Integrated multiple microarray studies by robust rank aggregation to identify immune-associated biomarkers in Crohn's disease based on three machine learning methods

PFOS-Induced Perturbations in Trophoblast Functions through the Oip5os1/miR-155/Rnd3 Axis in PE

The widespread use of perfluorooctanesulfonic acid (PFOS) has raised concerns regarding its potential on pregnant women, particularly in relation to the development of pre-eclampsia (PE). This study investigates the impact of PFOS exposure on the LncRNA/Rnd3 axis in pregnant mice and its association with trophoblast cell functions in PE. Bioinformatics analysis revealed PFOS-related gene alterations in PE, with pathways enriched in apoptotic signaling and cytokine interactions. Experimental findings showed the downregulation of Oip5os1 and Rnd3, along with the upregulation of miR-155, affecting trophoblast behavior. Animal experiments confirmed that PFOS-induced gene expression changes are linked to PE progression. PFOS exposure impairs trophoblast proliferation and migration via the Oip5os1/miR-155/Rnd3 axis, contributing to PE development.

Identification and immune landscape of sarcopenia-related molecular clusters in inflammatory bowel disease by machine learning and integrated bioinformatics

Sarcopenia, a prevalent comorbidity of inflammatory bowel disease (IBD), is characterized by diminished skeletal muscle mass and strength. Nevertheless, the underlying interconnected mechanisms remain elusive. This study identified distinct expression patterns of sarcopenia-associated genes (SRGs) across individuals with IBD and in samples of normal tissue. By analyzing SRG expression profiles, we effectively segregated 541 IBD samples into three distinct clusters, each marked by its unique immune landscape. To unravel the transcriptional disruptions underlying these clusters, the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm was employed to spotlight key genes linked to each cluster. A diagnostic model based on four key genes (TIMP1, PLAU, PHLDA1, TGFBI) was established using Random Forest and LASSO (least absolute shrinkage and selection operator) algorithms, and validated with the GSE179285 dataset. Moreover, the GSE112366 dataset facilitated the exploration of gene expression dynamics within the ileum mucosa of UC patients pre- and post-Ustekinumab treatment. Additionally, insights into the intricate relationship between immune cells and these pivotal genes were gleaned from the single-cell RNA dataset GSE162335. In conclusion, our findings collectively underscored the pivotal role of sarcopenia-related genes in the pathogenesis of IBD. Their potential as robust biomarkers for future diagnostic and therapeutic strategies is particularly promising, opening avenues for a deeper understanding and improved management of these interconnected conditions.

Exploring potential biomarkers and therapeutic targets in inflammatory bowel disease: insights from a mega-analysis approach

Background

Understanding the molecular pathogenesis of inflammatory bowel disease (IBD) has led to the discovery of new therapeutic targets that are more specific and effective. Our aim was to explore the molecular pathways and genes involved in IBD pathogenesis and to identify new therapeutic targets and novel biomarkers that can aid in the diagnosis of the disease.

Methods

To obtain the largest possible number of samples and analyze them comprehensively, we used a mega-analysis approach. This involved reprocessing raw data from multiple studies and analyzing them using bioinformatic and machine learning techniques.

Results

We analyzed a total of 697 intestinal biopsies of Ulcerative Colitis (n = 386), Crohn's disease (n = 183) and non-IBD controls (n = 128). A machine learning analysis detected 34 genes whose collective expression effectively distinguishes inflamed biopsies of IBD patients from non-IBD control samples. Most of these genes were upregulated in IBD. Notably, among these genes, three novel lncRNAs have emerged as potential contributors to IBD development: ENSG00000285744, ENSG00000287626, and MIR4435-2HG. Furthermore, by examining the expression of 29 genes, among the 34, in blood samples from IBD patients, we detected a significant upregulation of 12 genes (p-value < 0.01), underscoring their potential utility as non-invasive diagnostic biomarkers. Finally, by utilizing the CMap library, we discovered potential compounds that should be explored in future studies for their therapeutic efficacy in IBD treatment.

Conclusion

Our findings contribute to the understanding of IBD pathogenesis, suggest novel biomarkers for IBD diagnosis and offer new prospects for therapeutic intervention.

The Prokineticin System in Inflammatory Bowel Diseases: A Clinical and Preclinical Overview

Inflammatory bowel disease (IBD) includes Crohn's disease (CD) and ulcerative colitis (UC), which are characterized by chronic inflammation of the gastrointestinal (GI) tract. IBDs clinical manifestations are heterogeneous and characterized by a chronic relapsing-remitting course. Typical gastrointestinal signs and symptoms include diarrhea, GI bleeding, weight loss, and abdominal pain. Moreover, the presence of pain often manifests in the remitting disease phase. As a result, patients report a further reduction in life quality. Despite the scientific advances implemented in the last two decades and the therapies aimed at inducing or maintaining IBDs in a remissive condition, to date, their pathophysiology still remains unknown. In this scenario, the importance of identifying a common and effective therapeutic target for both digestive symptoms and pain remains a priority. Recent clinical and preclinical studies have reported the prokineticin system (PKS) as an emerging therapeutic target for IBDs. PKS alterations are likely to play a role in IBDs at multiple levels, such as in intestinal motility, local inflammation, ulceration processes, localized abdominal and visceral pain, as well as central nervous system sensitization, leading to the development of chronic and widespread pain. This narrative review summarized the evidence about the involvement of the PKS in IBD and discussed its potential as a druggable target.

Characterization of prokineticin system in Crohn's disease pathophysiology and pain, and its modulation by alcohol abuse: A preclinical study

BACKGROUND

Crohn's disease-(CD) pathogenesis is still unknown and chronic pain is a frequent symptom in CD-patients. Identifying novel therapeutic targets and predisposing factors is a primary goal. In this regard, prokineticin system-(PKS) appears a promising target.

AIMS AND METHODS

TNBS-model was used. DAI, abdominal and visceral pain, and muscle strength were monitored. CD-mice were sacrificed at two times (day 7 and 14 after TNBS) in order to identify PKS involvement in CD pathophysiology and pain. PKS characterization was performed in mesenteric lymph nodes-(MLN), colon, myenteric plexus-(MP), dorsal root ganglia-(DRGs) and spinal cord-(SC). Inflammation/neuroinflammation was also assessed in the same tissues. In order to evaluate alcohol abuse as a possible trigger for CD and its effect on PKS activation, naïve mice were administered (oral-gavage) with ethanol for 10 consecutive days. PKS as well as inflammation/neuroinflammation were evaluated in MLN, colon and MP.

RESULTS

TNBS treated-mice showed a rapid increase in DAI, abdominal/visceral hypersensitivity and a progressive strength loss. In all tissue analysed of CD-mice, a quick and significant increase of mRNA of PKs and PKRs was observed, associated with an increase of pro-inflammatory cytokines (IL-1β, IL-6 and TNFα) and macrophage/glia markers (iba1, CD11b and GFAP) levels. In alcohol abuse model, ethanol induced in colon and MP a significant PKS activation accompanied by inflammation/neuroinflammation.

CONCLUSIONS

We can assume that PKS may be involved in CD development and pain. Furthermore, alcohol appears to activate PKS and may be a trigger factor for CD.