Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion
Abstract
:1. Introduction
2. Experimental Section
2.1. Identification of Differentially Expressed Genes (DEGs) from Gene Expression Omnibus (GEO) Datasets of IC/BPS
2.2. Gene Ontology (GO) and Pathway Analysis of Common DEGs
2.3. Protein-Protein Interaction (PPI) Construction and Identification of Hub Genes
2.4. Construction of Hub Genes and the Transcriptional Factor (TF) Network
2.5. Clinical Sample Collection from IC/BPS and Normal Bladder Tissues
2.6. Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) Analyses
2.7. Statistical Analysis
3. Results
3.1. Identification of DEGs from IC/BPS Patient Tissues
3.2. Enrichment Analyses of DEGs from IC/BPS Patient Tissues
3.3. PPI Network Analyses of DEGs and Hub Gene Identification from IC/BPS Patient Tissues
3.4. Enrichment Analyses of Hub Genes from IC/BPS Patient Tissues
3.5. Expression Analysis of Hub Genes in GEO Datasets and IC/BPS Patient Tissues
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Hanno, P.M.; Burks, D.A.; Clemens, J.Q.; Dmochowski, R.R.; Erickson, D.; Fitzgerald, M.P.; Forrest, J.B.; Gordon, B.; Gray, M.; Mayer, R.D.; et al. AUA Guideline for the Diagnosis and Treatment of Interstitial Cystitis/Bladder Pain Syndrome. J. Urol. 2011, 185, 2162–2170. [Google Scholar] [CrossRef] [PubMed]
- Gormley, E.A.; Lightner, D.J.; Burgio, K.L.; Chai, T.C.; Clemens, J.Q.; Culkin, D.J.; Das, A.K.; Foster, H.E.; Scarpero, H.M.; Tessier, C.D.; et al. Diagnosis and Treatment of Overactive Bladder (Non-Neurogenic) in Adults: AUA/SUFU Guideline. J. Urol. 2012, 188, 2455–2463. [Google Scholar] [CrossRef] [PubMed]
- Abrams, P.; Hanno, P.; Wein, A. Overactive bladder and painful bladder syndrome: There need not be confusion. Neurourol. Urodyn. 2005, 24, 149–150. [Google Scholar] [CrossRef] [PubMed]
- Lai, H.H.; Vetter, J.; Jain, S.; Gereau, R.W.; Andriole, G.L. The overlap and distinction of self-reported symptoms between interstitial cystitis/bladder pain syndrome and overactive bladder: A questionnaire based analysis. J. Urol. 2014, 192, 1679–1685. [Google Scholar] [CrossRef]
- Berry, S.H.; Elliott, M.N.; Suttorp, M.; Bogart, L.M.; Stoto, M.A.; Eggers, P.; Nyberg, L.; Clemens, J.Q. Prevalence of Symptoms of Bladder Pain Syndrome/Interstitial Cystitis among Adult Females in the United States. J. Urol. 2011, 186, 540–544. [Google Scholar] [CrossRef] [Green Version]
- Keay, S.K.; Seillier-Moiseiwitsch, F.; Zhang, C.-O.; Chai, T.C.; Zhang, J. Changes in human bladder epithelial cell gene expression associated with interstitial cystitis or antiproliferative factor treatment. Physiol. Genom. 2003, 14, 107–115. [Google Scholar] [CrossRef] [Green Version]
- Gamper, M.; Viereck, V.; Geissbühler, V.; Eberhard, J.; Binder, J.; Moll, C.; Rehrauer, H.; Moser, R. Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis. BMC Genom. 2009, 10, 199. [Google Scholar] [CrossRef] [Green Version]
- Colaco, M.; Koslov, D.S.; Keys, T.; Evans, R.J.; Badlani, G.H.; Andersson, K.; Walker, S.J. Correlation of Gene Expression with Bladder Capacity in Interstitial Cystitis/Bladder Pain Syndrome. J. Urol. 2014, 192, 1123–1129. [Google Scholar] [CrossRef]
- Blalock, E.M.; Korrect, G.S.; Stromberg, A.J.; Erickson, D.R. Gene Expression Analysis of Urine Sediment: Evaluation for Potential Noninvasive Markers of Interstitial Cystitis/Bladder Pain Syndrome. J. Urol. 2012, 187, 725–732. [Google Scholar] [CrossRef]
- Pilarczyk, M.; Najafabadi, M.F.; Kouril, M.; Vasiliauskas, J.; Niu, W.; Shamsaei, B.; Mahi, N.; Zhang, L.; Clark, N.A.; Ren, Y.; et al. Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS. bioRxiv 2019, 826271. [Google Scholar] [CrossRef] [Green Version]
- Chen, E.Y.; Tan, C.M.; Kou, Y.; Duan, Q.; Wang, Z.; Meirelles, G.V.; Clark, N.R.; Ma’Ayan, A. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 2013, 14, 128. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kuleshov, M.V.; Jones, M.R.; Rouillard, A.; Fernandez, N.F.; Duan, Q.; Wang, Z.; Koplev, S.; Jenkins, S.L.; Jagodnik, K.M.; Lachmann, A.; et al. Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016, 44, W90–W97. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Szklarczyk, D.; Gable, A.L.; Lyon, D.; Junge, A.; Wyder, S.; Huerta-Cepas, J.; Simonovic, M.; Doncheva, N.T.; Morris, J.H.; Bork, P.; et al. STRING v11: Protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2018, 47, D607–D613. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Szklarczyk, D.; Morris, J.H.; Cook, H.V.; Kuhn, M.; Wyder, S.; Simonovic, M.; Santos, A.; Doncheva, N.T.; Roth, A.; Bork, P.; et al. The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2016, 45, D362–D368. [Google Scholar] [CrossRef]
- Chin, C.-H.; Chen, S.-H.; Wu, H.-H.; Ho, C.-W.; Ko, M.-T.; Lin, C.-Y. cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Syst. Boil. 2014, 8, S11. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lotia, S.; Montojo, J.; Dong, Y.; Bader, G.D.; Pico, A.R. Cytoscape app store. Bioinformatics 2013, 29, 1350–1351. [Google Scholar] [CrossRef] [Green Version]
- Xia, J.; E Gill, E.; Hancock, R.E.W. NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nat. Protoc. 2015, 10, 823–844. [Google Scholar] [CrossRef]
- Zhou, G.; Soufan, O.; Ewald, J.D.; Hancock, R.E.W.; Basu, N.; Xia, J. NetworkAnalyst 3.0: A visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Res. 2019, 47, W234–W241. [Google Scholar] [CrossRef] [Green Version]
- Patnaik, S.S.; Laganà, A.S.; Vitale, S.G.; Buttice, S.; Noventa, M.; Gizzo, S.; Valenti, G.; Rapisarda, A.M.C.; La Rosa, V.L.; Magno, C.; et al. Etiology, pathophysiology and biomarkers of interstitial cystitis/painful bladder syndrome. Arch. Gynecol. Obstet. 2017, 295, 1341–1359. [Google Scholar] [CrossRef]
- Hanno, P.M.; Erickson, D.; Moldwin, R.; Faraday, M.M. Diagnosis and Treatment of Interstitial Cystitis/Bladder Pain Syndrome: AUA Guideline Amendment. J. Urol. 2015, 193, 1545–1553. [Google Scholar] [CrossRef]
- Denson, M.A.; Griebling, T.L.; Cohen, M.B.; Kreder, K.J. Comparison of cystoscopic and histological findings in patients with suspected interstitial cystitis. Urology 2000, 164, 1908–1911. [Google Scholar] [CrossRef]
- Van De Merwe, J.P.; Nordling, J.; Bouchelouche, P.; Bouchelouche, K.; Cervigni, M.; Daha, L.K.; Elneil, S.; Fall, M.; Hohlbrugger, G.; Irwin, P.; et al. Diagnostic Criteria, Classification, and Nomenclature for Painful Bladder Syndrome/Interstitial Cystitis: An ESSIC Proposal. Eur. Urol. 2008, 53, 60–67. [Google Scholar] [CrossRef] [PubMed]
- Ueda, T.; Nakagawa, M.; Okamura, M.; Tanoue, H.; Yoshida, H.; Yoshimura, N. New cystoscopic diagnosis for interstitial cystitis/painful bladder syndrome using narrow-band imaging system. Int. J. Urol. 2008, 15, 1039–1043. [Google Scholar] [CrossRef] [PubMed]
- Furuya, R.; Masumori, N.; Furuya, S.; Oda, T.; Takahashi, S.; Takeuchi, M. Glomerulation Observed during Transurethral Resection of the Prostate for Patients with Lower Urinary Tract Symptoms Suggestive of Benign Prostatic Hyperplasia is a Common Finding But No Predictor of Clinical Outcome. Urology 2007, 70, 922–926. [Google Scholar] [CrossRef]
- Leiby, B.E.; Landis, J.R.; Propert, K.J.; Tomaszewski, J.E. Interstitial Cystitis Data Base Study Group Discovery of Morphological Subgroups That Correlate with Severity of Symptoms in Interstitial Cystitis: A Proposed Biopsy Classification System. J. Urol. 2007, 177, 142–148. [Google Scholar] [CrossRef]
- Bosch, P. A Randomized, Double-blind, Placebo-controlled Trial of Certolizumab Pegol in Women with Refractory Interstitial Cystitis/Bladder Pain Syndrome. Eur. Urol. 2018, 74, 623–630. [Google Scholar] [CrossRef]
- Van De Merwe, J.P. Interstitial cystitis and systemic autoimmune diseases. Nat. Clin. Pr. Urol. 2007, 4, 484–491. [Google Scholar] [CrossRef]
- Van De Merwe, J.P.; Yamada, T.; Sakamoto, Y. Systemic aspects of interstitial cystitis, immunology and linkage with autoimmune disorders. Int. J. Urol. 2003, 10, S35–S38. [Google Scholar] [CrossRef]
- Jhang, J.-F.; Hsu, Y.-H.; Peng, C.-W.; Jiang, Y.-H.; Ho, H.-C.; Kuo, H.-C. Epstein-Barr Virus as a Potential Etiology of Persistent Bladder Inflammation in Human Interstitial Cystitis/Bladder Pain Syndrome. J. Urol. 2018, 200, 590–596. [Google Scholar] [CrossRef]
- Lee, C.-K.; Tsai, C.-P.; Liao, T.-L.; Huang, W.-N.; Chen, Y.-M.; Lin, C.-H.; Chen, Y.-M. Overactive bladder and bladder pain syndrome/interstitial cystitis in primary Sjögren’s syndrome patients: A nationwide population-based study. PLoS ONE 2019, 14, e0225455. [Google Scholar] [CrossRef] [Green Version]
- Akiyama, Y.; Maeda, D.; Morikawa, T.; Niimi, A.; Nomiya, A.; Yamada, Y.; Igawa, Y.; Goto, A.; Fukayama, M.; Homma, Y. Digital quantitative analysis of mast cell infiltration in interstitial cystitis. Neurourol. Urodyn. 2017, 37, 650–657. [Google Scholar] [CrossRef] [Green Version]
- Chen, M.C.; Keshavan, P.; Gregory, G.D.; Klumpp, D.J. RANTES mediates TNF-dependent lamina propria mast cell accumulation and barrier dysfunction in neurogenic cystitis. Am. J. Physiol. Physiol. 2007, 292, F1372–F1379. [Google Scholar] [CrossRef] [PubMed]
- Sant, G.R.; Kempuraj, D.; Marchand, J.E.; Theoharides, T.C. The Mast Cell in Interstitial Cystitis: Role in Pathophysiology and Pathogenesis. Urology 2007, 69, S34–S40. [Google Scholar] [CrossRef] [PubMed]
- Jhang, J.-F.; Kuo, H.-C. Pathomechanism of Interstitial Cystitis/Bladder Pain Syndrome and Mapping the Heterogeneity of Disease. Int. Neurourol. J. 2016, 20, S95–S104. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Inclusion Criteria |
Persistent pelvic pain related to the bladder |
Pain worsening with bladder filling |
Duration of symptoms longer than 6 weeks |
Presence of Hunner lesions and glomerulation in cystoscopic finding |
Exclusion Criteria |
Untreated UTI, STD, or urinary stone |
Any defined neurological disease affecting the pelvic nerve |
History of endometriosis |
Urethral diverticulum |
Suspicious DRE or PSA ≥2.5 ng/mL |
Gene Symbol | Direction | Sequence |
---|---|---|
GADPH | Forward | GTC TCC TCT GAC TTC AAC AGC G |
Reverse | ACC ACC CTG TTG CTG TAG CCA A | |
CD38 | Forward | CAG ACT GGA GAA AGG ACT GC |
Reverse | TTT ACT GCG GGA TCC ATT GAG | |
CD5 | Forward | CGA GTT CTT GCC CTC CTT TGC T |
Reverse | TCC TGG CTG AAG AGC TGT CAC A | |
IL7R | Forward | ATC GCA GCA CTC ACT GAC CTG T |
Reverse | TCA GGC ACT TTA CCT CCA CGA G | |
ITGAL | Forward | CTG CTT TTG CCA GCC TCT CTG T |
Reverse | GCT CAC AGG TAT CTG GCT ATG G | |
KLRB1 | Forward | GTT CCA CCA AAG AAT CCA GCC TG |
Reverse | AAG AGC CGT TTA TCC ACT TCC AG | |
PSMB9 | Forward | CGA GAG GAC TTG TCT GCA CAT C |
Reverse | CAC CAA TGG CAA AAG GCT GTC G |
No. | Sex | Age | VAS Score | ICSI Score | ICPI Score | PUF Symptom Score | PUF Bother Score | Symptom Duration (months) |
---|---|---|---|---|---|---|---|---|
Non-IC/BPS 1 | M | 73 | 0 | 0 | 0 | 0 | 0 | 0 |
Non-IC/BPS 2 | M | 73 | 0 | 0 | 0 | 0 | 0 | 0 |
Non-IC/BPS 3 | M | 73 | 0 | 0 | 0 | 0 | 0 | 0 |
Non-IC/BPS 4 | M | 72 | 0 | 0 | 0 | 0 | 0 | 0 |
Non-IC/BPS 5 | M | 72 | 0 | 0 | 0 | 0 | 0 | 0 |
IC/BPS 1 | M | 26 | 8 | 18 | 18 | 22 | 12 | 24 |
IC/BPS 2 | F | 47 | 10 | 20 | 20 | 22 | 15 | 30 |
IC/BPS 3 | M | 57 | 8 | 18 | 20 | 20 | 12 | 38 |
IC/BPS 4 | F | 73 | 10 | 20 | 20 | 20 | 15 | 36 |
IC/BPS 5 | F | 74 | 10 | 18 | 20 | 22 | 15 | 26 |
IC/BPS 6 | F | 72 | 8 | 16 | 20 | 20 | 15 | 30 |
IC/BPS 7 | F | 70 | 8 | 20 | 20 | 28 | 15 | 30 |
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Saha, S.K.; Jeon, T.-I.; Jang, S.B.; Kim, S.J.; Lim, K.M.; Choi, Y.J.; Kim, H.G.; Kim, A.; Cho, S.-G. Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion. J. Clin. Med. 2020, 9, 1935. https://doi.org/10.3390/jcm9061935
Saha SK, Jeon T-I, Jang SB, Kim SJ, Lim KM, Choi YJ, Kim HG, Kim A, Cho S-G. Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion. Journal of Clinical Medicine. 2020; 9(6):1935. https://doi.org/10.3390/jcm9061935
Chicago/Turabian StyleSaha, Subbroto Kumar, Tak-Il Jeon, Soo Bin Jang, Se Jong Kim, Kyung Min Lim, Yu Jin Choi, Hyeong Gon Kim, Aram Kim, and Ssang-Goo Cho. 2020. "Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion" Journal of Clinical Medicine 9, no. 6: 1935. https://doi.org/10.3390/jcm9061935