Bioinformatics analysis of the Hub genes and key pathways of interstitial cystitis pathogenesis

An integrated machine learning framework for developing and validating a diagnostic model of major depressive disorder based on interstitial cystitis-related genes

BACKGROUND

Major depressive disorder (MDD) and interstitial cystitis (IC) are two highly debilitating conditions that often coexist with reciprocal effect, significantly exacerbating patients' suffering. However, the molecular underpinnings linking these disorders remain poorly understood.

METHODS

Transcriptomic data from GEO datasets including those of MDD and IC patients was systematically analyzed to develop and validate our model. Following removal of batch effect, differentially expressed genes (DEGs) between respective disease and control groups were identified. Shared DEGs of the conditions then underwent functional enrichment analyses. Additionally, immune infiltration analysis was quantified through ssGSEA. A diagnostic model for MDD was constructed by exploring 113 combinations of 12 machine learning algorithms with 10-fold cross-validation on the training sets following by external validation on test sets. Finally, the "Enrichr" platform was utilized to identify potential drugs for MDD.

RESULTS

Totally, 21 key genes closely associated with both MDD and IC were identified, predominantly involved in immune processes based on enrichment analyses. Immune infiltration analysis revealed distinct profiles of immune cell infiltration in MDD and IC compared to healthy controls. From these genes, a robust 11-gene (ABCD2, ATP8B4, TNNT1, AKR1C3, SLC26A8, S100A12, PTX3, FAM3B, ITGA2B, OLFM4, BCL7A) diagnostic signature was constructed, which exhibited superior performance over existing MDD diagnostic models both in training and testing cohorts. Additionally, epigallocatechin gallate and 10 other drugs emerged as potential targets for MDD.

CONCLUSION

Our work developed a diagnostic model for MDD employing a combination of bioinformatic techniques and machine learning methods, focusing on shared genes between MDD and IC.

Defining Molecular Treatment Targets for Bladder Pain Syndrome/Interstitial Cystitis: Uncovering Adhesion Molecules

Bladder pain syndrome/interstitial cystitis (BPS/IC) is a debilitating pain syndrome of unknown etiology that predominantly affects females. Clinically, BPS/IC presents in a wide spectrum where all patients report severe bladder pain together with one or more urinary tract symptoms. On bladder examination, some have normal-appearing bladders on cystoscopy, whereas others may have severely inflamed bladder walls with easily bleeding areas (glomerulations) and ulcerations (Hunner’s lesion). Thus, the reported prevalence of BPS/IC is also highly variable, between 0.06% and 30%. Nevertheless, it is rightly defined as a rare disease (ORPHA:37202). The aetiopathogenesis of BPS/IC remains largely unknown. Current treatment is mainly symptomatic and palliative, which certainly adds to the suffering of patients. BPS/IC is known to have a genetic component. However, the genes responsible are not defined yet. In addition to traditional genetic approaches, novel research methodologies involving bioinformatics are evaluated to elucidate the genetic basis of BPS/IC. This article aims to review the current evidence on the genetic basis of BPS/IC to determine the most promising targets for possible novel treatments.

[Interstitial cystitis: the latest findings on its aetiopathogenesis]

New findings provide progress in the understanding of the complicated aetiopathogenesis of interstitial cystitis/bladder pain syndrome (IC/BPS), whose causalities have only been deciphered in fragments so far. An increasingly complex network of pathomechanisms is emerging, in which the frequently mentioned mast cells and urothelial changes seem to be only a fragment of the pathological changes. The latest findings regarding a possible genetic and epigenetic predisposition are based on pedigree analyses, detection of single nucleotide polymorphisms and significant changes in differentially expressed genes. Multiple alterations can be detected at the molecular level. Platelet-activating factor, VEGF, corticotropin-releasing hormone and the inflammasome are important players in understanding the disease, but the pathomechanism underlying the "activation" of IC remains unclear. New starting points could be the detection of viruses (Epstein-Barr virus, BK polyomaviruses) or bacterial inflammation by pathogens that cannot be detected in standard cultures.

Biomarkers in the Light of the Etiopathology of IC/BPS

In this review, we focused on putatively interesting biomarkers of interstitial cystitis/bladder pain syndrome (IC/BPS) in relation to the etiopathology of this disease. Since its etiopathology is still under discussion, the development of novel biomarkers is critical for the correct classification of the patients in order to open personalized treatment options, on the one hand, and to separate true IC/BPS from the numerous confusable diseases with comparable symptom spectra on the other hand. There is growing evidence supporting the notion that the classical or Hunner-type IC (HIC) and the non-Hunner-type IC (NHIC) are different diseases with different etiopathologies and different pathophysiology at the full-blown state. While genetic alterations indicate close relationship to allergic and autoimmune diseases, at present, the genetic origin of IC/BPS could be identified. Disturbed angiogenesis and impairment of the microvessels could be linked to altered humoral signaling cascades leading to enhanced VEGF levels which in turn could enhance leucocyte and mast cell invasion. Recurrent or chronic urinary tract infection has been speculated to promote IC/BPS. New findings show that occult virus infections occurred in most IC/BPS patients and that the urinary microbiome was altered, supporting the hypothesis of infections as major players in IC/BPS. Environmental and nutritional factors may also influence IC/BPS, at least at a late state (e.g., cigarette smoking can enhance IC/BPS symptoms). The damage of the urothelial barrier could possibly be the result of many different causality chains and mark the final state of IC/BPS, the causes of this development having been introduced years ago. We conclude that the etiopathology of IC/BPS is complex, involving regulatory mechanisms at various levels. However, using novel molecular biologic techniques promise more sophisticated analysis of this pathophysiological network, resulting in a constantly improvement of our understanding of IC/BPS and related diseases.

Identification of key genes in human urothelial cells corresponding to interstitial cystitis/bladder pain syndrome in a lipopolysaccharide-induced cystitis model

AIMS

The cellular functions of bladder urothelial cells in interstitial cystitis/bladder pain syndrome (IC/BPS) have not been well revealed and understood. Thus, the study aims to identify key genes and significant pathways in urothelium corresponding to IC/BPS in a lipopolysaccharide (LPS)-induced cystitis model and provide novel clues related to diagnosis and treatment of IC/BPS.

METHODS

Human urothelial cells (HUCs) were incubated with LPS (50 μg/ml for 24 h). Microarray was applied to analyze the differentially expressed genes (DEGs) between HUCs under LPS treatment and the control group. DEGs in the two groups were identified and then used for enrichment analysis. Subsequently, protein-protein interaction (PPI) network based on DEGs was constructed. Lastly, the top five key genes were identified through the Cytoscape (version 3.7.2) using the "Clustering Coefficient" algorithm.

RESULTS

One hundred and seventy-one DEGs (96 upregulated genes and 75 downregulated genes) were identified between the LPS treatment and control group. The established PPI network was composed of 169 nodes and 678 edges. Moreover, C19orf33, TRIM31, MUC21, ELF3, and IFI27 were identified as hub genes in the PPI network. Subsequently, a statistically increased expression level of TRIM31 and ELF3 was validated by real-time quantitative-polymerase chain reaction and immunohistochemistry in bladder tissues from 20 patients with IC/BPS.

CONCLUSIONS

TRIM31 and ELF3 may be the two hub genes in urothelium corresponding to IC/BPS. More studies are warranted to further validate the findings. The identified marker genes may be useful targets for further studies to develop diagnostic tools and more effective therapies for a broader group of women with IC/PBS.