# Critical role for alternative splicing in conferring risk for type 1 diabetes

> **NIH NIH R01** · UNIVERSITY OF FLORIDA · 2021 · $411,469

## Abstract

Project Summary/Abstract:
 Classical immunogenetics, linkage studies, and genome-wide association studies (GWAS) have identified a
set of ~50 chromosomal regions which individually contribute significantly to risk for type 1 diabetes (T1D).
Knowledge of the genes in these regions provides an opportunity to probe the molecular underpinnings of the
disease, potentially facilitating improved disease prediction and/or novel strategies for prevention or
therapeutic intervention. ImmunoChip fine mapping in T1D indicates that the majority of credible causative
genetic variants for T1D overlap with tissue specific enhancer (but not promoter) elements, emphasizing the
need for a context dependent understanding of the mode of action for genes contributing to T1D pathogenesis
through the study of relevant cell types. To address this need, we have, in preliminary studies, processed more
than 800 RNA-Seq samples, transcriptionally profiling T and B lymphocyte subsets in both T1D cases and
controls. These preliminary studies have yielded three key observations: (1) Genes located in T1D-associated
chromosomal regions are significantly enriched for cell-type specific alternative splicing events. These
alternative splicing events are observed in 72% of T1D genes but only 32% of genes overall (P<0.0001) and
include event types such as intron retention or exon skipping that are likely to have significant effects on the
expression and function of the proteins encoded by these genes. (2) Non-coding polymorphisms in regulatory
regions that are identified as credible causative variants for T1D, are significantly associated with these
alternative splicing events in a highly tissue-specific manner. (3) Genes located in chromosomal regions
associated with T1D display correlated expression in lymphocytes, allowing them be clustered into co-
expression modules that provide insights into regulation and function.
 Our preliminary findings suggest that transcript isoforms, and, by implication, the protein isoforms that they
encode, are altered in T1D through genetically regulated shifts in exon usage in specific cell types. To gain a
comprehensive understanding of the impact of alternative splicing on T1D risk, and to identify and characterize
disease relevant transcripts and isoforms, we propose to apply long read sequencing to RNA from
lymphocytes in T1D and jointly analyze short and long read data to obtain reliable, cell type specific,
information on transcript structure and usage. We will then characterize the effects of alternative splicing and
transcript isoform usage on two candidate T1D genes that are part of a co-expression module in lymphocytes,
IKZF1 and SIRPG.

## Key facts

- **NIH application ID:** 10106620
- **Project number:** 5R01DK116954-04
- **Recipient organization:** UNIVERSITY OF FLORIDA
- **Principal Investigator:** Patrick Concannon
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $411,469
- **Award type:** 5
- **Project period:** 2018-04-01 → 2023-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10106620

## Citation

> US National Institutes of Health, RePORTER application 10106620, Critical role for alternative splicing in conferring risk for type 1 diabetes (5R01DK116954-04). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10106620. Licensed CC0.

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