Survival prediction and response to immune checkpoint inhibitors: A prognostic immune signature for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common cancers all over the world. Several studies have explored if immune-related genes and tumor immune microenvironment could play roles in HCC prognoses. This study is aimed at developing a prognostic signature of HCC based on immune-related genes or tumor immune microenvironment to predict survival and response to immune checkpoint inhibitors (ICIs). We constructed a prognostic signature using bioinformatics method and validated its predictive capability. The mechanisms of the signature prediction were explored with The Cancer Immunome Atlas (TCIA) and mutation analysis. We also explored the association between the signature and immunophenoscore (IPS), which is the marker of ICIs response. A 6 immune-related-gene (6-IRG) signature was developed. It was revealed in a multivariate analysis that the 6-IRG signature was an independent prognostic factor of overall survival and progression-free interval among HCC patients. In the high-risk group of 6-IRG signature score, macrophage M0 cells and regulatory T cells, which are observed associated with poor overall survival in our study, were higher. The low-risk group had a higher IPS, which meant a better response to ICIs. Taken together, we constructed a reliable 6-IRG signature for prediction of survival and response to ICIs. The signature needs further testing for clinical application.     

Plasma glucagon-immunoreactive components in early life in dogs

High plasma concentrations of C-terminal immunoreactive glucagon (IRG) have been found during early life in several mammalian species. We have analyzed the plasma IRG of 12 h to 60 day-old dogs in terms of the 4 peaks (IRG greater than 20,000, IRG9000, IRG3500 and IRG2000) obtained by gel filtration on Bio-Gel P-30. Significant changes with age and in response to administered agents were confined to IRG9000 and IRG3500. IRG9000 was 9-fold higher in 12-36 h old dogs than in adults (108 +/- 24 pg/ml pancreatic glucagon equivalents v. 12 +/- 3 pg/ml, mean +/- SEM) and showed a decline to 2-fold higher (27 +/- 5 pg/ml) at 31-60 days. IRG3500 was higher than in the adult only during the first 36 h of life (36 +/- 5 pg/ml v. 15 +/- 3 pg/ml). Arginine infusion (0.5 g/kg over 15 min) caused an increase in plasma levels of both IRG9000 and IRG3500 in the newborn, whereas in adult dogs only IRG3500 was increased. Insulin injection (0.2 U/kg intravenously) causing a marked hypoglycemia had no significant effect on the plasma level of any IRG component in newborn dogs. Dihydrosomatostatin infusion (10 micrograms/kg bolus +/- 90 micrograms/kg over 30 min) caused a decrease in both IRG9000 and IRG3500. The increased basal level and secretory response to arginine of IRG9000 in newborn dogs may reflect an immaturity of the A cells, whereby more of this component, which may represent a precursor of pancreatic glucagon, is secreted than in the adult. The immature A cells also appear to have an impaired secretory response to hypoglycemia.     

Effect of prednisone on type I interferon signature in rheumatoid arthritis: consequences for response prediction to rituximab

IntroductionElevated type I interferon (IFN) response gene (IRG) expression has proven clinical relevance in predicting rituximab non-response in rheumatoid arthritis (RA). Interference between glucocorticoids (GCs) and type I IFN signaling has been demonstrated in vitro. Since GC use and dose are highly variable among patients before rituximab treatment, the aim of this study was to determine the effect of GC use on IRG expression in relation to rituximab response prediction in RA.MethodsIn two independent cohorts of 32 and 182 biologic-free RA patients and a third cohort of 40 rituximab-starting RA patients, peripheral blood expression of selected IRGs was determined by microarray or quantitative real-time polymerase chain reaction (qPCR), and an IFN-score was calculated. The baseline IFN-score was tested for its predictive value towards rituximab response in relation to GC use using receiver operating characteristics (ROC) analysis in the rituximab cohort. Patients with a decrease in disease activity score (∆DAS28) >1.2 after 6 months of rituximab were considered responders.ResultsWe consistently observed suppression of IFN-score in prednisone users (PREDN⁺) compared to non-users (PREDN⁻). In the rituximab cohort, analysis on PREDN⁻ patients (n = 13) alone revealed improved prediction of rituximab non-response based on baseline IFN-score, with an area under the curve (AUC) of 0.975 compared to 0.848 in all patients (n = 40). Using a group-specific IFN-score cut-off for all patients and PREDN⁻ patients alone, sensitivity increased from 41% to 88%, respectively, combined with 100% specificity.ConclusionsBecause of prednisone-related suppression of IFN-score, higher accuracy of rituximab response prediction was achieved in PREDN⁻ patients. These results suggest that the IFN-score-based rituximab response prediction model could be improved upon implementation of prednisone use.     

A novel prognostic signature of immune‐related genes for patients with colorectal cancer

Colorectal cancer (CRC) is one of the most commonly diagnosed cancers with an estimated 1.8 million new cases worldwide and associated with high mortality rates of 881 000 CRC‐related deaths in 2018. Screening programs and new therapies have only marginally improved the survival of CRC patients. Immune‐related genes (IRGs) have attracted attention in recent years as therapeutic targets. The aim of this study was to identify an immune‐related prognostic signature for CRC. To this end, we combined gene expression and clinical data from the CRC data sets of The Cancer Genome Atlas (TCGA) into an integrated immune landscape profile. We identified a total of 476 IRGs that were differentially expressed in CRC vs normal tissues, of which 18 were survival related according to univariate Cox analysis. Stepwise multivariate Cox proportional hazards analysis established an immune‐related prognostic signature consisting of SLC10A2, FGF2, CCL28, NDRG1, ESM1, UCN, UTS2 and TRDC. The predictive ability of this signature for 3‐ and 5‐year overall survival was determined using receiver operating characteristics (ROC), and the respective areas under the curve (AUC) were 79.2% and 76.6%. The signature showed moderate predictive accuracy in the validation and GSE38832 data sets as well. Furthermore, the 8‐IRG signature correlated significantly with tumour stage, invasion, lymph node metastasis and distant metastasis by univariate Cox analysis, and was established an independent prognostic factor by multivariate Cox regression analysis for CRC. Gene set enrichment analysis (GSEA) revealed a relationship between the IRG prognostic signature and various biological pathways. Focal adhesions and ECM‐receptor interactions were positively correlated with the risk scores, while cytosolic DNA sensing and metabolism‐related pathways were negatively correlated. Finally, the bioinformatics results were validated by real‐time RT?qPCR. In conclusion, we identified and validated a novel, immune‐related prognostic signature for patients with CRC, and this signature reflects the dysregulated tumour immune microenvironment and has a potential for better CRC patient management.     

Gastric cancer peritoneal metastasis related signature predicts prognosis and sensitivity to immunotherapy in gastric cancer

Gastric cancer peritoneal metastases (GCPM) is a leading cause of GC-related death. Early detection of GCPM is critical for improving the prognosis of advanced GC. Differentially expressed genes (DEGs) were identified in the GSE62254 database to distinguish between GCPM and non-GCPM. The gastric cancer peritoneal metastases signature (GCPMs) was developed using DEGs. We analysed the effectiveness of GCPMs as indicators for prognosis, chemotherapy, and immune therapy response in GC patients. Subsequently, we analysed the correlation between GCPMs and immune microenvironment as well as immune escape in GC patients. Random forest model and immunohistochemistry was utilized to identify the crucial genes that can aid in the diagnosis of GCPM. We identified five DEGs and utilized their expression to construct GCPMs. Patients with high GCPMs had a higher likelihood of a poor prognosis, while those with low GCPMs appeared to potentially benefit more from chemotherapy. GCPMs were a dependable marker for predicting the response to immunotherapy. Additionally, GCPMs was found to be significantly linked to stromal score and cancer-associated fibroblasts. SYNPO2 has been identified as the gene with the highest significance in the diagnosis of GCPM. Immunohistochemistry suggests that SYNPO2-positive expression in tumour cells, fibroblasts, inflammatory cell may be associated with promoting peritoneal metastasis in GC. GCPMs have shown to be a promising biomarker for predicting the prognosis and response of GC patients to chemotherapy and immunotherapy. The use of GCPMs for individual tumour evaluation may pave the way for personalized treatment for GC patients in the future.     

Construction and validation of a TP53-associated immune prognostic model for gastric cancer

Increasing evidence indicates that TP53 mutation impacts the patients' prognosis by regulating the gastric cancer (GC) immunophenotype. An immune prognostic signature (IPS) was constructed based on TP53 status. The effects of the IPS on the immune microenvironment of GC were analyzed. We also constructed a nomogram integrating the IPS and other clinical factors. An IPS was constructed in the TCGA cohort and validated in the meta-GEO cohort. TP53 mutation resulted in the downregulation of the immune response in GC. Concretely, high-risk patients were characterized by increased monocyte, macrophage M0 and T cell follicular helper infiltration; increased stromal score, ESTIMATE score and immune score; higher TIM3 and BTLA expression; and decreased dendritic cell and T cell CD4 memory-activated infiltration and tumor purity. The nomogram also showed good predictive performance. These results suggest that the IPS is an effective prognostic indicator for GC patients, which might provide a theoretical foundation for immunotherapy.     

Immune response gene 1 deficiency aggravates high fat diet-induced nonalcoholic fatty liver disease via promotion of redox-sensitive AKT suppression

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder worldwide. Immune response gene 1 (IRG1) catalyzes the production of bio-active itaconate, which is actively involved in the regulation of signal transduction. A recent study has found that the expression of IRG1 was significantly down-regulated in obesity-associated fatty liver, but the potential roles of IRG1 in the development NAFLD remain unclear. The present study found that genetic deletion of IRG1 aggravated high fat diet (HFD)-induced metabolic disturbance, including obesity, dyslipidemia and insulin resistance. In addition, HFD induced more severe liver steatosis and higher serum ALT and AST level in IRG1 KO mice, which were accompanied with altered expression of genes involved in lipid uptake, synthesis and catabolism. RNA-seq and immunoblot analysis indicated that deficiency of IRG1 is associated with suppressed activation of AKT, a master metabolic regulator. Mechanistically, IRG1/itaconate enhanced the antioxidative NRF2 pathway and prevented redox-sensitive suppression of AKT. Interestingly, supplementation with 4-octyl itaconate (4-OI), a cell-permeable derivate of itaconate, alleviated HFD-induced oxidative stress, AKT suppression and liver steatosis. Therefore, IRG1 probably functions as a protective regulator in the development of NAFLD and the cell-permeable 4-OI might have potential value for the pharmacological intervention of NAFLD.     

Response of extrapancreatic immunoreactive glucagon to intraluminal nutrients in pancreatectomized dogs

To investigate the response of extrapancreatic glucagon to intraluminal stimuli, nutrients were administered to normal and pancreatectomized dogs through a stomach tube in a fully conscious state after an overnight fast. Plasma immunoreactive glucagon was determined with antisera specific and nonspecific to glucagon and was designated as IRG and total IRG, respectively. Oral glucose load elicited a decrease in plasma IRG and a remarkable rise of plasma total IRG in a group of 6 pancreatectomized dogs, as in the control dogs. When arginine was given, both plasma IRG and total IRG significantly increased in a group of 5 pancreatectomized dogs, while only total IRG rose significantly in the normal control dogs. Butter load did not reveal any changes in plasma IRG and total IRG in a group of 5 pancreatectomized dogs, whereas only total IRG increased in the normal control dogs. It is concluded that extrapancreatic glucagon responds to intraluminal administration of nutrients, as pancreatic glucagon does. In addition, gut glucagon-like immunoreactivity increased following glucose or arginine ingestion in pancreatectomized dogs. Furthermore, the failure in response of plasma IRG and total IRG to butter load in pancreatectomized animals suggests that its intraluminal hydrolysis is important in the secretion of extrapancreatic immunoreactive glucagon.     

Islet-activating protein (IAP)-induced adrenergic modulation of pancreatic A and B cell in dogs

Islet-activating protein (IAP) is a substance purified from the culture medium of Bordetella pertussis, and its main action is characterized by the enhancement of secretory response to glucose and other stimuli in pancreatic islet. In this experiment, the effect of IAP on epinephrine-induced secretion of immunoreactive insulin (IRI) and glucagon (IRG) was investigated in normal dogs. Epinephrine suppressed IRI secretion and it had a little increment to IRG secretion in control group, while IRI and IRG secretions were significantly increased by epinephrine in IAP pretreated group. Using beta-blocker (Propranolol) with epinephrine, these increments of IRI and IRG secretions in IAP pretreated group were abolished. However, using alpha-blocker (Phentolamine) with epinephrine, these secretions of IRI and IRG in IAP pretreated group were much more increased than epinephrine alone induced secretions. Blood glucose levels were lower in IAP pretreated group than in control group throughout the loading tests in all of the experiments. These findings suggest that (1) IAP decreases blood glucose level and (2) IAP enhances epinephrine-induced secretion of insulin and glucagon by acceleration of beta-adrenergic effect and by reduction of alpha-adrenergic suppression in dogs.     

Developing a risk scoring system based on immune-related lncRNAs for patients with gastric cancer

The immune system and the tumor interact closely during tumor development. Aberrantly expressed long non-coding RNAs (lncRNAs) may be potentially applied as diagnostic and prognostic markers for gastric cancer (GC). At present, the diagnosis and treatment of GC patients remain a formidable clinical challenge. The present study aimed to build a risk scoring system to improve the prognosis of GC patients. In the present study, ssGSEA was used to evaluate the infiltration of immune cells in GC tumor tissue samples, and the samples were split into a high immune cell infiltration group and a low immune cell infiltration group. About 1262 differentially expressed lncRNAs between the high immune cell infiltration group and the low immune cell infiltration group. About 3204 differentially expressed lncRNAs between GC tumor tissues and paracancerous tissues were identified. Then, 621 immune-related lncRNAs were screened using a Venn analysis based on the above results, and 85 prognostic lncRNAs were identified using a univariate Cox analysis. We constructed a prognostic signature using LASSO analysis and evaluated the predictive performance of the signature using ROC analysis. GO and KEGG enrichment analyses were performed on the lncRNAs using the R package, ‘clusterProfiler’. The TIMER online database was used to analyze correlations between the risk score and the abundances of the six types of immune cells. In conclusion, our study found that specific immune-related lncRNAs were clinically significant. These lncRNAs were used to construct a reliable prognostic signature and analyzed immune infiltrates, which may assist clinicians in developing individualized treatment strategies for GC patients.     

Identification of a prognostic gene signature based on an immunogenomic landscape analysis of bladder cancer

Cancer immune plays a critical role in cancer progression. Tumour immunology and immunotherapy are one of the exciting areas in bladder cancer research. In this study, we aimed to develop an immune‐related gene signature to improve the prognostic prediction of bladder cancer. Firstly, we identified 392 differentially expressed immune‐related genes (IRGs) based on TCGA and ImmPort databases. Functional enrichment analysis revealed that these genes were enriched in inflammatory and immune‐related pathways, including in ‘regulation of signaling receptor activity’, ‘cytokine‐cytokine receptor interaction’ and ‘GPCR ligand binding’. Then, we separated all samples in TCGA data set into the training cohort and the testing cohort in a ratio of 3:1 randomly. Data set {"type":"entrez-geo","attrs":{"text":"GSE13507","term_id":"13507"}}GSE13507 was set as the validation cohort. We constructed a prognostic six‐IRG signature with LASSO Cox regression in the training cohort, including AHNAK, OAS1, APOBEC3H, SCG2, CTSE and KIR2DS4. Six IRGs reflected the microenvironment of bladder cancer, especially immune cell infiltration. The prognostic value of six‐IRG signature was further validated in the testing cohort and the validation cohort. The results of multivariable Cox regression and subgroup analysis revealed that six‐IRG signature was a clinically independent prognostic factor for bladder cancer patients. Further, we constructed a nomogram based on six‐IRG signature and other clinicopathological risk factors, and it performed well in predict patients'' survival. Finally, we found six‐IRG signature showed significant difference in different molecular subtypes of bladder cancer. In conclusions, our research provided a novel immune‐related gene signature to estimate prognosis for patients'' survival with bladder cancer.     

Identification of a novel cell cycle-related gene signature predicting survival in patients with gastric cancer

Gastric cancer (GC) is one of the most fatal cancers in the world. Thousands of biomarkers have been explored that might be related to survival and prognosis via database mining. However, the prediction effect of single gene biomarkers is not specific enough. Increasing evidence suggests that gene signatures are emerging as a possible better alternative. We aimed to develop a novel gene signature to improve the prognosis prediction of GC. Using the messenger RNA (mRNA)-mining approach, we performed mRNA expression profiling in a large GC cohort (n = 375) from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) was performed, and we recovered genes related to the G2/M checkpoint, which we identified with a Cox proportional regression model. We identified a set of five genes (MARCKS, CCNF, MAPK14, INCENP, and CHAF1A), which were significantly associated with overall survival (OS) in the test series. Based on this five-gene signature, the test series patients could be classified into high-risk or low-risk subgroups. Multivariate Cox regression analysis indicated that the prognostic power of this five-gene signature was independent of clinical features. In conclusion, we developed a five-gene signature related to the cell cycle that can predict survival for GC. Our findings provide novel insight that is useful for understanding cell cycle mechanisms and for identifying patients with GC with poor prognoses.     

Factors associated with immunotherapy respond and survival in advanced non-small cell lung cancer patients

ObjectivesThis study aimed to explore factors associated with immunotherapy respond and survival in advanced non-small cell lung cancer (aNSCLC) patients treated with immune checkpoint inhibitors (ICIs).MethodsA total of 101 patients with aNSCLC receiving ICIs were included. The association between clinical factors and multiple endpoints including objective response rate (ORR), disease control rate (DCR), overall survival (OS) and progression-free survival (PFS) were investigated by multivariate analyses.ResultsMultivariate logistic analyses revealed that clinical stage, lactate dehydrogena (LDH), and any grade immune-related adverse events (irAEs) were independent predictors of ORR, while LDH and ICIs treatment type were independent predictors of DCR. In Multivariate Cox analysis, Eastern Cooperative Oncology Group performance status (ECOG PS), LDH, albumin (Alb), platelet to lymphocyte ratio (PLR), and any grade irAEs were independent factors for OS. Similarly, clinical stage, LDH, Alb, and any grade irAEs were independent factors for PFS. Pre-treatment prognostic score was established based on clinical stage, ECOG PS, LDH, Alb and PLR to classify patients into three groups: the good group (0–1 score), the intermediate group (2 scores) and the poor group (3-4 scores). The immunotherapy response was significantly different in various prognostic groups. Subset analyses showed pre-treatment prognostic score ≥ 3 tended to have a strong negative impact on survival among patients with programmed cell death-ligand 1 (PD-L1) expression ≥ 50%.ConclusionsPre-treatment prognostic score based on clinical stage, ECOG PS, LDH, Alb and PLR may help to identify aNSCLC patients who may benefit from ICIs.     

Immune signatures in cutaneous melanoma correlate with survival independently of immunotherapy treatment

Immune checkpoint inhibitors (ICIs) have fundamentally improved survival from advanced cutaneous melanoma. Significant efforts have been made to understand the ICI response to identify ways to further improve outcomes. One such approach has been to investigate gene expression associated with response to ICI, which has identified various immune-related mRNA signatures, including a six-gene IFN-γ signature (IFN-γ⁶), an expanded immune signature (IFN-γ¹⁸), an effector T-cell gene signature (T_eff), and a T_eff-associated and IFN-γ-associated gene signature (T_eff + IFN-γ). Given that these signatures appear to reflect expression from T cells and the level of tumour-infiltrating immune cells has been associated with survival, we hypothesised that the prognostic value of the signatures is not limited to ICI treatment and investigated if they were associated with survival also in patients who never received ICI. The signatures were not present in melanoma cell lines when compared with tumour samples, confirming that the signatures were likely derived from the samples' non-tumour (immune) components. We acquired expression and survival data from five melanoma cohorts with a wide range of disease stages, treatments and metrics for survival, and correlated the expression signatures with survival. All four signatures were significantly associated (p < .05) with survival in four of five cohorts, with hazard ratios ranging from 0.69 to 0.92. We conclude that these immune signatures' association with survival is not specific to ICI-treated patients, but present in a number of settings.     

Plasma glucagon response to intravenous alanine in obese and non-obese subjects

To investigate glucagon (IRG) and insulin (IRI) responses to alanine infusion in obesity and to assess the effect of body weight reduction with respect to hormonal balance, we compared six obese subjects with nine normal weight controls. None of the subjects were diabetic by OGTT criteria. Plasma IRI and IRG were measured following IV alanine at a rate of 0.1 g/kg over a period of 2 min. Our obese subjects had an increase in IRG response to alanine, which was due to decreased suppression of alpha-cell function due to insulin resistance. Weight reduction via calorie restriction reduced insulin demand, resulting in reduced plasma IRI by restoring beta-cell function, and the IRG response was paradoxically decreased as compared with that before weight loss. It is conceivable that improvements in insulin sensitivity after body weight reduction may re-establish the normalization of pancreatic beta-cell function and the insulin-induced inhibition of IRG secretion. Our obese subjects were characterized by decreased IRG secretion which was reflected in a change in body weight reduction.     

Development of a novel gene signature in patients without Helicobacter pylori infection gastric cancer

Gastric cancer (GC) is one of the most fatal common cancers in worldwide. Helicobacter pylori (H. pylori) infection is closely related to the development of GC, although the mechanism is still unclear. In our study, we aim to develop a robust messenger RNA (mRNA) signature associated with H. pylori (-) GC that can sensitively and efficiently predict the prognostic. The RNA-seq expression profile and corresponding clinical data of 598 gastric cancer samples and 63 normal samples obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database. Using gene set enrichment analysis H. pylori (+) GC and H. pylori (-) GC patients and normal samples to select certain genes for further analysis. Using univariate and multivariate Cox regression model to establish a gene signature for predicting the overall survival (OS). Finally, we identified G2/M related seven-mRNA signature (TGFB1, EGF, MKI67, ILF3, INCENP, TNPO2, and CHAF1A) closely related to the prognosis of patients with H. pylori (-) GC. The seven-mRNA signature was identified to act as an independent prognostic biomarker by stratified analysis and multivariate Cox regression analysis. It was also validated on two test groups from TCGA and GSE15460 and shown that patients with high-risk scores based on the expression of the seven mRNAs had significantly shorter survival times compared to patients with low-risk scores (P < .0001). In this study, we developed a seven-mRNA signature related to G2/M checkpoint from H. pylori (-) GCs that as an independent biomarker potentially with a good performance in predicting OS and might be valuable for the clinical management for patients with GC.     

Comparative immunoproteomics of identification and characterization of virulence factors from Helicobacter pylori related to gastric cancer

Helicobacter pylori is an important risk factor of gastric cancer (GC). Although many H. pylori virulence factors have been reported, the pathogenic mechanism by which H. pylori infection causes GC remains unclear. The aims of this study were to identify GC-related antigens from H. pylori and characterize their roles in the development of GC. As GC and duodenal ulcer (DU) are considered clinically divergent, we compared two-dimensional immunoblots of an acid-glycine extract of H. pylori probed with serum samples from 15 patients with GC and 15 with DU to find GC-related antigens, which were subsequently identified by mass spectrometry. Many protein spots were recognized by more than one serum, and 24 of these were better recognized by GC sera. The proteins showing higher frequency of recognition in GC group are threonine synthase, rod shape-determining protein, S-adenosylmethionine synthetase, peptide chain release factor 1, DNA-directed RNA polymerase alpha subunit, co-chaperonin GroES (monomeric and dimeric forms), response regulator OmpR, and membrane fusion protein. Of these proteins, GroES was identified as a dominant GC-related antigen with a much higher seropositivity of GC samples (64.2%, n = 95) compared with 30.9% for gastritis (n = 94) and 35.5% for DU (n = 124). GroES seropositivity was more commonly associated with antral GC than with non-antral GC (odds ratio = 2.7; 95% confidence interval, 1.1-6.7). In peripheral blood mononuclear cells, GroES stimulated production of interleukin (IL)-8, IL-6, granulocyte macrophage colony-stimulating factor, IL-1beta, tumor necrosis factor-alpha, cyclooxygenase-2, and prostaglandin E(2). Moreover when incubated with gastric epithelial cells, GroES induced expression of IL-8, cell proliferation, and up-regulation of c-jun, c-fos, and cyclin D1 but caused down-regulation of p27(Kip1). We conclude that GroES of H. pylori is a novel GC-associated virulence factor and may contribute to gastric carcinogenesis via induction of inflammation and promotion of cell proliferation.