Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs DOI Creative Commons
Shuai He,

Lin-he Wang,

Yang Liu

и другие.

Genome biology, Год журнала: 2020, Номер 21(1)

Опубликована: Дек. 1, 2020

Abstract Background As core units of organ tissues, cells various types play their harmonious rhythms to maintain the homeostasis human body. It is essential identify characteristics in organs and regulatory networks for understanding biological mechanisms related health disease. However, a systematic comprehensive single-cell transcriptional profile across multiple normal adult missing. Results We perform transcriptomes 84,363 derived from 15 tissue one donor generate an cell atlas. The atlas depicts 252 subtypes cells, including major such as T, B, myeloid, epithelial, stromal well novel COCH + fibroblasts FibSmo each which distinguished by marker genes profiles. These collectively contribute heterogeneity organs. Moreover, T B receptor repertoire comparisons trajectory analyses reveal direct clonal sharing with developmental states among different tissues. Furthermore, markers, transcription factors, ligand-receptor pairs are identified potential functional regulations maintaining Conclusions reveals inter- intra-organ provides useful resource uncovering key events during development diseases context

Язык: Английский

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity DOI Creative Commons
Ludovico Cantuti‐Castelvetri, Ravi Ojha, Liliana D. Pedro

и другие.

Science, Год журнала: 2020, Номер 370(6518), С. 856 - 860

Опубликована: Окт. 20, 2020

The causative agent of coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome 2 (SARS-CoV-2). For many viruses, tissue tropism determined by availability virus receptors and entry cofactors on surface host cells. In this study, we found that neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, an effect blocked a monoclonal blocking antibody against NRP1. A mutant with altered furin cleavage site did not depend NRP1 for infectivity. Pathological analysis olfactory epithelium obtained from human COVID-19 autopsies revealed infected NRP1-positive cells facing nasal cavity. Our data provide insight into cell infectivity define potential target antiviral intervention.

Язык: Английский

Процитировано

1783
A molecular cell atlas of the human lung from single-cell RNA sequencing DOI Open Access
Kyle J. Travaglini, Ahmad N. Nabhan,

Lolita Penland

и другие.

Nature, Год журнала: 2020, Номер 587(7835), С. 619 - 625

Опубликована: Ноя. 18, 2020

Язык: Английский

Процитировано

1350
Dictionary learning for integrative, multimodal and scalable single-cell analysis DOI Open Access
Yuhan Hao, Tim Stuart, Madeline H. Kowalski

и другие.

Nature Biotechnology, Год журнала: 2023, Номер 42(2), С. 293 - 304

Опубликована: Май 25, 2023

Язык: Английский

Процитировано

1297
A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells DOI Creative Commons
Sijin Cheng, Ziyi Li, Ranran Gao

и другие.

Cell, Год журнала: 2021, Номер 184(3), С. 792 - 809.e23

Опубликована: Фев. 1, 2021

Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the similarity and distinction of their fundamental properties across different tumors remain elusive. Here, by performing a pan-cancer analysis single from 210 patients 15 human cancer types, we identified distinct features TIMs types. Mast nasopharyngeal were found to be associated with better prognosis exhibited an anti-tumor phenotype high ratio TNF+/VEGFA+ cells. Systematic comparison between cDC1- cDC2-derived LAMP3+ cDCs revealed differences transcription factors external stimulus. Additionally, pro-angiogenic tumor-associated macrophages (TAMs) characterized diverse markers composition appeared certain somatic mutations gene expressions. Our results provide systematic view highly heterogeneous suggest future avenues for rational, targeted immunotherapies.

Язык: Английский

Процитировано

957
The protein expression profile of ACE2 in human tissues DOI
Feria Hikmet, Loren Méar, Åsa Edvinsson

и другие.

Molecular Systems Biology, Год журнала: 2020, Номер 16(7)

Опубликована: Июль 1, 2020

Язык: Английский

Процитировано

945
Single‐cell RNA sequencing technologies and applications: A brief overview DOI

Dragomirka Jovic,

Xue Liang, Zeng Hua

и другие.

Clinical and Translational Medicine, Год журнала: 2022, Номер 12(3)

Опубликована: Март 1, 2022

Язык: Английский

Процитировано

652
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans DOI Open Access

The Tabula Sapiens Consortium,

Robert C. Jones, Jim Karkanias

и другие.

Science, Год журнала: 2022, Номер 376(6594)

Опубликована: Май 12, 2022

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing biology and enabling new insights into the physiology human organs. We created a reference atlas comprising nearly 500,000 cells from 24 different tissues organs, many same donor. This enabled molecular more than 400 types, their distribution across tissues, tissue-specific variation in gene expression. Using multiple single donor identification clonal T between mutation rate B cells, analysis cycle state proliferative potential shared tissues. Cell type–specific RNA splicing was discovered analyzed within an individual.

Язык: Английский

Процитировано

652
Cross-tissue immune cell analysis reveals tissue-specific features in humans DOI Creative Commons
Cecilia Domínguez Conde, Chuan Xu, Lorna B. Jarvis

и другие.

Science, Год журнала: 2022, Номер 376(6594)

Опубликована: Май 12, 2022

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the compartment 16 from 12 adult donors by single-cell RNA sequencing VDJ generating a dataset ~360,000 cells. To systematically resolve cell heterogeneity across tissues, we developed CellTypist, machine learning tool for rapid precise type annotation. Using this approach, combined with detailed curation, determined tissue distribution finely phenotyped types, revealing hitherto unappreciated tissue-specific features clonal architecture T B Our multitissue approach lays foundation identifying highly resolved types leveraging common reference dataset, tissue-integrated expression analysis, antigen receptor sequencing.

Язык: Английский

Процитировано

571
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly DOI
Hongjie Li, Jasper Janssens, Maxime De Waegeneer

и другие.

Science, Год журнала: 2022, Номер 375(6584)

Опубликована: Март 3, 2022

For more than 100 years, the fruit fly

Язык: Английский

Процитировано

548
UCell: Robust and scalable single-cell gene signature scoring DOI Creative Commons
Massimo Andreatta, Santiago J. Carmona

Computational and Structural Biotechnology Journal, Год журнала: 2021, Номер 19, С. 3796 - 3798

Опубликована: Янв. 1, 2021

UCell is an R package for evaluating gene signatures in single-cell datasets. signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, their calculation demands less computing time memory than other available methods, enabling processing of large datasets a few minutes even machines with limited power. can be applied any data matrix, includes functions directly interact Seurat objects. The documentation GitHub at https://github.com/carmonalab/UCell.

Язык: Английский

Процитировано

518