Genome-based expression profiles as a single standardized microarray platform for the diagnosis of experimental interstitial cystitis: an array of 75 genes model

Integrating single-cell RNA sequencing with spatial transcriptomics reveals immune landscape for interstitial cystitis

Interstitial cystitis (IC) is a severely debilitating and chronic disorder with unclear etiology and pathophysiology, which makes the diagnosis difficult and treatment challenging. To investigate the role of immunity in IC bladders, we sequenced 135,091 CD45⁺ immune cells from 15 female patients with IC and 9 controls with stress urinary incontinence using single-cell RNA sequencing (scRNA-seq). 22 immune subpopulations were identified in the constructed landscape. Among them, M2-like macrophages, inflammatory CD14⁺ macrophages, and conventional dendritic cells had the most communications with other immune cells. Then, a significant increase of central memory CD4⁺ T cells, regulatory T cells, GZMK⁺CD8⁺ T cells, activated B cells, un-switched memory B cells, and neutrophils, and a significant decrease of CD8⁺ effector T cells, Th17 cells, follicular helper T cells, switched memory B cells, transitional B cells, and macrophages were noted in IC bladders. The enrichment analysis identified a virus-related response during the dynamic change of cell proportion, furthermore, the human polyomavirus-2 was detected with a positive rate of 95% in urine of patients with IC. By integrating the results of scRNA-seq with spatial transcriptomics, we found nearly all immune subpopulations were enriched in the urothelial region or located close to fibroblasts in IC bladders, but they were discovered around urothelium and smooth muscle cells in control bladders. These findings depict the immune landscape for IC and might provide valuable insights into the pathophysiology of IC.

Neuropilins: expression and roles in the epithelium

Initially found expressed in neuronal and then later in endothelial cells, it is well established that the transmembrane glycoproteins neuropilin-1 (NRP1) and neuropilin-2 (NRP2) play essential roles in axonal growth and guidance and in physiological and pathological angiogenesis. Neuropilin expression and function in epithelial cells has received little attention when compared with neuronal and endothelial cells. Overexpression of NRPs is shown to enhance growth, correlate with invasion and is associated with poor prognosis in various tumour types, especially those of epithelial origin. The contribution of NRP and its ligands to tumour growth and metastasis has spurred a strong interest in NRPs as novel chemotherapy drug targets. Given NRP's role as a multifunctional co-receptor with an ability to bind with disparate ligand families, this has sparked new areas of research implicating NRPs in diverse biological functions. Here, we review the growing body of research demonstrating NRP expression and role in the normal and neoplastic epithelium.

Genome-based expression profiling study of Hunner's ulcer type interstitial cystitis: an array of 40-gene model

INTRODUCTION AND HYPOTHESIS

The aim of this study was to explore potential molecular mechanisms contributing to the pathogenesis of Hunner's ulcer type interstitial cystitis (IC).

METHODS

Dataset acquisitions from Gene Expression Omnibus under platform accession no GSE 11783. We compared global gene expression profiles in bladder epithelial cells from IC patients with Hunner's ulcer corresponding to normal controls. We re-sampling and exploit the correlation structure presented in the dataset through the transcriptional response. For each patient, two bladder biopsies were studied, one from an ulcer area and one from a non-ulcer area. RNA was extracted, and all labeled samples were hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix, CA, USA).

RESULTS

The Mahalanobis distance in hierarchical cluster analysis revealed a model of 40 genes expression which is increased in IC and ulcerated IC. Our results can be summarized as follows: First, the expressions of major histocompatibility complex (MHC) class IF and II molecules, leukocyte immunoglobulin-like receptors, hepatitis A virus cellular receptor 2, and interleukin 32 were increased in bladder epithelial from IC and ulcerative IC area. Next, there is an indication of antigen-mediated aggregation of the high-affinity Fc epsilon and gamma RI leading to allergic inflammation through the disease status. Third, the high-affinity Fc gamma RI subunit facilitated T-cell-mediated immune response through the disease status. Such changes, jointly termed "bladder remodeling," can constitute an important long-term consequence of Hunner's ulcer type IC.

CONCLUSIONS

Our results indicate that genome-based expression profiling can be used for the diagnostic tests of Hunner's ulcer type IC in clinical practice.

Genome-based expression profiling study following spinal cord injury in the rat: An array of 48-gene model

AIM

To explore the potential molecular mechanisms underlying experimental neurogenic bladder dysfunction.

METHODS

With the aid of Affymetrix GeneChip Rat Genome U34A arrays, we examined microarray gene expression profiles in bladder wall tissue from female Sprague-Dawley rats within the first 3 weeks following spinal cord injury. Gene transcripts expressed in rat bladder wall tissue at 3 days, 7 days, and 3 weeks following spinal cord injury were compared to normal rat bladder wall tissue.

RESULTS

The Mahalanobis distance in hierarchical cluster analysis revealed a 48-gene model, which contained high expressions in rat bladder wall tissue at 3 days, 7 days, and 3 weeks following spinal cord injury. According to gene ontology, plausible molecular alterations in rat bladder wall tissue following spinal cord injury include: (1) the release of nerve growth factor (NGF) and transforming growth factor beta 1 (Tgfb1) (2) the secretion of histamine from mast cells, (3) the occurrence of blood coagulation, (4) the occurrence of N-terminal protein myristoylation, and (5) Axon guidance mediated by Ena/Vasodilator-stimulated phosphoprotein (Ena/VASP) promotes reestablishment of the bladder reflex following spinal cord injury. Such changes, jointly termed "bladder remodeling," can constitute an important long-term consequence of neurogenic bladder dysfunction.

CONCLUSION

The success of this innovation has supported the use of microarray-based expression profiling as a commonplace platform for the pathogenesis and therapeutic interventions of experimental neurogenic bladder dysfunction. dysfunction.