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Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis
Acute pancreatitis (AP) is an acute inflammatory disease of the exocrine pancreas. The pathogenesis of AP is still unclear, and there is currently no specific treatment. A variety of immune cells infiltrate in AP, which may play an important role in the progression of the disease. In this study, for...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9855877/ https://www.ncbi.nlm.nih.gov/pubmed/36671463 http://dx.doi.org/10.3390/biom13010078 |
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author | Fang, Zhen Li, Jie Cao, Feng Li, Fei |
author_facet | Fang, Zhen Li, Jie Cao, Feng Li, Fei |
author_sort | Fang, Zhen |
collection | PubMed |
description | Acute pancreatitis (AP) is an acute inflammatory disease of the exocrine pancreas. The pathogenesis of AP is still unclear, and there is currently no specific treatment. A variety of immune cells infiltrate in AP, which may play an important role in the progression of the disease. In this study, for the first time, scRNA-Seq and Bulk RNA-Seq data were used to show the characteristics of immune cell infiltration in AP, and to explore the specific molecular markers of different cell types. The present study also investigated cell-to-cell communication networks using the CellChat package, and AP-specific gene signatures (Clic1, Sat1, Serpina3n, Atf3, Lcn2, Osmr, Ccl9, Hspb1, Anxa2, Krt8, Cd44, Cd9, Hsp90aa1, Tmsb10, Hmox1, Fxyd5, Plin2, Pnp) were identified through integrative analysis of multiple sequencing datasets. We also defined disease-specific associated genes in different cell types, revealing dynamic changes through cell trajectory and pseudo-time analysis using the Monocle2 package. The results showed that macrophages were significantly increased in acute pancreatitis, and the number of interactions and interaction weight/strength of the macrophages in AP were significantly higher than those in the controls. The activities of various signaling pathways were abnormally regulated such as apoptosis, oxidative stress, lysosome, autophagy, ferroptosis, and inflammatory responses signaling pathways. In conclusion, this study comprehensively depicted the immune microenvironment of AP, explored the interaction network between different cell types, and defined AP-specific gene signatures, providing many new directions for basic research in AP. |
format | Online Article Text |
id | pubmed-9855877 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-98558772023-01-21 Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis Fang, Zhen Li, Jie Cao, Feng Li, Fei Biomolecules Article Acute pancreatitis (AP) is an acute inflammatory disease of the exocrine pancreas. The pathogenesis of AP is still unclear, and there is currently no specific treatment. A variety of immune cells infiltrate in AP, which may play an important role in the progression of the disease. In this study, for the first time, scRNA-Seq and Bulk RNA-Seq data were used to show the characteristics of immune cell infiltration in AP, and to explore the specific molecular markers of different cell types. The present study also investigated cell-to-cell communication networks using the CellChat package, and AP-specific gene signatures (Clic1, Sat1, Serpina3n, Atf3, Lcn2, Osmr, Ccl9, Hspb1, Anxa2, Krt8, Cd44, Cd9, Hsp90aa1, Tmsb10, Hmox1, Fxyd5, Plin2, Pnp) were identified through integrative analysis of multiple sequencing datasets. We also defined disease-specific associated genes in different cell types, revealing dynamic changes through cell trajectory and pseudo-time analysis using the Monocle2 package. The results showed that macrophages were significantly increased in acute pancreatitis, and the number of interactions and interaction weight/strength of the macrophages in AP were significantly higher than those in the controls. The activities of various signaling pathways were abnormally regulated such as apoptosis, oxidative stress, lysosome, autophagy, ferroptosis, and inflammatory responses signaling pathways. In conclusion, this study comprehensively depicted the immune microenvironment of AP, explored the interaction network between different cell types, and defined AP-specific gene signatures, providing many new directions for basic research in AP. MDPI 2022-12-30 /pmc/articles/PMC9855877/ /pubmed/36671463 http://dx.doi.org/10.3390/biom13010078 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Fang, Zhen Li, Jie Cao, Feng Li, Fei Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title | Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title_full | Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title_fullStr | Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title_full_unstemmed | Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title_short | Integration of scRNA-Seq and Bulk RNA-Seq Reveals Molecular Characterization of the Immune Microenvironment in Acute Pancreatitis |
title_sort | integration of scrna-seq and bulk rna-seq reveals molecular characterization of the immune microenvironment in acute pancreatitis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9855877/ https://www.ncbi.nlm.nih.gov/pubmed/36671463 http://dx.doi.org/10.3390/biom13010078 |
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