Cargando…

Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination

BACKGROUND: According to the Global Cancer Statistics in 2020, the incidence and mortality of colorectal cancer (CRC) rank third and second among all tumors. The disturbance of ubiquitination plays an important role in the initiation and development of CRC, but the ubiquitinome of CRC cells and the...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhang, Wei, Yang, Yan, Lin, Liewen, He, Jingquan, Dong, Jingjing, Yan, Bin, Cai, Wanxia, Chen, Yumei, Yin, Lianghong, Tang, Donge, Liu, Fanna, Dai, Yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9528151/
https://www.ncbi.nlm.nih.gov/pubmed/36184622
http://dx.doi.org/10.1186/s12967-022-03645-8
_version_ 1784801247543427072
author Zhang, Wei
Yang, Yan
Lin, Liewen
He, Jingquan
Dong, Jingjing
Yan, Bin
Cai, Wanxia
Chen, Yumei
Yin, Lianghong
Tang, Donge
Liu, Fanna
Dai, Yong
author_facet Zhang, Wei
Yang, Yan
Lin, Liewen
He, Jingquan
Dong, Jingjing
Yan, Bin
Cai, Wanxia
Chen, Yumei
Yin, Lianghong
Tang, Donge
Liu, Fanna
Dai, Yong
author_sort Zhang, Wei
collection PubMed
description BACKGROUND: According to the Global Cancer Statistics in 2020, the incidence and mortality of colorectal cancer (CRC) rank third and second among all tumors. The disturbance of ubiquitination plays an important role in the initiation and development of CRC, but the ubiquitinome of CRC cells and the survival-relevant ubiquitination are poorly understood. METHODS: The ubiquitinome of CRC patients (n = 6) was characterized using our own data sets of proteomic and ubiquitin-proteomic examinations. Then, the probable survival-relevant ubiquitination was searched based on the analyses of data sets from public databases. RESULTS: For the ubiquitinomic examination, we identified 1690 quantifiable sites and 870 quantifiable proteins. We found that the highly-ubiquitinated proteins (n ≥ 10) were specifically involved in the biological processes such as G-protein coupling, glycoprotein coupling, and antigen presentation. Also, we depicted five motif sequences frequently recognized by ubiquitin. Subsequently, we revealed that the ubiquitination content of 1172 proteins were up-regulated and 1700 proteins were down-regulated in CRC cells versus normal adjacent cells. We demonstrated that the differentially ubiquitinated proteins were relevant to the pathways including metabolism, immune regulation, and telomere maintenance. Then, integrated with the proteomic datasets from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) (n = 98), we revealed that the increased ubiquitination of FOCAD at Lys583 and Lys587 was potentially associated with patient survival. Finally, we depicted the mutation map of FOCAD and elucidated its potential functions on RNA localization and translation in CRC. CONCLUSIONS: The findings of this study described the ubiquitinome of CRC cells and identified abnormal ubiquitination(s) potentially affecting the patient survival, thereby offering new probable opportunities for clinical treatment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-022-03645-8.
format Online
Article
Text
id pubmed-9528151
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-95281512022-10-04 Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination Zhang, Wei Yang, Yan Lin, Liewen He, Jingquan Dong, Jingjing Yan, Bin Cai, Wanxia Chen, Yumei Yin, Lianghong Tang, Donge Liu, Fanna Dai, Yong J Transl Med Research BACKGROUND: According to the Global Cancer Statistics in 2020, the incidence and mortality of colorectal cancer (CRC) rank third and second among all tumors. The disturbance of ubiquitination plays an important role in the initiation and development of CRC, but the ubiquitinome of CRC cells and the survival-relevant ubiquitination are poorly understood. METHODS: The ubiquitinome of CRC patients (n = 6) was characterized using our own data sets of proteomic and ubiquitin-proteomic examinations. Then, the probable survival-relevant ubiquitination was searched based on the analyses of data sets from public databases. RESULTS: For the ubiquitinomic examination, we identified 1690 quantifiable sites and 870 quantifiable proteins. We found that the highly-ubiquitinated proteins (n ≥ 10) were specifically involved in the biological processes such as G-protein coupling, glycoprotein coupling, and antigen presentation. Also, we depicted five motif sequences frequently recognized by ubiquitin. Subsequently, we revealed that the ubiquitination content of 1172 proteins were up-regulated and 1700 proteins were down-regulated in CRC cells versus normal adjacent cells. We demonstrated that the differentially ubiquitinated proteins were relevant to the pathways including metabolism, immune regulation, and telomere maintenance. Then, integrated with the proteomic datasets from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) (n = 98), we revealed that the increased ubiquitination of FOCAD at Lys583 and Lys587 was potentially associated with patient survival. Finally, we depicted the mutation map of FOCAD and elucidated its potential functions on RNA localization and translation in CRC. CONCLUSIONS: The findings of this study described the ubiquitinome of CRC cells and identified abnormal ubiquitination(s) potentially affecting the patient survival, thereby offering new probable opportunities for clinical treatment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-022-03645-8. BioMed Central 2022-10-02 /pmc/articles/PMC9528151/ /pubmed/36184622 http://dx.doi.org/10.1186/s12967-022-03645-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Zhang, Wei
Yang, Yan
Lin, Liewen
He, Jingquan
Dong, Jingjing
Yan, Bin
Cai, Wanxia
Chen, Yumei
Yin, Lianghong
Tang, Donge
Liu, Fanna
Dai, Yong
Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title_full Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title_fullStr Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title_full_unstemmed Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title_short Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
title_sort comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9528151/
https://www.ncbi.nlm.nih.gov/pubmed/36184622
http://dx.doi.org/10.1186/s12967-022-03645-8
work_keys_str_mv AT zhangwei comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT yangyan comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT linliewen comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT hejingquan comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT dongjingjing comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT yanbin comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT caiwanxia comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT chenyumei comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT yinlianghong comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT tangdonge comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT liufanna comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination
AT daiyong comprehensivecharacterizationofubiquitinomeofhumancolorectalcancerandidentificationofpotentialsurvivalrelatedubiquitination