The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events

Zhe Liu; Xudong Liu; Fang Liu; Hui Zhao; Yu Zhang; Yafan Wang; Ying Ma; Fuzhou Wang; Weitong Zhang; Olutomilayo Olayemi Petinrin; Zhongyu Yao; Jingbo Liang; Qian He; Dayun Feng; Lei Wang; Ka-Chun Wong

doi:10.1016/j.gene.2022.146657

The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events

Zhe Liu
, Xudong Liu
, Fang Liu
, Hui Zhao
, Yu Zhang
, Yafan Wang
, Ying Ma
, Fuzhou Wang
, Weitong Zhang
, Olutomilayo Olayemi Petinrin
, Zhongyu Yao
, Jingbo Liang
, Qian He
, Dayun Feng^*
, Lei Wang^*
, Ka-Chun Wong^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

13 Citations (Scopus)

Abstract

Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.

Original language	English
Article number	146657
Journal	Gene
Volume	835
Online published	13 Jun 2022
DOIs	https://doi.org/10.1016/j.gene.2022.146657
Publication status	Published - 15 Aug 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Research Keywords

Alternative splicing (AS)
Splicing factor (SF)
Bladder urothelial carcinoma (BLCA)
TCGA
Prognostic analysis

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10.1016/j.gene.2022.146657

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@article{98393cc384c744a89dc5960e1576271c,

title = "The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events",

abstract = "Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.",

keywords = "Alternative splicing (AS), Splicing factor (SF), Bladder urothelial carcinoma (BLCA), TCGA, Prognostic analysis",

author = "Zhe Liu and Xudong Liu and Fang Liu and Hui Zhao and Yu Zhang and Yafan Wang and Ying Ma and Fuzhou Wang and Weitong Zhang and Petinrin, \{Olutomilayo Olayemi\} and Zhongyu Yao and Jingbo Liang and Qian He and Dayun Feng and Lei Wang and Ka-Chun Wong",

year = "2022",

month = aug,

day = "15",

doi = "10.1016/j.gene.2022.146657",

language = "English",

volume = "835",

journal = "Gene",

issn = "0378-1119",

publisher = "Elsevier B.V.",

}

TY - JOUR

T1 - The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events

AU - Liu, Zhe

AU - Liu, Xudong

AU - Liu, Fang

AU - Zhao, Hui

AU - Zhang, Yu

AU - Wang, Yafan

AU - Ma, Ying

AU - Wang, Fuzhou

AU - Zhang, Weitong

AU - Petinrin, Olutomilayo Olayemi

AU - Yao, Zhongyu

AU - Liang, Jingbo

AU - He, Qian

AU - Feng, Dayun

AU - Wang, Lei

AU - Wong, Ka-Chun

PY - 2022/8/15

Y1 - 2022/8/15

N2 - Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.

AB - Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.

KW - Alternative splicing (AS)

KW - Splicing factor (SF)

KW - Bladder urothelial carcinoma (BLCA)

KW - TCGA

KW - Prognostic analysis

UR - https://www.scopus.com/pages/publications/85132760407

UR - https://www.scopus.com/pages/publications/85132760407#tab=impact

U2 - 10.1016/j.gene.2022.146657

DO - 10.1016/j.gene.2022.146657

M3 - RGC 21 - Publication in refereed journal

SN - 0378-1119

VL - 835

JO - Gene

JF - Gene

M1 - 146657

ER -

The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events

Abstract

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Research Keywords

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HMRF: Development of Big Data Tools for High-Throughput Sequencing Data with Applications to Colorectal Cancer Genomes

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The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events

Abstract

UN SDGs

Research Keywords

Access Output

Other Access Options

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Other Files and Links

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Projects

HMRF: Development of Big Data Tools for High-Throughput Sequencing Data with Applications to Colorectal Cancer Genomes

Cite this