(T1330-02-09) Examining PDGFRA Gene Downregulation in the Peripheral Blood of Patients with Functional Dyspepsia

Purpose: Functional Dyspepsia (FD) is a common worldwide disorder, with one or more symptoms including postprandial fullness, early satiety, epigastric pain, or epigastric burning. The major feature of FD is regarded as the dysfunction of gastric motility. The challenge in diagnosing FD using gastroscopy lies in the absence of visible abnormal legions. Also, there are no suitable drugs to cure functional dyspepsia. To understand the molecular mechanism of FD, we performed RNA sequencing (RNA-seq) in the peripheral blood of the patients. Furthermore, we aim to identify biomarker candidates in peripheral blood for the diagnosis and treatment of FD.

Methods: We performed RNA-seq from the peripheral blood of the FD patient group (N = 14) and the healthy control group (N = 15). The differentially expressed genes (DEGs) between the FD patient group and the healthy control group were identified with a fold change > 1.5 and p-value < 0.05 using edgeR program [1]. Among the DEGs, the biological pathways related to downregulated genes were enriched for Gene Set Enrichment Analysis (GSEA) using Metascape website [2]. In addition, protein-protein Interaction (PPI) network was created based on DEGs related to gastric motility identified through GSEA using STRING database [3]. By PPI network analysis, biomarker candidates were selected by significantly higher betweenness centrality and degree centrality than other genes. To compare gene expression value (counts per million) of biomarker candidates in peripheral blood and stomach tissue with other five diseases, RNA-seq data was collected from gastritis(GS), gastroparesis(GP), and inflammatory bowel disease(IBD), diseases characterized by impaired gastric motility, as well as from diabetes mellitus(DM) and sepsis(SP), associated with inflammation. The RNA-seq data were collected from a total of 13 projects including 1,374 samples (control: 499, case: 875). In the dataset, samples from gastritis and gastroparesis were obtained from gastric tissue biopsy, while the remaining samples were collected from peripheral blood. The datasets were collected from NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/).

Results: RNA-seq analysis revealed the downregulation of pathways related to gastric motility including smooth muscle contraction and relaxation. PPI network analysis identified 22 genes belonging to smooth muscle contraction and relaxation. Among the genes, Platelet Derived Growth Factor Receptor Alpha (PDGFRA) was significantly downregulated in patients with FD (Fold change = -3.05, p-value = 0.01). PDGFRA is described as a specific marker of SIP syncytium related to gastric motility [4]. In the comparison of fold change and odds ratio of PDGFRA with six diseases, the fold change of PDGFRA revealed a significant downregulation of PDGFRA in the patients with FD, with a notable fold change of -3.05. Also, downregulation with a fold change of -2.23 was observed in gastric tissue biopsy from the patients with gastroparesis (GSE115601) (Fig 1). Conversely, no significant changes were demonstrated in the other four diseases with fold changes < 2 or p-value > 0.05. To measure of association between PDGFRA and six diseases including FD, we calculated odds ratios between PDGFRA and diseases. As a result, the odds ratio of PDGFRA in FD was 1.63 which implied that a decrease in PDGFRA expression values had great odds of an increase in FD (Fig 2). In addition, a significant effect of the decreased PDGFRA expression was observed in gastroparesis although less prominently compared to FD. However, PDGFRA indicated no significant association with other diseases below 1.00 or p-value > 0.05.

Conclusion: We aimed to understand the molecular mechanisms of functional dyspepsia with delayed gastric emptying through RNA-seq. The RNA-seq analysis revealed that dysfunction of gastric motility was characterized by a complex dysfunction involving smooth muscle contraction and relaxation. Among genes involving the pathway, PDGFRA, a significant marker of the SIP syncytium, was downregulated in patients with functional dyspepsia and gastroparesis. Interestingly, PDGFRA emerged the potential of PDGFRA to serve as a biomarker for FD diagnosis in peripheral blood samples.

References: 1. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. doi:10.1093/bioinformatics/btp616
2. Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523. Published 2019 Apr 3. doi:10.1038/s41467-019-09234-6
3. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290-295. doi:10.1038/nbt.3122
4. Sanders KM, Ward SM, Koh SD. Interstitial cells: regulators of smooth muscle function. Physiol Rev. 2014;94(3):859-907. doi:10.1152/physrev.00037.2013

Acknowledgements: This work was supported by the National Research Foundation of Korea grant funded by the Korea government (MSIT) (No. 1711173730) and by the Korea Institute of Toxicology, Republic of Korea (Grant No. 1711195891).