Cargando…
Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing
The papillary thyroid carcinoma (PTC) microenvironment consists of various cancer and surrounding cells, and the communication between them is mainly performed through ligand–receptor (LR) interactions. Single-cell RNA sequencing (scRNA-seq) has been performed to investigate the role of intercellula...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354623/ https://www.ncbi.nlm.nih.gov/pubmed/35935973 http://dx.doi.org/10.3389/fimmu.2022.902550 |
_version_ | 1784763112929361920 |
---|---|
author | Cao, Zhe Xu Weng, Xin Huang, Jiang Sheng Long, Xia |
author_facet | Cao, Zhe Xu Weng, Xin Huang, Jiang Sheng Long, Xia |
author_sort | Cao, Zhe Xu |
collection | PubMed |
description | The papillary thyroid carcinoma (PTC) microenvironment consists of various cancer and surrounding cells, and the communication between them is mainly performed through ligand–receptor (LR) interactions. Single-cell RNA sequencing (scRNA-seq) has been performed to investigate the role of intercellular communication networks in tumor progression. In addition, scRNA-seq can accurately identify the characteristics of immune cell subsets, which is of great significance for predicting the efficacy of immunotherapy. In this study, the cell–cell communication network was analyzed through LR pairs, and a new PTC molecular phenotype was developed based on LR pairs. Furthermore, a risk model was established to predict patient response to PD-1 blockade immunotherapy. The scRNA-seq dataset was obtained from GSE184362, and the bulk tumor RNA-seq dataset was obtained from The Cancer Genome Atlas. CellPhoneDB was used for cellular communication analysis. LR pair correlations were calculated and used to identify molecular subtypes, and the least absolute shrinkage and selection operator (Lasso) Cox regression was used to develop a risk model based on LR pairs. The IMvigor210 and GSE78220 cohorts were used as external validations for the LR.score to predict responses to PD-L1 blockade therapy. A total of 149 LR pairs with significant expression and prognostic correlation were included, and three PTC molecular subtypes were obtained from those with significant prognostic differences. Then, five LR pairs were selected to construct the risk scoring model, a reliable and independent prognostic factor in the training set, test set, and whole dataset. Furthermore, two external validation sets confirmed the predictive efficacy of the LR.score for response to PD-1 blockade therapy. |
format | Online Article Text |
id | pubmed-9354623 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93546232022-08-06 Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing Cao, Zhe Xu Weng, Xin Huang, Jiang Sheng Long, Xia Front Immunol Immunology The papillary thyroid carcinoma (PTC) microenvironment consists of various cancer and surrounding cells, and the communication between them is mainly performed through ligand–receptor (LR) interactions. Single-cell RNA sequencing (scRNA-seq) has been performed to investigate the role of intercellular communication networks in tumor progression. In addition, scRNA-seq can accurately identify the characteristics of immune cell subsets, which is of great significance for predicting the efficacy of immunotherapy. In this study, the cell–cell communication network was analyzed through LR pairs, and a new PTC molecular phenotype was developed based on LR pairs. Furthermore, a risk model was established to predict patient response to PD-1 blockade immunotherapy. The scRNA-seq dataset was obtained from GSE184362, and the bulk tumor RNA-seq dataset was obtained from The Cancer Genome Atlas. CellPhoneDB was used for cellular communication analysis. LR pair correlations were calculated and used to identify molecular subtypes, and the least absolute shrinkage and selection operator (Lasso) Cox regression was used to develop a risk model based on LR pairs. The IMvigor210 and GSE78220 cohorts were used as external validations for the LR.score to predict responses to PD-L1 blockade therapy. A total of 149 LR pairs with significant expression and prognostic correlation were included, and three PTC molecular subtypes were obtained from those with significant prognostic differences. Then, five LR pairs were selected to construct the risk scoring model, a reliable and independent prognostic factor in the training set, test set, and whole dataset. Furthermore, two external validation sets confirmed the predictive efficacy of the LR.score for response to PD-1 blockade therapy. Frontiers Media S.A. 2022-07-22 /pmc/articles/PMC9354623/ /pubmed/35935973 http://dx.doi.org/10.3389/fimmu.2022.902550 Text en Copyright © 2022 Cao, Weng, Huang and Long https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Immunology Cao, Zhe Xu Weng, Xin Huang, Jiang Sheng Long, Xia Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title | Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title_full | Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title_fullStr | Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title_full_unstemmed | Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title_short | Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
title_sort | receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing |
topic | Immunology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354623/ https://www.ncbi.nlm.nih.gov/pubmed/35935973 http://dx.doi.org/10.3389/fimmu.2022.902550 |
work_keys_str_mv | AT caozhexu receptorligandpairtypingandprognosticriskmodelforpapillarythyroidcarcinomabasedonsinglecellsequencing AT wengxin receptorligandpairtypingandprognosticriskmodelforpapillarythyroidcarcinomabasedonsinglecellsequencing AT huangjiangsheng receptorligandpairtypingandprognosticriskmodelforpapillarythyroidcarcinomabasedonsinglecellsequencing AT longxia receptorligandpairtypingandprognosticriskmodelforpapillarythyroidcarcinomabasedonsinglecellsequencing |