# Alternate splicing as a source of shared neoantigens in a non-small cell lung cancer

> **NIH NIH F30** · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · 2023 · $52,694

## Abstract

PROJECT SUMMARY/ABSTRACT
Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality in the United States. Immune
checkpoint inhibitors (ICIs) like anti-PD-1 have increased overall survival in NSCLC, but most patients still do
not respond to treatment. Cancer vaccines that target tumor-specific antigens, known as neoantigens, may
increase the efficacy of ICIs and other immunotherapies by expanding neoantigen-reactive CD8+ T cells that
can recognize and destroy tumor cells. Alternative splicing is a ubiquitous post-transcriptional regulatory process
that allows cells to produce different mRNA and protein sequences from the same gene. Alternative splicing is
broadly dysregulated in many cancer types including NSCLC and may generate novel peptide sequences absent
from normal tissue that can be recognized as neoantigens by CD8+ T cells. To identify alternative splicing-
derived neoantigens in NSCLC, we used long-read RNA sequencing to comprehensively map full-length mRNA
isoforms in NSCLC tumors and predict the proteins they encode with high accuracy. We found 145,914 predicted
peptides that were specific to tumors and shared by up to 70% of NSCLC patients. To identify which of these
peptides might be immunogenic, we used immunopeptidomics to directly sequence peptides bound to MHC
Class I in three NSCLC cell lines. We identified 21 peptides that are bound to MHC Class I on NSCLC cells and
are encoded by tumor-specific alternatively spliced mRNA isoforms. These splicing-derived peptides are
potentially shared neoantigens that might represent vaccine targets for NSCLC. Therefore, Aim 1 will test
whether any of these 21 splicing-derived peptides can be recognized by CD8+ T cells from NSCLC patients. We
will examine whether patient CD8+ T cells can proliferate, secrete cytokines like interferon-gamma, and lyse
target cells in response to these peptides. The experiments proposed in Aim 1 will provide crucial insight into the
frequency and immunogenicity of alternative splicing-derived neoantigens in NSCLC. Aim 2 will examine which
regulators of alternative splicing are driving production of these peptides. To this end, we will leverage publicly
available databases to identify splicing factors whose expression in tumors or target binding sites suggest an
association with the mRNA isoforms that code for the 21 splicing-derived peptides. We will use targeted genetic
approaches to study whether candidate splicing factors directly regulate peptide-coding isoform splicing in vitro.
This work will highlight mechanisms that can drive the production of tumor-specific splicing-derived peptides and
may reveal novel targets that can be exploited to enhance NSCLC immunogenicity. Altogether, these studies
may identify candidates for new immunotherapies, including personalized NSCLC cancer vaccines that can be
used to treat multiple patients who share expression of immunogenic splicing-derived neoantigens. This proposal
will provide me excellent trainin...

## Key facts

- **NIH application ID:** 10750090
- **Project number:** 1F30CA278494-01A1
- **Recipient organization:** UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
- **Principal Investigator:** Ryan Englander
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $52,694
- **Award type:** 1
- **Project period:** 2023-09-01 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10750090

## Citation

> US National Institutes of Health, RePORTER application 10750090, Alternate splicing as a source of shared neoantigens in a non-small cell lung cancer (1F30CA278494-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10750090. Licensed CC0.

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