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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Impact Journals
2023
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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. |
format | Online Article Text |
id | pubmed-10333080 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Impact Journals |
record_format | MEDLINE/PubMed |
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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