Immune-related Signaling Pathways Research Articles

Pan-cancer analysis of BRK1 as a potential immunotherapeutic target

ABSTRACT Increasing evidence supports the connection between the progression of several cancers and BRK1. However, the clinical significance of aberrant BRK1 gene expression in cancer is unknown. This study is conducted to investigate the possibility and effect of BRK1 as a potential immunotherapy target, to deliver a better option for liver cancer immunotherapy. We explored the predictive role of BRK1 expression in a variety of cancers from different bioinformatics, including differential expression in different cancers, tumor microenvironment (TME), microsatellite instability (MSI), tumor mutational burden (TMB), immune checkpoint molecules, immune-related and cell cycle-related signalling pathways, and drug response sensitivity. Finally, we verified the expression of BRK1 in hepatocellular carcinoma using immunohistochemistry. BRK1 is overexpressed in multiple cancers and displays a negative association with prognosis and progression of disease in a wide range of main cancer types. Additionally, the expression of BRK1 is related to MSI and TMB of tumors. There was also a remarkable correlation between the expression of BRK1 and immune score, immune infiltration, immune checkpoint molecules and a stromal score of tumors. In hepatocellular carcinoma, BRK1 is associated with several signaling pathways and immune cell infiltration may affect several key immune-related regulatory genes, making it an excellent biomarker and may be a sensitive target for immune drugs.Our research suggests that BRK1 may be a potential prognostic marker and target for immunotherapy and may be associated with poor prognosis in diverse malignancies, including hepatocellular carcinoma.

Identification of immunodiagnostic blood biomarkers associated with spinal cord injury severity.

Blood always shows some immune changes after spinal cord injury (SCI), and detection of such changes in blood may be helpful for diagnosis and treatment of SCI. However, studies to date on blood immune changes after SCI in humans are not comprehensive. Therefore, to obtain the characteristics of blood immune changes and immunodiagnostic blood biomarkers of SCI and its different grades, a human blood transcriptome sequencing dataset was downloaded and analyzed to obtain differentially expressed immune-related genes (DEIGs), related functions and signaling pathways related to SCI and its various grades. Characteristic biomarkers of SCI and its different grades were identified by using weighted gene coexpression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) logistic regression. Expression of biomarkers was verified through experiments. The area under the curve (AUC) of biomarkers was calculated to evaluate their diagnostic value, and differences in immune cell content were examined. In this study, 17 kinds of immune cells with different contents between the SCI group and healthy control (HC) group were identified, with 7 immune cell types being significantly increased. Differences in the content of immune cells between different grades of SCI and the HC group were also discovered. DEIGs were identified, with alteration in some immune-related signaling pathways, vascular endothelial growth factor signaling pathways, and axon guidance signaling pathways. The SCI biomarkers identified and those of American Spinal Injury Society Impairment Scale (AIS) A and AIS D of SCI have certain diagnostic sensitivity. Analysis of the correlation of immune cells and biomarkers showed that biomarkers of SCI, AIS A grade and AIS D grade correlated positively or negatively with some immune cells. CKLF, EDNRB, FCER1G, SORT1, and TNFSF13B can be used as immune biomarkers for SCI. Additionally, GDF11and HSPA1L can be used as biomarkers of SCI AIS A grade; PRKCA and CMTM2 can be used as biomarkers of the SCI AIS D grade. Detecting expression of these putative biomarkers and changes in related immune cells may be helpful for predicting the severity of SCI.

Transcriptome Analysis Reveals the Immunoregulation of Replacing Fishmeal with Cottonseed Protein Concentrates on Litopenaeus vannamei

Cottonseed protein concentrate (CPC) is a new non-food protein source with high crude protein, low price, and abundant resources, making it an ideal substitute for fishmeal. In this study, we investigated the effects of CPC re placing fishmeal on the immune response of Litopenaeus vannamei using transcriptome sequencing. L. vannamei (initial body weight: 0.42 ± 0.01 g) were fed four isonitrogenous and isolipid feeds for eight weeks, with CPC replacing fishmeal at 0% (control, FM), 15% (CPC15), 30% (CPC30), and 45% (CPC45), respectively. At the end of the feeding trial, the changes of the activities and expression of immune-related enzymes were consistent in L. vannamei in the CPC-containing group when compared with the FM group. Among them, the activities of ACP, PO, and LZM in the group whose diet was CPC30 were significantly higher than those in the FM group. Moreover, the activities of AKP, SOD, and CAT were significantly higher in the group containing CPC than in the FM group. Furthermore, all CPC groups had considerably lower MDA levels than the FM group. This suggests that the substitution of fishmeal with CPC leads to a significant immune response in L. vannamei. Compared with the FM group, transcriptome analysis identified 805 differentially expressed genes (DEGs) (484 down and 321 up), 694 (266 down and 383 up), and 902 (434 down and 468 up) in CPC15, CPC30, and CPC45, respectively. Among all DEGs, 121 DEGs were shared among different CPC-containing groups compared with the FM group. Most of these differential genes are involved in immune-related signaling pathways. The top 20 signaling pathways enriched for differential genes contained toxoplasmosis, pathogenic Escherichia coli infection, insulin resistance, and Toll and immune deficiency (IMD) pathways, in which NF-kappa-B inhibitor Cactus were involved. In addition, trend analysis comparison of the DEGs shared by the group with CPC in the diet and the FM group showed that Cactus genes were significantly down-regulated in the group with CPC in the diet and were lowest in the CPC30 group. Consistently, the expression of antimicrobial peptide genes was significantly higher in both diet-containing CPC groups than in the FM group. In conclusion, the moderate amount of CPC substituted for fishmeal may improve the immunity of L. vannamei by suppressing the expression of Cactus genes, thereby increasing the expression of antimicrobial peptide (AMP) genes.

Prediction and Verification of Curcumin as a Potential Drug for Inhibition of PDCoV Replication in LLC-PK1 Cells.

Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus (CoV) that causes lethal watery diarrhea in neonatal pigs and poses economic and public health burdens. Currently, there are no effective antiviral agents against PDCoV. Curcumin is the active ingredient extracted from the rhizome of turmeric, which has a potential pharmacological value because it exhibits antiviral properties against several viruses. Here, we described the antiviral effect of curcumin against PDCoV. At first, the potential relationships between the active ingredients and the diarrhea-related targets were predicted through a network pharmacology analysis. Twenty-three nodes and 38 edges were obtained using a PPI analysis of eight compound-targets. The action target genes were closely related to the inflammatory and immune related signaling pathways, such as the TNF signaling pathway, Jak-STAT signaling pathway, and so on. Moreover, IL-6, NR3C2, BCHE and PTGS2 were identified as the most likely targets of curcumin by binding energy and 3D protein-ligand complex analysis. Furthermore, curcumin inhibited PDCoV replication in LLC-PK1 cells at the time of infection in a dose-dependent way. In poly (I:C) pretreated LLC-PK1 cells, PDCoV reduced IFN-β production via the RIG-I pathway to evade the host's antiviral innate immune response. Meanwhile, curcumin inhibited PDCoV-induced IFN-β secretion by inhibiting the RIG-I pathway and reduced inflammation by inhibiting IRF3 or NF-κB protein expression. Our study provides a potential strategy for the use of curcumin in preventing diarrhea caused by PDCoV in piglets.

Significance of CD80 as a Prognostic and Immunotherapeutic Biomarker in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) is the primary cause of death among pulmonary cancer patients. Upregulation of CD80 may interact with cytotoxic T lymphocyte antigen 4 (CTLA4) to promote tumor progression and provide a potential target for biological antitumor therapy. However, the role of CD80 in LUAD is still unclear. To investigate the function of CD80 in LUAD, we collected transcriptomic data from 594 lung samples from The Cancer Genome Atlas of America (TCGA) database, along with the corresponding clinical information. We systematically explored the role of CD80 in LUAD using bioinformatics methods, including GO enrichment analysis, KEGG pathway analysis, Gene Set Enrichment Analysis (GSEA), co-expression analysis, and the CIBERSORT algorithm. Finally, we investigated the differences between the two subgroups of CD80 expression in terms of some drug sensitivity, using the pRRophetic package to screen small molecular drugs for therapeutic use. A predictive model based on CD80 for LUAD patients was successfully constructed. In addition, we discovered that the CD80-based prediction model was an independent prognostic factor. Co-expression analysis revealed 10 CD80-related genes, including oncogenes and immune-related genes. Functional analysis showed that the differentially expressed genes in patients with high CD80 expression were mainly located in immune-related signaling pathways. CD80 expression was also associated with immune cell infiltration and immune checkpoints. Highly expressing patients were more sensitive to several drugs, such as rapamycin, paclitaxel, crizotinib, and bortezomib. Finally, we found evidence that 15 different small molecular drugs may benefit the treatment of LUAD patients. This study found that elevated CD80 pairs could improve the prognosis of LUAD patients. CD80 is likely to be a potential as a prognostic and therapeutic target. The future use of small molecular drugs in combination with immune checkpoint blockade to enhance antitumor therapy and improve prognosis for LUAD patients is promising.

Akkermansia muciniphila plays a neuroprotective role in HMC3 cells through the 'gut-brain' axis.

Aims: We investigated the neuroprotective effects of Akkermansia muciniphila through the 'gut-brain' axis. Methods: Human colon cancer (Caco-2) cells treated with A. muciniphila metabolites were used to create theconditioned medium from Caco-2 cells treated with A. muciniphila metabolites (AC medium)medium, then treated human microglial clone 3 (HMC3) cells to simulate the gut-brainaxis in vitro. Bioinformatics analyses were performed to investigate the molecular mechanisms by which the AC medium affected HMC3 cells. Results: The secretion of inflammatory cytokines IL-6 (0.37±0.80-fold) and IL-17A (0.05±0.18-fold) by HMC3 cells was inhibited by the AC medium. Differentially expressed genes were mainly enriched in immune-related signaling pathways, such as the cAMP and TGF-β signaling pathways. Conclusion: A. muciniphila might be a source of therapeutic approaches to alleviate microglia-mediated neuroinflammatory diseases.

Tumor necrosis factor-related lncRNAs predict prognosis and immunotherapy response for patients with lung adenocarcinoma.

Lung adenocarcinoma (LUAD) has become one of the most lethal cancers, for which the recurrence and survival rates remain unfavorable. The tumor necrosis factor (TNF) family is involved in tumorigenesis and tumor progression. Various long non-coding RNAs (lncRNAs) play important roles by mediating the TNF family in cancer. Therefore, this study aimed to construct a TNF-related lncRNA signature to predict prognosis and immunotherapy response in LUAD. The expression of TNF family members and their related lncRNAs in a total of 500 enrolled LUAD patients was collected from The Cancer Genome Atlas (TCGA). Univariate Cox and the least absolute shrinkage and selection operator (LASSO)-Cox analysis was used to construct a TNF family-related lncRNA prognostic signature. Kaplan-Meier (KM) survival analysis was used to evaluate survival status. The time-dependent area under the receiver operating characteristic (ROC) curve (AUC) values were used to assess the predictive value of the signature to 1-, 2-, and 3-year overall survival (OS). Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied to identify the signature-related biological pathways. Furthermore, tumor immune dysfunction and exclusion (TIDE) analysis was employed to evaluate immunotherapy response. A total of 8 TNF-related lncRNAs significantly associated with OS of LUAD patients were used to construct a TNF family-related lncRNA prognostic signature. According to risk score, these patients were divided into high- and low-risk subgroups. The KM survival analysis indicated that patients in the high-risk group showed significantly less favorable OS than that of low-risk group. The AUC values in predicting 1-, 2-, and 3-year OS were 0.740, 0.738, and 0.758, respectively. Moreover, the GO and KEGG pathway analyses demonstrated that these lncRNAs were closely involved in immune-related signaling pathways. The further TIDE analysis indicated that high-risk patients had a lower TIDE score than that of low-risk patients, indicating that high-risk patients may be appropriate candidates for immunotherapy. For the first time, this study constructed and validated a prognostic predictive signature of LUAD patients based on TNF-related lncRNAs, and the signature showed good performance to predict immunotherapy response. Therefore, this signature may provide new strategies for individualized treatment of LUAD patients.

Abstract P6-14-11: Exosome-mediated Circ-CRSP1 promotes tumor proliferation and metastasis through stabilizing ELAVL1 protein and suppresses anti-tumor immune response in regulating the progression of Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) is one of the most malignant subtype of breast cancer. Lacking targetable molecular drivers, chemotherapy is almost the only effective systematic treatment for TNBC. Compared with other types of breast cancer, TNBC shows a higher long-term recurrence rate and worse prognostic outcome, and its main cause of death is tumor metastasis. Therefore, there is an urgent clinical need to explore underlying molecular mechanisms and find novel targets for therapeutic intervention, as well as biomarkers for early clinical diagnosis. Materials & Methods: To explore the signal pathways and target molecules related to tumor immunity by bioinformatics analysis of tissue samples [TNBC (n = 55), Her2 (n = 39), Luminal B (n = 30), Luminal A (n = 29), healthy (n = 11)]. Co-culture experiment was conducted to study the effect of TNBC-derived exosome-mediated molecules on the proliferation and migration of breast cancer. qRT-PCR assay was used to confirm the expression level of Circ-CRSP1 in tumor tissues, breast cancer cells, exosomes of breast cancer cells and serum exosomes of breast cancer patients. Overexpression and knockout experiments investigated the role of Circ-CRSP1 in promoting the proliferation and migration of TNBC cells. Protein molecular docking technique was used to predict the possible targeting binding protein ELAVL1, and molecular experiments and nude mice model were used to study the mechanism of Circ-CRSP1-ELAVL1 complex in tumor immunity. Results: TNBC-derived exosome-mediated molecular transmission promotes the proliferation and migration of breast cancer, and may promote distant metastasis of breast cancer by changing the tumor microenvironment (TME) before metastasis. Bioinformatics analysis of TNBC tumor samples confirmed that TNBC is strongly associated with tumor immune-related biological processes and signal pathways. Circ-CRSP1 is highly expressed in TNBC tumor tissues, TNBC cells, exosome derived from TNBC cells and serum exosomes of TNBC patients, and is related to the poor clinical prognosis of TNBC patients. Overexpression of Circ-CRSP1 enhanced the proliferation and migration ability of TNBC cells, and the expression levels of EMT and cell-cycle related genes altered. Circ-CRSP1 binds to protein ELAVL1 at the physical level. The target gene of Circ-CRSP1-ELAVL1 complex is involved in the immune response, and the overexpression of Circ-CRSP1 significantly down-regulates the expression level of immune-related genes. Conclusion: Exosome-mediated Circ-CRSP1 promotes the transport of ELAVL1 from nucleus to cytoplasm through targeted binding with ELAVL1, and then regulates cytoplasmic proliferation and metastasis and inhibits the stability and translation of anti-tumor immune-related gene mRNA, thus finally promotes the proliferation, invasion and metastasis of TNBC. This study can further understand the mechanism of circRNA in the growth and metastasis of TNBC from the theoretical level, further explore the feasibility of Circ-CRSP1 as a molecular target for gene therapy, and provide theoretical basis and pre-clinical data for Circ-CRSP1 in serum exosomes as a high risk screening index and prognostic marker for TNBC patients. Citation Format: Sujin Yang, Jinhai Tang. Exosome-mediated Circ-CRSP1 promotes tumor proliferation and metastasis through stabilizing ELAVL1 protein and suppresses anti-tumor immune response in regulating the progression of Triple-Negative Breast Cancer. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-14-11.

Bioinformatics-based diagnosis and evaluation of several pivotal genes and pathways associated with immune infiltration at different time points in spinal cord injury

ABSTRACT Spinal Cord Injury (SCI) is a devastating neurological event. To assess the degree of spinal cord damage and classify the injury, it is recommended to use the 2019 version of the AIS standard. The severity of trauma was evaluated using the Trauma Severity Score, and various classification systems have been proposed for injuries at different parts and segments of the spine. Understanding the regulated signaling pathways and immune processes following SCI can lead to a better understanding of SCI-induced biomarkers and their underlying mechanisms. In this study, two gene expression datasets (GSE464 and GSE45006) from the Gene Expression Omnibus database were utilized. Differential gene expression and co-expression network analysis were performed, revealing 370 shared genes in the 3-day group and 111 shared genes in the 14-day group after SCI. The study used functional enrichment analysis methods such as Gene Set Enrichment Analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes. The ssGSEA method was used to assess the levels and composition of immune infiltration in both the sham (control) and SCI groups. The single-cell transcriptomics dataset GSE182803 was analyzed to identify genes associated with immune marker cells. Four key genes (Ptgs2, Fn1, Ccl2, and Icam1) were identified in the 3-day group, while only one gene (Cyp51) was identified in the 14-day group after SCI. The findings offer significant insights into the immune-related genes and signaling pathways involved in secondary SCI at different time points and hold potential for the development of intervention strategies for acute and chronic post-SCI.

Transcriptome, intestinal microbiome and histomorphology profiling of differences in the response of Chinese sea bass (Lateolabrax maculatus) to Aeromonas hydrophila infection.

The Chinese sea bass (Lateolabrax maculatus) is an important aquaculture fish, but diseases caused by Aeromonas hydrophila have led to severe economic losses to the aquaculture industry in recent years. To date, only a few studies have focused on the relationship between the intestinal immune response and changes in intestinal microbes by A. hydrophila infection. Here, we report the transcriptome and intestinal changes in infected sea bass. Histopathological results showed that severe steatosis and vacuolation occurred in the liver and that the intestinal villi and mesentery were seriously affected after infection. By extracting total RNA from intestinal tissue and studying the transcriptome profile, 1,678 genes (1,013 upregulated and 665 downregulated) were identified as significantly differentially expressed genes (DEGs). These genes are involved in many immune-related signalling pathways, such as the NOD-like receptor, C-type lectin receptor, and Toll-like receptor signalling pathways. Moreover, the intestinal microbes of sea bass changed significantly after infection. Interestingly, at the genus level, there was an increase in Serratia, Candida arthromitus and Faecalibacterium as well as a decrease in Akkermansia and Parabacteroides after infection. The results also indicated that some of the DEGs involved in the immune response were related to the genus level of intestinal microbiota. Finally, there was a relationship between gene expression patterns and the bacterial structure in the host intestine. Our study provides a reference for the study of the immune response and particular functions of intestinal microbes of sea bass after pathogen infection.

Novel Bruton's tyrosine kinase inhibitor TAS5315 suppresses the progression of inflammation and joint destruction in rodent collagen-induced arthritis.

Rheumatoid arthritis is an inflammatory autoimmune disease, characterized by autoantibody production, synovial inflammation, and joint destruction. Its pathogenesis is due to environmental factors and genetic backgrounds. Bruton's tyrosine kinase is a cytoplasmic non-receptor tyrosine kinase, expressed in most hematopoietic cell lineages, except T cells and plasma cells, and regulates various immune-related signaling pathways, thereby playing a crucial role in pathogenesis. Thus, inhibiting Bruton's tyrosine kinase may prove beneficial in treating autoimmune diseases. In the present study, we characterized Bruton's tyrosine kinase inhibitor, TAS5315, in vitro and evaluated its therapeutic effects in experimental arthritis models. TAS5315 markedly inhibited Bruton's tyrosine kinase enzyme activity and suppressed the B-cell receptor signaling pathway in Ramos cells. Moreover, it suppressed the expression of CD69, CD86, and MHC class II in mouse B lymphocytes and the production of TNF-α and MIP-1α in mouse macrophages and decreased bone resorption activity in mouse osteoclasts. Furthermore, it ameliorated the pathological changes in two rodent models of collagen-induced arthritis in vivo. TAS5315 improved bone mineral density and bone intensity. Thus, these results suggest that TAS5315 could be a promising therapeutic option for the treatment of rheumatoid arthritis.

Identification of Immune-Related Risk Genes in Osteoarthritis Based on Bioinformatics Analysis and Machine Learning.

In this research, we aimed to perform a comprehensive bioinformatic analysis of immune cell infiltration in osteoarthritic cartilage and synovium and identify potential risk genes. Datasets were downloaded from the Gene Expression Omnibus database. We integrated the datasets, removed the batch effects and analyzed immune cell infiltration along with differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) was used to identify the positively correlated gene modules. LASSO (least absolute shrinkage and selection operator)-cox regression analysis was performed to screen the characteristic genes. The intersection of the DEGs, characteristic genes and module genes was identified as the risk genes. The WGCNA analysis demonstrates that the blue module was highly correlated and statistically significant as well as enriched in immune-related signaling pathways and biological functions in the KEGG and GO enrichment. LASSO-cox regression analysis screened 11 characteristic genes from the hub genes of the blue module. After the DEG, characteristic gene and immune-related gene datasets were intersected, three genes, PTGS1, HLA-DMB and GPR137B, were identified as the risk genes in this research. In this research, we identified three risk genes related to the immune system in osteoarthritis and provide a feasible approach to drug development in the future.

The Efficacy and Mechanism of Qinghua Jianpi Recipe in Inhibiting Canceration of Colorectal Adenoma Based on Inflammatory Cancer Transformation.

This study is aimed at exploring the effect of Qinghua Jianpi Recipe on preventing colon polyp recurrence and inhibiting the progress of "inflammatory cancer transformation." And another goal is to explore the changes of intestinal flora structure and intestinal inflammatory (immune) microenvironment of mice with colon polyps treated by Qinghua Jianpi Recipe and to clarify its mechanism. Clinical trials were conducted to confirm the therapeutic effect of Qinghua Jianpi Recipe on patients with inflammatory bowel disease. The inhibitory effect of Qinghua Jianpi Recipe on "inflammatory cancer transformation" of colon cancer was confirmed by an adenoma canceration mouse model. Histopathological examination was used to evaluate the effects of Qinghua Jianpi Recipe on intestinal inflammatory state, adenoma number, and pathological changes of adenoma model mice. The changes of inflammatory indexes in intestinal tissue were tested by ELISA. Intestinal flora was detected by 16S rRNA high-throughput sequencing. Short-chain fatty acid metabolism in the intestine was analyzed by targeted metabolomics. Network pharmacology analysis of possible mechanism of Qinghua Jianpi Recipe on colorectal cancer was performed. Western blot was used to detect the protein expression of the related signaling pathways. Qinghua Jianpi Recipe can significantly improve intestinal inflammation status and function in patients with inflammatory bowel disease. Qinghua Jianpi Recipe could significantly improve the intestinal inflammatory activity and pathological damage of adenoma model mice and reduce the number of adenoma. Qinghua Jianpi Recipe significantly increased the levels of Peptostreptococcales_Tissierellales, NK4A214_group, Romboutsia, and other intestinal flora after intervention. Meanwhile, the treatment group of Qinghua Jianpi Recipe could reverse the changes of short-chain fatty acids. Network pharmacology analysis and experimental studies showed that Qinghua Jianpi Recipe inhibited the "inflammatory cancer transformation" of colon cancer by regulating intestinal barrier function-related proteins, inflammatory and immune-related signaling pathways, and free fatty acid receptor 2 (FFAR2). Qinghua Jianpi Recipe can improve the intestinal inflammatory activity and pathological damage of patient and adenoma cancer model mice. And its mechanism is related to the regulation of intestinal flora structure and abundance, short-chain fatty acid metabolism, intestinal barrier function, and inflammatory pathways.

Dual RNA-seq of spleens extracted from channel catfish infected with Aeromonas veronii reveals novel insights into host-pathogen interactions

Interactions between host and pathogen are involving various dynamic changes in transcript expression and critical for understanding host immunity against infections and its associated pathogenesis. Herein, we established a model of channel catfish infected with Aeromonas veronii. The infected fish had prominent body surface bleeding, and the spleen showed hyperemia and swelling. Then, the spleen of channel catfish infected with A. veronii was analyzed by dual RNA sequencing (RNA-seq), and the transcriptome data were compared with uninfected channel catfish spleen or bacteria cultured in vitro. The transcript expression profile of pathogen-host interaction between A. veronii and channel catfish was successfully studied. During infection, the host was enriched for multiple immune-related signaling pathways, such as the Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, and T cell receptor signaling pathway; and significantly upregulated for many innate immune-related genes, including IL-8. At the same time, we found that A. veronii mainly harmed the host spleen through hemolysin. Our current findings are of great significance in clarifying the pathogenesis of channel catfish induced by A. veronii and provide gene targets for developing preventive measures.

The role of gene expression of CD47 in colorectal cancer (CRC).

240 Background: CD47 belongs to the immunoglobulin superfamily and is overexpressed in many tumor types. CD47 plays an important role in suppressing phagocytosis through binding to transmembrane protein SIRP-alpha on macrophages. Targeting CD47 is a novel strategy for cancer immunotherapy and is being evaluated in ongoing clinical trials. However, molecular characteristics of CD47-overexpressed colorectal cancer (CRC) are largely unknown. Methods: We retrospectively reviewed CRC patient samples (n = 14786) submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry were performed. Correlation of CD47 expression with danger-associated molecular pattern (DAMP)-related genes ( HMGB1, CALR, ANXA1, HSP90AA1, HSPA1A, and CXCL10) expressions was tested. DAMP signature calculated as composite z-score of the DAMP related genes was compared between CD47-high and -low patients classified according to the median level of CD47 expression. Distributions of KRAS and BRAF mutations, consensus molecular subtype (CMS), and signatures of oncogenic signaling pathways were compared between CD47-high and -low patients. In addition, overall survival (OS) was compared between CD47-high and -low patients available for survival data. Results: CD47 expression level was significantly higher in metastatic compared to primary lesions (1.07-fold, q < 0.05) and microsatellite instability high tumors compared to microsatellite stable tumors (1.15-fold, q < 0.05). CD47 expression was positively correlated with DAMP genes expression except for HSPA1A, and the DAMP signature (median score [MS]: 2.66 vs -2.29, q < 0.05) was significantly increased in CD47-high patients. KRAS mutations were less prevalent (45.87% vs 50.05%) and CMS1(17.72% vs 14.42%) and CMS4 (40.33% vs 27.28%) were more prevalent in CD47-high patients, while no difference was observed in the prevalence of BRAF mutations between CD47-high and -low patients. Signatures of EMT (MS:2.91 vs -3.19), TGF-beta (MS:3.72 vs -3.52), angiogenesis (MS:2.95 vs -2.78), MAPK (MS:4.99 vs -4.12), PI3K (MS:2.41 vs -2.03), and immune-related signaling pathways (MS:1.20 vs -2.51) were significantly enriched in CD47-high patients (all q < 0.05). CD47-high patients (n = 4873) showed significantly worse OS than CD47-low patients (n = 4898) (median OS, 32.4 vs 37.6 months; hazard ratio = 1.158, p< 0.01). Conclusions: Highly CD47-expressed CRC harbored activation of DAMPs and oncogenic signaling pathways that linked to aberrant tumor microenvironment and worse prognosis. Our results support intensive treatment strategies using CD47 inhibitors combined with cytotoxic agents and molecular targeted agents (such as anti-VEGF agents) in CD47-overexpressed CRC.

Development of a Novel KCNN4-Related ceRNA Network and Prognostic Model for Renal Clear Cell Carcinoma

Background. Clear cell renal cell carcinoma (ccRCC) accounts for more than 80% of renal cell carcinomas. Yet, it has not been fully understood about the derivation and progression of the tumor, as well as the long-term benefits from multimodality therapy. Therefore, reliable and applicable molecular markers are urgently needed for the prediction of diagnosis and prognosis of ccRCC patients. Methods. Genetic and clinical information of 533 ccRCC patients from The Cancer Genome Atlas database was collected for comprehensive bioinformatic analyses. UALCAN was used to detect gene expression in paired tumor samples. Two data sets from Gene Expression Omnibus database were analyzed to identify differentially expressed genes (DEGs), and Gene Set Enrichment Analysis was applied for the functional enrichment of DEGs. Tumor Immune Single Cell Hub and Tumor IMmune Estimation Resource databases were separately used for analyses of single-immune cell and immune cell infiltration. Encyclopedia of RNA Interactomes database was explored to predict targeted microRNAs (miRNAs) and corresponding long non-coding RNAs (lncRNAs). Cox regression analysis was performed for the construction of risk signature and prognosis model. Finally, quantitative real-time polymerase chain reaction and western blot were conducted for KCNN4 expression detection in cell lines and clinical samples. Small interfering RNA was employed to knock down KCNN4, and corresponding functional experiments were conducted on ccRCC cells as well. Results. KCNN4 showed elevated expression in tumors and prominent clinical correlation in ccRCC. In total, 41 KCNN4-related genes were enriched, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed they were intimately related to immune-related signaling pathways. Spearman’s analysis revealed the significantly positive correlation of KCNN4 with immune cell infiltration. By integrating hub miRNA-let-7e-5p and four critical lncRNA, a competitive endogenous RNA network-based risk signature was constructed. The prognosis model derived from it showed considerable predictive value for survival of ccRCC patients. Finally, in vitro experiments confirmed the remarkable tumor-promoting role of KCNN4 in ccRCC cells. Conclusion. KCNN4 significantly affected the immune status of tumor microenvironment and immunotherapy elements, through which it promoted tumor progression in ccRCC, and it could be a potential biomarker for prognosis and immunotherapy effects of ccRCC patients.

A novel risk model based on anoikis: Predicting prognosis and immune infiltration in cutaneous melanoma.

Cutaneous melanoma (CM) is a highly aggressive malignancy with a dimal prognosis and limited treatment options. Anoikis is believed to involve in the regeneration, migration, and metastasis of tumor. The exact role of anoikis-related genes (ARGs) in the development and progression of cutaneous melanoma, however, remains elusive. Four ARGs (SNAI2, TFDP1, IKBKG, and MCL1) with significant differential expression were selected through Cox regression and LASSO analyses. Data for internal and external cohorts validated the accuracy and clinical utility of the prognostic risk model based on ARGs. The Kaplan-Meier curve indicated a much better overall survival rate of low-risk patients. Notably, we also found that the action of ARGs in the CM was mediated by immune-related signaling pathways. Consensus clustering and TIME landscape analysis also indicated that the low-risk score patients have excellent immune status. Moreover, the results of immunotherapy response and drug sensitivity also confirmed the potential implications of informing individualized immune therapeutic strategies for CM. Collectively, the predictive risk model constructed based on ARGs provides an excellent and accurate prediction tool for CM patients. This present research provides a rationale for the joint application of targeted therapy and immunotherapy in CM treatment. The approach could have great therapeutic value and make a contribution to personalized medicine therapy.

Identification and validation of immune cells and hub genes alterations in recurrent implantation failure: A GEO data mining study.

Introduction: Recurrent implantation failure (RIF) is a distressing problem in assisted reproductive technology (ART). Immunity plays a vital role in recurrent implantation failure (RIF) occurrence and development, but its underlying mechanism still needs to be fully elucidated. Through bioinformatics analysis, this study aims to identify the RIF-associated immune cell types and immune-related genes. Methods: The differentially expressed genes (DEGs) were screened based on RIF-associated Gene Expression Omnibus (GEO) datasets. Then, the enrichment analysis and protein-protein interaction (PPI) analysis were conducted with the DEGs. The RIF-associated immune cell types were clarified by combining single sample gene set enrichment analysis (ssGSEA) and CIBERSORT. Differentially expressed immune cell types-related modules were identified by weighted gene co-expression network analysis (WGCNA) and local maximal quasi-clique merger (lmQCM) analysis. The overlapping genes between DEGs and genes contained by modules mentioned above were delineated as candidate hub genes and validated in another two external datasets. Finally, the microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) that interacted with hub genes were predicted, and the competing endogenous RNA (ceRNA) regulatory network was structured. Results: In the present study, we collected 324 DEGs between RIF and the control group, which functions were mainly enriched in immune-related signaling pathways. Regarding differential cell types, the RIF group had a higher proportion of activated memory CD4 T cells and a lower proportion of γδ T cells in the endometrial tissue. Finally, three immune-related hub genes (ALOX5AP, SLC7A7, and PTGS2) were identified and verified to effectively discriminate RIF from control individuals with a specificity rate of 90.8% and a sensitivity rate of 90.8%. In addition, we constructed a key ceRNA network that is expected to mediate molecular mechanisms in RIF. Conclusion: Our study identified the intricate correlation between immune cell types and RIF and provided new immune-related hub genes that offer promising diagnostic and therapeutic targets for RIF.

Identification and validation of novel biomarkers associated with immune infiltration for the diagnosis of osteosarcoma based on machine learning.

Objectives: Osteosarcoma is the most common primary malignant tumor in children and adolescents, and the 5-year survival of osteosarcoma patients gained no substantial improvement over the past decades. Effective biomarkers in diagnosing osteosarcoma are warranted to be developed. This study aims to explore novel biomarkers correlated with immune cell infiltration in the development and diagnosis of osteosarcoma. Methods: Three datasets (GSE19276, GSE36001, GSE126209) comprising osteosarcoma samples were extracted from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression. Then, differentially expressed genes (DEGs) were identified by limma and potential biological functions and downstream pathways enrichment analysis of DEGs was performed. The machine learning algorithms LASSO regression model and SVM-RFE (support vector machine-recursive feature elimination) analysis were employed to identify candidate hub genes for diagnosing patients with osteosarcoma. Receiver operating characteristic (ROC) curves were developed to evaluate the discriminatory abilities of these candidates in both training and test sets. Furthermore, the characteristics of immune cell infiltration in osteosarcoma, and the correlations between these potential genes and immune cell abundance were illustrated using CIBERSORT. qRT-PCR and western blots were conducted to validate the expression of diagnostic candidates. Results: GEO datasets were divided into the training (merged GSE19276, GSE36001) and test (GSE126209) groups. A total of 71 DEGs were screened out in the training set, including 10 upregulated genes and 61 downregulated genes. These DEGs were primarily enriched in immune-related biological functions and signaling pathways. After machine learning by SVM-RFE and LASSO regression model, four biomarkers were chosen for the diagnostic nomogram for osteosarcoma, including ASNS, CD70, SRGN, and TRIB3. These diagnostic biomarkers all possessed high diagnostic values (AUC ranging from 0.900 to 0.955). Furthermore, these genes were significantly correlated with the infiltration of several immune cells, such as monocytes, macrophages M0, and neutrophils. Conclusion: Four immune-related candidate hub genes (ASNS, CD70, SRGN, TRIB3) with high diagnostic value were confirmed for osteosarcoma patients. These diagnostic genes were significantly connected with the immune cell abundance, suggesting their critical roles in the osteosarcoma tumor immune microenvironment. Our study provides highlights on novel diagnostic candidate genes with high accuracy for diagnosing osteosarcoma patients.

Anti-inflammatory effect of dental pulp stem cells.

Dental pulp stem cells (DPSCs) have received a lot of attention as a regenerative medicine tool with strong immunomodulatory capabilities. The excessive inflammatory response involves a variety of immune cells, cytokines, and has a considerable impact on tissue regeneration. The use of DPSCs for controlling inflammation for the purpose of treating inflammation-related diseases and autoimmune disorders such as supraspinal nerve inflammation, inflammation of the pulmonary airways, systemic lupus erythematosus, and diabetes mellitus is likely to be safer and more regenerative than traditional medicines. The mechanism of the anti-inflammatory and immunomodulatory effects of DPSCs is relatively complex, and it may be that they themselves or some of the substances they secrete regulate a variety of immune cells through inflammatory immune-related signaling pathways. Most of the current studies are still at the laboratory cellular level and animal model level, and it is believed that through the efforts of more researchers, DPSCs/SHED are expected to be transformed into excellent drugs for the clinical treatment of related diseases.