Page 33 - G. Cell differentiation. division. and death

Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling
Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome
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Subbroto Kumar Saha , Tak-Il Jeon , Soo Bin Jang , Se Jong Kim , Kyung Min Lim , Yu Jin
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Choi , Hyeong Gon Kim , Aram Kim * and Ssang-Goo Cho *
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BACKGROUND AIM
Interstitial cystitis/bladder pain syndrome (IC/BPS) is a The purpose of this study is to assess the potential of
prevalent condition that presents with symptoms of a genetic diagnosis of IC/BPS, since there is no single
disrupted urine storage and pelvic pain. The syndrome
lacks definitive diagnostic tests or markers and is defined definition of IC/BPS that can identify all IC/BPS cases.
by a collection of symptoms reported by patients, making We conducted an extensive bioinformatic analysis to
diagnosis subjective and clinician dependent. Under these identify genes and transcriptional factors to determine
circumstances, chronic inflammation has been reported to whether these biomarkers meet the clinical criteria to
have arisen after surgery in IC/BPS patients, which is
frequently misdiagnosed. The purpose of this study is to confirm the diagnosis of IC/BPS. Thus, we
assess the potential of a genetic diagnosis of IC/BPS. systematically predict the significant biomarkers.
METHODS
To identify Differentially Expressed Genes (DEGs) in IC/BPS, we utilized the Gene Expression Omnibus (GEO)
datasets: GSE621, GSE11783, GSE28242, and GSE57560. The possible pathway and Gene Ontology of the
common upregulated and downregulated DEGs were analyzed using Enrich web server. To construct the PPI
network, we carried out the Cytoscape v3.7.2 software using common DEGs. We also constructed a hub gene and
transcriptional factor network using the web-based tool NetworkAnalyst. We obtained IC/BPS patient-derived tissues
from Konkuk University Medical Center and confirmed the gene expression via real-time qPCR.
RESULTS

Figure 1 Figure 2 Figure 3 Figure 4

Figure 5 Figure 6 Figure 7 Figure 8

Volcano plots show the transcript expression between normal and IC/BPS patients and was identified several DEGs
from the four GEO datasets (Figure 1). These DEGs were separately obtained 51 overlapping upregulated and two
downregulated (Figure 2 and 3), and putative pathways and Gene Ontology (GO) (Figure 4). We identified a PPI
network and Hub genes from datasets (Figure 5-7), and finally analyzed mRNA expression from patients (Figure 8).
CONCLUSION REFERENCES ACKNOWLEDGEMENTS

In this study, we carried out a bioinformatics [1] Hanno P.M., Burks D.A., et This research was supported by a grant
analysis using patient-derived tissue genomics al. AUA Guideline for the from the National Research Foundation
Diagnosis and Treatment of
data to reveal the molecular signs of IC/BPS. The Interstitial Cystitis/Bladder (NRF) funded by the Korean
identified common DEGs were mostly enriched in Pain Syndrome. J. Urol. (2011) government.
[2] Berry S.H., Elliott M.N.,
immune and metabolic signaling mechanisms. As Suttorp M., Bogart L.M., Stoto Contact information
a result, at least five out of six hub genes were M.A., Eggers P., Nyberg L.,
finally selected. Thus, these five hub genes might Clemens J.Q. Prevalence of BuruBuru6586@naver.com (S.B.J.)
Symptoms of Bladder Pain
play a potential role in IC/BPS development and Syndrome/Interstitial Cystitis jeonti94@naver.com (T.I.J.)
serve as diagnostic biomarkers of IC/BPS, which among Adult Females in the
United States. J. Urol. (2011)
deserves further detailed investigation. ssangoo@konkuk.ac.kr (S.-G.C.)