LncRNA-miRNA-mRNA Network Analysis Reveals the Potential Biomarkers in Crohn’s Disease Rats Treated with Herb-Partitioned Moxibustion

The role of long non-coding RNA in Crohn's disease

Emerging evidence has illuminated the pivotal role of long noncoding RNAs (lncRNAs) in orchestrating immunological functions and autoimmune responses. In the context of Crohn's disease (CD), an array of novel lncRNAs has been identified in the plasma and intestinal tissues of afflicted individuals, suggesting a dualistic influence on the disease progression, either exacerbating or mitigating its course. Current research has demonstrated the involvement of lncRNAs in competitive endogenous RNA, the inflammation process, epithelial barrier function, gut microbiota imbalance, and epigenetic regulation. This review aims to encapsulate the current knowledge on the lncRNA contribution to CD and underscore potential avenues for future research. LncRNAs are increasingly recognized as significant biomarkers and potential therapeutic targets, holding a key position in the pathogenesis of CD. Furthermore, the unique attributes of circulating lncRNAs, such as minimal side effects, combinational therapy potential, and personalized medicine, render them as promising therapeutic tools for individual health management in CD.

Moxibustion alleviates intestinal inflammation in ulcerative colitis rats by modulating long non-coding RNA LOC108352929 and inhibiting Phf11 expression

Long noncoding RNA (lncRNAs) are involved in the pathogenesis of ulcerative colitis (UC). Moxibustion, a traditional Chinese medicine, can improve symptoms in patients with UC and reduce intestinal inflammation in rats with UC. However, it remains unclear whether the ameliorative effect of moxibustion on intestinal mucosal inflammation in UC is related to lncRNAs. Thirty-two rats were randomly assigned to four groups: normal control, UC, moxibustion (MOX), and sulfasalazine (SASP). The UC rat model was induced by administering 4% dextran sulfate sodium (DSS) in drinking water. Rats in the moxibustion group underwent bilateral Tianshu (ST25) moxibustion using the herbs-partition moxibustion method. Rats in the sulfasalazine group received SASP solution via gavage twice daily for seven consecutive days. Our results revealed that, compared with the UC group [2.00 (1.00, 2.50)], the DAI score [0.25 (0.00, 0.50)] was significantly lower in the MOX group (P < 0.05). Compared with the UC group [13.00 (11.25, 14.00)], the histopathological score [5.50 (4.00, 7.75)] was significantly lower in the MOX group (P < 0.05). In addition, the CMDI and macroscopic scores were decreased in the MOX group (P < 0.05). Moxibustion significantly decreased the protein expression of inflammatory factors TNF-α, IFN-γ, and IL-1β in the colonic tissues of UC rats (P <0.05), thereby suppressing the inflammatory response. Moreover, moxibustion exerted a regulatory influence on colon lncRNA and mRNA expression profiles, upregulating LOC108352929 and downregulating Phf11 in rats with UC (P <0.05). Moxibustion also led to a reduction in the expression and colocalization of Phf11 and NF-κB in the colons of UC rats. Moreover, knockdown of LOC108352929 in rat enteric glial cells demonstrated a significant upregulation of TNF-α mRNA expression (P <0.05). In summary, these data illustrate that moxibustion effectively ameliorates DSS-induced colonic injury and inflammation while exerting regulatory control over the lncRNA-mRNA co-expression network in UC rats. Collectively, the in vivo and in vitro studies suggested that LOC108352929-Phf11 may serve as a potential biological marker for moxibustion in the treatment of UC.

CXCL8 as a Potential Biomarker for Crohn's Disease is Associated with Immune Infiltration and RNA Methylation

TRP channels have an important role in regulating the function of gastrointestinal epithelial cells. The aim of this study was to investigate the molecular mechanisms of genes associated with TRP channels in Crohn's disease (CD) by bioinformatics approach and to identify potential key biomarkers. In our study, we identified TRP channel-related differentially expressed genes (DEGs) based on the GSE95095 dataset and the TRP channel-related gene set from the GeneCards database. Hub genes (CXCL8, HIF1A, NGF, JUN, IL1A) were identified by the PPI network and validated by the external GSE52746 dataset. Immune infiltration analysis revealed that CXCL8 was significantly correlated with B cells memory, NK cells activated, Mast cells resting, Mast cells activated, and Neutrophils. GSEA of CXCL8 results showed inositol phosphate metabolism, RNA polymerase, propanoate metabolism, MAPK signaling pathway, base excision repair, and Calcium signaling pathway. In addition, we constructed a lncRNA-miRNA-mRNA ceRNA network and a drug-gene interaction network. Finally, we performed in vitro experiments to verify that LPS induced CXCL8 expression in HT-29 cells and that knockdown of CXCL8 inhibited the inflammatory stimulatory effects of LPS. This study reveals that CXCL8 plays an important role in the pathogenesis of Crohn's disease and is expected to be a novel biomarker.

The significance of long non-coding RNAs in the pathogenesis, diagnosis and treatment of inflammatory bowel disease

Inflammatory bowel diseases (IBD) are a group of chronic relapsing gastrointestinal inflammatory diseases with significant global incidence. Although the pathomechanism of IBD has been extensively investigated, several aspects of its pathogenesis remain unclear. Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides in length that have potential protein-coding functions. LncRNAs play important roles in biological processes such as epigenetic modification, transcriptional regulation and post-transcriptional regulation. In this review, we summarize recent advances in research on IBD-related lncRNAs from the perspective of the overall intestinal microenvironment, as well as their potential roles as immune regulators, diagnostic biomarkers and therapeutic targets or agents for IBD.

LncRNA-XR_002792574.1-mediated ceRNA network reveals potential biomarkers in myopia-induced retinal ganglion cell damage

BACKGROUND

Long noncoding RNAs (lncRNAs) play a key role in the occurrence and progression of myopia. However, the function of lncRNAs in retinal ganglion cells (RGCs) in the pathogenesis of myopia is still unknown. The aim of our study was to explore the lncRNA-mediated competing endogenous RNA (ceRNA) network in RGCs during the development of myopia.

METHODS

RNA sequencing was performed to analyze lncRNA and mRNA expression profiles in RGCs between guinea pigs with form-deprived myopia (FDM) and normal control guinea pigs, and related ceRNA networks were constructed. Then, potentially important genes in ceRNA networks were verified by qRT‒PCR, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore biological functions in the RGCs of FDM guinea pigs. The important genes and related signaling pathways were further verified by qRT‒PCR, immunohistochemistry, immunofluorescence and Western blot in myopia in FDM guinea pigs, FDM mice, and highly myopic adults.

RESULTS

The distribution of RGCs was uneven, the number of RGCs was decreased, and RGC apoptosis was increased in FDM guinea pigs. In total, 873 lncRNAs and 2480 mRNAs were determined to be differentially expressed genes in RGCs from normal control and FDM guinea pigs. Via lncRNA-mediated ceRNA network construction and PCR verification, we found that lncRNA-XR_002792574.1 may be involved in the development of myopia through the miR-760-3p/Adcy1 pathway in RGCs. Further verification in FDM guinea pigs, FDM mice, and highly myopic adults demonstrated that the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis in RGCs might be related to cGMP/PKG, the apelin signaling pathway and scleral remodeling.

CONCLUSION

We demonstrated that the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis in RGCs might be related to myopia. On the one hand, the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis might inhibit the cGMP/PKG and apelin signaling pathways in RGCs, thereby causing RGC damage in myopia. On the other hand, the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis may cause myopic scleral remodeling through the ERK-MMP-2 pathway. These findings may reveal novel potential targets in myopia and provide reference value for exploration and development of gene editing therapeutics for hereditary myopia.

Phosphatidylinositol 3-kinase signaling pathway and inflammatory bowel disease: Current status and future prospects

Inflammatory bowel disease (IBD) is a chronic life-limiting disease of gastrointestinal tract characterized by widespread enteric inflammation. IBD is a multifactorial disease, and different environmental, microbial, and immune-related factors give rise to the development of disease. Among several factors, the preponderance of pro-inflammatory T helper 17 cells over the anti-inflammatory regulatory T cells augments inflammation in the intestinal mucosa. Prevailing evidence accentuates that PI3K signaling pathway plays a central role in the pathophysiology of the condition by regulating the inflammatory process in the gut mucosa. By recognizing the implications of PI3K in the pathogenesis of IBD, agents that could modulate this pathway have recently been at the focus of research, yielding encouraging results mainly in the experimental IBD models. In this review, we have summarized the recent advances, which may hold the keys to identify novel therapeutic strategies for IBD.

Tempol modulates lncRNA-miRNA-mRNA ceRNA networks in ovaries of DHEA induced PCOS rats

Polycystic ovary syndrome (PCOS) is one of the most common endocrine and metabolic disorders in reproductive age women. Our previous results demonstrated that tempol was able to ameliorate PCOS phenotype in rats. However, the exact pathophysiological effect of tempol on PCOS remains largely unknown. To extend this research, deep RNA-sequencing was performed to investigate the long noncoding RNA (lncRNA) associated ceRNA mechanisms in the ovarian tissues of control rats, dehydropiandrosterone (DHEA) induced PCOS rats and tempol treated PCOS rats. Our results identified total 164, 79, and 914 significantly dysregulated lncRNAs, miRNAs, and mRNAs in three groups, respectively. The total of 7 lncRNAs, 8 mRNAs and 5 miRNAs were involved in lncRNA-associated ceRNA networks were constructed. Among them, mRNAs including C1qtnf1, Dipk2a, IL4r and lncRNAs including MSTRG.16751.2, MSTRG.8065.2 had high RNA connectivity in the ceRNA network, which also showed significant alterations in these three groups by using qPCR validation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the involvement of the identified ceRNA networks in regulating the development of PCOS from distinct origins, such as metabolic pathway, immune cell differentiation. The study presents the first systematic dissection of lncRNA-associated ceRNA profiles in tempol treated PCOS rats. The identified ceRNA networks could provide insights that help facilitate PCOS diagnosis and treatment.

Suppression of microRNA-222-3p ameliorates ulcerative colitis and colitis-associated colorectal cancer to protect against oxidative stress via targeting BRG1 to activate Nrf2/HO-1 signaling pathway

Oxidative stress is an important pathogenic factor in ulcerative colitis (UC) and colitis-associated colorectal cancer (CAC), further impairing the entire colon. Intestinal epithelial cells (IECs) are crucial components of innate immunity and play an important role in maintaining intestinal barrier function. Recent studies have indicated that microRNA-222-3p (miR-222-3p) is increased in colon of UC and colorectal cancer (CRC) patients, and miR-222-3p is a crucial regulator of oxidative stress. However, whether miR-222-3p influences IEC oxidative stress in UC and CAC remains unknown. This study investigated the effect of miR-222-3p on the regulation of IEC oxidative stress in UC and CAC. An in vitro inflammation model was established in NCM460 colonic cells, mouse UC and CAC models were established in vivo, and IECs were isolated. The biological role and mechanism of miR-222-3p-mediated oxidative stress in UC and CAC were determined. We demonstrated that miR-222-3p expression was notably increased in dextran sulfate sodium (DSS)-induced NCM460 cells and IECs from UC and CAC mice. In vitro, these results showed that the downregulation of miR-222-3p reduced oxidative stress, caspase-3 activity, IL-1β and TNF-α in DSS-induced NCM460 cells. We further identified BRG1 as the target gene of miR-222-3p, and downregulating miR-222-3p alleviated DSS-induced oxidative injury via promoting BRG1-mediated activation Nrf2/HO-1 signaling in NCM460 cells. The in vivo results demonstrated that inhibiting miR-222-3p in IECs significantly relieved oxidative stress and inflammation in the damaged colons of UC and CAC mice, as evidenced by decreases in ROS, MDA, IL-1β and TNF-α levels and increases in GSH-Px levels. Our study further demonstrated that inhibiting miR-222-3p in IECs attenuated oxidative damage by targeting BRG1 to activate the Nrf2/HO-1 signaling. In summary, inhibiting miR-222-3p in IECs attenuates oxidative stress by targeting BRG1 to activate the Nrf2/HO-1 signaling, thereby reducing colonic inflammation and tumorigenesis.

Exploration of the Common Gene Characteristics and Molecular Mechanism of Parkinson's Disease and Crohn's Disease from Transcriptome Data

Parkinson's disease (PD) is the second most common neurodegenerative disorder, and the mechanism of its occurrence is still not fully elucidated. Accumulating evidence has suggested that the gut acts as a potential origin of PD pathogenesis. Recent studies have identified that inflammatory bowel disease acts as a risk factor for Parkinson's disease, although the underlying mechanisms remain elusive. The aim of this study was to further explore the molecular mechanism between PD and Crohn's disease (CD). The gene expression profiles of PD (GSE6613) and CD (GSE119600) were downloaded from the Gene Expression Omnibus (GEO) database and were identified as the common differentially expressed genes (DEGs) between the two diseases. Next, analyses were performed, including functional enrichment analysis, a protein-protein interaction network, core genes identification, and clinical correlation analysis. As a result, 178 common DEGs (113 upregulated genes and 65 downregulated genes) were found between PD and CD. The functional analysis found that they were enriched in regulated exocytosis, immune response, and lipid binding. Twelve essential hub genes including BUB1B, BUB3, DLGAP5, AURKC, CBL, PCNA, RAF1, LYN, RPL39L, MRPL13, RSL24D1, and MRPS11 were identified from the PPI network by using cytoHubba. In addition, inflammatory and metabolic pathways were jointly involved in these two diseases. After verifying expression levels in an independent dataset (GSE99039), a correlation analysis with clinical features showed that LYN and RAF1 genes were associated with the severity of PD. In conclusion, our study revealed the common pathogenesis of PD and CD. These common pathways and hub genes may provide novel insights for mechanism research.