Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

ABSTRACTStopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans.Bullet pointsWe generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19.ACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2.ACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities.We unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry.

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Lifelong single-cell profiling of cranial neural crest diversification

10.1101/2021.08.19.456710 ◽

2021 ◽

Author(s):

Peter Fabian ◽

Kuo-Chang Tseng ◽

Mathi Thiruppathy ◽

Claire Arata ◽

Hung-Jhen Chen ◽

...

Keyword(s):

Neural Crest ◽

Single Cell ◽

Cell Fate ◽

Intrinsic Property ◽

Chromatin Accessibility ◽

Specific Cell ◽

List Type ◽

Cranial Neural Crest ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractThe cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being an intrinsic property of cranial neural crest, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse neural crest lineage potential.HighlightsSingle-cell transcriptome and chromatin atlas of cranial neural crestProgressive emergence of region-specific cell fate competencyChromatin accessibility mapping identifies candidate lineage regulatorsGata3 function linked to gill-specific respiratory programGraphical Abstract

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Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

Genome Research ◽

10.1101/gr.207704.116 ◽

2017 ◽

Vol 27 (3) ◽

pp. 451-461 ◽

Cited By ~ 46

Author(s):

Santiago J. Carmona ◽

Sarah A. Teichmann ◽

Lauren Ferreira ◽

Iain C. Macaulay ◽

Michael J.T. Stubbington ◽

...

Keyword(s):

Single Cell ◽

Immune Cells ◽

Transcriptome Analysis ◽

Immune Cell ◽

Cell Types ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Insight Into

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A Single-Cell Transcriptome Profiling of Anterior Kidney Leukocytes From Nile Tilapia (Oreochromis niloticus)

Frontiers in Immunology ◽

10.3389/fimmu.2021.783196 ◽

2021 ◽

Vol 12 ◽

Author(s):

Liting Wu ◽

Along Gao ◽

Lan Li ◽

Jianlin Chen ◽

Jun Li ◽

...

Keyword(s):

T Cells ◽

B Cells ◽

B Cell ◽

Single Cell ◽

Nile Tilapia ◽

Immune Cell ◽

Cell Types ◽

Cell Transcriptome ◽

B Cell Subsets ◽

Single Cell Transcriptome

Teleost fish anterior kidney (AK) is an important hematopoietic organ with multifarious immune cells, which have immune functions comparable to mammalian bone marrow. Myeloid and lymphoid cells locate in the AK, but the lack of useful specific gene markers and antibody-based reagents for the cell subsets makes the identification of the different cell types difficult. Single-cell transcriptome sequencing enables single-cell capture and individual library construction, making the study on the immune cell heterogeneity of teleost fish AK possible. In this study, we examined the transcriptional patterns of 11,388 AK leukocytes using 10× Genomics single-cell RNA sequencing (scRNA-seq). A total of 22 clusters corresponding to five distinct immune cell subsets were identified, which included B cells, T cells, granulocytes, macrophages, and dendritic cells (DCs). However, the subsets of myeloid cells (granulocytes, macrophages, and DCs) were not identified in more detail according to the known specific markers, even though significant differences existed among the clusters. Thereafter, we highlighted the B-cell subsets and identified them as pro/pre B cells, immature/mature B cells, activated B/plasmablasts, or plasma cells based on the different expressions of the transcription factors (TFs) and cytokines. Clustering of the differentially modulated genes by pseudo-temporal trajectory analysis of the B-cell subsets showed the distinct kinetics of the responses of TFs to cell conversion. Moreover, we classified the T cells and discovered that CD3+CD4−CD8−, CD3+CD4+CD8+, CD4+CD8−, and CD4−CD8+ T cells existed in AK, but neither CD4+CD8− nor CD4−CD8+ T cells can be further classified into subsets based on the known TFs and cytokines. Pseudotemporal analysis demonstrated that CD4+CD8− and CD4−CD8+ T cells belonged to different states with various TFs that might control their differentiation. The data obtained above provide a valuable and detailed resource for uncovering the leukocyte subsets in Nile tilapia AK, as well as more potential markers for identifying the myeloid and lymphoid cell types.

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Lifelong single-cell profiling of cranial neural crest diversification in zebrafish

Nature Communications ◽

10.1038/s41467-021-27594-w ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Peter Fabian ◽

Kuo-Chang Tseng ◽

Mathi Thiruppathy ◽

Claire Arata ◽

Hung-Jhen Chen ◽

...

Keyword(s):

Neural Crest ◽

Single Cell ◽

Cell Types ◽

Chromatin Accessibility ◽

Cranial Neural Crest ◽

Cell Fates ◽

Regulatory Circuit ◽

Lineage Priming ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractThe cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe progressive and region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being established during cranial neural crest specification, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse potential.

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Single cell transcriptome atlas of mouse mammary epithelial cells across development

Breast Cancer Research ◽

10.1186/s13058-021-01445-4 ◽

2021 ◽

Vol 23 (1) ◽

Author(s):

Bhupinder Pal ◽

Yunshun Chen ◽

Michael J. G. Milevskiy ◽

François Vaillant ◽

Lexie Prokopuk ◽

...

Keyword(s):

Epithelial Cells ◽

Single Cell ◽

Developmental Stages ◽

Mammary Epithelial Cells ◽

Expression Profiles ◽

Single Cells ◽

Chromatin Accessibility ◽

Mammary Epithelial ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing

Science Advances ◽

10.1126/sciadv.aba1190 ◽

2020 ◽

Vol 6 (37) ◽

pp. eaba1190

Author(s):

Q. R. Xing ◽

C. A. El Farran ◽

P. Gautam ◽

Y. S. Chuah ◽

T. Warrier ◽

...

Keyword(s):

Single Cell ◽

Chromatin Accessibility ◽

Human Cells ◽

Cellular Reprogramming ◽

Surface Markers ◽

Low Efficiency ◽

Cell Transcriptome ◽

Intermediate Cells ◽

Single Cell Transcriptome ◽

Accessible Chromatin

Cellular reprogramming suffers from low efficiency especially for the human cells. To deconstruct the heterogeneity and unravel the mechanisms for successful reprogramming, we adopted single-cell RNA sequencing (scRNA-Seq) and single-cell assay for transposase-accessible chromatin (scATAC-Seq) to profile reprogramming cells across various time points. Our analysis revealed that reprogramming cells proceed in an asynchronous trajectory and diversify into heterogeneous subpopulations. We identified fluorescent probes and surface markers to enrich for the early reprogrammed human cells. Furthermore, combinatory usage of the surface markers enabled the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 and a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Together, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part list of the reprogramming machinery.

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High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports ◽

10.1016/j.celrep.2019.04.054 ◽

2019 ◽

Vol 27 (7) ◽

pp. 2241-2247.e4 ◽

Cited By ~ 57

Author(s):

Christine N. Shulse ◽

Benjamin J. Cole ◽

Doina Ciobanu ◽

Junyan Lin ◽

Yuko Yoshinaga ◽

...

Keyword(s):

Single Cell ◽

Plant Cell ◽

High Throughput ◽

Transcriptome Profiling ◽

Cell Types ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity

Nature Communications ◽

10.1038/s41467-020-18207-z ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Yehuda Schlesinger ◽

Oshri Yosefov-Levi ◽

Dror Kolodkin-Gal ◽

Roy Zvi Granit ◽

Luriano Peters ◽

...

Keyword(s):

Single Cell ◽

Malignant Lesion ◽

Tumor Development ◽

Initial Step ◽

Cell Types ◽

Tumor Formation ◽

Specific Cell ◽

Preinvasive Lesions ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Abstract Acinar metaplasia is an initial step in a series of events that can lead to pancreatic cancer. Here we perform single-cell RNA-sequencing of mouse pancreas during the progression from preinvasive stages to tumor formation. Using a reporter gene, we identify metaplastic cells that originated from acinar cells and express two transcription factors, Onecut2 and Foxq1. Further analyses of metaplastic acinar cell heterogeneity define six acinar metaplastic cell types and states, including stomach-specific cell types. Localization of metaplastic cell types and mixture of different metaplastic cell types in the same pre-malignant lesion is shown. Finally, single-cell transcriptome analyses of tumor-associated stromal, immune, endothelial and fibroblast cells identify signals that may support tumor development, as well as the recruitment and education of immune cells. Our findings are consistent with the early, premalignant formation of an immunosuppressive environment mediated by interactions between acinar metaplastic cells and other cells in the microenvironment.

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Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants

10.1101/2021.09.27.461256 ◽

2021 ◽

Author(s):

Zhouhuan Xi ◽

Bilge E. Ozturk ◽

Molly E. Johnson ◽

Leah C. Byrne

Keyword(s):

Single Cell ◽

Viral Vector ◽

Cell Types ◽

Adeno Associated Virus ◽

Altered Expression ◽

Gene Therapies ◽

Retinal Tissue ◽

Retinal Explants ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Gene therapy is a rapidly developing field, and adeno-associated virus (AAV) is a leading viral vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models, due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue, and are thus important for the validation of candidate AAV vectors. In this study, we evaluated 18 wildtype and engineered AAV capsids in human retinal explants using a recently developed single-cell RNA-Seq AAV engineering pipeline (scAAVengr). Human retinal explants retained the same major cell types as fresh retina, with similar expression of cell-specific markers, except for a cone population with altered expression of cone-specific genes. The efficiency and tropism of AAVs in human explants were quantified, with single-cell resolution. The top performing serotypes, K91, K912, and 7m8, were further validated in non-human primate and human retinal explants. Together, this study provides detailed information about the transcriptome profiles of retinal explants, and quantifies the infectivity of leading AAV serotypes in human retina, accelerating the translation of retinal gene therapies to the clinic.

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A Single-Cell Transcriptome Atlas for Zebrafish Development

10.1101/738344 ◽

2019 ◽

Cited By ~ 1

Author(s):

Dylan R. Farnsworth ◽

Lauren Saunders ◽

Adam C. Miller

Keyword(s):

Gene Expression ◽

Single Cell ◽

Cell Types ◽

Developmental Time ◽

Cell Type ◽

Specific Expression ◽

Transcriptional Profiles ◽

Larval Stages ◽

Cell Transcriptome ◽

Single Cell Transcriptome

ABSTRACTThe ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome Atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic (mutant) or functional analysis, to launch an effort to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.

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