Related Experiment Video

Updated: Dec 14, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.2K

ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq

Zhanbing Zhang1, Chi Zhou1, Lihua Tang2

  • 1Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China.

Aging
|July 23, 2020
PubMed

Insights

This study introduces ASNEO, a tool identifying cancer neoantigens from alternative splicing events using RNA-seq. These novel neoantigens show higher immune scores and can predict patient survival, advancing personalized cancer vaccines.

Area of Science:

  • Oncology
  • Immunology
  • Bioinformatics

Background:

  • Cancer neoantigens are crucial for immunotherapy.
  • Current methods primarily identify neoantigens from SNVs, indels, or gene fusions.
  • Alternative splicing is prevalent in tumors and generates neoantigens.

Purpose of the Study:

  • To present ASNEO, a computational pipeline for identifying personalized alternative splicing-based neoantigens (ASNEOs) from RNA-seq data.
  • To validate ASNEO's capability in identifying MHC I-presented neopeptides.
  • To explore the clinical relevance of ASNEOs in cancer immunotherapy.

Main Methods:

  • Development of the ASNEO pipeline for alternative splicing neoantigen identification.
  • Validation using mass spectrometry data for MHC I presentation.
  • Application of ASNEO to immunotherapy-treated patient cohorts.

Main Results:

  • ASNEO successfully identified neopeptides presented by MHC I.
  • Alternative splicing-based neopeptides exhibited higher immune scores compared to somatic neoantigens.
  • ASNEOs demonstrated potential as biomarkers for predicting patient survival.

Conclusions:

  • ASNEO enhances the understanding of the tumor immune landscape by including alternative splicing-derived neoantigens.
  • ASNEOs represent a promising avenue for developing personalized cancer vaccines.
  • The identification of ASNEOs contributes to more comprehensive neoantigen discovery for cancer immunotherapy.
Keywords:
RNA-seqalternative splicingcancerimmunotherapyneoantigen

More Related Videos

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

14.2K
Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay11:22

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

Published on: August 26, 2018

9.2K

Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
24.3K
Alternative RNA Splicing02:18

Alternative RNA Splicing

4.6K
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
59.9K
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.5K
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K