Identification of miRNA Signature Associated With Erectile Dysfunction in Type 2 Diabetes Mellitus by Support Vector Machine-Recursive Feature Elimination

Comprehensive analysis of biological landscape of oxidative stress-related genes in diabetic erectile dysfunction

Oxidative stress plays a pivotal role in the pathogenesis of diabetic erectile dysfunction, while specific mechanisms have not been illuminated. The study aims to reveal the genetic expression patterns of oxidative stress in diabetic erectile dysfunction. Transcriptome data of diabetic erectile dysfunction and oxidative stress-related genes (OSRGs) in the Gene Expression Omnibus database were downloaded and analyzed based on differential expression. Functional enrichment analyses were conducted to clarify the biological functions. A protein interaction framework was established, and significant gene profiles were validated in the cavernous endothelial cells, clinical patients, and rat models. A miRNA-OSRGs network was predicted and validated. The results were analyzed using Student's t-test. The analysis screened 203 differentially expressed OSRGs (p < 0.05), which had a close association with oxidoreductase activities, glutathione metabolism, and autophagy. A four-gene signature comprised of EPS8L2 (p = 0.044), GSTA3 (p = 0.015), LOX (p < 0.001) and MGST1 (p = 0.002) was well validated and regarded as the hub OSRGs. Compared with the control group, notable increases and decreases were observed in the expressions of GSTA3 (3.683 ± 0.636 vs. 0.416 ± 0.507) and LOX (2.104 ± 1.895 vs. 18.804 ± 2.751) in the validated diabetic erectile dysfunction group. The hub OSRGs-related miRNAs participated in smooth muscle cell proliferation. Besides, miR-125a-3p (p = 0.034) and miR-138-2-3p (p = 0.012) were validated as promising oxidative stress-related miRNA biomarkers. Our findings revealed the genetic alternations of oxidative stress in diabetic erectile dysfunction. These results will be instructive to explore the molecular landscape and the potential treatment for diabetic erectile dysfunction.

Uncovering the genetic links of diabetic erectile dysfunction and chronic prostatitis/chronic pelvic pain syndrome

Background: Clinical associations between erectile dysfunction and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) have been noticed, but the common pathogenic mechanisms between them remain elusive. The aim of the study was to mine shared genetic alterations between ED and chronic prostatitis/chronic pelvic pain syndrome. Method: Transcriptome data of ED and chronic prostatitis/chronic pelvic pain syndrome-related genes (CPRGs) were retrieved from relevant databases and differentially expressed analysis was used to obtain significant CPRGs. Then function enrichment and interaction analyses were performed to show shared transcriptional signature, including gene ontology and pathway enrichment, the construction of protein-protein interaction (PPI) network, cluster analysis, and co-expression analysis. Hub CPRGs and key cross-link were selected by validating these genes in clinical samples, chronic prostatitis/chronic pelvic pain syndrome and ED-related datasets. Then the miRNA-OSRGs co-regulatory network was predicted and validated. Subpopulation distribution and disease association of hub CPRGs were further identified. Result: Differentially expressed analysis revealed 363 significant CPRGs between ED and chronic prostatitis/chronic pelvic pain syndrome, functioning in inflammatory reaction, oxidative stress, apoptosis, smooth muscle cell proliferation, and extracellular matrix organization. A PPI network containing 245 nodes and 504 interactions was constructed. Module analysis depicted that multicellular organismal process and immune metabolic process were enriched. 17 genes were screened in PPI via topological algorithms, and reactive oxygen species as well as interleukin-1 metabolism were regarded as the bridging interactive mechanism. After screening and validation, a hub-CPRG signature consisting of COL1A1, MAPK6, LPL, NFE2L2 and NQO1 were identified and associated miRNA were verified. These miRNAs played an important role in immune and inflammatory response likewise. Finally, NQO1 was identified as a key genetic link between ED and chronic prostatitis/chronic pelvic pain syndrome. It was predominately enriched in corpus cavernosum endothelial cell, and correlated with other male urogenital and immune system diseases tightly. Conclusion: We identified the genetic profiles as well as corresponding regulatory network underlying interaction between ED and chronic prostatitis/chronic pelvic pain syndrome via multi-omics analysis. These findings expanded a new understanding for the molecular mechanism of ED with chronic prostatitis/chronic pelvic pain syndrome.

Combination of machine learning-based bulk and single-cell genomics reveals necroptosis-related molecular subtypes and immunological features in autism spectrum disorder

Background

Necroptosis is a novel form of controlled cell death that contributes to the progression of various illnesses. Nonetheless, the function and significance of necroptosis in autism spectrum disorders (ASD) remain unknown and require further investigation.

Methods

We utilized single-nucleus RNA sequencing (snRNA-seq) data to assess the expression patterns of necroptosis in children with autism spectrum disorder (ASD) based on 159 necroptosis-related genes. We identified differentially expressed NRGs and used an unsupervised clustering approach to divide ASD children into distinct molecular subgroups. We also evaluated immunological infiltrations and immune checkpoints using the CIBERSORT algorithm. Characteristic NRGs, identified by the LASSO, RF, and SVM-RFE algorithms, were utilized to construct a risk model. Moreover, functional enrichment, immune infiltration, and CMap analysis were further explored. Additionally, external validation was performed using RT-PCR analysis.

Results

Both snRNA-seq and bulk transcriptome data demonstrated a greater necroptosis score in ASD children. Among these cell subtypes, excitatory neurons, inhibitory neurons, and endothelials displayed the highest activity of necroptosis. Children with ASD were categorized into two subtypes of necroptosis, and subtype2 exhibited higher immune activity. Four characteristic NRGs (TICAM1, CASP1, CAPN1, and CHMP4A) identified using three machine learning algorithms could predict the onset of ASD. Nomograms, calibration curves, and decision curve analysis (DCA) based on 3-NRG have been shown to have clinical benefit in children with ASD. Furthermore, necroptosis-based riskScore was found to be positively associated with immune activation. Finally, RT-PCR demonstrated differentially expressed of these four NRGs in human peripheral blood samples.

Conclusion

A comprehensive identification of necroptosis may shed light on the underlying pathogenic process driving ASD onset. The classification of necroptosis subtypes and construction of a necroptosis-related risk model may yield significant insights for the individualized treatment of children with ASD.

Non-Coding RNAs: New Dawn for Diabetes Mellitus Induced Erectile Dysfunction

Erectile dysfunction (ED) is a common sexual dysfunction in males, with multifactorial alterations which consist of psychological and organic. Diabetes mellitus (DM) induced erectile dysfunction (DMED) is a disconcerting and critical complication of DM, and remarkably different from non-diabetic ED. The response rate of phosphodiesterase type 5 inhibitor (PDE5i), a milestone for ED therapy, is far from satisfactory in DMED. Unfortunately, the contributing mechanisms of DMED remains vague. Hence, It is urgent to seek for novel prospective biomarkers or targets of DMED. Numerous studies have proved that non-coding RNAs (ncRNAs) play essential roles in the pathogenesis process of DM, which comprise of long non-coding RNAs (lncRNAs) and small non-coding RNAs (sncRNAs) like microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and circular RNAs (circRNAs). However, the implications of ncRNAs in DMED are still understudied. This review highlights the pathophysiology of DMED, summarizes identified mechanisms of ncRNAs associated with DMED and covers the topic of perspectives for ncRNAs in DMED.