Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Wang, Ting You; Yang, Rendong

doi:10.1016/j.xpro.2021.100788

Cited by 10 publications

(9 citation statements)

References 19 publications

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“…117,125,126 The production of neoantigens from skipped exons, also known as "neojunctions", occurs more frequently and is more likely to be shared among patients than those generated from SNV mutations. 29,117,127,128 A recent study has identified exitron splicing, a non-canonical splicing mechanism, as a new source of tumor neoantigens. Exitrons are exon-embedded cryptic introns distinguished from conventional introns in that they have both splicing (intron) and protein-coding (exon) potential while lacking stop codons or premature termination codons.…”

Section: Transcriptomic Variantsmentioning

confidence: 99%

“…Accordingly, exitrons splicing creates more validated neoantigens with higher immunogenicity in malignancies with low TMB. 128,129 Trans-acting alterations in splicing factors. Trans-acting alterations, in which a somatic mutation in a splicing factor results in an altered splicing variant, induce the production of neoantigens throughout the genome.…”

Section: Transcriptomic Variantsmentioning

confidence: 99%

See 1 more Smart Citation

Neoantigens: promising targets for cancer therapy

Xie

Shen

Gao

et al. 2023

Sig Transduct Target Ther

317

150

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Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.

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Section: Transcriptomic Variantsmentioning

confidence: 99%

Section: Transcriptomic Variantsmentioning

confidence: 99%

Neoantigens: promising targets for cancer therapy

Xie

Shen

Gao

et al. 2023

Sig Transduct Target Ther

317

150

View full text Add to dashboard Cite

show abstract

“…3B ). Wang and Yang (2021) , using a bioinformatic tool named ScanExitron, identified exitron splicing in 33 cancer types across 9599 tumour transcriptome data. They observed that exitron splicing affected 63 % of the coding genes of humans, and 95 % of these exitronic events were tumour specific.…”

Section: Function Of Exitronsmentioning

confidence: 99%

“…They identified exitron splicing-derived neo-epitopes, which can bind to MHC Class I or II and potentially be targeted for immunotherapy. An integrated protocol for the identification of exitron and exitron-derived neo-antigen using RNA-seq data using bioinformatic tools like ScanExitron and Scan Neo was developed by Wang and Yang (2021) . Splicing of exitrons was observed in genes like TAF15 , FUS and EWSR1 , which may be involved in promoting cancer progression ( Zhang et al 2022 ).…”

Section: Function Of Exitronsmentioning

confidence: 99%

Exitrons: offering new roles to retained introns—the novel regulators of protein diversity and utility

Shamnas v,

Singh,

Kumar

et al. 2024

AoB PLANTS

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Exitrons are exonic-introns. This subclass of intron-retention alternative splicing does not contain a Pre-Terminating stop Codon. Therefore, when retained, they are always a part of a protein. Intron retention is a frequent phenomenon predominantly found in plants, which results in either the degradation of the transcripts or can serve as a stable intermediate to be processed upon induction by specific signals or the cell status. Interestingly, exitrons have coding ability and may confer additional attributes to the proteins that retain them. Therefore, exitron-containing and exitron-spliced isoforms will be a driving force for creating protein diversity in the proteome of an organism. This review establishes a basic understanding of exitron, discussing its genesis, key features, identification methods, and functions. We also try to depict its other potential roles. The present review also aims to provide a fundamental background to those who found such exitronic sequences in their gene(s) and to speculate the future course of studies.

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“…INDELs were called by TransIndel [40] followed by neoepitopes analysis by ScanNeo [41] and calls present in healthy controls were removed. Exitrons were called by ScanExitron [42] and ScanNeo further predicted neoantigens (Table S1). visual overview of workflow.…”

Section: Neoepitopes Derived From Indels and Exitronsmentioning

confidence: 99%

Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype

Bahrambeigi

Lee

Branchi

et al. 2022

Preprint

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Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunity for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of plasma extracellular vesicles (EVs) RNA, we successfully predict consensus molecular subtypes in metastatic colorectal cancer (mCRC) patients and analogous RNA-based subtypes in patients with pancreatic ductal adenocarcinoma (PDAC). We further demonstrate the ability monitor changes in transcriptomic subtype under treatment selection pressure. Our approach also identified gene fusions and neoepitopes from plasma EVs, which were validated in matched tissue samples. These results demonstrate the feasibility of transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to identification of expressed fusions and neoantigens as potential therapeutic targets, sans the need for tissue-based sampling

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Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Cited by 10 publications

References 19 publications

Neoantigens: promising targets for cancer therapy

Neoantigens: promising targets for cancer therapy

Exitrons: offering new roles to retained introns—the novel regulators of protein diversity and utility

Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype

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