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Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis

Currently, the role of liquid-liquid phase separation (LLPS) in cancer has been preliminarily explained. However, the significance of LLPS in breast cancer is unclear. In this study, single cell sequencing datasets GSE188600 and GSE198745 for breast cancer were downloaded from the GEO database. Tran...

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Autores principales: Xie, Jiaheng, Chen, Liang, Wu, Dan, Liu, Shengxuan, Pei, Shengbin, Tang, Qikai, Wang, Yue, Ou, Mengmeng, Zhu, Zhechen, Ruan, Shujie, Wang, Ming, Shi, Jingping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10333080/
https://www.ncbi.nlm.nih.gov/pubmed/37338518
http://dx.doi.org/10.18632/aging.204812
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author Xie, Jiaheng
Chen, Liang
Wu, Dan
Liu, Shengxuan
Pei, Shengbin
Tang, Qikai
Wang, Yue
Ou, Mengmeng
Zhu, Zhechen
Ruan, Shujie
Wang, Ming
Shi, Jingping
author_facet Xie, Jiaheng
Chen, Liang
Wu, Dan
Liu, Shengxuan
Pei, Shengbin
Tang, Qikai
Wang, Yue
Ou, Mengmeng
Zhu, Zhechen
Ruan, Shujie
Wang, Ming
Shi, Jingping
author_sort Xie, Jiaheng
collection PubMed
description Currently, the role of liquid-liquid phase separation (LLPS) in cancer has been preliminarily explained. However, the significance of LLPS in breast cancer is unclear. In this study, single cell sequencing datasets GSE188600 and GSE198745 for breast cancer were downloaded from the GEO database. Transcriptome sequencing data for breast cancer were downloaded from UCSC database. We divided breast cancer cells into high-LLPS group and low-LLPS group by down dimension clustering analysis of single-cell sequencing data set, and obtained differentially expressed genes between the two groups. Subsequently, weighted co-expression network analysis (WGCNA) was performed on transcriptome sequencing data, and the module genes most associated with LLPS were obtained. COX regression and Lasso regression were performed and the prognostic model was constructed. Subsequently, survival analysis, principal component analysis, clinical correlation analysis, and nomogram construction were used to evaluate the significance of the prognostic model. Finally, cell experiments were used to verify the function of the model’s key gene, PGAM1. We constructed a LLPS-related prognosis model consisting of nine genes: POLR3GL, PLAT, NDRG1, HMGB3, HSPH1, PSMD7, PDCD2, NONO and PGAM1. By calculating LLPS-related risk scores, breast cancer patients could be divided into high-risk and low-risk groups, with the high-risk group having a significantly worse prognosis. Cell experiments showed that the activity, proliferation, invasion and healing ability of breast cancer cell lines were significantly decreased after knockdown of the key gene PGAM1 in the model. Our study provides a new idea for prognostic stratification of breast cancer and provides a novel marker: PGAM1.
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spelling pubmed-103330802023-07-12 Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis Xie, Jiaheng Chen, Liang Wu, Dan Liu, Shengxuan Pei, Shengbin Tang, Qikai Wang, Yue Ou, Mengmeng Zhu, Zhechen Ruan, Shujie Wang, Ming Shi, Jingping Aging (Albany NY) Research Paper Currently, the role of liquid-liquid phase separation (LLPS) in cancer has been preliminarily explained. However, the significance of LLPS in breast cancer is unclear. In this study, single cell sequencing datasets GSE188600 and GSE198745 for breast cancer were downloaded from the GEO database. Transcriptome sequencing data for breast cancer were downloaded from UCSC database. We divided breast cancer cells into high-LLPS group and low-LLPS group by down dimension clustering analysis of single-cell sequencing data set, and obtained differentially expressed genes between the two groups. Subsequently, weighted co-expression network analysis (WGCNA) was performed on transcriptome sequencing data, and the module genes most associated with LLPS were obtained. COX regression and Lasso regression were performed and the prognostic model was constructed. Subsequently, survival analysis, principal component analysis, clinical correlation analysis, and nomogram construction were used to evaluate the significance of the prognostic model. Finally, cell experiments were used to verify the function of the model’s key gene, PGAM1. We constructed a LLPS-related prognosis model consisting of nine genes: POLR3GL, PLAT, NDRG1, HMGB3, HSPH1, PSMD7, PDCD2, NONO and PGAM1. By calculating LLPS-related risk scores, breast cancer patients could be divided into high-risk and low-risk groups, with the high-risk group having a significantly worse prognosis. Cell experiments showed that the activity, proliferation, invasion and healing ability of breast cancer cell lines were significantly decreased after knockdown of the key gene PGAM1 in the model. Our study provides a new idea for prognostic stratification of breast cancer and provides a novel marker: PGAM1. Impact Journals 2023-06-19 /pmc/articles/PMC10333080/ /pubmed/37338518 http://dx.doi.org/10.18632/aging.204812 Text en Copyright: © 2023 Xie et al. https://creativecommons.org/licenses/by/3.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/3.0/) (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Paper
Xie, Jiaheng
Chen, Liang
Wu, Dan
Liu, Shengxuan
Pei, Shengbin
Tang, Qikai
Wang, Yue
Ou, Mengmeng
Zhu, Zhechen
Ruan, Shujie
Wang, Ming
Shi, Jingping
Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title_full Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title_fullStr Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title_full_unstemmed Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title_short Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis
title_sort significance of liquid-liquid phase separation (llps)-related genes in breast cancer: a multi-omics analysis
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10333080/
https://www.ncbi.nlm.nih.gov/pubmed/37338518
http://dx.doi.org/10.18632/aging.204812
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