Dataset Information

Structure prediction of novel isoforms from uveal melanoma by AlphaFold.

ABSTRACT: Alternative splicing is an important mechanism that enhances protein functional diversity. To date, our understanding of alternative splicing variants has been based on mRNA transcript data, but due to the difficulty in predicting protein structures, protein tertiary structures have been largely unexplored. However, with the release of AlphaFold, which predicts three-dimensional models of proteins, this challenge is rapidly being overcome. Here, we present a dataset of 315 predicted structures of abnormal isoforms in 18 uveal melanoma patients based on second- and third-generation transcriptome-sequencing data. This information comprises a high-quality set of structural data on recurrent aberrant isoforms that can be used in multiple types of studies, from those aimed at revealing potential therapeutic targets to those aimed at recognizing of cancer neoantigens at the atomic level.

SUBMITTER: Zhang Z

PROVIDER: S-EPMC10403560 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Structure prediction of novel isoforms from uveal melanoma by AlphaFold.

Zhang Zhe Z Li Chen C Li Qian Q Su Xiaoming X Li Jiayi J Zhu Lili L Lin Xinhua James XJ Shen Jianfeng J

Scientific data 20230804 1

Alternative splicing is an important mechanism that enhances protein functional diversity. To date, our understanding of alternative splicing variants has been based on mRNA transcript data, but due to the difficulty in predicting protein structures, protein tertiary structures have been largely unexplored. However, with the release of AlphaFold, which predicts three-dimensional models of proteins, this challenge is rapidly being overcome. Here, we present a dataset of 315 predicted structures o ...[more]

PMID: 37542084

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Project description:BackgroundUveal melanoma (UVM) is a form of eye cancer with a poor prognosis, particularly in metastatic patients. This study aimed to elucidate the cellular heterogeneity within UVM and identify prognostic biomarkers.MethodsWe performed single-cell RNA sequencing (scRNA-seq) on primary and metastatic UVM samples. A UVM-specific gene signature was constructed using LASSO regression and validated via ROC curve analysis in the TCGA-UVM and GSE84976 cohorts. AlphaFold 3 was used to predict the 3D structures of key proteins. T-cell populations were analyzed using pseudotime trajectory mapping and interaction network visualization. CRISPR-Cas9 screening analysis was conducted to identify hub genes and cytokine pathways that may serve as therapeutic targets. Additionally, we constructed the Dictionary of Immune Responses to Cytokines at single-cell resolution to evaluate cytokine signatures.ResultsScRNA-seq revealed five major cell types within UVMs and subdivided them into seven distinct subtypes. Cytokine signaling analysis revealed differential expression of cytokine signaling in immune-related genes (CSIRGs) across these subtypes in primary and metastatic tumors. The UVM-specific gene signature demonstrated high predictive accuracy in ROC curve analysis and was associated with overall survival in Kaplan-Meier survival analyses. Additionally, AlphaFold 3 predicted the 3D structures of key proteins with high confidence. T-cell population analysis revealed complex developmental pathways and interaction networks in UVM. Myeloid-derived suppressor cells (MDSCs) were found to be increased in metastatic UVM, correlating with the enrichment of GM-CSF. CRISPR-Cas9 screening analysis identified hub genes and cytokine pathways with low gene effect scores across cell lines, indicating their potential importance in UVM.ConclusionThis study identified critical cellular subtypes and prognostic biomarkers in UVM, shedding light on targeted therapies. The insights into cytokine signaling and T-cell dynamics within the UVM microenvironment provide a foundation for developing personalized therapeutic strategies to improve patient outcomes.

Dataset Information

Structure prediction of novel isoforms from uveal melanoma by AlphaFold.

Publications

Structure prediction of novel isoforms from uveal melanoma by AlphaFold.

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