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Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer

Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer...

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Autores principales: Zhang, Xingda, Zeng, Jiaqi, Wang, Jianyu, Yang, Zihan, Gao, Song, Liu, Honghao, Li, Guozheng, Zhang, Xin, Gu, Yue, Pang, Da
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777589/
https://www.ncbi.nlm.nih.gov/pubmed/36553667
http://dx.doi.org/10.3390/genes13122400
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author Zhang, Xingda
Zeng, Jiaqi
Wang, Jianyu
Yang, Zihan
Gao, Song
Liu, Honghao
Li, Guozheng
Zhang, Xin
Gu, Yue
Pang, Da
author_facet Zhang, Xingda
Zeng, Jiaqi
Wang, Jianyu
Yang, Zihan
Gao, Song
Liu, Honghao
Li, Guozheng
Zhang, Xin
Gu, Yue
Pang, Da
author_sort Zhang, Xingda
collection PubMed
description Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas database were categorized according to the expression level of NAT10, which drives acetylation of cytidine in RNA to N(4)-acetylcytidine (ac4C) and affects mRNA stability. A total of 703 differentially expressed long non-coding RNAs (lncRNAs) were found between high- and low-expressed NAT10 groups in TNBC. Twenty of these lncRNAs were significantly associated with prognosis. Two breast cancer tissues and their paired normal tissues were sequenced at the whole genome level using acetylated RNA immunoprecipitation sequencing (acRIP-seq) technology to identify acetylation features in TNBC, and 180 genes were significantly differentially ac4c acetylated in patients. We also analyzed the genome-wide lncRNA expression profile and constructed a co-expression network, containing 116 ac4C genes and 1080 lncRNAs. Three of these lncRNAs were prognostic risk lncRNAs affected by NAT10 and contained in the network. The corresponding reciprocal pairs were “LINC01614-COL3A1”, “OIP5-AS1-USP8”, and “RP5-908M14.9-TRIR”. These results indicate that RNA ac4c acetylation involves lncRNAs and affects the tumor process and prognosis of TNBC. This will aid the prediction of drug targets and drug sensitivity.
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spelling pubmed-97775892022-12-23 Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer Zhang, Xingda Zeng, Jiaqi Wang, Jianyu Yang, Zihan Gao, Song Liu, Honghao Li, Guozheng Zhang, Xin Gu, Yue Pang, Da Genes (Basel) Article Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas database were categorized according to the expression level of NAT10, which drives acetylation of cytidine in RNA to N(4)-acetylcytidine (ac4C) and affects mRNA stability. A total of 703 differentially expressed long non-coding RNAs (lncRNAs) were found between high- and low-expressed NAT10 groups in TNBC. Twenty of these lncRNAs were significantly associated with prognosis. Two breast cancer tissues and their paired normal tissues were sequenced at the whole genome level using acetylated RNA immunoprecipitation sequencing (acRIP-seq) technology to identify acetylation features in TNBC, and 180 genes were significantly differentially ac4c acetylated in patients. We also analyzed the genome-wide lncRNA expression profile and constructed a co-expression network, containing 116 ac4C genes and 1080 lncRNAs. Three of these lncRNAs were prognostic risk lncRNAs affected by NAT10 and contained in the network. The corresponding reciprocal pairs were “LINC01614-COL3A1”, “OIP5-AS1-USP8”, and “RP5-908M14.9-TRIR”. These results indicate that RNA ac4c acetylation involves lncRNAs and affects the tumor process and prognosis of TNBC. This will aid the prediction of drug targets and drug sensitivity. MDPI 2022-12-18 /pmc/articles/PMC9777589/ /pubmed/36553667 http://dx.doi.org/10.3390/genes13122400 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
Zhang, Xingda
Zeng, Jiaqi
Wang, Jianyu
Yang, Zihan
Gao, Song
Liu, Honghao
Li, Guozheng
Zhang, Xin
Gu, Yue
Pang, Da
Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title_full Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title_fullStr Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title_full_unstemmed Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title_short Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer
title_sort revealing the potential markers of n(4)-acetylcytidine through acrip-seq in triple-negative breast cancer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777589/
https://www.ncbi.nlm.nih.gov/pubmed/36553667
http://dx.doi.org/10.3390/genes13122400
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