therapeutic vulnerability to PRC1 inhibition.
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Affiliation(s)
- Thomas Köhnke
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
| | - Kevin A. Nuno
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
| | | | - Eric J. Gars
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
| | - Paul Phan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
| | - Amy C. Fan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Stanford School of Medicine, Stanford, California
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8
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 2024; 629:1165-1173. [PMID: 38720076 DOI: 10.1038/s41586-024-07429-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
The nucleus is highly organized, such that factors involved in the transcription and processing of distinct classes of RNA are confined within specific nuclear bodies1,2. One example is the nuclear speckle, which is defined by high concentrations of protein and noncoding RNA regulators of pre-mRNA splicing3. What functional role, if any, speckles might play in the process of mRNA splicing is unclear4,5. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are located farther from nuclear speckles. Gene organization around nuclear speckles is dynamic between cell types, and changes in speckle proximity lead to differences in splicing efficiency. Finally, directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Together, our results integrate the long-standing observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a crucial role for dynamic three-dimensional spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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Affiliation(s)
- Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alex Burr
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Isabel N Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Allen W Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wesley Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jose Lorenzo M Ferrer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elizabeth Soehalim
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Say-Tar Goh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Delaney K Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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9
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Izzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli S, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, El Ghaity-Beckley S, Arandela J, Raviram R, Choi DC, Hoffman R, Chaligné R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA. Mapping genotypes to chromatin accessibility profiles in single cells. Nature 2024; 629:1149-1157. [PMID: 38720070 PMCID: PMC11139586 DOI: 10.1038/s41586-024-07388-y] [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: 05/22/2022] [Accepted: 04/04/2024] [Indexed: 05/19/2024]
Abstract
In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from patients with myeloproliferative neoplasms with JAK2V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT-ChA will empower broad future investigations of the critical link between somatic mutations and epigenetic alterations across clonal populations in malignant and non-malignant contexts.
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Affiliation(s)
- Franco Izzo
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saravanan Ganesan
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Levan Mekerishvili
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Sanjay Kottapalli
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Tamara Prieto
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Elliot O Eton
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theo Botella
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Andrew J Dunbar
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L Bowman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Catherine Potenski
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Eleni P Mimitou
- New York Genome Center, New York, NY, USA
- Immunai, New York, NY, USA
| | - Maximilian Stahl
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Oncology, Division of Leukemia, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sebastian El Ghaity-Beckley
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - JoAnn Arandela
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ramya Raviram
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daniel C Choi
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, NY, USA
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ronald Hoffman
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ronan Chaligné
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- SAIL: Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irene M Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joseph M Scandura
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, NY, USA
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bridget Marcellino
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ross L Levine
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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10
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Bush SJ, Nikola R, Han S, Suzuki S, Yoshida S, Simons BD, Goriely A. Adult Human, but Not Rodent, Spermatogonial Stem Cells Retain States with a Foetal-like Signature. Cells 2024; 13:742. [PMID: 38727278 PMCID: PMC11083513 DOI: 10.3390/cells13090742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Spermatogenesis involves a complex process of cellular differentiation maintained by spermatogonial stem cells (SSCs). Being critical to male reproduction, it is generally assumed that spermatogenesis starts and ends in equivalent transcriptional states in related species. Based on single-cell gene expression profiling, it has been proposed that undifferentiated human spermatogonia can be subclassified into four heterogenous subtypes, termed states 0, 0A, 0B, and 1. To increase the resolution of the undifferentiated compartment and trace the origin of the spermatogenic trajectory, we re-analysed the single-cell (sc) RNA-sequencing libraries of 34 post-pubescent human testes to generate an integrated atlas of germ cell differentiation. We then used this atlas to perform comparative analyses of the putative SSC transcriptome both across human development (using 28 foetal and pre-pubertal scRNA-seq libraries) and across species (including data from sheep, pig, buffalo, rhesus and cynomolgus macaque, rat, and mouse). Alongside its detailed characterisation, we show that the transcriptional heterogeneity of the undifferentiated spermatogonial cell compartment varies not only between species but across development. Our findings associate 'state 0B' with a suppressive transcriptomic programme that, in adult humans, acts to functionally oppose proliferation and maintain cells in a ready-to-react state. Consistent with this conclusion, we show that human foetal germ cells-which are mitotically arrested-can be characterised solely as state 0B. While germ cells with a state 0B signature are also present in foetal mice (and are likely conserved at this stage throughout mammals), they are not maintained into adulthood. We conjecture that in rodents, the foetal-like state 0B differentiates at birth into the renewing SSC population, whereas in humans it is maintained as a reserve population, supporting testicular homeostasis over a longer reproductive lifespan while reducing mutagenic load. Together, these results suggest that SSCs adopt differing evolutionary strategies across species to ensure fertility and genome integrity over vastly differing life histories and reproductive timeframes.
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Affiliation(s)
- Stephen J. Bush
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Rafail Nikola
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Seungmin Han
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Shinnosuke Suzuki
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Shosei Yoshida
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Benjamin D. Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome—MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Science, University of Cambridge, Cambridge CB3 0WA, UK
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- NIHR Biomedical Research Centre, Oxford OX3 7JX, UK
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11
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Su Z, Tong Y, Wei GW. Hodge Decomposition of Single-Cell RNA Velocity. J Chem Inf Model 2024; 64:3558-3568. [PMID: 38572676 PMCID: PMC11035094 DOI: 10.1021/acs.jcim.4c00132] [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: 01/24/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
RNA velocity has the ability to capture the cell dynamic information in the biological processes; yet, a comprehensive analysis of the cell state transitions and their associated chemical and biological processes remains a gap. In this work, we provide the Hodge decomposition, coupled with discrete exterior calculus (DEC), to unveil cell dynamics by examining the decomposed curl-free, divergence-free, and harmonic components of the RNA velocity field in a low dimensional representation, such as a UMAP or a t-SNE representation. Decomposition results show that the decomposed components distinctly reveal key cell dynamic features such as cell cycle, bifurcation, and cell lineage differentiation, regardless of the choice of the low-dimensional representations. The consistency across different representations demonstrates that the Hodge decomposition is a reliable and robust way to extract these cell dynamic features, offering unique analysis and insightful visualization of single-cell RNA velocity fields.
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Affiliation(s)
- Zhe Su
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yiying Tong
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East
Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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12
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Rich JM, Moses L, Einarsson PH, Jackson K, Luebbert L, Booeshaghi AS, Antonsson S, Sullivan DK, Bray N, Melsted P, Pachter L. The impact of package selection and versioning on single-cell RNA-seq analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588111. [PMID: 38617255 PMCID: PMC11014608 DOI: 10.1101/2024.04.04.588111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat and Scanpy are the most widely-used packages implementing such workflows, and are generally thought to implement individual steps similarly. We investigate in detail the algorithms and methods underlying Seurat and Scanpy and find that there are, in fact, considerable differences in the outputs of Seurat and Scanpy. The extent of differences between the programs is approximately equivalent to the variability that would be introduced in benchmarking scRNA-seq datasets by sequencing less than 5% of the reads or analyzing less than 20% of the cell population. Additionally, distinct versions of Seurat and Scanpy can produce very different results, especially during parts of differential expression analysis. Our analysis highlights the need for users of scRNA-seq to carefully assess the tools on which they rely, and the importance of developers of scientific software to prioritize transparency, consistency, and reproducibility for their tools.
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Affiliation(s)
- Joseph M Rich
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- USC-Caltech MD/PhD Program, Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Lambda Moses
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Pétur Helgi Einarsson
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, Reykjavík, Iceland
| | - Kayla Jackson
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- USC-Caltech MD/PhD Program, Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Laura Luebbert
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - A. Sina Booeshaghi
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Sindri Antonsson
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, Reykjavík, Iceland
| | - Delaney K. Sullivan
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Páll Melsted
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, Reykjavík, Iceland
| | - Lior Pachter
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
- Lead Contact
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13
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Caron DP, Specht WL, Chen D, Wells SB, Szabo PA, Jensen IJ, Farber DL, Sims PA. Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.06.547944. [PMID: 37461466 PMCID: PMC10350048 DOI: 10.1101/2023.07.06.547944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and dissecting transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins, as in cells of the immune system. Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell type annotation requires a classifier that integrates multimodal data. Here, we describe MultiModal Classifier Hierarchy (MMoCHi), a marker-based approach for classification, reconciling gene and protein expression without reliance on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal novel subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.
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Affiliation(s)
- Daniel P. Caron
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - William L. Specht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - David Chen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Steven B. Wells
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter A. Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Isaac J. Jensen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Donna L. Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
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14
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Yuan CU, Quah FX, Hemberg M. Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing. Mol Aspects Med 2024; 96:101255. [PMID: 38368637 DOI: 10.1016/j.mam.2024.101255] [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: 11/17/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Single-cell technologies have transformed biomedical research over the last decade, opening up new possibilities for understanding cellular heterogeneity, both at the genomic and transcriptomic level. In addition, more recent developments of spatial transcriptomics technologies have made it possible to profile cells in their tissue context. In parallel, there have been substantial advances in sequencing technologies, and the third generation of methods are able to produce reads that are tens of kilobases long, with error rates matching the second generation short reads. Long reads technologies make it possible to better map large genome rearrangements and quantify isoform specific abundances. This further improves our ability to characterize functionally relevant heterogeneity. Here, we show how researchers have begun to combine single-cell, spatial transcriptomics, and long-read technologies, and how this is resulting in powerful new approaches to profiling both the genome and the transcriptome. We discuss the achievements so far, and we highlight remaining challenges and opportunities.
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Affiliation(s)
- Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Hemberg
- Gene Lay Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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15
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Booeshaghi AS, Chen X, Pachter L. A machine-readable specification for genomics assays. Bioinformatics 2024; 40:btae168. [PMID: 38579259 PMCID: PMC11009023 DOI: 10.1093/bioinformatics/btae168] [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] [Revised: 10/04/2023] [Accepted: 04/04/2024] [Indexed: 04/07/2024] Open
Abstract
MOTIVATION Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries. RESULTS We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays. AVAILABILITY AND IMPLEMENTATION The specification and associated seqspec command line tool is available at https://www.doi.org/10.5281/zenodo.10213865.
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Affiliation(s)
- Ali Sina Booeshaghi
- Department of Bioengineering, University of California, Berkeley, CA, 94720, United States
| | - Xi Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, United States
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16
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Adewale Q, Khan AF, Bennett DA, Iturria-Medina Y. Single-nucleus RNA velocity reveals critical synaptic and cell-cycle dysregulations in neuropathologically confirmed Alzheimer's disease. Sci Rep 2024; 14:7269. [PMID: 38538816 PMCID: PMC10973452 DOI: 10.1038/s41598-024-57918-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Typical differential single-nucleus gene expression (snRNA-seq) analyses in Alzheimer's disease (AD) provide fixed snapshots of cellular alterations, making the accurate detection of temporal cell changes challenging. To characterize the dynamic cellular and transcriptomic differences in AD neuropathology, we apply the novel concept of RNA velocity to the study of single-nucleus RNA from the cortex of 60 subjects with varied levels of AD pathology. RNA velocity captures the rate of change of gene expression by comparing intronic and exonic sequence counts. We performed differential analyses to find the significant genes driving both cell type-specific RNA velocity and expression differences in AD, extensively compared these two transcriptomic metrics, and clarified their associations with multiple neuropathologic traits. The results were cross-validated in an independent dataset. Comparison of AD pathology-associated RNA velocity with parallel gene expression differences reveals sets of genes and molecular pathways that underlie the dynamic and static regimes of cell type-specific dysregulations underlying the disease. Differential RNA velocity and its linked progressive neuropathology point to significant dysregulations in synaptic organization and cell development across cell types. Notably, most of the genes underlying this synaptic dysregulation showed increased RNA velocity in AD subjects compared to controls. Accelerated cell changes were also observed in the AD subjects, suggesting that the precocious depletion of precursor cell pools might be associated with neurodegeneration. Overall, this study uncovers active molecular drivers of the spatiotemporal alterations in AD and offers novel insights towards gene- and cell-centric therapeutic strategies accounting for dynamic cell perturbations and synaptic disruptions.
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Affiliation(s)
- Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - Ahmed F Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada.
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada.
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17
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Chamberlin JT, Lee Y, Marth GT, Quinlan AR. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments. Genome Res 2024; 34:179-188. [PMID: 38355308 PMCID: PMC10984380 DOI: 10.1101/gr.278253.123] [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: 07/07/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing and analyzing single-cell and single-nucleus RNA sequencing experiments. Nuclei contain the same pre-mRNA population as cells, but they contain a small subset of the mRNAs. Nonetheless, early studies argued that single-nucleus analysis yielded results comparable to cellular samples if pre-mRNA measurements were included. However, typical workflows do not distinguish between pre-mRNA and mRNA when estimating gene expression, and variation in their relative abundances across cell types has received limited attention. These gaps are especially important given that incorporating pre-mRNA has become commonplace for both assays, despite known gene length bias in pre-mRNA capture. Here, we reanalyze public data sets from mouse and human to describe the mechanisms and contrasting effects of mRNA and pre-mRNA sampling on gene expression and marker gene selection in single-cell and single-nucleus RNA-seq. We show that pre-mRNA levels vary considerably among cell types, which mediates the degree of gene length bias and limits the generalizability of a recently published normalization method intended to correct for this bias. As an alternative, we repurpose an existing post hoc gene length-based correction method from conventional RNA-seq gene set enrichment analysis. Finally, we show that inclusion of pre-mRNA in bioinformatic processing can impart a larger effect than assay choice itself, which is pivotal to the effective reuse of existing data. These analyses advance our understanding of the sources of variation in single-cell and single-nucleus RNA-seq experiments and provide useful guidance for future studies.
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Affiliation(s)
- John T Chamberlin
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
- Seoul National University, College of Veterinary Medicine, Seoul, 08826, South Korea
| | - Gabor T Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Aaron R Quinlan
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
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18
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Barcenas M, Bocci F, Nie Q. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. Biophys J 2024:S0006-3495(24)00201-7. [PMID: 38504523 DOI: 10.1016/j.bpj.2024.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024] Open
Abstract
Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high-resolution single-cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to "tipping points" whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single-cell transcriptomics data to infer the stability and gene regulatory networks (GRNs) along cell lineages. Our method uses the unspliced and spliced counts from single-cell RNA sequencing data and cell ordering along lineage trajectories to train an RNA splicing multivariate model, from which cell-state stability along the lineage is inferred based on spectral analysis of the model's Jacobian matrix. Moreover, the model infers the RNA cross-species interactions resulting in GRNs and their variation along the cell lineage. When applied to epithelial-mesenchymal transition in ovarian and lung cancer-derived cell lines, our model predicts a saddle-node transition between the epithelial and mesenchymal states passing through an unstable, intermediate cell state. Furthermore, we show that the underlying GRN controlling epithelial-mesenchymal transition rearranges during the transition, resulting in denser and less modular networks in the intermediate state. Overall, our method represents a flexible tool to study cell lineages with a combination of theory-driven modeling and single-cell transcriptomics data.
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Affiliation(s)
- Manuel Barcenas
- Department of Mathematics, University of California Irvine, Irvine, California
| | - Federico Bocci
- Department of Mathematics, University of California Irvine, Irvine, California; NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, California.
| | - Qing Nie
- Department of Mathematics, University of California Irvine, Irvine, California; NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, California.
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19
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Lodewijk GA, Kozuki S, Han C, Topacio BR, Zargari A, Lee S, Knight G, Ashton R, Qi LS, Shariati SA. Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583597. [PMID: 38496557 PMCID: PMC10942404 DOI: 10.1101/2024.03.05.583597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Embryonic stem cells (ESCs) can self-organize in vitro into developmental patterns with spatial organization and molecular similarity to that of early embryonic stages. This self-organization of ESCs requires transmission of signaling cues, via addition of small molecule chemicals or recombinant proteins, to induce distinct embryonic cellular fates and subsequent assembly into structures that can mimic aspects of early embryonic development. During natural embryonic development, different embryonic cell types co-develop together, where each cell type expresses specific fate-inducing transcription factors through activation of non-coding regulatory elements and interactions with neighboring cells. However, previous studies have not fully explored the possibility of engineering endogenous regulatory elements to shape self-organization of ESCs into spatially-ordered embryo models. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize ESCs into early embryonic models. Our results show that CRISPR-based activation (CRISPRa) of only two endogenous regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that the emergence of spatially-ordered embryonic patterns happens through the intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-Programmed Embryo Models (CPEMs) show highly consistent composition of major embryonic cell types that are spatially-organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CPEMs with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings offer a programmable embryo model and demonstrate that minimum intrinsic epigenome editing is sufficient to self-organize ESCs into highly consistent pre-gastrulation embryo models.
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Affiliation(s)
- Gerrald A Lodewijk
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
- Equal contribution to this work
| | - Sayaka Kozuki
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
- Equal contribution to this work
| | - Clara Han
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Benjamin R Topacio
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Abolfazl Zargari
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA
| | - Seungho Lee
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Gavin Knight
- Neurosetta LLC, Madison, WI
- Wisconsin Institute for Discovery, Madison, WI
| | - Randolph Ashton
- Neurosetta LLC, Madison, WI
- Wisconsin Institute for Discovery, Madison, WI
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA
- Sarafan ChEM-H, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA
| | - S Ali Shariati
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
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20
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Weatherbee BAT, Weberling A, Gantner CW, Iwamoto-Stohl LK, Barnikel Z, Barrie A, Campbell A, Cunningham P, Drezet C, Efstathiou P, Fishel S, Vindel SG, Lockwood M, Oakley R, Pretty C, Chowdhury N, Richardson L, Mania A, Weavers L, Christie L, Elder K, Snell P, Zernicka-Goetz M. Distinct pathways drive anterior hypoblast specification in the implanting human embryo. Nat Cell Biol 2024; 26:353-365. [PMID: 38443567 PMCID: PMC10940163 DOI: 10.1038/s41556-024-01367-1] [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: 12/12/2022] [Accepted: 01/24/2024] [Indexed: 03/07/2024]
Abstract
Development requires coordinated interactions between the epiblast, which generates the embryo proper; the trophectoderm, which generates the placenta; and the hypoblast, which forms both the anterior signalling centre and the yolk sac. These interactions remain poorly understood in human embryogenesis because mechanistic studies have only recently become possible. Here we examine signalling interactions post-implantation using human embryos and stem cell models of the epiblast and hypoblast. We find anterior hypoblast specification is NODAL dependent, as in the mouse. However, while BMP inhibits anterior signalling centre specification in the mouse, it is essential for its maintenance in human. We also find contrasting requirements for BMP in the naive pre-implantation epiblast of mouse and human embryos. Finally, we show that NOTCH signalling is important for human epiblast survival. Our findings of conserved and species-specific factors that drive these early stages of embryonic development highlight the strengths of comparative species studies.
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Affiliation(s)
- Bailey A T Weatherbee
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
- Center for Stem Cell and Organoid Medicine, Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Antonia Weberling
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
- All Souls College, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Carlos W Gantner
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | - Lisa K Iwamoto-Stohl
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | - Lucy Richardson
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, UK
| | | | | | | | - Kay Elder
- Bourn Hall Fertility Clinic, Bourn, UK
| | | | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.
- Stem Cells Self-Organization Group, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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21
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He D, Gao Y, Chan SS, Quintana-Parrilla N, Patro R. Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577813. [PMID: 38370848 PMCID: PMC10871212 DOI: 10.1101/2024.02.01.577813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motivation Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing dynamics in scRNA-seq data is challenging, with inherent difficulty in even the seemingly straightforward task of elucidating the splicing status of the molecules from which sequenced fragments are drawn. This difficulty arises, in part, from the limited read length and positional biases, which substantially reduce the specificity of the sequenced fragments. As a result, the splicing status of many reads in scRNA-seq is ambiguous because of a lack of definitive evidence. We are therefore in need of methods that can recover the splicing status of ambiguous reads which, in turn, can lead to more accuracy and confidence in downstream analyses. Results We develop Forseti, a predictive model to probabilistically assign a splicing status to scRNA-seq reads. Our model has two key components. First, we train a binding affinity model to assign a probability that a given transcriptomic site is used in fragment generation. Second, we fit a robust fragment length distribution model that generalizes well across datasets deriving from different species and tissue types. Forseti combines these two trained models to predict the splicing status of the molecule of origin of reads by scoring putative fragments that associate each alignment of sequenced reads with proximate potential priming sites. Using both simulated and experimental data, we show that our model can precisely predict the splicing status of reads and identify the true gene origin of multi-gene mapped reads. Availability Forseti and the code used for producing the results are available at https://github.com/COMBINE-lab/forseti under a BSD 3-clause license.
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Affiliation(s)
- Dongze He
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- Program in Computational Biology, Bioinformatics and Genomices, University of Maryland, College Park, MD 20742, USA
| | - Yuan Gao
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- Program in Computational Biology, Bioinformatics and Genomices, University of Maryland, College Park, MD 20742, USA
| | - Spencer Skylar Chan
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | | | - Rob Patro
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
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22
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Morris JA, Sun JS, Sanjana NE. Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis. Trends Genet 2024; 40:118-133. [PMID: 37989654 PMCID: PMC10872607 DOI: 10.1016/j.tig.2023.10.012] [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: 08/01/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Programmable genome-engineering technologies, such as CRISPR (clustered regularly interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens that capitalize on this programmability, have transformed biomedical science. These screens connect genes and noncoding genome elements to disease-relevant phenotypes, but until recently have been limited to individual phenotypes such as growth or fluorescent reporters of gene expression. By pairing massively parallel screens with high-dimensional profiling of single-cell types/states, we can now measure how individual genetic perturbations or combinations of perturbations impact the cellular transcriptome, proteome, and epigenome. We review technologies that pair CRISPR screens with single-cell multiomics and the unique opportunities afforded by extending pooled screens using deep multimodal phenotyping.
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Affiliation(s)
- John A Morris
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Jennifer S Sun
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA.
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23
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Crespo-Garcia S, Fournier F, Diaz-Marin R, Klier S, Ragusa D, Masaki L, Cagnone G, Blot G, Hafiane I, Dejda A, Rizk R, Juneau R, Buscarlet M, Chorfi S, Patel P, Beltran PJ, Joyal JS, Rezende FA, Hata M, Nguyen A, Sullivan L, Damiano J, Wilson AM, Mallette FA, David NE, Ghosh A, Tsuruda PR, Dananberg J, Sapieha P. Therapeutic targeting of cellular senescence in diabetic macular edema: preclinical and phase 1 trial results. Nat Med 2024; 30:443-454. [PMID: 38321220 DOI: 10.1038/s41591-024-02802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Compromised vascular endothelial barrier function is a salient feature of diabetic complications such as sight-threatening diabetic macular edema (DME). Current standards of care for DME manage aspects of the disease, but require frequent intravitreal administration and are poorly effective in large subsets of patients. Here we provide evidence that an elevated burden of senescent cells in the retina triggers cardinal features of DME pathology and conduct an initial test of senolytic therapy in patients with DME. In cell culture models, sustained hyperglycemia provoked cellular senescence in subsets of vascular endothelial cells displaying perturbed transendothelial junctions associated with poor barrier function and leading to micro-inflammation. Pharmacological elimination of senescent cells in a mouse model of DME reduces diabetes-induced retinal vascular leakage and preserves retinal function. We then conducted a phase 1 single ascending dose safety study of UBX1325 (foselutoclax), a senolytic small-molecule inhibitor of BCL-xL, in patients with advanced DME for whom anti-vascular endothelial growth factor therapy was no longer considered beneficial. The primary objective of assessment of safety and tolerability of UBX1325 was achieved. Collectively, our data suggest that therapeutic targeting of senescent cells in the diabetic retina with a BCL-xL inhibitor may provide a long-lasting, disease-modifying intervention for DME. This hypothesis will need to be verified in larger clinical trials. ClinicalTrials.gov identifier: NCT04537884 .
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Affiliation(s)
- Sergio Crespo-Garcia
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
- École d'optométrie, University of Montreal, Montreal, Quebec, Canada
| | - Frédérik Fournier
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Roberto Diaz-Marin
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Sharon Klier
- UNITY Biotechnology, South San Francisco, CA, USA
| | - Derek Ragusa
- UNITY Biotechnology, South San Francisco, CA, USA
| | | | - Gael Cagnone
- Departments of Pediatrics Ophthalmology, and Pharmacology, Centre Hospitalier Universitaire Sainte Justine Research Center, Montreal, Quebec, Canada
| | - Guillaume Blot
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Ikhlas Hafiane
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Agnieszka Dejda
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Rana Rizk
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Rachel Juneau
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Manuel Buscarlet
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Sarah Chorfi
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | | | | | - Jean-Sebastien Joyal
- Departments of Pediatrics Ophthalmology, and Pharmacology, Centre Hospitalier Universitaire Sainte Justine Research Center, Montreal, Quebec, Canada
| | - Flavio A Rezende
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Masayuki Hata
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Alex Nguyen
- UNITY Biotechnology, South San Francisco, CA, USA
| | | | | | - Ariel M Wilson
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Frédérick A Mallette
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | | | | | | | | | - Przemyslaw Sapieha
- Department of Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada.
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO-HMR) Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada.
- UNITY Biotechnology, South San Francisco, CA, USA.
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24
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat Cell Biol 2024; 26:250-262. [PMID: 38321203 DOI: 10.1038/s41556-023-01337-z] [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: 08/07/2022] [Accepted: 12/13/2023] [Indexed: 02/08/2024]
Abstract
A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.
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Affiliation(s)
- Rachel K Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Petr Kasparek
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Viragova
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Weichselbaum
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Kara L McKinley
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Asoka Rathnayake
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dedeepya Vaka
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Vinh Nguyen
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Efren Reyes
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander R Gupta
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Chan Zuckerberg BioHub and Center for Cellular Construction 94158, University of California San Francisco, San Francisco, CA, USA
| | - Richard M Locksley
- Department of Medicine and Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - James M Gardner
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
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25
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Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568164. [PMID: 38045414 PMCID: PMC10690192 DOI: 10.1101/2023.11.21.568164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data.
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Affiliation(s)
- Delaney K Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | | | - Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Lambda Moses
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Nicolas L Bray
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Harold Pimentel
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - A Sina Booeshaghi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Páll Melsted
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
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26
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Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun 2024; 15:476. [PMID: 38216587 PMCID: PMC10786948 DOI: 10.1038/s41467-023-40408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 01/14/2024] Open
Abstract
Mechanisms specifying cancer cell states and response to therapy are incompletely understood. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas, the most common tumors of the peripheral nervous system. We find schwannomas are comprised of 2 molecular groups that are distinguished by activation of neural crest or nerve injury pathways that specify tumor cell states and the architecture of the tumor immune microenvironment. Moreover, we find radiotherapy is sufficient for interconversion of neural crest schwannomas to immune-enriched schwannomas through epigenetic and metabolic reprogramming. To define mechanisms underlying schwannoma groups, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of tumor evolution and establish a paradigm of epigenetic and metabolic reprograming of cancer cells that shapes the immune microenvironment in response to radiotherapy.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Tim Casey-Clyde
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nam Woo Cho
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Jason Swinderman
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark C Dougherty
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Kyla Foster
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Joanna Pak
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Jonathan D Breshears
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ursula E Lang
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Dermatology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Charlotte D Eaton
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kamir J Hiam-Galvez
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Erica Stevenson
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kuei-Ho Chen
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Brian V Lien
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Wu
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Penny K Sneed
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, 60611, USA
| | - Daniel Lim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Marlan R Hansen
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Matthew H Spitzer
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Luke Gilbert
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Philip V Theodosopoulos
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.
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27
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Millet A, Ledo JH, Tavazoie SF. An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer's brains. Immunity 2024; 57:153-170.e6. [PMID: 38159571 PMCID: PMC10805152 DOI: 10.1016/j.immuni.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/04/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
The dominant risk factors for late-onset Alzheimer's disease (AD) are advanced age and the APOE4 genetic variant. To examine how these factors alter neuroimmune function, we generated an integrative, longitudinal single-cell atlas of brain immune cells in AD model mice bearing the three common human APOE alleles. Transcriptomic and chromatin accessibility analyses identified a reactive microglial population defined by the concomitant expression of inflammatory signals and cell-intrinsic stress markers whose frequency increased with age and APOE4 burden. An analogous population was detectable in the brains of human AD patients, including in the cortical tissue, using multiplexed spatial transcriptomics. This population, which we designate as terminally inflammatory microglia (TIM), exhibited defects in amyloid-β clearance and altered cell-cell communication during aducanumab treatment. TIM may represent an exhausted-like state for inflammatory microglia in the AD milieu that contributes to AD risk and pathology in APOE4 carriers and the elderly, thus presenting a potential therapeutic target for AD.
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Affiliation(s)
- Alon Millet
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA
| | - Jose Henrique Ledo
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Department of Pathology and Laboratory of Medicine, Department of Neuroscience, South Carolina Alzheimer's Disease Research Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA.
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28
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George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte N, Zhao L, Thanki A, Yu I, Marugan Calles J, Erdos K, Vilmovsky L, Kurri S, Vathrakokoili-Pournara A, Osumi-Sutherland D, Prakash A, Wang S, Tello-Ruiz M, Kumari S, Ware D, Goutte-Gattat D, Hu Y, Brown N, Perrimon N, Vizcaíno JA, Burdett T, Teichmann S, Brazma A, Papatheodorou I. Expression Atlas update: insights from sequencing data at both bulk and single cell level. Nucleic Acids Res 2024; 52:D107-D114. [PMID: 37992296 PMCID: PMC10767917 DOI: 10.1093/nar/gkad1021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.
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Affiliation(s)
- Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Alfonso Munoz Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Yalan Bi
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Haider Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Upendra Kumbham
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Nadja Francesca Nolte
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Lingyun Zhao
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Anil S Thanki
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Iris D Yu
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Jose C Marugan Calles
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Karoly Erdos
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Liora Vilmovsky
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Sandeep R Kurri
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | | | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Marcela K Tello-Ruiz
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Doreen Ware
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA, Plant Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853, USA
| | - Damien Goutte-Gattat
- FlyBase-Cambridge, Department of Physiology, Development and Neuroscience, University of Cambridge Downing Street, Cambridge CB2 3DY, UK
| | - Yanhui Hu
- Perrimon Lab, Department of Genetics, Harvard Medical School, Boston MA 02115, USA
| | - Nick Brown
- FlyBase-Cambridge, Department of Physiology, Development and Neuroscience, University of Cambridge Downing Street, Cambridge CB2 3DY, UK
| | - Norbert Perrimon
- Perrimon Lab, Department of Genetics, Harvard Medical School, Boston MA 02115, USA
- FlyBase-Harvard Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Sarah Teichmann
- Wellcome Trust Sanger Institute. Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
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29
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Sun N, Teyssier N, Wang B, Drake S, Seyler M, Zaltsman Y, Everitt A, Teerikorpi N, Willsey HR, Goodarzi H, Tian R, Kampmann M, Willsey AJ. Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573108. [PMID: 38187634 PMCID: PMC10769323 DOI: 10.1101/2023.12.22.573108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent studies have identified over one hundred high-confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses on smaller subsets of these genes have consistently implicated excitatory neurogenesis. However, the extent to which the broader set of hcASD genes are involved in this process has not been explored systematically nor have the biological pathways underlying this convergence been identified. Here, we leveraged CROP-Seq to repress 87 hcASD genes in a human in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cellular state characterized by disruptions in proliferation, differentiation, cell cycle, microtubule biology, and RNA-binding proteins (RBPs). We also characterized over 3,000 differentially expressed genes, 286 of which had expression profiles correlated with changes in developmental trajectory. Overall, we uncovered transcriptional disruptions downstream of hcASD gene perturbations, correlated these disruptions with distinct differentiation phenotypes, and reinforced neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.
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30
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Gayoso A, Weiler P, Lotfollahi M, Klein D, Hong J, Streets A, Theis FJ, Yosef N. Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nat Methods 2024; 21:50-59. [PMID: 37735568 PMCID: PMC10776389 DOI: 10.1038/s41592-023-01994-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/23/2023]
Abstract
RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in snapshot single-cell data; however, current approaches for estimating RNA velocity lack effective strategies for quantifying uncertainty and determining the overall applicability to the system of interest. Here, we present veloVI (velocity variational inference), a deep generative modeling framework for estimating RNA velocity. veloVI learns a gene-specific dynamical model of RNA metabolism and provides a transcriptome-wide quantification of velocity uncertainty. We show that veloVI compares favorably to previous approaches with respect to goodness of fit, consistency across transcriptionally similar cells and stability across preprocessing pipelines for quantifying RNA abundance. Further, we demonstrate that veloVI's posterior velocity uncertainty can be used to assess whether velocity analysis is appropriate for a given dataset. Finally, we highlight veloVI as a flexible framework for modeling transcriptional dynamics by adapting the underlying dynamical model to use time-dependent transcription rates.
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Affiliation(s)
- Adam Gayoso
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Philipp Weiler
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Mohammad Lotfollahi
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Cambridge, UK
| | - Dominik Klein
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Justin Hong
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Aaron Streets
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
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31
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Fair T, Pavlovic BJ, Schaefer NK, Pollen AA. Mapping cis- and trans-regulatory target genes of human-specific deletions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573461. [PMID: 38234800 PMCID: PMC10793408 DOI: 10.1101/2023.12.27.573461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution1,2. Comparative genetic studies of primates2,3 have identified thousands of human-specific deletions (hDels), and the cis-regulatory potential of short (≤31 base pairs) hDels has been assessed using reporter assays4. However, how structural variant-sized (≥50 base pairs) hDels influence molecular and cellular processes in their native genomic contexts remains unexplored. Here, we design genome-scale libraries of single-guide RNAs targeting 7.2 megabases of sequence in 6,358 hDels and present a systematic CRISPR interference (CRISPRi) screening approach to identify hDels that modify cellular proliferation in chimpanzee pluripotent stem cells. By intersecting hDels with chromatin state features and performing single-cell CRISPRi (Perturb-seq) to identify their cis- and trans-regulatory target genes, we discovered 19 hDels controlling gene expression. We highlight two hDels, hDel_2247 and hDel_585, with tissue-specific activity in the liver and brain, respectively. Our findings reveal a molecular and cellular role for sequences lost in the human lineage and establish a framework for functionally interrogating human-specific genetic variants.
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Affiliation(s)
- Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan K Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
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32
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Song Y, Zhang C, Omenn GS, O’Meara MJ, Welch JD. Predicting the Structural Impact of Human Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572928. [PMID: 38187531 PMCID: PMC10769328 DOI: 10.1101/2023.12.21.572928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
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Affiliation(s)
- Yuxuan Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D. Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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33
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Booeshaghi AS, Min KH(J, Gehring J, Pachter L. Quantifying orthogonal barcodes for sequence census assays. BIOINFORMATICS ADVANCES 2023; 4:vbad181. [PMID: 38213823 PMCID: PMC10783946 DOI: 10.1093/bioadv/vbad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/02/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Summary Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs. Availability and implementation https://github.com/pachterlab/kb_python, https://github.com/pachterlab/qcbc.
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Affiliation(s)
- A Sina Booeshaghi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Kyung Hoi (Joseph) Min
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jase Gehring
- Arcadia Science, Berkeley, CA 94702, United States
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, United States
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34
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Kulkarni S, Saha M, Slosberg J, Singh A, Nagaraj S, Becker L, Zhang C, Bukowski A, Wang Z, Liu G, Leser JM, Kumar M, Bakhshi S, Anderson MJ, Lewandoski M, Vincent E, Goff LA, Pasricha PJ. Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease. eLife 2023; 12:RP88051. [PMID: 38108810 PMCID: PMC10727506 DOI: 10.7554/elife.88051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
The enteric nervous system (ENS), a collection of neural cells contained in the wall of the gut, is of fundamental importance to gastrointestinal and systemic health. According to the prevailing paradigm, the ENS arises from progenitor cells migrating from the neural crest and remains largely unchanged thereafter. Here, we show that the lineage composition of maturing ENS changes with time, with a decline in the canonical lineage of neural-crest derived neurons and their replacement by a newly identified lineage of mesoderm-derived neurons. Single cell transcriptomics and immunochemical approaches establish a distinct expression profile of mesoderm-derived neurons. The dynamic balance between the proportions of neurons from these two different lineages in the post-natal gut is dependent on the availability of their respective trophic signals, GDNF-RET and HGF-MET. With increasing age, the mesoderm-derived neurons become the dominant form of neurons in the ENS, a change associated with significant functional effects on intestinal motility which can be reversed by GDNF supplementation. Transcriptomic analyses of human gut tissues show reduced GDNF-RET signaling in patients with intestinal dysmotility which is associated with reduction in neural crest-derived neuronal markers and concomitant increase in transcriptional patterns specific to mesoderm-derived neurons. Normal intestinal function in the adult gastrointestinal tract therefore appears to require an optimal balance between these two distinct lineages within the ENS.
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Affiliation(s)
- Subhash Kulkarni
- Division of Gastroenterology, Dept of Medicine, Beth Israel Deaconess Medical CenterBostonUnited States
- Division of Medical Sciences, Harvard Medical SchoolBostonUnited States
| | - Monalee Saha
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Jared Slosberg
- Department of Genetic Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Alpana Singh
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Sushma Nagaraj
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Laren Becker
- Division of Gastroenterology, Stanford University – School of MedicineStanfordUnited States
| | - Chengxiu Zhang
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Alicia Bukowski
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Zhuolun Wang
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Guosheng Liu
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Jenna M Leser
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Mithra Kumar
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Shriya Bakhshi
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Matthew J Anderson
- Center for Cancer Research, National Cancer InstituteFrederickUnited States
| | - Mark Lewandoski
- Center for Cancer Research, National Cancer InstituteFrederickUnited States
| | - Elizabeth Vincent
- Department of Genetic Medicine, Johns Hopkins University – School of MedicineBaltimoreUnited States
| | - Loyal A Goff
- Department of Neuroscience, Johns Hopkins University – School of MedicineBaltimoreUnited States
- Kavli Neurodiscovery Institute, Johns Hopkins University – School of MedicineBaltimoreUnited States
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35
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Ivanova EN, Shwetar J, Devlin JC, Buus TB, Gray-Gaillard S, Koide A, Cornelius A, Samanovic MI, Herrera A, Mimitou EP, Zhang C, Karmacharya T, Desvignes L, Ødum N, Smibert P, Ulrich RJ, Mulligan MJ, Koide S, Ruggles KV, Herati RS, Koralov SB. mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection. iScience 2023; 26:108572. [PMID: 38213787 PMCID: PMC10783604 DOI: 10.1016/j.isci.2023.108572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/21/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell analysis of blood from COVID-19 patients and healthy volunteers receiving the SARS-CoV-2 vaccine and booster. We profiled immune responses via transcriptional analysis and lymphocyte repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. B and T cell repertoire analysis revealed clonal expansion among effector cells in COVID-19 patients and memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, expansion of clonal γδ T cells was found only in infected individuals. Our dataset enables side-by-side comparison of immune responses to infection versus vaccination, including clonal B and T cell responses. Our comparative analysis shows that vaccination induces a robust, durable clonal B and T cell responses, without the severe inflammation associated with infection.
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Affiliation(s)
- Ellie N. Ivanova
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jasmine Shwetar
- Institute of Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Joseph C. Devlin
- Institute of Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Terkild B. Buus
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sophie Gray-Gaillard
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
| | - Akiko Koide
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Amber Cornelius
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
| | - Marie I. Samanovic
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alberto Herrera
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Chenzhen Zhang
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Trishala Karmacharya
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
| | - Ludovic Desvignes
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- High Containment Laboratories, Office of Science and Research, New York University Langone Health, New York, NY 10016, USA
| | - Niels Ødum
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Robert J. Ulrich
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Mark J. Mulligan
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly V. Ruggles
- Institute of Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ramin S. Herati
- New York University Langone Vaccine Center, New York University Langone Health, New York, NY 10016, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine, 430 East 29th Street, New York, NY 10016, USA
| | - Sergei B. Koralov
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
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36
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Bredel D, Tihic E, Mouraud S, Danlos FX, Susini S, Aglave M, Alfaro A, Mohamed-Djalim C, Rouanne M, Halse H, Bigorgne A, Tselikas L, Dalle S, Hartl DM, Baudin E, Guettier C, Vibert E, Rosmorduc O, Robert C, Ferlicot S, Parier B, Albiges L, de Montpreville VT, Besse B, Mercier O, Even C, Breuskin I, Classe M, Radulescu C, Lebret T, Pautier P, Gouy S, Scoazec JY, Zitvogel L, Marabelle A, Bonvalet M. Immune checkpoints are predominantly co-expressed by clonally expanded CD4 +FoxP3 + intratumoral T-cells in primary human cancers. J Exp Clin Cancer Res 2023; 42:333. [PMID: 38057799 DOI: 10.1186/s13046-023-02897-6] [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: 07/14/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND In addition to anti-PD(L)1, anti-CTLA-4 and anti-LAG-3, novel immune checkpoint proteins (ICP)-targeted antibodies have recently failed to demonstrate significant efficacy in clinical trials. In these trials, patients were enrolled without screening for drug target expression. Although these novel ICP-targeted antibodies were expected to stimulate anti-tumor CD8 + T-cells, the rationale for their target expression in human tumors relied on pre-clinical IHC stainings and transcriptomic data, which are poorly sensitive and specific techniques for assessing membrane protein expression on immune cell subsets. Our aim was to describe ICP expression on intratumoral T-cells from primary solid tumors to better design upcoming neoadjuvant cancer immunotherapy trials. METHODS We prospectively performed multiparameter flow cytometry and single-cell RNA sequencing (scRNA-Seq) paired with TCR sequencing on freshly resected human primary tumors of various histological types to precisely determine ICP expression levels within T-cell subsets. RESULTS Within a given tumor type, we found high inter-individual variability for tumor infiltrating CD45 + cells and for T-cells subsets. The proportions of CD8+ T-cells (~ 40%), CD4+ FoxP3- T-cells (~ 40%) and CD4+ FoxP3+ T-cells (~ 10%) were consistent across patients and indications. Intriguingly, both stimulatory (CD25, CD28, 4-1BB, ICOS, OX40) and inhibitory (PD-1, CTLA-4, PD-L1, CD39 and TIGIT) checkpoint proteins were predominantly co-expressed by intratumoral CD4+FoxP3+ T-cells. ScRNA-Seq paired with TCR sequencing revealed that T-cells with high clonality and high ICP expressions comprised over 80% of FoxP3+ cells among CD4+ T-cells. Unsupervised clustering of flow cytometry and scRNAseq data identified subsets of CD8+ T-cells and of CD4+ FoxP3- T-cells expressing certain checkpoints, though these expressions were generally lower than in CD4+ FoxP3+ T-cell subsets, both in terms of proportions among total T-cells and ICP expression levels. CONCLUSIONS Tumor histology alone does not reveal the complete picture of the tumor immune contexture. In clinical trials, assumptions regarding target expression should rely on more sensitive and specific techniques than conventional IHC or transcriptomics. Flow cytometry and scRNAseq accurately characterize ICP expression within immune cell subsets. Much like in hematology, flow cytometry can better describe the immune contexture of solid tumors, offering the opportunity to guide patient treatment according to drug target expression rather than tumor histological type.
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Affiliation(s)
- Delphine Bredel
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
| | - Edi Tihic
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
| | - Séverine Mouraud
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
| | - François-Xavier Danlos
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Gustave Roussy, Département d'Innovation Thérapeutique Et d'Essais Précoces (DITEP), 94805, Villejuif, France
| | - Sandrine Susini
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
| | - Marine Aglave
- Gustave Roussy, Plateforme de bioinformatique, F-94805, Villejuif, France
| | - Alexia Alfaro
- Gustave Roussy, Université Paris-Saclay, UMS 23/3655, Plateforme Imagerie Et Cytométrie, Villejuif, France
| | - Chifaou Mohamed-Djalim
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
| | - Mathieu Rouanne
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, USA
| | - Héloise Halse
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Institut Imagine, Université Paris Descartes, 75015, Paris, France
| | - Amélie Bigorgne
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Institut Imagine, Université Paris Descartes, 75015, Paris, France
| | - Lambros Tselikas
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Gustave Roussy, Université Paris Saclay, Département d'Anesthésie, Chirurgie et Imagerie Interventionnelle, F-94805, Villejuif, France
| | - Stéphane Dalle
- Department of Dermatology, HCL Cancer Institute, Lyon Cancer Research Center, 69495, Lyon, France
| | - Dana M Hartl
- Gustave Roussy, Université Paris Saclay, Département d'Anesthésie, Chirurgie et Imagerie Interventionnelle, F-94805, Villejuif, France
| | - Eric Baudin
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
| | - Catherine Guettier
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Service d'Anatomie Pathologique, Hôpital Bicêtre, AP-HP, 94270, Le Kremlin-Bicêtre, France
- UMR-S 1193, Hôpital Paul Brousse Université Paris Saclay, 94800, Villejuif, France
| | - Eric Vibert
- UMR-S 1193, Hôpital Paul Brousse Université Paris Saclay, 94800, Villejuif, France
- Centre Hépato-Biliaire, Hôpital Paul Brousse, AP-HP, 94800, Villejuif, France
| | - Olivier Rosmorduc
- Centre Hépato-Biliaire, Hôpital Paul Brousse, AP-HP, 94800, Villejuif, France
| | - Caroline Robert
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U981, Gustave Roussy, 94805, Villejuif, France
| | - Sophie Ferlicot
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Service d'Anatomie Pathologique, Hôpital Bicêtre, AP-HP, 94270, Le Kremlin-Bicêtre, France
- Centre National de Recherche Scientifique (CNRS), Gustave Roussy, Université Paris-Saclay, UMR 9019, 94805, Villejuif, France
| | - Bastien Parier
- Service de Chirurgie Urologique, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, France
| | - Laurence Albiges
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
| | | | - Benjamin Besse
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
| | - Olaf Mercier
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
- Service de Chirurgie Thoracique Et Transplantation Cardio-Pulmonaire, Hôpital Marie-Lannelongue, UMR_S 999 INSERM, Université Paris-Saclay, GHPSJ, 92350, Le Plessis-Robinson, France
| | - Caroline Even
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
| | - Ingrid Breuskin
- Gustave Roussy, Université Paris Saclay, Département d'Anesthésie, Chirurgie et Imagerie Interventionnelle, F-94805, Villejuif, France
| | - Marion Classe
- Gustave Roussy, Département de Biopathologie, F-94805, Villejuif, France
| | - Camélia Radulescu
- Département de Pathologie, Hôpital Foch, UVSQ, Université Paris-Saclay, 92150, Suresnes, France
| | - Thierry Lebret
- Département d'Urologie, Hôpital Foch, UVSQ-Université Paris-Saclay, 92150, Suresnes, France
| | - Patricia Pautier
- Gustave Roussy, Département d'Oncologie Médicale, F-94805, Villejuif, France
| | - Sébastien Gouy
- Gustave Roussy, Université Paris Saclay, Département d'Anesthésie, Chirurgie et Imagerie Interventionnelle, F-94805, Villejuif, France
| | - Jean-Yves Scoazec
- Gustave Roussy, Département de Biopathologie, F-94805, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Aurélien Marabelle
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France.
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France.
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France.
- Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.
- Gustave Roussy, Département d'Innovation Thérapeutique Et d'Essais Précoces (DITEP), 94805, Villejuif, France.
| | - Mélodie Bonvalet
- Gustave Roussy, 114 Rue Édouard Vaillant, 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) U1015, Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), 94805, Villejuif, France
- Institut National de La Santé Et de La Recherche Médicale (INSERM) CIC1428, Centre d'Investigation Clinique BIOTHERIS, 94805, Villejuif, France
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Farias-Jofre M, Romero R, Galaz J, Xu Y, Miller D, Garcia-Flores V, Arenas-Hernandez M, Winters AD, Berkowitz BA, Podolsky RH, Shen Y, Kanninen T, Panaitescu B, Glazier CR, Pique-Regi R, Theis KR, Gomez-Lopez N. Blockade of IL-6R prevents preterm birth and adverse neonatal outcomes. EBioMedicine 2023; 98:104865. [PMID: 37944273 PMCID: PMC10665693 DOI: 10.1016/j.ebiom.2023.104865] [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: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Preterm birth preceded by spontaneous preterm labour often occurs in the clinical setting of sterile intra-amniotic inflammation (SIAI), a condition that currently lacks treatment. METHODS Proteomic and scRNA-seq human data were analysed to evaluate the role of IL-6 and IL-1α in SIAI. A C57BL/6 murine model of SIAI-induced preterm birth was developed by the ultrasound-guided intra-amniotic injection of IL-1α. The blockade of IL-6R by using an aIL-6R was tested as prenatal treatment for preterm birth and adverse neonatal outcomes. QUEST-MRI evaluated brain oxidative stress in utero. Targeted transcriptomic profiling assessed maternal, foetal, and neonatal inflammation. Neonatal biometrics and neurodevelopment were tested. The neonatal gut immune-microbiome was evaluated using metagenomic sequencing and immunophenotyping. FINDINGS IL-6 plays a critical role in the human intra-amniotic inflammatory response, which is associated with elevated concentrations of the alarmin IL-1α. Intra-amniotic injection of IL-1α resembles SIAI, inducing preterm birth (7% vs. 50%, p = 0.03, Fisher's exact test) and neonatal mortality (18% vs. 56%, p = 0.02, Mann-Whitney U-test). QUEST-MRI revealed no foetal brain oxidative stress upon in utero IL-1α exposure (p > 0.05, mixed linear model). Prenatal treatment with aIL-6R abrogated IL-1α-induced preterm birth (50% vs. 7%, p = 0.03, Fisher's exact test) by dampening inflammatory processes associated with the common pathway of labour. Importantly, aIL-6R reduces neonatal mortality (56% vs. 22%, p = 0.03, Mann-Whitney U-test) by crossing from the mother to the amniotic cavity, dampening foetal organ inflammation and improving growth. Beneficial effects of prenatal IL-6R blockade carried over to neonatal life, improving survival, growth, neurodevelopment, and gut immune homeostasis. INTERPRETATION IL-6R blockade can serve as a strategy to treat SIAI, preventing preterm birth and adverse neonatal outcomes. FUNDING NICHD/NIH/DHHS, Contract HHSN275201300006C. WSU Perinatal Initiative in Maternal, Perinatal and Child Health.
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Affiliation(s)
- Marcelo Farias-Jofre
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Yi Xu
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Derek Miller
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Valeria Garcia-Flores
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marcia Arenas-Hernandez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Andrew D Winters
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MO, USA
| | - Bruce A Berkowitz
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine; Detroit, MI, USA
| | - Robert H Podolsky
- Division of Biostatistics and Design Methodology, Center for Translational Research, Children's National Hospital, Silver Spring, MD, USA
| | - Yimin Shen
- Department of Radiology, School of Medicine, Wayne State University School of Medicine, Detroit, MI, USA
| | - Tomi Kanninen
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bogdan Panaitescu
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Catherine R Glazier
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Roger Pique-Regi
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kevin R Theis
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MO, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MO, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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Kavaliauskaite G, Madsen JS. Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops. NAR Genom Bioinform 2023; 5:lqad101. [PMID: 38025048 PMCID: PMC10657416 DOI: 10.1093/nargab/lqad101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/05/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei enabling comprehensive characterization of cell types and states. However, isolation of cells or nuclei for sxRNA-seq releases contaminating RNA, which can distort biological signals, through, for example, cell damage and transcript leakage. Thus, identifying barcodes containing high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, an automated method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics, and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with distinct biological signals. We benchmark valiDrops and show that biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops compared to existing tools. Finally, we show that valiDrops can predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to improve data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.
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Affiliation(s)
- Gabija Kavaliauskaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Odense M 5230, Denmark
| | - Jesper Grud Skat Madsen
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Odense M 5230, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M 5230, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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39
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Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, Saliba AE, Groeber-Becker F, Engstler M. Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms. Nat Commun 2023; 14:7660. [PMID: 37996412 PMCID: PMC10667367 DOI: 10.1038/s41467-023-43437-2] [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: 07/10/2021] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly's bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites' development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
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Affiliation(s)
- Christian Reuter
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Laura Hauf
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Core Unit Systems Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Rituparno Sen
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Philipp Fey
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Tamara Finger
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Heike Walles
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
- Core Facility Tissue Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Institute of Molecular Infection Biology (IMIB), Faculty of Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Florian Groeber-Becker
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany.
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40
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Schnell A, Huang L, Regan BML, Singh V, Vonficht D, Bollhagen A, Wang M, Hou Y, Bod L, Sobel RA, Chihara N, Madi A, Anderson AC, Regev A, Kuchroo VK. Targeting PGLYRP1 promotes antitumor immunity while inhibiting autoimmune neuroinflammation. Nat Immunol 2023; 24:1908-1920. [PMID: 37828379 PMCID: PMC10864036 DOI: 10.1038/s41590-023-01645-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Co-inhibitory and checkpoint molecules suppress T cell function in the tumor microenvironment, thereby rendering T cells dysfunctional. Although immune checkpoint blockade is a successful treatment option for multiple human cancers, severe autoimmune-like adverse effects can limit its application. Here, we show that the gene encoding peptidoglycan recognition protein 1 (PGLYRP1) is highly coexpressed with genes encoding co-inhibitory molecules, indicating that it might be a promising target for cancer immunotherapy. Genetic deletion of Pglyrp1 in mice led to decreased tumor growth and an increased activation/effector phenotype in CD8+ T cells, suggesting an inhibitory function of PGLYRP1 in CD8+ T cells. Surprisingly, genetic deletion of Pglyrp1 protected against the development of experimental autoimmune encephalomyelitis, a model of autoimmune disease in the central nervous system. PGLYRP1-deficient myeloid cells had a defect in antigen presentation and T cell activation, indicating that PGLYRP1 might function as a proinflammatory molecule in myeloid cells during autoimmunity. These results highlight PGLYRP1 as a promising target for immunotherapy that, when targeted, elicits a potent antitumor immune response while protecting against some forms of tissue inflammation and autoimmunity.
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Affiliation(s)
- Alexandra Schnell
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Linglin Huang
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Brianna M L Regan
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vasundhara Singh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dominik Vonficht
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina Bollhagen
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mona Wang
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yu Hou
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Lloyd Bod
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raymond A Sobel
- Palo Alto Veteran's Administration Health Care System and Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norio Chihara
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Asaf Madi
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Ana C Anderson
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay K Kuchroo
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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41
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van Loo B, Ten Den SA, Araújo-Gomes N, de Jong V, Snabel RR, Schot M, Rivera-Arbeláez JM, Veenstra GJC, Passier R, Kamperman T, Leijten J. Mass production of lumenogenic human embryoid bodies and functional cardiospheres using in-air-generated microcapsules. Nat Commun 2023; 14:6685. [PMID: 37865642 PMCID: PMC10590445 DOI: 10.1038/s41467-023-42297-0] [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: 08/17/2022] [Accepted: 10/05/2023] [Indexed: 10/23/2023] Open
Abstract
Organoids are engineered 3D miniature tissues that are defined by their organ-like structures, which drive a fundamental understanding of human development. However, current organoid generation methods are associated with low production throughputs and poor control over size and function including due to organoid merging, which limits their clinical and industrial translation. Here, we present a microfluidic platform for the mass production of lumenogenic embryoid bodies and functional cardiospheres. Specifically, we apply triple-jet in-air microfluidics for the ultra-high-throughput generation of hollow, thin-shelled, hydrogel microcapsules that can act as spheroid-forming bioreactors in a cytocompatible, oil-free, surfactant-free, and size-controlled manner. Uniquely, we show that microcapsules generated by in-air microfluidics provide a lumenogenic microenvironment with near 100% efficient cavitation of spheroids. We demonstrate that upon chemical stimulation, human pluripotent stem cell-derived spheroids undergo cardiomyogenic differentiation, effectively resulting in the mass production of homogeneous and functional cardiospheres that are responsive to external electrical stimulation. These findings drive clinical and industrial adaption of stem cell technology in tissue engineering and drug testing.
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Affiliation(s)
- Bas van Loo
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Simone A Ten Den
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
| | - Nuno Araújo-Gomes
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Vincent de Jong
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Rebecca R Snabel
- Radboud University, Radboud Institute for Molecular Life Sciences, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, The Netherlands
| | - Maik Schot
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - José M Rivera-Arbeláez
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
- University of Twente, TechMed Centre, Max Planck Center for Complex Fluid Dynamics, BIOS Lab-on-a-Chip Group, Enschede, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Radboud Institute for Molecular Life Sciences, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, The Netherlands
| | - Robert Passier
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
- Leiden University Medical Centre, Department of Anatomy and Embryology, Leiden, Netherlands
| | - Tom Kamperman
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
- IamFluidics B.V., De Veldmaat 17, 7522NM, Enschede, The Netherlands
| | - Jeroen Leijten
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands.
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42
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Gorin G, Vastola JJ, Pachter L. Studying stochastic systems biology of the cell with single-cell genomics data. Cell Syst 2023; 14:822-843.e22. [PMID: 37751736 PMCID: PMC10725240 DOI: 10.1016/j.cels.2023.08.004] [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: 05/29/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
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Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John J Vastola
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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43
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Gorin G, Yoshida S, Pachter L. Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing. Bull Math Biol 2023; 85:114. [PMID: 37828255 DOI: 10.1007/s11538-023-01213-9] [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: 11/22/2022] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
The serial nature of reactions involved in the RNA life-cycle motivates the incorporation of delays in models of transcriptional dynamics. The models couple a transcriptional process to a fairly general set of delayed monomolecular reactions with no feedback. We provide numerical strategies for calculating the RNA copy number distributions induced by these models, and solve several systems with splicing, degradation, and catalysis. An analysis of single-cell and single-nucleus RNA sequencing data using these models reveals that the kinetics of nuclear export do not appear to require invocation of a non-Markovian waiting time.
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Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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44
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Zhong J, Aires R, Tsissios G, Skoufa E, Brandt K, Sandoval-Guzmán T, Aztekin C. Multi-species atlas resolves an axolotl limb development and regeneration paradox. Nat Commun 2023; 14:6346. [PMID: 37816738 PMCID: PMC10564727 DOI: 10.1038/s41467-023-41944-w] [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: 03/16/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Humans and other tetrapods are considered to require apical-ectodermal-ridge (AER) cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, a primary model organism for regeneration, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first establish that axolotls contain cells with AER characteristics. Further analyses and spatial transcriptomics reveal that axolotl limbs do not fully re-form AER cells during regeneration. Moreover, the axolotl mesoderm displays part of the AER machinery, revealing a program for limb (re)growth. These results clarify the debate about the axolotl AER and the extent to which the limb developmental program is recapitulated during regeneration.
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Affiliation(s)
- Jixing Zhong
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Rita Aires
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Georgios Tsissios
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Evangelia Skoufa
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Kerstin Brandt
- Paul Langerhans Institute Dresden, Helmholtz Centre Munich, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tatiana Sandoval-Guzmán
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Paul Langerhans Institute Dresden, Helmholtz Centre Munich, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | - Can Aztekin
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015, Lausanne, Switzerland.
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45
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He D, Patro R. simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry. Bioinformatics 2023; 39:btad614. [PMID: 37802884 PMCID: PMC10580267 DOI: 10.1093/bioinformatics/btad614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/02/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023] Open
Abstract
SUMMARY The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry's single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. AVAILABILITY AND IMPLEMENTATION Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf that have been developed can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.
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Affiliation(s)
- Dongze He
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, United States
| | - Rob Patro
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, United States
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46
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Meng R, Yin S, Sun J, Hu H, Zhao Q. scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention. Comput Biol Med 2023; 165:107414. [PMID: 37660567 DOI: 10.1016/j.compbiomed.2023.107414] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating cellular heterogeneity and structure. However, analyzing scRNA-seq data remains challenging, especially in the context of COVID-19 research. Single-cell clustering is a key step in analyzing scRNA-seq data, and deep learning methods have shown great potential in this area. In this work, we propose a novel scRNA-seq analysis framework called scAAGA. Specifically, we utilize an asymmetric autoencoder with a gene attention module to learn important gene features adaptively from scRNA-seq data, with the aim of improving the clustering effect. We apply scAAGA to COVID-19 peripheral blood mononuclear cell (PBMC) scRNA-seq data and compare its performance with state-of-the-art methods. Our results consistently demonstrate that scAAGA outperforms existing methods in terms of adjusted rand index (ARI), normalized mutual information (NMI), and adjusted mutual information (AMI) scores, achieving improvements ranging from 2.8% to 27.8% in NMI scores. Additionally, we discuss a data augmentation technology to expand the datasets and improve the accuracy of scAAGA. Overall, scAAGA presents a robust tool for scRNA-seq data analysis, enhancing the accuracy and reliability of clustering results in COVID-19 research.
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Affiliation(s)
- Rui Meng
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Shuaidong Yin
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi, 276000, China
| | - Huan Hu
- Institute of Applied Genomics, Fuzhou University, Fuzhou, 350108, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
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47
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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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48
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Weatherbee BAT, Gantner CW, Iwamoto-Stohl LK, Daza RM, Hamazaki N, Shendure J, Zernicka-Goetz M. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 2023; 622:584-593. [PMID: 37369347 PMCID: PMC10584688 DOI: 10.1038/s41586-023-06368-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
The human embryo undergoes morphogenetic transformations following implantation into the uterus, but our knowledge of this crucial stage is limited by the inability to observe the embryo in vivo. Models of the embryo derived from stem cells are important tools for interrogating developmental events and tissue-tissue crosstalk during these stages1. Here we establish a model of the human post-implantation embryo, a human embryoid, comprising embryonic and extraembryonic tissues. We combine two types of extraembryonic-like cell generated by overexpression of transcription factors with wild-type embryonic stem cells and promote their self-organization into structures that mimic several aspects of the post-implantation human embryo. These self-organized aggregates contain a pluripotent epiblast-like domain surrounded by extraembryonic-like tissues. Our functional studies demonstrate that the epiblast-like domain robustly differentiates into amnion, extraembryonic mesenchyme and primordial germ cell-like cells in response to bone morphogenetic protein cues. In addition, we identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells2. Modulation of the subpopulations in the hypoblast-like compartment demonstrates that extraembryonic-like cells influence epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, we present a modular, tractable, integrated3 model of the human embryo that will enable us to probe key questions of human post-implantation development, a critical window during which substantial numbers of pregnancies fail.
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Affiliation(s)
- Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Lisa K Iwamoto-Stohl
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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49
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Jackson CA, Beheler-Amass M, Tjärnberg A, Suresh I, Hickey ASM, Bonneau R, Gresham D. Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558277. [PMID: 37790443 PMCID: PMC10542544 DOI: 10.1101/2023.09.21.558277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Cells respond to environmental and developmental stimuli by remodeling their transcriptomes through regulation of both mRNA transcription and mRNA decay. A central goal of biology is identifying the global set of regulatory relationships between factors that control mRNA production and degradation and their target transcripts and construct a predictive model of gene expression. Regulatory relationships are typically identified using transcriptome measurements and causal inference algorithms. RNA kinetic parameters are determined experimentally by employing run-on or metabolic labeling (e.g. 4-thiouracil) methods that allow transcription and decay rates to be separately measured. Here, we develop a deep learning model, trained with single-cell RNA-seq data, that both infers causal regulatory relationships and estimates RNA kinetic parameters. The resulting in silico model predicts future gene expression states and can be perturbed to simulate the effect of transcription factor changes. We acquired model training data by sequencing the transcriptomes of 175,000 individual Saccharomyces cerevisiae cells that were subject to an external perturbation and continuously sampled over a one hour period. The rate of change for each transcript was calculated on a per-cell basis to estimate RNA velocity. We then trained a deep learning model with transcriptome and RNA velocity data to calculate time-dependent estimates of mRNA production and decay rates. By separating RNA velocity into transcription and decay rates, we show that rapamycin treatment causes existing ribosomal protein transcripts to be rapidly destabilized, while production of new transcripts gradually slows over the course of an hour. The neural network framework we present is designed to explicitly model causal regulatory relationships between transcription factors and their genes, and shows superior performance to existing models on the basis of recovery of known regulatory relationships. We validated the predictive power of the model by perturbing transcription factors in silico and comparing transcriptome-wide effects with experimental data. Our study represents the first step in constructing a complete, predictive, biophysical model of gene expression regulation.
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Affiliation(s)
- Christopher A Jackson
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Maggie Beheler-Amass
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Andreas Tjärnberg
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Ina Suresh
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Angela Shang-mei Hickey
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | | | - David Gresham
- Center For Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558726. [PMID: 37790430 PMCID: PMC10542170 DOI: 10.1101/2023.09.20.558726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar-ẟ and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.
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