Response-related Genes Research Articles

The needle in the haystack: Identifying and validating common genes of depression, insomnia, and inflammation

BackgroundInsomnia, inflammation, and depression are often co-occurring conditions. The mechanisms underlying these conditions remain unclear. Materials and methodsWe collected microarray datasets of depression and insomnia from GEO and analyzed them for differentially expressed genes (DEGs). We then overlapped the DEGs with a list of inflammatory response-related genes to identify genes associated with all three conditions. We next performed analyses of enrichment analyses, KEGG mapping, and protein-protein interaction to identify hub genes. Furthermore, we established a depression rat model with inflammation and insomnia to validate the potential genes. At last, a two-sample Mendelian randomization (MR) study was conducted to confirm the association of identified target genes with depression outcomes. ResultsWe obtained 32 common DEGs associated with the depression, insomnia and inflammatory, and found that the PI3K-AKT signaling pathway might be involved in the inflammatory response in insomnia and depression. CREB1, CYBB, FYN, and CCR5 were identified as targets for the next validation. In model rats, the CCR5 and PI3K-AKT pathways were significantly up-regulated, while the model group exhibited significantly lower hippocampal p-CREB protein expression. The MR study suggested a potential causal relationship between CREB1 and the risk of depression (OR = 1.11, p = 0.013). LimitationsThe identified potential genes and pathways require further laboratory and clinical evidence verification. ConclusionWe identified four potential inflammatory related-genes (CREB1, CYBB, FYN, and CCR5). CREB1 may be a potential inflammatory response-related biomarker and drug target for depression and insomnia, as validated by the followed rat model and MR study.

Glycerol monolaurate improved intestinal barrier, antioxidant capacity, inflammatory response and microbiota dysbiosis in large yellow croaker (Larimichthys crocea) fed with high soybean oil diets

Glycerol monolaurate (GML) is a potential candidate for regulating metabolic syndrome and inflammatory response. However, the role of GML in modulating intestinal health in fish has not been well determined. In this study, a 70-d feeding trial was conducted to evaluate the effect of GML on intestinal barrier, antioxidant capacity, inflammatory response and microbiota community of large yellow croaker (13.05 ± 0.09 g) fed with high level soybean oil (SO) diets. Two basic diets with fish oil (FO) or SO were formulated. Based on the SO group diet, three different levels of GML 0.02% (SO0.02), 0.04% (SO0.04) and 0.08% (SO0.08) were supplemented respectively. Results showed that intestinal villus height and perimeter ratio were increased in SO0.04 treatment compared with the SO group. The mRNA expressions of intestinal physical barrier-related gene odc and claudin-11 were significantly up-regulated in different addition of GML treatments compared with the SO group. Fish fed SO diet with 0.04% GML addition showed higher activities of acid phosphatase and lysozyme compared with the SO group. The content of malonaldehyde was significantly decreased and activities of catalase and superoxide dismutase were significantly increased in 0.02% and 0.04% GML groups compared with those in the SO group. The mRNA transcriptional levels of inflammatory response-related genes (il-1β, il-6, tnf-α and cox-2) in 0.04% GML treatment were notably lower than those in the SO group. Meanwhile, sequencing analysis of bacterial 16S rRNA V4–V5 region showed that GML addition changed gut microbiota structure and increased alpha diversity of large yellow croaker fed diets with a high level of SO. The correlation analysis results indicated that the change of intestinal microbiota relative abundance strongly correlated with intestinal health indexes. In conclusion, these results demonstrated that 0.02%–0.04% GML addition could improve intestinal morphology, physical barrier, antioxidant capacity, inflammatory response and microbiota dysbiosis of large yellow croaker fed diets with a high percentage of SO.

Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem

BackgroundSomatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution.ResultsWe generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay.ConclusionsThis study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.

Vitamin D3 activates the innate immune response and xenophagy against Nocardia seriolae through the VD receptor in liver of largemouth bass (Micropterus salmoides)

Nocardia seriolae is a pathogenic bacterium that commonly infects largemouth bass (Micropterus salmoides), causing chronic wasting disease characterized by multiple nodules. The mechanism by which Vitamin D3 (VD3) can resist Nocardia seriolae (N. seriolae)infection is unknown, although VD3 has been found to regulate innate immune response and xenophagy in mammals. Therefore, we investigated the effects of VD3 on the immune response and xenophagy of largemouth bass after N. seriolae challenge. The results demonstrate that increasing dietary VD3 intake can alleviate focal necrosis of liver cells, increase mRNA and protein levels of innate immune response-related genes, such as cGAS, STING1, TBK1, IRF3, and IFNα, decrease the content of liver autophagosomes, and increase the content of liver autophagolysosomes. Additionally, VD3 can increase mRNA expression and protein levels of genes related to liver autophagosome-lysosome fusion, including ATG16L1, ATPV0Ca, ATPV0Cb, ATPV1D, LAMP2, STX17, and VAMP8, as well as VDR. These findings suggest that VD3 contributes to the resistance of largemouth bass to N. seriolae infection by activating innate immune response and xenophagy through VDR-mediated immunomodulation.

Effects of dietary lipid levels on lipid accumulation and health status of adult Onychostomamacrolepis

The effects of different dietary lipid levels on lipid accumulation, inflammatory response, serum bio-chemical index and histological features of intestine and hepatopancreas of O.macrolepis was experimentally evaluated in an eight-weeks study. Fish (initial weight 50.11 ± 2.86 g) were fed with five iso-nitrogenous diets (around 390 g/kg protein) varying with lipid level (5%, 7%, 9%, 11%, 13%, being LL5, LL7, LL9, LL11, and LL13 respectively) in triplicates. Results showed that the content of crude lipid in carcass and hepatopancreas were not affected by dietary lipid levels (P > 0.05). Serum ALT, TP, HDL-c and MDA, etc., were not significantly affected by diets (P > 0.05), while serum total antioxidant capacity in LL9 and LL11 groups were significantly higher than the other groups (P < 0.05). Histological features of hepatopancreas and intestine showed no significant difference among the five diets (P > 0.05), while the height of intestine villus showed the higher trend in LL9 compared with other groups. The relative expression of lipid metabolism related genes (ppar α, cpt-1α, fas, and hsl) and immune response related genes (tlr 22, nrf 2, tnfα, and il-γ) in the hepatopancreas of fish fed diets differing in their crude lipid levels were not significantly different (P > 0.05). The results suggested that a proper dietary lipid level of 9%–11% could maintain higher antioxidant and health status of adult O.macrolepis.

Undesirable ER stress induced by bavachin contributed to follicular atresia in zebrafish ovary

Fructus psoraleae (FP) is a commonly used herb with potential reproductive toxicity. Bavachin (BV), one of essential active ingredients of FP, was found to exhibit estrogenic activity, but its effect on female reproductive system remains unknown. In this study, the impact of BV on the female zebrafish reproductive system and underlying molecular mechanism were determined in vivo and ex vivo. The results showed that BV could accumulate in zebrafish ovary, leading to obvious follicular atresia and increase in gonadal index and vitellogenin content. Endoplasmic reticulum (ER) swelling and hypertrophy were observed in the BV-treated zebrafish ovary, accompanied by an increase in the expressions of ER stress and unfolded protein response (UPR) related genes, namely atf6, ire-1α and xbp1s. In the ex vivo study, BV was found to decrease the survival rate and maturation rate of oocytes, while increasing the expression of Ca2+. Additionally, BV led to an elevation in the level of estrogen receptor ESR1 and the expressions of genes involved in ER stress and UPR, including atf6, ire-1α, xbp1s, chop and perk. Moreover, molecular docking revealed that BV could directly bind to immunoglobulin heavy chain binding protein (BiP) and estrogen receptor 1 (ESR1). Besides, the alterations induced by BV could be partially reversed by fulvestrant (FULV) and 4-phenylbutyric acid (4-PBA), respectively. Thus, long-termed BV-containing medicine treatment could generate reproductive toxicity in female zebrafish by causing follicular atresia through BiP- and ESR-mediated ER stress and UPR, providing a potential target for the prevention of reproductive toxicity caused by BV.

Integrative Analysis of Inflammatory Response-Related Gene for Predicting Prognosis and Immunotherapy in Glioma

Inflammatory response plays a crucial role in the development and progression of gliomas. Whereas the prognostic esteem of inflammatory response-related genes has never been comprehensively explored in glioma, the RNA-seq information and clinical data of patients with glioma were extracted from TCGA, CGGA, and Rembrandt databases. The differentially expressed genes (DEGs) were picked out between glioma tissue and non-tumor brain tissue (NBT). Then, the least absolute shrinkage and selection operator (LASSO) regression analysis was performed to construct the prognostic signature in the TCGA cohort and verified in other cohorts. Kaplan–Meier survival analyses were conducted to compare the overall survival (OS) between the high and low-risk groups. Univariate and multivariate Cox analyses were subsequently used to confirm the independent prognostic factors of OS, and then, the nomogram was established based them. Furthermore, immune infiltration, immune checkpoints, and immunotherapy were also probed and compared between high and low-risk groups. The four genes were also analyzed by qRT-PCR, immunohistochemistry, and western blot trials between glioma tissue and NBT. The 39 DEGs were identified between glioma tissue and NBT, of which 31 genes are associated to the prognosis of glioma. The 8 optimal inflammatory response-related genes were selected to construct the prognostic inflammatory response-related signature (IRRS) through the LASSO regression. The effectiveness of the IRRS was verified in the TCGA, CGGA, and Rembrandt cohorts. Meanwhile, a nomogram with better accuracy was established to predict OS based on the independent prognostic factors. The IRRS was highly correlated with clinicopathological features, immune infiltration, and genomic alterations in glioma patients. In addition, four selective genes also verified the difference between glioma tissue and NBT. A novel prognostic signature was associated with the prognosis, immune infiltration, and immunotherapy effect in patients with gliomas. Thus, this study could provide a perspective for glioma prognosis and treatment.

Integrated bioinformatic analysis and experimental validation for exploring the key molecular of brain inflammaging.

Integrating bioinformatics and experimental validation to explore the mechanisms of inflammaging in the Brain. After dividing the GSE11882 dataset into aged and young groups, we identified co-expressed differentially expressed genes (DEGs) in different brain regions. Enrichment analysis revealed that the co-expressed DEGs were mainly associated with inflammatory responses. Subsequently, we identified 12 DEGs that were related to the inflammatory response and used the DGIdb website for drug prediction. By using both the least absolute shrinkage and selection operator (LASSO) and random forest (RF), four biomarkers were screened and an artificial neural network (ANN) was developed for diagnosis. Subsequently, the biomarkers were validated through animal studies. Then we utilized AgeAnno to investigate the roles of biomarkers at the single cell level. Next, a consensus clustering approach was used to classify the aging samples and perform differential analysis to identify inflammatory response-related genes. After conducting a weighted gene co-expression network analysis (WGCNA), we identified the genes that are correlated with both four brain regions and aging. Wayne diagrams were used to identify seven inflammaging-related genes in different brain regions. Finally, we performed immuno-infiltration analysis and identified macrophage module genes. Inflammaging may be a major mechanism of brain aging, and the regulation of macrophages by CX3CL1 may play a role in the development of inflammaging. In summary, targeting CX3CL1 can potentially delay inflammaging and immunosenescence in the brain.

Optic Nerve Head Gene Transcription Sequelae to a Single Elevated IOP Exposure Provides Insights Into Known Responses to Chronically Elevated IOP.

To clarify the optic nerve head (ONH) gene expression responses associated with a single, axon-damaging exposure to elevated IOP in relation to the composite cellular events previously identified in models of chronically elevated IOP. Anesthetized rats were exposed unilaterally to an 8-hour pulse-train controlled elevation of IOP (PT-CEI) at 60mm Hg, while others received normotensive CEI at 20mm Hg. ONH RNA was harvested at 0hours and 1, 2, 3, 7, and 10 days after either CEI and from naïve animals. RNA sequencing was performed to analyze ONH gene expression. DAVID Bioinformatics tools were used to identify significant functional annotation clusters. Gene function was compared between PT-CEI and two models of chronic ocular hypertension from the literature. The number of significantly changed genes peaked immediately (n = 1354) after PT-CEI (0hours). This was followed by a lull (<4 genes per time point) at 1 and 2days after PT-CEI. Gene activity increased again at 3 days (136 genes) and persisted at 7 (78 genes) and 10 (339 genes) days. Significant gene functional categories included an immediate upregulation of Defense Response at 0hours, followed by upregulation in Cell Cycle, a reduction in Axonal-related genes at 3 to 10 days, and upregulation of Immune Response-related genes at 10 days following PT-CEI. The most commonly upregulated gene expression across our PT-CEI study and two chronic models of ocular hypertension were cell cycle related. The PT-CEI model places in sequence ONH gene expression responses previously reported in models with chronically elevated IOP and may provide insights into their role in optic nerve damage.

Th1 cells inducing IFNγ response improves immunotherapy efficacy in gastric cancer.

Cancer immunotherapy has made remarkable advances in recent years, but its effectiveness in treating gastric cancer is often limited by the complexity of the tumor microenvironment and the lack of effective biomarkers. This study aimed to identify effective biomarkers for immunotherapy treatment by characterizing the tumor microenvironment. We retrieved the RNA-seq data from gastric cancer patients treated with the programmed death 1 (PD-1) blockade pembrolizumab. Differentially expressed genes associated with clinical outcomes were identified and further analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Gene signature scores were calculated by single sample Gene Set Enrichment Analysis (ssGSEA). The infiltration levels of immune cells were quantified using the xCell website. Cell type enrichment analysis was performed to compare treatment response and non-response groups, and regression analysis was used to investigate the relationship between interferon gamma (IFNγ) immune response and immune cell infiltration. Biomarkers were identified using least absolute shrinkage and selection operator (LASSO) analysis. Compared to normal tissues, cytokine activity and interleukin-6 production were highly activated in gastric tumors. Responders to pembrolizumab showed significantly up-regulated expression of IFNγ response-related genes. Cell type enrichment analysis revealed that Th1 cells were significantly enriched in the tumor microenvironment of responders. Regression analysis indicated that Th1 cells induced IFNγ response more efficiently than other cell types. Using signatures of Th1 cells, stromal cells and IFNγ response, a set of eight genes were identified that effectively predicted the efficacy of immunotherapy treatment and patient prognosis. Th1 cells promote therapeutic efficacy of PD-1 blockade by promoting IFNγ immune response in gastric cancer. The identified biomarkers have the potential to improve the effectiveness of immunotherapy treatment for gastric cancer patients.

Single and combined effects of polyethylene microplastics and acetochlor on accumulation and intestinal toxicity of zebrafish (Danio rerio)

The co-exposure of microplastics (MPs) and other contaminants has aroused extensive attention, but the combined impacts of MPs and pesticides remain poorly understood. Acetochlor (ACT), a widely used chloroacetamide herbicide, has raised concerns for its potential bio-adverse effects. This study evaluated the influences of polyethylene microplastics (PE-MPs) for acute toxicity, bioaccumulation, and intestinal toxicity in zebrafish to ACT. We found that PE-MPs significantly enhanced ACT acute toxicity. Also, PE-MPs increased the accumulation of ACT in zebrafish and aggravate the oxidative stress damage of ACT in intestines. Exposure to PE-MPs or/and ACT causes mild damage to the gut tissue of zebrafish and altered gut microbial composition. In terms of gene transcription, ACT exposure triggered a significant increase in inflammatory response-related gene expressions in the intestines, while some pro-inflammatory factors were found to be inhibited by PE-MPs. This study provides a new perspective on the fate of MPs in the environment and on the assessment of the combined effects of MPs and pesticides on organisms.

Fructo-oligosaccharide-mediated alteration in claudin expression in small intestinal absorptive Caco-2 cells is positively associated with the induction of inflammatory genes and the glucan receptor gene CLEC7A

ObjectivesIndigestible carbohydrates may strengthen tight junctions (TJs) independently of intestinal bacteria. This study investigated whether indigestible carbohydrates (i.e., fructo-oligosaccharides [FOS]) promote TJs directly to intestinal absorptive Caco-2 cells and examined the association between the expression of genes constructing TJs and other genes using mRNA microarray analysis. MethodsCaco-2 cells at 1.0 × 105/mL were seeded in a type I collagen plate and cultured in high-glucose Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS); the cells reached confluence at 7 d after seeding. Ten days after the cells reached confluency, they were cultured for 24 h in 10% FCS-containing DMEM medium supplemented with 0%, 5%, or 10% FOS. We performed mRNA microarray to identify the genes whose expression was altered by FOS. Subsequently, quantitative reverse transcription polymerase chain reaction was performed for these altered genes, including CLEC7A encoding the glucan receptor, and for the claudin (CLDN) family genes. The expression of CLDN2, CLDN4, and CLEC7A proteins was assessed using western blot analysis. ResultsFOS decreased the mRNA and protein expression of CLDN2, which weakens TJs, and increased those of CLDN4, which strengthens TJs, in Caco-2 cells. FOS treatment (10%) reduced the mRNA expression of antioxidative genes and induced the expression of immune response–related genes, including CLEC7A, CCL2, and ITGA2. Furthermore, the expression of CLEC7A protein was enhanced by FOS. ConclusionsInduction of TJ-strengthening CLDN4 and reduction of TJ-weakening CLDN2 by FOS treatment in small intestinal absorptive Caco-2 cells is positively associated with the induction of inflammatory genes, including CLEC7A.

1479-P: Targeted Exome Sequencing for Long-Term Efficacy and Weight Loss of Dulaglutide in Type 2 Diabetes

Introduction: There are individual differences in glucose lowering effect and weight reduction of dulaglutide, long-acting glucagon-like peptide-1 (GLP-1) receptor agonist. It is expected that genetic variations in the mechanism of action of drugs are involved in treatment response to drugs. This study aims to investigate genetic variants associated with long-term efficacy and weight reduction of dulaglutide using targeted next-generation sequencing. Methods: We recruited 77 patients those who were treated with dulaglutide at least one year after switching from DPP-4 inhibitors (±basal insulin) due to uncontrolled type 2 diabetes (HbA1c ≥8.0%) at Korean VHS medical center between September 2018 and October 2019, and followed up until March 2021. The responder was defined by ≥1.0% HbA1c reduction at 24 weeks and achievement of HbA1c ≤7.5% at 52 weeks. We designed targeted exome panel based on the mechanism of drug action, and candidate genetic variants included known GLP-1 response related genes (n=10), gastric emptying related genes (n=18), pancreatic insulin secretion related genes (n=25). At the same time, we also performed whole exome sequencing. Results: During follow-up period of median 2.5±1.3 years, HbA1c was 9.7±1.3% at baseline and reduced to 8.2±1.5% at 6 months, and maintained thereafter up to 4 years. Glycemic response was associated with GNB3, SPARC, and COL4A1 genes. Weight loss (n=13) was more frequently observed in patients with minor G alleles of COL4A1 gene (OR 2.516, 95% CI 1.013, 6.249, p=0.047). Glycemic effectiveness of dulaglutide therapy is associated with genetic variants (OR 2.106, 95% CI 1.358, 3.265, p=0.001) as well as baseline HbA1c (OR 1.682, 95% CI 1.067, 2.650, p=0.025). Conclusion: The glucose lowering effect of dulaglutide, which exempts some patients from insulin therapy, has been associated with GNB3, SPARC, and COL4A1 variants. Polymorphisms in COL4A1 gene was associated with weight loss, although further studies are needed for validation. Disclosure Y.Kim: None. J.Seo: None. Funding VHS Medical Center (VHSMC20026)

Integrated transcriptomics reveals the brain and blood biomarkers in Alzheimer's disease.

The systematic molecular associations between the peripheral blood cells and brain in Alzheimer's disease (AD) remains unclear, which hinders our understanding of AD pathological mechanisms and the exploration of new diagnostic biomarkers. Here, we performed an integrated analysis of the brain and peripheral blood cells transcriptomics to establish peripheral biomarkers of AD. By employing multiple statistical analyses plus machine learning, we identified and validated multiple regulated central and peripheral network in patients with AD. By bioinformatics analysis, a total of 243 genes were differentially expressed in the central and peripheral systems, mainly enriched in three modules: immune response, glucose metabolism and lysosome. In addition, lysosome related gene ATP6V1E1 and immune response related genes (IL2RG, OSM, EVI2B TNFRSF1A, CXCR4, STAT5A) were significantly correlated with Aβ or Tau pathology. Finally, receiver operating characteristic (ROC) analysis revealed that ATP6V1E1 showed high-diagnostic potential for AD. Taken together, our data identified the main pathological pathways in AD progression, particularly the systemic dysregulation of the immune response, and provided peripheral biomarkers for AD diagnosis.

Development and validation of an inflammatory response-related signature in triple negative breast cancer for predicting prognosis and immunotherapy.

Inflammation is one of the most important characteristics of tumor tissue. Signatures based on inflammatory response-related genes (IRGs) can predict prognosis and treatment response in a variety of tumors. However, the clear function of IRGs in the triple negative breast cancer (TNBC) still needs to be explored. IRGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO). Verification analyses were conducted to show the robustness of the signature. The expression of risk genes was identified by RT-qPCR. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool. The IRGs signature, comprised of four genes, was developed and was shown to be highly correlated with the prognoses of TNBC patients. In contrast with the performance of the other individual predictors, we discovered that the IRGs signature was remarkably superior. Also, the ImmuneScores were elevated in the low-risk group. The immune cell infiltration showed significant difference between the two groups, as did the expression of immune checkpoints. The IRGs signature could act as a biomarker and provide a momentous reference for individual therapy of TNBC.

Effects of dietary vitamin E on the growth performance, immunity and digestion of Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂ by physiology, pathology and RNA-seq

Vitamin E (VE) is an essential nutrient for most animals. Investigating the requirement and effects of vitamin E for Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂ would be meaningful. In the study, a 12-week feeding trial was conducted via the juvenile fish (initial body weight: 20.48 ± 0.20 g), and the physiological and biochemical indexes detection, histology observation and transcriptome analysis were operated to reach our goals. The results showed that vitamin E deficiency would result in bad effects on the growth, immunity and digestion, and induced some injury for the tissues. The analyse of quadratic regression curve and broken-line regression curve for some representative parameters revealed the optimal dosage of dietary VE for the fish was at 130.12–156.52 mg/kg. Comparative transcriptomic analyses revealed that VE mainly regulated the inflammatory response related genes(IL-1β, Irak3, Irak4, Nfkbia), immune related genes (Cd40, Fos, Cxcl9, Ccl20, Cxcr, Tnfaip3, Akt, Calca), membrane stability genes (Fgf1, Mrl and Gadd45b) and metabolism related genes (Gck and Ins) to influence the liver function and for the foregut, the functional metabolism related genes were Try3, Prss2, Cel, Pla2g1b, Ins Socs3 and Sqle and the Socs3 maybe also an important function gene in maintaining a good status of the foregut. Our study provided a new insight of VE function on the fish, meanwhile, it enriched the bioinformatic data of this species, as well as contributed to the healthy culture of the fish.

Prodigiosin from Serratia rubidaea MJ 24 impedes Helicoverpa armigera development by the dysregulation of Juvenile hormone-dopamine system

Prodigiosin pigment is a secondary metabolite produced by many bacterial species and is known for its medicinal properties. A few of these prodigiosin-producing bacteria are also reported to be entomopathogenic. It is intriguing to unravel the role of prodigiosin in insecticidal activities and its mode of action. In this study, we have shown the production and characterization of prodigiosin from the Serratia rubidaea MJ 24 isolated from the soil of the Western Ghats, India. Further, we assessed the effect of this pigment on the lepidopteran agricultural pest, Helicoverpa armigera. Prodigiosin-fed H. armigera indicated defective development of insect growth upon treatment. Due to defective early development, about 50% mortality and 40% reduction in body weight were observed in insects fed on a 500 ppm prodigiosin-containing diet. The transcriptomic analysis of these insects indicated significant dysregulation of Juvenile hormone synthesis and response related genes. In addition, dopamine related processes and their resultant melanization and sclerotization processes were also found to be affected. The changes in the expression levels of the key transcripts were further validated using real-time quantitative PCR. The metabolome data confirmed the developmental dysregulation of precursors and products of differentially regulated genes due to prodigiosin. Therefore, the corroborated data suggests that prodigiosin majorly affects H. armigera development through dysregulation of the Juvenile hormone-dopamine system and can be considered as a bioactive scaffold to design insect-pest management compounds. This study provides the first report of in-depth analysis of insecticidal system dynamics in H. armigera insects upon prodigiosin feeding via gene expression and metabolic change via omics approach.

A novel predictive model based on inflammatory response-related genes for predicting endometrial cancer prognosis and its experimental validation.

Inflammatory response is an important feature of most tumors. Local inflammation promotes tumor cell immune evasion and chemotherapeutic drug resistance. We aimed to build a prognostic model for endometrial cancer patients based on inflammatory response-related genes (IRGs). RNA sequencing and clinical data for uterine corpus endometrial cancer were obtained from TCGA datasets. LASSO-penalized Cox regression was used to obtain the risk formula of the model: the score = esum(corresponding coefficient × each gene's expression). The "ESTIMATE" and "pRRophetic" packages in R were used to evaluate the tumor microenvironment and the sensitivity of patients to chemotherapy drugs. Data sets from IMvigor210 were used to evaluate the efficacy of immunotherapy in cancer patients. For experimental verification, 37 endometrial cancer and 43 normal endometrial tissues samples were collected. The mRNA expression of the IRGs was measured using qRT-PCR. The effects of IRGs on the malignant biological behaviors of endometrial cancer were detected using CCK-8, colony formation, Transwell invasion, and apoptosis assays. We developed a novel prognostic signature comprising 13 IRGs, which is an independent prognostic marker for endometrial cancer. A nomogram was developed to predict patient survival accurately. Three key IRGs (LAMP3, MEP1A, and ROS1) were identified in this model. Furthermore, we verified the expression of the three key IRGs using qRT-PCR. Functional experiments also confirmed the influence of the three key IRGs on the malignant biological behavior of endometrial cancer. Thus, a characteristic model constructed using IRGs can predict the survival, chemotherapeutic drug sensitivity, and immunotherapy response in patients with endometrial cancer.

Inflammatory response-related genes predict prognosis in patients with HNSCC

BackgroundHead and neck squamous cell carcinoma (HNSCC) is the most common malignancy of the head and neck, and the inflammatory microenvironment can impact the prognosis of HNSCC. However, the contribution of inflammation to tumour progression has not been fully elucidated. MethodsThe mRNA expression profiles and corresponding clinical data of HNSCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) Cox analysis model was used to identify prognostic genes. The overall survival (OS) between high- and low-risk patients was compared by Kaplan‒Meier analysis. The independent predictors of OS were determined by univariate and multivariate Cox analyses. Single-sample gene set enrichment analysis (ssGSEA) was used to assess immune cell infiltration and immune-related pathway activity. GSEA was used to analyse Gene Ontology (GO) terms and Kyoto encyclopaedia of Genes and Genomes (KEGG) pathways. The Gene Expression Profiling Interactive Analysis (GEPIA) database was used to examine prognostic genes in HNSCC patients. Immunohistochemistry was used to verify the protein expression of prognostic genes in HNSCC samples. ResultsAn inflammatory response-related gene signature was constructed by LASSO Cox regression analysis. HNSCC patients in the high-risk group showed significantly reduced OS compared with those in the low-risk group. The predictive capacity of the prognostic gene signature was confirmed by ROC curve analysis. Multivariate Cox analysis revealed that the risk score was an independent predictor for OS. Functional analysis indicated that the immune status was markedly different between the two risk groups. The risk score was significantly related to tumour stage and immune subtype. The expression levels of the prognostic genes were significantly related to the sensitivity of cancer cells to antitumour drugs. Furthermore, high expression of the prognostic genes significantly predicted poor prognosis of HNSCC patients. ConclusionsThe novel signature containing 9 inflammatory response-related genes reflects the immune status of HNSCC and can be used for prognosis prediction. Furthermore, the genes may be potential targets for HNSCC treatment.

Abstract B031: Investigation of the ubiquitin ligase RNF31 as a mediator of immune evasion in advanced prostate cancer

Abstract Background: Metastatic Castration-Resistance Prostate cancer (mCRPC) is a disease state associated with poor survival. Current FDA-approved therapies are non-curative and can only extend mCRPC patient survival by a few months. Therefore, there is an unmet need to improve therapies for patients with advanced disease. Immunotherapy is an effective treatment strategy for a number of cancers but showed limited success in mCRPC patients. Prostate cancer cells exhibit reduced surface expression of major histocompatibility complex (MHC) molecules as an evasive mechanism from cytotoxic CD8+ T-cells. Natural killer (NK) cells are another class of immune cells with anti-tumor characteristics and can target cancer cells independently of MHC expression. Increased NK cell infiltration and activity in prostate cancer has been associated with favorable patient outcomes, but cancer cells have evolved resistance mechanisms against NK cell targeting. We hypothesize that there are druggable pathways that can be exploited to enhance anti-tumor activities of NK cells and improve efficacy of immunotherapies. Methods: To investigate these pathways, we established and characterized an in vitro co-culture system between prostate cancer and NK cells. We conducted the first targeted pool CRISPR screen identifying genes that, when knockout (KO) in prostate cancer cells, enhance killing by NK cells. We validated the screen by individually KO the gene hits. To explore the potential resistance mechanisms conferred by these hits, we performed RNA seq in control and KO cells. Results: Our screen nominated several known ligands of NK cells including CD58 and PVRL2, as well as RNF31 as the top novel target in promoting NK-mediated kill of cancer cells. RNF31 is upregulated in prostate cancer and is part of a druggable linear ubiquitin chain assembly complex (LUBAC). Single sgRNA validation experiments confirmed that RNF31 KO significantly sensitized LNCaP cells to NK92-mediated depletion. Importantly, RNF31 KO did not affect cancer cell proliferation, suggesting that the observed effects are due to the actions of NK cells. We observed that immune response related genes were upregulated in the RNF31 KO cells compare to the wildtype cells. Furthermore, pharmacologic inhibiting RNF31 via LUBAC inhibitor Hopin-8 sensitizes LNCaP cell to NK cell mediated kill. Conclusions: We anticipate that results from this study will yield insights into a novel tumor-intrinsic mechanism of immune evasion in prostate cancer and evaluate the therapeutic potential of targeting this pathway. We hope this work will help identify new therapeutic options or combination treatments that can improve the efficacy of immunotherapy in prostate cancer and significantly extend the lives of patients with advanced prostate cancer. Acknowledgements: This study was supported by the DOD Early Investigator Research Award to TL. Citation Format: Tianyi Liu, Haolong Li, Tony Junjie Hua, Hyunjin Shin, Tanushree Shenoy, Martin Sjoestroem, Arian Lundberg, Luke Gilbert, David Quigley, Alan Ashworth, Lewis Lanier, Felix Feng. Investigation of the ubiquitin ligase RNF31 as a mediator of immune evasion in advanced prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B031.