# USING SINGLE-CELL RNA AND PROTEIN APPROACHES TO ELUCIDATE MOLECULAR DETERMINANTS  AND PREDICTORS OF INFLAMMATORY BOWEL DISEASES

> **NIH NIH K23** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $194,057

## Abstract

Abstract
Inflammatory bowel diseases (IBD) represent a spectrum of complicated intestinal pathology characterized by
dysregulation of the adaptive and innate immune responses in genetically susceptible hosts. The precise
molecular mechanisms underlying the pathophysiology and immune dysregulation have yet to be fully
elucidated. A significant barrier to better understanding of the disease pathogenesis is the heterogeneity of
intestinal tissue. Furthermore, substantial heterogeneity may exist even within the same phenotypic cell subset,
limiting the ability to detect differences using bulk RNA sequencing or flow cytometry. Single cell RNA sequencing
and single cell protein identification in combination, however, represent a significant technologic advance with
the capability to identify novel cell subsets and states that could not be previously detected. We propose
exploiting this technology to generate a single cell atlas of the intestinal and peripheral blood immune response
in two subsets of IBD: ulcerative colitis (UC) and ileal Crohn’s disease. The overall objective of this proposal is
to define molecular determinants of IBD in tissue and blood, then to harness these differences in gene expression
to develop novel diagnostic testing for IBD using peripheral blood. Specific Aim 1 proposes to identify abnormal
states of differentiation and pathogenic cell subtypes that are enriched in the intestinal tissue and peripheral
blood from UC and Crohn’s ileitis as compared to healthy controls. The differences in gene expression between
the intestinal cells from IBD patients and healthy controls will provide insight into molecular determinants of
disease that are specific to UC and Crohn’s ileitis. Specific Aim 2 proposes to utilize the differences in single cell
gene expression from the peripheral blood in a larger cohort of patients to develop diagnostic testing for UC and
Crohn’s ileitis. Non-invasive testing with single cell gene expression has the potential to predict not only disease
status but also severity of disease activity with potential therapeutic targets. In sum, this proposal aims to use
single cell gene and protein expression to understand disease pathophysiology of IBD and develop novel
diagnostic biomarkers.

## Key facts

- **NIH application ID:** 9871279
- **Project number:** 1K23DK123406-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Brigid S Boland
- **Activity code:** K23 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $194,057
- **Award type:** 1
- **Project period:** 2020-04-01 → 2023-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9871279

## Citation

> US National Institutes of Health, RePORTER application 9871279, USING SINGLE-CELL RNA AND PROTEIN APPROACHES TO ELUCIDATE MOLECULAR DETERMINANTS  AND PREDICTORS OF INFLAMMATORY BOWEL DISEASES (1K23DK123406-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9871279. Licensed CC0.

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