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Identification of Potential Biomarkers for Abdominal Pain in IBS Patients by Bioinformatics Approach

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Identification of Potential Biomarkers for Abdominal Pain in IBS Patients by Bioinformatics Approach Lin et al. BMC Gastroenterol (2021) 21:48 https://doi.org/10.1186/s12876-021-01626-7 RESEARCH ARTICLE Open Access Identifcation of potential biomarkers for abdominal pain in IBS patients by bioinformatics approach Zhongyuan Lin1†, Yimin Wang2†, Shiqing Lin1, Decheng Liu1, Guohui Mo1, Hui Zhang2* and Yunling Dou1* Abstract Background: Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disease characterized by chronic abdominal discomfort and pain. The mechanisms of abdominal pain, as a relevant symptom, in IBS are still unclear. We aimed to explore the key genes and neurobiological changes specially involved in abdominal pain in IBS. Methods: Gene expression data (GSE36701) was downloaded from Gene Expression Omnibus database. Fifty-three rectal mucosa samples from 27 irritable bowel syndrome with diarrhea (IBS-D) patients and 40 samples from 21 healthy volunteers as controls were included. Diferentially expressed genes (DEGs) between two groups were identi- fed using the GEO2R online tool. Functional enrichment analysis of DEGs was performed on the DAVID database. Then a protein–protein interaction network was constructed and visualized using STRING database and Cytoscape. Results: The microarray analysis demonstrated a subset of genes (CCKBR, CCL13, ACPP, BDKRB2, GRPR, SLC1A2, NPFF, P2RX4, TRPA1, CCKBR, TLX2, MRGPRX3, PAX2, CXCR1) specially involved in pain transmission. Among these genes, we identifed GRPR, NPFF and TRPA1 genes as potential biomarkers for irritating abdominal pain of IBS patients. Conclusions: Overexpression of certain pain-related genes (GRPR, NPFF and TRPA1) may contribute to chronic visceral hypersensitivity, therefore be partly responsible for recurrent abdominal pain or discomfort in IBS patients. Several synapses modifcation and biological process of psychological distress may be risk factors of IBS. Keywords: Bioinformatics analysis, Biomarker, Visceral hypersensitivity, Abdominal pain, Irritable bowel syndrome Background Abdominal pain in IBS is thought to be secondary to Chronic abdominal pain is an important symptom of visceral hypersensitivity (VH), which has been described irritable bowel syndrome (IBS), which afects 3.8–9.2% as low thresholds of stimuli perception arising from the of the global population [1]. Recurrent abdominal pain gut [3]. Visceral hypersensitivity is characterized by two can substantially reduce quality of life in IBS patients components: allodynia, a painful response to stimuli that and there is no efective and standard treatment cur- are normally not painful and hyperalgesia, an enhanced rently [2]. In order to identify new therapies, it is impor- response to a painful stimulus [4]. Te underlying patho- tant to understand the underlying mechanism of chronic genesis that lead to VH in patients who have IBS is not abdominal pain. fully understood. However, the prevailing viewpoint in the pathogenesis involves psychosocial factors, subtle *Correspondence: [email protected]; [email protected] infammation and alteration in the neuronal excitability †Zhongyuan Lin and Yimin Wang have contributed equally to this work of gut sensory pathways, which is responsible for trans- 1 Department of Anesthesiology, The First Afliated Hospital of Sun Yat- sen University, Guangzhou 510000, Guangdong, China mitting nociceptive information from the periphery to 2 Department of Anesthesiology, Guangdong Second Provincial General the central nervous system [5]. Specifc changes of a vari- Hospital, Guangzhou 510000, Guangdong, China ety of receptors and ion channels both in the expression © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Lin et al. BMC Gastroenterol (2021) 21:48 Page 2 of 8 and function have been documented in visceral pain con- Hochberg false discovery rate method for adjustment of ditions relevant to irritable bowel syndrome. Researches the P values. In our study, DEGs between healthy volun- have shown genetic factors may play a role in those teers and IBS-D patients were screened and selected by specifc changes in IBS [6]. Beyder and colleagues have the cut-of point of FC ≥ 1.2 and P value < 0.05. reported that a mutation of the SCN5A-encoded voltage- gated sodium channel, type V (alpha subunit) was asso- Functional enrichment analysis ciated with abdominal pain [7]. Other investigators have Te selected DEGs were submitted to the Database for investigated genetic changes related to enteric infection, Annotation, Visualization, and Integrated Discovery epithelial barrier function and immune regulation, sero- (DAVID) for further analysis. Te DAVID database, ver- tonin signaling, cannabinoid receptors, and bile acid syn- sion 6.8 Beta (https ://david -d.ncifc rf.gov/), ofers biologi- thesis, with varying results [8]. cal function annotation for researchers [9]. In this study, Bioinformatics analysis provides tools to produce over- Gene Ontology (GO) analysis and Te Kyoto Encyclope- views of genetic networks and potential biological path- dia of Genes and Genomes (KEGG) pathways of DEGs ways based on large-scale information. Tis study aimed were obtained from the DAVID database. Te biologi- to explore the molecular mechanisms specially involved cal processes and pathways might contribute to verify in pain transmission underlying IBS and to identify hub the signifcative DEGs and to IBS treatments. Functional genes and potential pathways associated with the patho- annotation analysis was performed by two-sided hyper- genesis of IBS. geometric test and Benjamini and Hochberg meth- ods was applied for multiple testing correction. Min. Methods Count ≥ 2 and P value < 0.05 was chosen as the threshold. Microarray data search and selection of eligible data set Te microarray data of GSE36701 was downloaded from Protein–protein interaction (PPI) analysis the GEO database (www.ncbi.nlm.nih.gov/geo/) with Ten we constructed PPI network of DEGs from Search its microarray platform as GPL570 (Afymetrix Human Tool for the Retrieval of Interacting Genes (STRING, Genome U133 Plus 2.0 Array). In this microarray, 53 http://strin g-db.org/) [10]. STRING is a public database samples of rectal mucosa from 27 IBS-D patients with of known and predicted protein–protein interactions. In obvious abdominal pain were obtained and 40 samples this study, we selected confdence score > 0.4 as a thresh- from 21 healthy volunteers as controls. Subjects com- old to construct the PPI network. Te combined score pleted a Talley IBS symptom questionnaire modifed is calculated by combining the probabilities from the to include days with pain. IBS was diagnosed according diferent evidence channels, including high throughput to the Rome II criteria. Tose with IBS also completed experimental data and literature, and corrected for the IBS quality of life questionnaire and the IBS Symptom probability of randomly observing an association [11]. Severity Score Questionnaire including severity of vis- Ten, the list of PPI pairs was downloaded for further ceral pain. Tose agreeing to take part underwent sig- analysis. Module clustering analysis for the network was moidoscopy without bowel preparation. Two biopsies then performed to identify the potential functional mod- from each donor were obtained using endoscopic biopsy ules in the network, using the Molecular Complex Detec- forceps and the mRNA were extracted for further analy- tion (MCODE 1.6.1) in Cytoscape 3.7.1 plugin [12, 13]. sis. After RNA extraction and Microarray processing, Te degree cut-of value to 2 and the node score cut-of samples without visible 18S and 28S rRNA peaks were to 0.2 were set as criteria in the MCODE process. excluded. Tere was one donor in IBS-D group and two donors in HV group only obtained one microarray data. Results Details of clinical data collection, RNA extraction and Screening and prioritization for DEGs microarray processing can be found in GSE36701 dataset An available Expression profiling data set (GSE36701) citation (https ://www.ncbi.nlm.nih.gov/geo/query /acc. in NCBI was selected in this study to identify differ- cgi?acc=GSE36 701). entially expressed genes in the comparisons between IBS-D patients and the healthy volunteers. Then the DEGs’ screening differentially expressed genes were further filtered Te expression profles were expressed as FC (fold for functional associations with neurotransmitters/ change) to produce a normally distributed variable. We mediators of pain. Each array was normalized by screened out DEGs using the online tool GEO2R/R, quantile, and then the DEGs
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