Cross-species transcriptomic atlas of dorsal root ganglia reveals species-specific programs for sensory function

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 23, 2023

Sensory neurons of the dorsal root ganglion (DRG) are critical for maintaining tissue homeostasis by sensing and initiating responses to stimuli. While most preclinical studies DRGs conducted in rodents, much less is known about mechanisms sensory perception primates. We generated a transcriptome atlas mouse, guinea pig, cynomolgus monkey, human implementing common laboratory workflow multiple data-integration approaches generate high-resolution cross-species mappings neuron subtypes. Using our atlas, we identified conserved core modules highlighting subtype-specific biological processes related inflammatory response. also divergent expression key genes involved DRG function, suggesting species-specific adaptations specifically nociceptors that likely point function nociceptors. Among these, validated TAFA4, member druggable genome, was expressed distinct populations across species, programs therapeutic development.

Язык: Английский

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A reference cell tree will serve science better than a reference cell atlas

Cell, Год журнала: 2023, Номер 186(6), С. 1103 - 1114

Опубликована: Март 1, 2023

Язык: Английский

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Spatiotemporal omics for biology and medicine

Cell, Год журнала: 2024, Номер 187(17), С. 4488 - 4519

Опубликована: Авг. 1, 2024

Язык: Английский

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Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Frontiers in Cell and Developmental Biology, Год журнала: 2021, Номер 9

Опубликована: Окт. 1, 2021

Zebrafish have been found to be a premier model organism in biological and regeneration research. However, the comprehensive cell compositions molecular dynamics during tissue zebrafish remain poorly understood. Here, we utilized Microwell-seq analyze more than 250,000 single cells covering major types constructed systematic landscape. We revealed single-cell for 18 both embryo adult stages. Single-cell mapping of caudal fin unique characteristic blastema population key genetic regulation involved repair. Overall, our datasets demonstrate utility landscape resources various fields

Язык: Английский

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Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application

Molecular Neurodegeneration, Год журнала: 2022, Номер 17(1)

Опубликована: Март 2, 2022

Abstract Alzheimer’s disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical genomic studies have revealed biomarkers, risk factors, pathways, targets AD in past decade. However, exact molecular basis development progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into disease. Here we systematically review state-of-the-art bioinformatics approaches to analyze data their applications 14 major directions, including 1) quality control normalization, 2) dimension reduction feature extraction, 3) cell clustering analysis, 4) type inference annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation 8) integration multi-omics, 9) epigenomic 10) gene network 11) prioritization subpopulations, 12) integrative analysis human mouse sc-RNA-seq data, 13) spatial transcriptomics, 14) comparison single model studies. We also address challenges using postmortem tissues outline future developments analysis. Importantly, implemented our recommended workflow for each analytic direction applied them a large nucleus RNA-sequencing (snRNA-seq) dataset AD. Key results are reported while scripts shared with research community through GitHub. In summary, this comprehensive provides various offers specific guidelines study design variety directions. accompanied software tools will serve as valuable resource studying cellular mechanisms AD, other diseases, or biological systems at level.

Язык: Английский

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Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development

Nature Genetics, Год журнала: 2022, Номер 54(7), С. 1051 - 1061

Опубликована: Июль 1, 2022

Язык: Английский

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A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июль 13, 2022

Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using single-cell chromatin accessibility RNA sequencing data. The integrated map enables in-depth dissection comparison molecular dynamics, cell-type compositions cellular heterogeneity tissues organs. Using transcriptomic data, infer pseudotime trajectories cell-cell communications to uncover key signatures underlying their processes. Furthermore, identify various cell-specific cis-regulatory elements construct organ-specific gene regulatory networks at the level. Finally, perform comparative analyses landscapes among mouse, monkey human. We show has strikingly higher degree similarities terms immune-associated expression patterns human than mouse. Taken together, our study provides valuable resource for non-human primate biology.

Язык: Английский

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An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

EvoDevo, Год журнала: 2024, Номер 15(1)

Опубликована: Май 10, 2024

Abstract Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house Parasteatoda tepidariorum , has made important contributions to understanding evolution animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about cells build embryos, their gene expression profiles fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes cellular genetics range animals. Therefore, carried out single-cell RNA sequencing P. embryos at stages 7, 8 9, which encompass establishment patterning body plan, initial differentiation many tissues organs. We identified 20 cell clusters, 18.5 k cells, were marked by developmental toolkit genes, as well plethora genes not previously investigated. found differences cycle transcriptional signatures, suggestive different proliferation dynamics, related distinctions between endodermal some mesodermal compared with ectodermal clusters. Hox markers ohnologs often present This provided additional evidence sub- and/or neo-functionalisation after whole genome duplication an arachnopulmonate ancestor (spiders, scorpions, orders). also examined spatial marker for each cluster generate comprehensive atlas embryonic stages. revealed new insights into basis genetic regulation head patterning, hematopoiesis, limb gut posterior segmentation. will serve platform future analysis specification fate, studying processes among animals resolution.

Язык: Английский

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Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types

Nature Genetics, Год журнала: 2022, Номер 54(11), С. 1711 - 1720

Опубликована: Окт. 13, 2022

Язык: Английский

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Cell landscape of larval and adult Xenopus laevis at single-cell resolution

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июль 25, 2022

Abstract The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity animals. A large number organism-wide atlases have been constructed for vertebrates such as Homo sapiens , Macaca fascicularis Mus musculus and Danio rerio . However, an intermediate taxon that links mammals more ancient origin is still lacking. Here, we construct the first Xenopus landscape date, including larval adult organs. Common lineage-specific transcription factors identified in vertebrates, fish, amphibians mammals. comparison erythrocytes identifies stage-specific hemoglobin subtypes, well common type cluster containing both hemoglobin, mainly at NF59. In addition, lineages originating from all three layers exhibits antigen processing presentation during metamorphosis, indicating regulatory mechanism metamorphosis. Overall, our study provides large-scale resource research on metamorphosis

Язык: Английский

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