Cargando…

Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer

Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through...

Descripción completa

Detalles Bibliográficos
Autores principales: Xu, Xiaochen, Zhang, Xinwen, Lin, Qiumei, Qin, Yuling, Liu, Yihao, Tang, Weizhong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10403602/
https://www.ncbi.nlm.nih.gov/pubmed/37542061
http://dx.doi.org/10.1038/s41598-023-39412-y
_version_ 1785085105630347264
author Xu, Xiaochen
Zhang, Xinwen
Lin, Qiumei
Qin, Yuling
Liu, Yihao
Tang, Weizhong
author_facet Xu, Xiaochen
Zhang, Xinwen
Lin, Qiumei
Qin, Yuling
Liu, Yihao
Tang, Weizhong
author_sort Xu, Xiaochen
collection PubMed
description Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC.
format Online
Article
Text
id pubmed-10403602
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-104036022023-08-06 Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer Xu, Xiaochen Zhang, Xinwen Lin, Qiumei Qin, Yuling Liu, Yihao Tang, Weizhong Sci Rep Article Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC. Nature Publishing Group UK 2023-08-04 /pmc/articles/PMC10403602/ /pubmed/37542061 http://dx.doi.org/10.1038/s41598-023-39412-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Xu, Xiaochen
Zhang, Xinwen
Lin, Qiumei
Qin, Yuling
Liu, Yihao
Tang, Weizhong
Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title_full Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title_fullStr Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title_full_unstemmed Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title_short Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
title_sort integrated single-cell and bulk rna sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10403602/
https://www.ncbi.nlm.nih.gov/pubmed/37542061
http://dx.doi.org/10.1038/s41598-023-39412-y
work_keys_str_mv AT xuxiaochen integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer
AT zhangxinwen integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer
AT linqiumei integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer
AT qinyuling integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer
AT liuyihao integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer
AT tangweizhong integratedsinglecellandbulkrnasequencinganalysisidentifiesaprognosticsignaturerelatedtoferroptosisdependenceincolorectalcancer