Identifying immune cell infiltration and effective diagnostic biomarkers in Crohn's disease by bioinformatics analysis

Phellodendrine ameliorates intestinal inflammation and protects mucosal barrier via modulating COL1A1, VCAM1 and IL-17 a

BACKGROUND

Phellodendrine (PHE) has anti-inflammatory and antioxidant effects. However, the function of PHE in treating inflammatory bowel disease (IBD) has not been fully elucidated. The aim of this study was to investigate the effects and mechanisms of PHE on IBD with in vivo and in vitro assays.

MATERIALS AND METHODS

Bioinformatics was used to identify hub genes associated with IBD pathogenesis. Virtual screening was applied to predicting the natrual compounds targeting hub genes. A mouse model with colitis was established by oral administration of 3 % dextran sulfate (DSS), and the mice were treated with normal saline or PHE (30 mg/kg/day or 80 mg/kg/day). On day 14, the mice were sacrificed and their colons were collected for measurement and histological analysis. The pathological change and inflammation of the tissues in different groups also were evaluated. In addition, the intestinal epithelial Caco-2 cell line was treated with lipopolysaccharide (LPS) to establish an in vitro intestinal inflammation model. CCK-8 assay and flow cytometry were used to detect the effects of PHE (10 μM or 40 μM) on cell viability and apoptosis. Western blot was used to the investigate the regulatory effects of PHE on the expression levels of zonula occludens 1 (ZO-1), occludin, claudin-1, collagen type I alpha 1 (COL1A1), vascular cell adhesion molecule 1 (VCAM1), interleukin-17 A (IL-17 A), phosphorylated AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR).

RESULTS

COL1A1 and VCAM1 were identified as therapeutic targets in IBD. PHE was identified as a natural drug simultaneously targeting COL1A1 and VCAM1. PHE treatment alleviates the weight loss and symptoms of mice induced by acute colitis. PHE treatment reduced myeloperoxidase (MPO) activity and pro-inflammatory cytokine levels in colonic tissues, and inhibited expression levels of COL1A1, VCAM1 and IL-17 A, and promoted expression levels of ZO-1, occludin and claudin-1. In vitro, PHE treatment also protected Caco-2 cells from LPS-induced inflammation, which was dependent on AMPK/mTOR pathway.

CONCLUSION

PHE ameliorates intestinal inflammation and intestinal barrier injury, probably via modulating COL1A1, VCAM1 and IL-17 A, and acting on AMPK/mTOR pathway. PHE may be a potential natural drug for IBD treatment.

Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn's disease by bioinformatics analysis and machine learning

Crohn's disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differentially expressed ubiquitination-related genes were identified by intersecting differentially expressed genes (DEGs) from the GSE95095 dataset in the Gene Expression Omnibus (GEO) database with a set of ubiquitination-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Key genes were selected by combining hub genes from the protein-protein interaction (PPI) network with feature genes identified by Lasso and Random Forest (RF) algorithms. Additionally, the correlation between key genes and immune infiltration was assessed, and Gene Set Enrichment Analysis (GSEA) of key genes was conducted. The efficacy of key genes was validated using ROC curves in an external dataset, and their expression was confirmed in LPS-induced Caco-2 cells through RT-qPCR. A total of 32 ubiquitination-related DEGs were identified, and two key genes (UBE2R2, NEDD4L) were selected. The infiltration of M2 macrophages was reduced in CD patients, with UBE2R2 expression negatively correlated and NEDD4L expression positively correlated with M2 macrophage infiltration. GSEA indicated that UBE2R2 was enriched in terpenoid backbone biosynthesis, regulation of autophagy, and limonene and pinene degradation, while NEDD4L was enriched in lysosome, Wnt signaling, and calcium signaling pathways. ROC curves demonstrated superior efficacy for NEDD4L. In LPS-induced Caco-2 cells, UBE2R2 expression increased, while NEDD4L expression decreased. A comprehensive analysis of the functional relationship between ubiquitination-related genes and CD can enhance understanding of CD pathogenesis and suggest potential therapeutic targets.

Exploring the mechanisms of chronic obstructive pulmonary disease and Crohn's disease: a bioinformatics-based study

This study explored the comorbid mechanisms between Crohn's disease (CD) and chronic obstructive pulmonary disease (COPD) using bioinformatics analysis. From the Gene Expression Omnibus (GEO) microarray dataset, 349 common differentially expressed genes (coDEGs) were identified, and 8 shared hub genes were found: CCL2, CXCL1, TLR2, ICAM1, PTPRC, ITGAX, PTGS2, and MMP9, which were vital for immune function and regulation of inflammatory responses. In addition, the study also analyzed the association between coDEGs and immune cell infiltration using the single-sample gene set enrichment algorithm (ssGSEA). Potential drugs related to these genes were identified using the connectivity map (CMap). These findings provided new perspectives for understanding the interaction between CD and COPD.

Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli

BACKGROUND

Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.

RESULTS

We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.

CONCLUSION

This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.

Key Disease-Related Genes and Immune Cell Infiltration Landscape in Inflammatory Bowel Disease: A Bioinformatics Investigation

Inflammatory Bowel Diseases (IBD), which encompass ulcerative colitis (UC) and Crohn's disease (CD), are characterized by chronic inflammation and tissue damage of the gastrointestinal tract. This study aimed to uncover novel disease-gene signatures, dysregulated pathways, and the immune cell infiltration landscape of inflamed tissues. Eight publicly available transcriptomic datasets, including inflamed and non-inflamed tissues from CD and UC patients were analyzed. Common differentially expressed genes (DEGs) were identified through meta-analysis, revealing 180 DEGs. DEGs were implicated in leukocyte transendothelial migration, PI3K-Akt, chemokine, NOD-like receptors, TNF signaling pathways, and pathways in cancer. Protein-protein interaction network and cluster analysis identified 14 central IBD players, which were validated using eight external datasets. Disease module construction using the NeDRex platform identified nine out of 14 disease-associated genes (CYBB, RAC2, GNAI2, ITGA4, CYBA, NCF4, CPT1A, NCF2, and PCK1). Immune infiltration profile assessment revealed a significantly higher degree of infiltration of neutrophils, activated dendritic cells, plasma cells, mast cells (resting/activated), B cells (memory/naïve), regulatory T cells, and M0 and M1 macrophages in inflamed IBD tissue. Collectively, this study identified the immune infiltration profile and nine disease-associated genes as potential modulators of IBD pathogenesis, offering insights into disease molecular mechanisms, and highlighting potential disease modulators and immune cell dynamics.

Food-Protein-Induced Proctocolitis in Pre-Term Newborns with Bloody Stools in a Neonatal Intensive Care Unit

The bloody stools of newborns may be a clue for several clinical entities of varying severity, ranging from idiopathic neonatal transient colitis to food-protein-induced allergic proctocolitis (FPIAP) or necrotizing enterocolitis (NEC). Distinguishing among them at an early stage is challenging but crucial, as the treatments and prognoses are different. We conducted a monocentric retrospective study including all pre-term infants with bloody stools admitted to the Neonatal Intensive Care Unit (NICU) of the Vittore Buzzi Children's Hospital (Milan) from December 2022 to May 2024. Patients diagnosed with NEC exhibited significantly lower eosinophil counts and higher procalcitonin levels than both patients with FPIAP and patients with idiopathic neonatal transient colitis, as well as a statistically significant increase in pathological features from abdomen ultrasounds and abdominal X-rays. In contrast, no lab markers or imaging techniques have been demonstrated to be useful in distinguishing between idiopathic neonatal transient colitis and FPIAP. Thus, after excluding a diagnosis of NEC, the only way to confirm FPIAP is through the oral food challenge, which can be performed in premature newborns presenting with bloody stools who are otherwise healthy and under medical supervision, in order to identify infants who may benefit from a cow's-milk-free diet.

Unveiling the Links Between Microbial Alteration and Host Gene Disarray in Crohn's Disease via TAHMC

A compelling correlation method linking microbial communities and host gene expression in tissues is currently absent. A novel pipeline is proposed, dubbed Transcriptome Analysis of Host-Microbiome Crosstalk (TAHMC), designed to concurrently restore both host gene expression and microbial quantification from bulk RNA-seq data. Employing this approach, it discerned associations between the tissue microbiome and host immunity in the context of Crohn's disease (CD). Further, machine learning is utilized to separately construct networks of associations among host mRNA, long non-coding RNA, and tissue microbes. Unique host genes and tissue microbes are extracted from these networks for potential utility in CD diagnosis. Experimental validation of the predicted host gene regulation by microbes from the association network is achieved through the co-culturing of Faecalibacterium prausnitzii with Caco-2 cells. Collectively, the TAHMC pipeline accurately recovers both host gene expression and microbial quantification from CD RNA-seq data, thereby illuminating potential causal links between shifts in microbial composition as well as diversity within CD mucosal tissues and aberrant host gene expression.

Intestinal strictures in Crohn's disease: An update from 2023

Crohn's disease (CD) is a chronic inflammatory disease that leads to intestinal stricture in nearly 35% of cases within 10 years of initial diagnosis. The unknown pathogenesis, lack of universally accepted criteria, and absence of an effective management approach remain unconquered challenges in structuring CD. The pathogenesis of stricturing CD involves intricate interactions between factors such as immune cell dysbiosis, fibroblast activation, and microecology imbalance. New techniques such as single-cell sequencing provide a fresh perspective. Non-invasive diagnostic tools such as serum biomarkers and novel cross-sectional imaging techniques offer a precise understanding of intestinal fibrostenosis. Here, we provide a timely and comprehensive review of the worthy advancements in intestinal strictures in 2023, aiming to dispense cutting-edge information regarding fibrosis and to build a cornerstone for researchers and clinicians to make greater progress in the field of intestinal strictures.

FPR1, as a Potential Biomarker of Diagnosis and Infliximab Therapy Responses for Crohn's Disease, is Related to Disease Activity, Inflammation and Macrophage Polarization

Purpose

Crohn's disease (CD) represents a multifaceted inflammatory gastrointestinal condition, with a profound significance placed on unraveling its molecular pathways to enhance both diagnostic capabilities and therapeutic interventions. This study focused on identifying a robust macrophage-related signatures (MacroSig) for diagnosing CD, emphasizing the role of FPR1 in macrophage polarization and its implications in CD.

Patients and Methods

Expression profiles from intestinal biopsies and macrophages of 1804 CD patients were retrieved from the Gene Expression Omnibus (GEO). Utilizing CIBERSORTx, differential expression analysis, and weighted correlation network analysis to to identify macrophage-related genes (MRGs). By unsupervised clustering, distinct clusters of CD were identified. Potential biomarkers were identified via using four machine learning algorithms, leading to the establishment of MacroSig which combines insights from 12 machine learning algorithms. Furthermore, the expression of FPR1 was verified in intestinal biopsies of CD patients and two murine experimental colitis models. Finally, we further explored the role of FPR1 in macrophage polarization through single-cell analysis as well as through the study of RAW264.7 cells and peritoneal macrophages.

Results

Two distinct clusters with differential levels of macrophage infiltration and inflammation were identified. The MacroSig, which included FPR1 and LILRB2, exhibited high diagnostic accuracy and outperformed existing biomarkers and signatures. Clinical analysis demonstrated a strong correlation of FPR1 with disease activity, endoscopic inflammation status, and response to infliximab treatment. The expression levels of FPR1 were validated in our CD cohort by immunohistochemistry and confirmed in two colitis mouse models. Single-cell analysis indicated that FPR1 is predominantly expressed in macrophages and monocytes. In vitro studies demonstrated that FPR1 was upregulated in M1 macrophages, and its activation promoted M1 polarization.

Conclusion

We developed a promising diagnostic signature for CD, and targeting FPR1 to modulate macrophage polarization may represent a novel therapeutic strategy.

Dendritic cells: the yin and yang in disease progression

Dendritic cells (DCs) are antigen presenting cells that link innate and adaptive immunity. DCs have been historically considered as the most effective and potent cell population to capture, process and present antigens to activate naïve T cells and originate favorable immune responses in many diseases, such as cancer. However, in the last decades, it has been observed that DCs not only promote beneficial responses, but also drive the initiation and progression of some pathologies, including inflammatory bowel disease (IBD). In line with those notions, different therapeutic approaches have been tested to enhance or impair the concentration and role of the different DC subsets. The blockade of inhibitory pathways to promote DCs or DC-based vaccines have been successfully assessed in cancer, whereas the targeting of DCs to inhibit their functionality has proved to be favorable in IBD. In this review, we (a) described the general role of DCs, (b) explained the DC subsets and their role in immunogenicity, (c) analyzed the role of DCs in cancer and therapeutic approaches to promote immunogenic DCs and (d) analyzed the role of DCs in IBD and therapeutic approaches to reduced DC-induced inflammation. Therefore, we aimed to highlight the "yin-yang" role of DCs to improve the understand of this type of cells in disease progression.