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人类浆细胞分化的整合单细胞染色质和转录组分析

Integrative single-cell chromatin and transcriptome analysis of human plasma cell differentiation.

作者信息

Alaterre Elina, Ovejero Sara, Bret Caroline, Dutrieux Laure, Sika Dassou, Fernandez Perez Raul, Espéli Marion, Fest Thierry, Cogné Michel, Martin-Subero José Ignacio, Milpied Pierre, Cavalli Giacomo, Moreaux Jérôme

机构信息

Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France.

Department of Biological Hematology, CHU Montpellier, Montpellier, France.

出版信息

Blood. 2024 Aug 1;144(5):496-509. doi: 10.1182/blood.2023023237.


DOI:10.1182/blood.2023023237
PMID:38643512
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11406183/
Abstract

Plasma cells (PCs) are highly specialized cells representing the end stage of B-cell differentiation. We have shown that PC differentiation can be reproduced in vitro using elaborate culture systems. The molecular changes occurring during PC differentiation are recapitulated in this in vitro differentiation model. However, a major challenge exists to decipher the spatiotemporal epigenetic and transcriptional programs that drive the early stages of PC differentiation. We combined single cell (sc) RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with high throughput sequencing (scATAC-seq) to decipher the trajectories involved in PC differentiation. ScRNA-seq experiments revealed a strong heterogeneity of the preplasmablastic and plasmablastic stages. Among genes that were commonly identified using scATAC-seq and scRNA-seq, we identified several transcription factors with significant stage specific potential importance in PC differentiation. Interestingly, differentially accessible peaks characterizing the preplasmablastic stage were enriched in motifs of BATF3, FOS and BATF, belonging to activating protein 1 (AP-1) transcription factor family that may represent key transcriptional nodes involved in PC differentiation. Integration of transcriptomic and epigenetic data at the single cell level revealed that a population of preplasmablasts had already undergone epigenetic remodeling related to PC profile together with unfolded protein response activation and are committed to differentiate in PC. These results and the supporting data generated with our in vitro PC differentiation model provide a unique resource for the identification of molecular circuits that are crucial for early and mature PC maturation and biological functions. These data thus provide critical insights into epigenetic- and transcription-mediated reprogramming events that sustain PC differentiation.

摘要

浆细胞(PCs)是高度特化的细胞,代表B细胞分化的终末阶段。我们已经表明,使用精细的培养系统可以在体外重现PC分化过程。在这个体外分化模型中概括了PC分化过程中发生的分子变化。然而,要破译驱动PC分化早期阶段的时空表观遗传和转录程序,存在一个重大挑战。我们结合单细胞(sc)RNA测序(RNA-seq)和转座酶可及染色质高通量测序分析(scATAC-seq)来破译PC分化所涉及的轨迹。ScRNA-seq实验揭示了前浆母细胞和浆母细胞阶段的强烈异质性。在使用scATAC-seq和scRNA-seq共同鉴定出的基因中,我们确定了几个在PC分化中具有重要阶段特异性潜在重要性的转录因子。有趣的是,表征前浆母细胞阶段的差异可及峰在BATF3、FOS和BATF的基序中富集,它们属于激活蛋白1(AP-1)转录因子家族,可能代表参与PC分化的关键转录节点。在单细胞水平上整合转录组和表观遗传数据表明,一群前浆母细胞已经经历了与PC谱相关的表观遗传重塑以及未折叠蛋白反应激活,并致力于分化为PC。这些结果以及我们体外PC分化模型产生的支持数据为鉴定对早期和成熟PC成熟及生物学功能至关重要的分子回路提供了独特资源。因此,这些数据为维持PC分化的表观遗传和转录介导的重编程事件提供了关键见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/d03b7514d217/BLOOD_BLD-2023-023237-gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/4a89f8ef2e65/BLOOD_BLD-2023-023237-ga1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/ea8886145a49/BLOOD_BLD-2023-023237-gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/eab1ea3cbb8d/BLOOD_BLD-2023-023237-gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/c5ee2dc8f84f/BLOOD_BLD-2023-023237-gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/40234c7c4b97/BLOOD_BLD-2023-023237-gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/2a814289e5c7/BLOOD_BLD-2023-023237-gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/8e3794167c88/BLOOD_BLD-2023-023237-gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/d03b7514d217/BLOOD_BLD-2023-023237-gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/4a89f8ef2e65/BLOOD_BLD-2023-023237-ga1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/ea8886145a49/BLOOD_BLD-2023-023237-gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/eab1ea3cbb8d/BLOOD_BLD-2023-023237-gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/c5ee2dc8f84f/BLOOD_BLD-2023-023237-gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/40234c7c4b97/BLOOD_BLD-2023-023237-gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/2a814289e5c7/BLOOD_BLD-2023-023237-gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/8e3794167c88/BLOOD_BLD-2023-023237-gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4c3f/11406183/d03b7514d217/BLOOD_BLD-2023-023237-gr7.jpg

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本文引用的文献

[1]
An atlas of cells in the human tonsil.

Immunity. 2024-2-13

[2]
Understanding heterogeneity of human bone marrow plasma cell maturation and survival pathways by single-cell analyses.

Cell Rep. 2023-7-25

[3]
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Elife. 2023-3-2

[4]
A CRISPR/Cas9-mediated screen identifies determinants of early plasma cell differentiation.

Front Immunol. 2022

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Integrated Single-Cell (Phospho-)Protein and RNA Detection Uncovers Phenotypic Characteristics and Active Signal Transduction of Human Antibody-Secreting Cells.

Mol Cell Proteomics. 2023-2

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Nat Commun. 2022-7-15

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Blood. 2022-4-14

[8]
Committed Human CD23-Negative Light-Zone Germinal Center B Cells Delineate Transcriptional Program Supporting Plasma Cell Differentiation.

Front Immunol. 2021

[9]
Early Emergence of Adaptive Mechanisms Sustaining Ig Production: Application to Antibody Therapy.

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[10]
Genetic manipulation and immortalized culture of ex vivo primary human germinal center B cells.

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