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.

Exploring the glycolytic cross-talk genes between inflammatory bowel disease and colorectal cancer.

Patients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer (CRC). Glycolysis is involved in the development of both IBD and CRC. However, the mechanisms and outcomes of glycolysis shared between IBD and CRC remain unclear. This study aimed to explore the glycolytic cross-talk genes between IBD and CRC integrating bioinformatics and machine learning. With WGCNA, LASSO, COX, and SVM-RFE algorithms, P4HA1 and PMM2 were identified as glycolytic cross-talk genes. The independent risk signature of P4HA1 and PMM2 was constructed to predict the overall survival rate of patients with CRC. The risk signature correlated with clinical characteristics, prognosis, tumor microenvironment, immune checkpoint, mutants, cancer stemness, and chemotherapeutic drug sensitivity. CRC patients with high risk have increased microsatellite instability, tumor mutation burden. The nomogram integrating risk score, tumor stage, and age showed high accuracy for predicting overall survival rate. In addition, the diagnostic model for IBD based on P4HA1 and PMM2 showed excellent accuracy. Finally, immunohistochemistry results showed that P4HA1 and PMM2 were significantly upregulated in IBD and CRC. Our study reveals the presence of glycolytic cross-talk genes P4HA1 and PMM2 between IBD and CRC. This may prove to be beneficial in advancing research on the mechanism of development of IBD-associated CRC.

Landscape of sialylation patterns identify biomarkers for diagnosis and prediction of response to anti-TNF therapy in crohn's disease.

Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), causes chronic gastrointestinal tract inflammation. Thirty percent of patients do not respond to anti-tumor necrosis factor (TNF) therapy. Sialylation is involved in the pathogenesis of IBD. We aimed to identify potential biomarkers for diagnosing CD and predicting anti-TNF medication outcomes in CD. Three potential biomarkers (SERPINB2, TFPI2, and SLC9B2) were screened using bioinformatics analysis and machine learning based on sialylation-related genes. Moreover, the combined model of SERPINB2, TFPI2, and SLC9B2 showed excellent diagnostic value in both the training and validation cohorts. Importantly, a Sial-score was constructed based on the expression of SERPINB2, TFPI2, and SLC9B2. The Sial-low group showed a lower level of immune infiltration than the Sial-high group. Anti-TNF therapy was effective for 94.4% of patients in the Sial-low group but only 15.8% in the Sial-high group. The Sial-score had an outstanding ability to predict and distinguish between responders and non-responders. Our comprehensive analysis indicates that SERPINB2, TFPI2, and SLC9B2 play essential roles in pathogenesis and anti-TNF therapy resistance in CD. Furthermore, it may provide novel concepts for customizing treatment for individual patients with CD.

Identification of a Ferroptosis-Related Prognostic Signature in Sepsis via Bioinformatics Analyses and Experiment Validation.

Ferroptosis is a new type of programmed cell death that is different from apoptosis, cell necrosis, and autophagy, which might be involved in development of sepsis. However, the potential role of ferroptosis-related genes (FRGs) in sepsis remained unclear. We identified 41 ferroptosis-related differential expression genes by weighted correlation network and differential expression analysis. The hub module of 41 ferroptosis-related differential expression genes in the protein-protein interaction network was identified. Next, we estimated diagnostic values of genes in hub modules. TLR4, WIPI1, and GABARAPL2 with high diagnostic value were selected for construction of risk prognostic model. The high risk-scored patients had significantly higher mortality than the patients with low risk scores in discovery dataset. Furthermore, the risk scores of nonsurvivor were higher than those of survivor in validation dataset. It suggested that risk score was significantly correlated to prognosis in sepsis. Then, we constructed a nomogram for improving the clinical applicability of risk signature. Moreover, the risk score was significantly associated with immune infiltration in sepsis. Our comprehensive analysis of FRGs in sepsis demonstrated the potential roles in diagnosis, prognosis, and immune infiltration. This work may benefit in understanding FRGs in sepsis and pave a new path for diagnosis and assessment of prognosis.

Characterization of Two TNF-Related Subtypes Predicting Infliximab Therapy Responses in Crohn's Disease.

Background: Anti-tumor necrosis factor (TNF) therapy is widely used to treat Crohn's disease (CD). Unfortunately, 10%-40% of patients have primary non-response to anti-TNF therapy. TNF family genes play crucial roles in inflammation and immune regulation; however, the effects of TNF family genes on CD remain unclear. Methods: CD expression profiles were downloaded from the Gene Expression Omnibus database. Unsupervised clustering was then used to identify the gene subtypes in CD based on the expressions of TNF family genes. The features of the gene subtypes were characterized using functional enrichment and immune infiltration analyses, and biomarkers of the gene subtypes were identified. Results: Patients with CD were divided on the basis of unsupervised clustering into two gene subtypes: immune and metabolic. Gene subtype A was significantly correlated with leukocyte migration and cytokine interactions, whereas gene subtype B was associated with metabolic pathways. Whereas 89.5% of the patients in gene subtype B responded to infliximab, only 16.7% of patients in gene subtype A responded. In addition, a combination of interleukin 1 beta (IL1ß), interleukin 6 (IL6), and Toll-like receptor 4 (TLR4) can effectively distinguish between gene subtypes A and B. Conclusion: Comprehensive analyses of the TNF family genes may reveal the underlying pathogenesis of CD. The classification of subtypes may provide new ideas for the personalized treatment of patients with CD.

PgtE Enzyme of Salmonella enterica Shares the Similar Biological Roles to Plasminogen Activator (Pla) in Interacting With DEC-205 (CD205), and Enhancing Host Dissemination and Infectivity by Yersinia pestis.

Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.

Construction of ceRNA Network to Reveal Potential Biomarkers in Crohn's Disease and Validation in a TNBS Induced Mice Model.

PURPOSE: We aimed to construct a competing endogenous RNA (ceRNA) network and explore the potential biomarkers in Crohn's disease (CD) via bioinformatics analysis. Validation of candidate biomarkers in a 2,4,6-trinitrobenzene sulfonic acid (TNBS) induced experimental colitis model and ceRNA network in an HCT116 cell line was also an aim, along with purposing to reveal the pathogenesis of CD. METHODS: GSE102134 and GSE67106 datasets were obtained and used to screen the differentially expressed genes. WCGNA was applied to identify the relative model to construct the ceRNA network. Furthermore, the relationship between candidate gene and immune infiltration was investigated. Then, the expression of potential biomarkers was validated via qRT-PCR in a TNBS induced experimental colitis model. Finally, the ceRNA network was confirmed by RNAi experiments in an HCT116 cell line. RESULTS: The ceRNA network, consisting of four lncRNAs, four miRNAs, and eight mRNAs, was constructed and the ROC analysis showed four mRNAs (PTGS2, LPL, STAT1, and TRIB2) had high diagnostic accuracy (AUC>0.9). In addition, upregulated PTGS2 was positively correlated with immune cell infiltration, including Natural killer cells, exhausted T-cells, monocytes, and Dendritic cells. The outcome of this TNBS induced experimental colitis model verified that the expression of PTGS2 and mir-429 was consistent with results of previous bioinformatics analysis. Furthermore, the predicted ceRNA network MIR3142HG/mir-429/PTGS2 were validated via RNA interference. Knockout of MIR3142HG decreased the mRNA level of PTGS2, whereas inhibition of mir-429 increased the mRNA level of PTGS2 in the HCT116 cell line. CONCLUSION: The exploration of the ceRNA network in this work might contribute to understanding the pathogenesis of CD. The constructed MIR3142HG/mir-429/PTGS2 ceRNA network may play a role in CD, and PTGS2 can be a potential immune-related biomarker in CD.

Murine SIGNR1 (CD209b) Contributes to the Clearance of Uropathogenic Escherichia coli During Urinary Tract Infections.

Uropathogenic Escherichia coli (UPEC), a Gram-negative bacterial pathogen, is a major causative agent of urinary tract infections (UTIs). However, the molecular mechanisms of how UPEC causes infections have not been determined. Recent studies indicated that certain enteric Gram-negative bacteria interact with and hijack innate immune receptors DC-SIGN (CD209a) and SIGNR1 (CD209b), often expressed by antigen-presenting cells (APCs), such as macrophages, leading to dissemination and infection. It was not known whether UPEC could utilize DC-SIGN receptors to promote its infection and dissemination similarly to the enteric pathogens. The results of this study reveal that UPEC interacts with CD209-expressing macrophages and transfectants. This interaction is inhibited by anti-CD209 antibody, indicating that CD209s are receptors for UPEC. Additionally, in contrast to the results of previous studies, mice lacking SIGNR1 are more susceptible to infection of this uropathogen, leading to prolonged bacterial persistence. Overall, the results of our study indicate that the innate immune receptor CD209s participate in the clearance of UPEC during UTIs.

Metalloporphyrin-indomethacin conjugates as new photosensitizers for photodynamic therapy.

Photodynamic therapy (PDT) is a promising cancer treatment approach with the advantages of low toxicity and noninvasive characteristics. In this study, a series of metalloporphyrin-indomethacin conjugates tethered with poly(ethylene glycol) (PEG) chains were prepared and characterized. The singlet oxygen production of the conjugates was evaluated through 2', 7'-dichlorofluorescin (DCFH) method. Because of the heavy atom effect, the metal porphyrin complexes exhibited the higher singlet oxygen (1O2) quantum yield than that of free base porphyrin. The order of 1O2 yield of the synthesized porphyrins was PtPor > PdPor > ZnPor > Por. The MTT assay using HeLa cells verified the low cytotoxicity of porphyrin-indomethacin conjugates in the dark. Upon irradiation, the platinated porphyrin (PtPor) showed the highest therapeutic activity among these conjugates, probably due to its high efficiency of 1O2 generation. The cellular uptake and subcellular localization of the conjugates were further evaluated through a confocal laser scanning microscope. The results showed that the conjugates were primarily localized in the lysosomes of HeLa cells.

Platinated porphyrin as a new organelle and nucleus dual-targeted photosensitizer for photodynamic therapy.

Organelle and nucleus dual-targeted anticancer drugs are being increasingly used for efficient cancer therapy as they can attack the double vital sites of tumor cells. In this work, we synthesized and characterized two new porphyrin compounds Pt-Por-RB and Me-Por-RB. The spectral titration results suggest that both Pt-Por-RB and Me-Por-RB bind to DNA efficiently in an intercalation binding mode. Upon irradiation, Pt-Por-RB with low dark-cytotoxicity can rapidly generate singlet oxygen to damage the tumor cells through the process of photodynamic therapy. Compared with Me-Por-RB, Pt-Por-RB was not only internalized in the organelles, but also in the nuclei of HeLa cells, probably due to the presence of platinum complexes, as analyzed using the confocal laser scanning microscope. Thus, with the combination of organelle and nucleus dual-targeting property and high efficiency of singlet oxygen generation, Pt-Por-RB showed a significant therapeutic activity against tumor cells.

Photocytotoxicity, cellular uptake and subcellular localization of amidinophenylporphyrins as potential photodynamic therapeutic agents: An in vitro cell study.

The cell-based studies of 5, 10, 15, 20-Tetrakis (4-amidinophenyl) porphyrin (Por1), its Zn complex (Por2) and amidinophenyl bisporphyrin (Por3) were carried out to examine their photocytotoxicity, cellular uptake and sub-cellular localization with human nasopharyngeal carcinoma cell (HK-1), using 5, 10, 15, 20-Tetrakis (N-methyl-4-pyridyl) porphyrin (H2TMPyP) as a reference. These porphyrins showed low dark-cytotoxicity and high photo-cytotoxicity against HK-1. The amphiphilic amidinophenyl bisporphyrin (Por3) displayed better cellular uptake than the single hydrophilic Por1, Por2 and H2TMPyP. As seen from the extent of overlapping of the fluorescence profiles, lysosomal localization of amidinophenylporphyrin Por1-Por3 and mito/lyso localization of the H2TMPyP occurred in the cells. The results suggest these porphyrins with amidine group could be used as potential agents in photodynamic therapy.