Immune Marker Genes Research Articles

Hexokinase 2 expression in apical enterocytes correlates with inflammation severity in patients with inflammatory bowel disease

BackgroundInflammation is characterized by a metabolic switch promoting glycolysis and lactate production. Hexokinases (HK) catalyze the first reaction of glycolysis and inhibition of epithelial HK2 protected from colitis in mice. HK2 expression has been described as elevated in patients with intestinal inflammation; however, there is conflicting data from few cohorts especially with severely inflamed individuals; thus, systematic studies linking disease activity with HK2 levels are needed.MethodsWe examined the relationship between HK2 expression and inflammation severity using bulk transcriptome data derived from the mucosa of thoroughly phenotyped inflammatory bowel disease (IBD) patients of two independent cohorts including both subtypes Crohn’s disease (CD) and ulcerative colitis (UC). Publicly available single-cell RNA sequencing data were analyzed, and immunofluorescence staining on colonic biopsies of unrelated patients with intestinal inflammation was performed to confirm the RNA-based findings on cellular and protein level.ResultsHK2 expression gradually increased from mild to intermediate inflammation, yet strongly declined at high inflammation scores. Expression of epithelial marker genes also declined at high inflammation scores, whereas that of candidate immune marker genes increased, indicating a cellular remodeling of the mucosa during inflammation with an infiltration of HK2-negative immune cells and a loss of terminal differentiated epithelial cells in the apical epithelium—the main site of HK2 expression. Normalizing for the enterocyte loss clearly identified epithelial HK2 expression as gradually increasing with disease activity and remaining elevated at high inflammation scores. HK2 protein expression was mostly restricted to brush border enterocytes, and these cells along with HK2 levels vanished with increasing disease severity.ConclusionsOur findings clearly define dysregulated epithelial HK2 expression as an indicator of disease activity in intestinal inflammation and suggest targeted HK2-inhibition as a potential therapeutic avenue.

Bursaphelenchus xylophilus Venom Allergen-Like Protein BxVAP1, Triggering Plant Defense-Related Programmed Cell Death, Plays an Important Role in Regulating Pinus massoniana Terpene Defense Responses.

Bursaphelenchus xylophilus (pine wood nematode, PWN), a migratory plant-parasitic nematode, acts as an etiological agent, inflicting considerable damage to pine forests worldwide. Plant immunity constitutes a crucial factor in resisting various pathogenic invasions. The primary defensive responses of host pines against PWN infection encompass terpene accumulation, defense response-related gene expression, and programmed cell death. Venom allergen-like proteins (VAPs), as potential effectors, are instrumental in facilitating the successful colonization of PWNs. In this study, we investigated the inhibition of B. xylophilus VAP (BxVAP1) expression by RNA interference in vitro. Following BxVAP1 silencing, the reproduction rate and migration rate of the PWN population in Pinus massoniana decreased, the expression of the α-pinene synthase gene was induced, other terpene synthase and pathogenesis-related genes were inhibited and delayed, the peak times and levels of terpene-related substances were changed, and the degree of cavitation in P. massoniana was diminished. Transient expression of BxVAP1 in Nicotiana benthamiana revealed that BxVAP1 was expressed in both the cell membrane and nucleus, inducing programmed cell death and the expression of pathogen-associated molecular pattern-triggered immunity marker genes (NbAcre31 and NbPTI5). This study is the first to demonstrate that silencing the BxVAP1 gene affects host defense responses, including terpenoid metabolism in P. massoniana, and that BxVAP1 can be recognized by N. benthamiana as an effector to trigger its innate immunity, expanding our understanding of the parasitic mechanism of B. xylophilus.

The MAP4 kinase NbM4K3 regulates immune responses in Nicotiana benthamiana

The mitogen-activated protein kinase kinase kinase kinase (M4K) family is evolutionarily conserved across plants and animals. In Arabidopsis, the protein kinase SIK1, an M4K member, is known to positively modulate reactive oxygen species (ROS) production during pattern-triggered immunity (PTI) by stabilizing BIK1, a key receptor-like cytoplasmic kinase (RLCK). While homologs of SIK1 exhibit conserved protein domain architectures across a range of land plants, their functional conservation remains incompletely understood. This study investigates the functional conservation and divergence of SIK1 homologs, focusing particularly on NbM4K3 in Nicotiana benthamiana. Silencing NbM4K3 resulted in an impairment of the flg22-induced ROS burst and expression of PTI marker genes. Additionally, silencing NbM4K3 led to diminished protein accumulation of RLCKs, while overexpression of the RLCKs prominently enhanced the flg22-induced ROS burst in NbM4K3-silenced plants. Furthermore, NbM4K3-silenced plants exhibited a compromised hypersensitive response (HR), reduced ROS accumulation, and diminished expression of effector-triggered immunity (ETI) marker genes when challenged with the avirulent strains Ralstonia solanacearum GMI1000 and Pseudomonas syringae DC3000, suggesting that NbM4K3 is a positive regulator of ETI. The attenuated HR phenotype observed in NbM4K3-silenced plants upon expression of RipP1 or RipE1, two avirulent type III effectors of GMI1000, further supports the affirmative role of NbM4K3 in ETI. In summary, our data indicate that the M4K NbM4K3 positively regulates both PTI and ETI in N. benthamiana, potentially by stabilizing RLCKs. These findings not only strengthen the role of M4K family in plant immunity but also suggest its potential in improving disease resistance in plants.

Construction and Evaluation of a Prognostic Risk Prediction Model of Pancreatic Ductal Adenocarcinoma Based on Immune-Related Genes

Objective To construct a risk prediction model by integrating the molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) and immune-related genes.Methods With GSE71729 data set (n=145) as the training set,the differentially expressed genes and differential immune-related genes between the squamous and non-squamous subtypes of PDAC were integrated to construct a regulatory network,on the basis of which five immune marker genes regulating the squamous subtype were screened out.An integrated immune score (IIS) model was constructed based on patient survival information and immune marker genes to predict the clinical prognosis of PDAC patients,and its predictive performance was tested with 5 validation sets (n=758).Results PDAC patients were assigned into high risk and low risk groups according to the IIS.In both training and validation sets,the overall survival of patients in the high risk group was shorter than that in the low risk group (both P<0.001).The multivariable Cox regression showed that IIS was an independent prognostic factor for PDAC (HR=2.16,95%CI=1.50-3.10,P<0.001).Conclusion IIS can be used for risk stratification of PDAC patients and may become a potential prognostic marker for PDAC.

Potential marker genes for chronic obstructive pulmonary disease revealed based on single-cell sequencing and Mendelian randomization analysis.

Progress is being made in the prevention and treatment of chronic obstructive pulmonary disease (COPD), but it is still unsatisfactory. With the development of genetic technology, validated genetic information can better explain COPD. The study utilized scRNA-seq and Mendelian randomization analysis of eQTLs to identify crucial genes and potential mechanistic pathways underlying COPD pathogenesis. Single-cell sequencing data were used to identify marker genes for immune cells in the COPD process. Data on eQTLs for immune cell marker genes were obtained from the eQTLGen consortium. To estimate the causal effect of marker genes on COPD, we selected an independent cohort (ukb-b-16751) derived from the UK Biobank database for two-sample Mendelian randomization analysis. Subsequently, we performed immune infiltration analysis, gene set enrichment analysis (GSEA), and co-expression network analysis on the key genes. The 154 immune cell-associated marker genes identified were mainly involved in pathways such as vacuolar cleavage, positive regulation of immune response and regulation of cell activation. Mendelian randomization analysis screened four pairs of marker genes (GZMH, COTL1, CSTA and CD14) were causally associated with COPD. These four key genes were significantly associated with immune cells. In addition, we have identified potential transcription factors associated with these key genes using the Cistrome database, thus contributing to a deeper understanding of the regulatory network of these gene expressions. This eQTLs Mendelian randomization study identified four key genes (GZMH, COTL1, CSTA, and CD14) causally associated with COPD, providing new insights for prevention and treatment of COPD.

Immune Rejection Mediated by prf1 and gzmb Affects the Colonization of Fat Greenling (Hexagrammos otakii) Spermatogonia in Heterotransplantation.

Fish germ cell transplantation holds great potential for conserving endangered species, improving cultured fish breeds, and exploring reproductive techniques. However, low transplantation efficiency is a common issue in heterotransplantation. This study transplanted fat greenling (Hexagrammos otakii) spermatogonia into the testes of spotted sea bass (Lateolabrax maculatus) to investigate factors that might affect the colonization and fixation of heterologous transplanted germ cells. Results indicated that transplanted fat greenling spermatogonia cells were successfully detected in the early transplantation phase in spotted sea bass. Their numbers gradually decreased over time, and after 10 days post-transplantation, more than 90% of the transplanted cells underwent apoptosis. Transcriptome sequencing analysis of the testes of spotted sea bass and fat greenling spermatogonia on days 1 and 10 post-transplantation revealed that this apoptosis process involved many immune-related genes and their associated signaling pathways. Acute immune rejection marker genes prf1 and gzmb were detected in the spotted sea bass testes, while immune tolerance genes lck and zap-70 were expressed in the fat greenling spermatogonia. Additionally, differential expression of prf1 and gzmb genes was screened from spotted sea bass, with experimental evidence indicating that PRF1 and GZMB protein from spotted sea bass primarily induce apoptosis in transplanted fat greenling spermatogonia via the mitochondrial apoptosis pathway, at the protein level. This suggests that the difficulties in heterotransplantation are primarily related to acute immune rejection, with PRF1 and GZMB playing significant roles.

Virus-specific antibody secreting cells reside in the peritoneal cavity and systemic immune sites of Atlantic salmon (Salmo salar) challenged intraperitoneally with salmonid alphavirus

The development and persistence of antibody secreting cells (ASC) after antigenic challenge remain inadequately understood in teleosts. In this study, intraperitoneal (ip) injection of Atlantic salmon (Salmo salar) with salmonid alphavirus (WtSAV3) increased the total ASC response, peaking 3–6 weeks post injection (wpi) locally in the peritoneal cavity (PerC) and in systemic lymphoid tissues, while at 13 wpi the response was only elevated in PerC. At the same time point a specific ASC response was induced by WtSAV3 in PerC and systemic tissues, with the highest frequency in PerC, suggesting a local role. Inactivated SAV (InSAV1) induced comparatively lower ASC responses in all sites, and specific serum antibodies were only induced by WtSAV3 and not by InSAV1. An InSAV1 boost did not increase these responses. Expression of immune marker genes implies a role for PerC adipose tissue in the PerC immune response. Overall, the study suggests the Atlantic salmon PerC as a secondary immune site and an ASC survival niche.

Cordycepin enhances anti-tumor immunity in breast cancer by enhanceing ALB expression

ObjectiveThe treatment of breast cancer still faces great challenges, and it is necessary to continuously explore effective drugs and targets to promote immune precision medicine. This study aims to investigate the immune-related regulatory mechanism of cordycepin in breast cancer. MethodsNetwork pharmacology was employed to discovery the action of cordyceps on breast cancer targets, molecular docking was employed to analyze the interaction pattern between core components and targets, and biological information analysis was used to explore the target-related immune mechanism and verified in vitro experiments. ResultsThe results of this study indicate that cordycepin can effectively inhibit breast cancer. The roles of cordycepin's active component and its target gene ALB were elucidated through the combined use of network pharmacology and molecular docking. Bioinformatics analysis revealed convincing associations between ALB and many immune pathway marker genes. ALB was inhibited in tumor expression, and cordycepin was found to enhance the expression of ALB in vitro to play an anti-tumor role. ConclusionCordycepin regulates immune suppression of tumor, which is expected to open a new chapter of breast cancer immunotherapy.

CCDC58 is a potential biomarker for diagnosis, prognosis, immunity, and genomic heterogeneity in pan-cancer

Coiled-coil domain-containing 58 (CCDC58) is a member of the CCDC protein family. Similar to other members, CCDC58 exhibits potential tumorigenic roles in a variety of malignancies. However, there is no systematic and comprehensive pan-cancer analysis to investigate the diagnosis, prognosis, immune infiltration, and other related functions of CCDC58. We used several online websites and databases, such as TCGA, GTEx, UALCAN, HPA, CancerSEA, BioGRID, GEPIA 2.0, TIMER 2.0, and TISIDB, to extract CCDC58 expression data and clinical data of patients in pan-cancer. Then, the relationship between CCDC58 expression and diagnosis, prognosis, genetic alterations, DNA methylation, genomic heterogeneity, and immune infiltration level were determined. In addition, the biological function of CCDC58 in liver hepatocellular carcinoma (LIHC) was investigated. Pan-cancer analysis results showed that CCDC58 was differentially expressed in most tumors and showed excellent performance in diagnosis and prediction of prognosis. The expression of CCDC58 was highly correlated with genetic alterations, DNA methylation, and genomic heterogeneity in some tumors. In addition, the correlation analysis of CCDC58 with the level of immune infiltration and immune checkpoint marker genes indicated that CCDC58 might affect the composition of the tumor immune microenvironment. Enrichment analysis showed that CCDC58-related genes were mainly linked to mitosis, chromosome, and cell cycle. Finally, biological function experiments demonstrated that CCDC58 plays an important role in tumor cell proliferation and migration. CCDC58 was first identified as a pan-cancer biomarker. It may be used as a potential therapeutic target to improve the prognosis of patients in the future.

Class II diacylglycerol kinases participate in the basal immune responses of Nicotiana benthamiana to Ralstonia solanacearum

Phospholipid signaling plays an important role in Nicotiana benthamiana immune responses to phytopathogenic bacteria. In this study, we isolated three orthologs encoding class II diacylglycerol kinase (NbDGK4-1, NbDGK4-2 and NbDGK7) in the N. benthamiana genome. In contrast to the undetectable expression of NbDGK4-2, the NbDGK4-1 and NbDGK7 expression levels increased in response to Ralstonia solanacearum and the flg22 peptide. The induction of the hypersensitive response was not affected, but bacterial growth increased and the onset of bacterial wilt symptoms was accelerated in the NbDGK4-1-silenced and NbDGK7-silenced plants challenged with R. solanacearum. The expression levels of NbPR-1 and NbPR-4 (marker genes for salicylic acid and jasmonic acid signaling, respectively) decreased in the NbDGK4-1-silenced and NbDGK7-silenced plants inoculated with R. solanacearum. The expression of pathogen-associated molecular pattern-triggered immunity (PTI) marker genes were also inhibited in the NbDGK4-1-silenced and NbDGK7-silenced plants infiltrated with the type III secretion system (T3SS)-deficient R. solanacearum mutant or flg22. Accordingly, the T3SS-deficient R. solanacearum bacterial population increased in the NbDGK4-1-silenced and NbDGK7-silenced plants. Moreover, flg22-induced resistance and callose deposition were also compromised in the NbDGK4-1-silenced and NbDGK7-silenced plants. Considered together, the study results indicate class II diacylglycerol kinases may be important for N. benthamiana basal disease resistance (e.g., PTI responses).

Abstract 7036: Integrative biomarker profiling for predicting immunotherapy outcomes in gynecologic cancers

Abstract Immunotherapy with immune checkpoint inhibitors (ICI) has proven effective for various solid tumors, such as those in the lungs, urinary tract, and skin. However, its efficacy in gynecologic (GYN) cancers has been limited, with response rates of 11-17% in recurrent cases. Only a minority of patients with DNA mismatch repair deficiencies exhibit favorable responses to PD-1 inhibitors. The predictability of PD-L1 expression in GYN cancers remains inconsistent. Our research aimed to identify and prioritize biomarkers and mechanisms linked to ICI resistance in GYN oncology, targeting those who could benefit from these treatments.We gathered clinical and pathological data from 49 patients with ovarian, endometrial, and cervical cancers at various stages, all treated with ICI. We performed comprehensive analyses, including transcriptome-based immune cell abundance estimation, signaling pathway enrichment, and correlation with ICI treatment responses and survival outcomes. Our previous work highlighted TGF-β and CD47's roles in immunotherapy resistance, facilitating an immunosuppressive environment within our GYN cancer cohort. Moreover, we conducted a stoichiometry constraint-based genome-scale metabolic model and computed correlation-grouped metabolic activity scores (cgScore) using metabolic enzyme gene expression as constraints. Among 1533 metabolic reactions, pyruvate transport and folate metabolism stood out as the most upregulated in responders versus those who progressed.Upon identifying several promising biomarkers, we used logistic regression classifiers to decipher the predictive value of each. Our model included clinical-demographic (age, BMI, cancer type, stage) and molecular-genomic features (immune marker gene expression, TopTGF-β score, immune cell abundance from transcriptomic deconvolution, and the top 2 cgScores). Analysis divided into training and testing sets highlighted features such as stage, BMI, eosinophils, CD274, CD47, and the pyruvate transport reaction as significant predictors of ICI response. The model achieved an 80% accuracy rate on the test set, confirmed by permutation importance from scikit-learn. We also used a Regularized Cox model to link predictors with progression-free survival, emphasizing the roles of BMI, plasma cells, CD276, pyruvate transport reaction, and folate metabolism. In conclusion, there are immunological and metabolic markers have the potential to serve as predictive indicators for ICI treatment response and survival in GYN cancers. Understanding these predictors can profoundly influence clinical decision-making in immunotherapy, ultimately leading to enhanced patient outcomes and personalized treatment approaches. Citation Format: Gideon Idumah, Lin Li, Haider Mahdi, Ying Ni. Integrative biomarker profiling for predicting immunotherapy outcomes in gynecologic cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7036.

A novel lectin receptor kinase gene, AtG-LecRK-I.2, enhances bacterial pathogen resistance through regulation of stomatal immunity in Arabidopsis

The S-locus lectin receptor kinases (G-LecRKs) have been suggested as receptors for microbe/damage-associated molecular patterns (MAMPs/DAMPs) and to be involved in the pathogen defense responses, but the functions of most G-LecRKs in biotic stress response have not been characterized. Here, we identified a member of this family, G-LecRK-I.2, that positively regulates flg22- and Pseudomonas syringae pv. tomato (Pst) DC3000-induced stomatal closure. G-LecRK-I.2 was rapidly phosphorylated under flg22 treatment and could interact with the FLS2/BAK1 complex. Two T-DNA insertion lines, glecrk-i.2–1 and glecrk-i.2–2, had lower levels of reactive oxygen species (ROS) and nitric oxide (NO) production in guard cells, as compared with the wild-type Col-0, under Pst DC3000 infection. Also, the immunity marker genes CBP60g and PR1 were induced at lower levels under Pst DC3000 hrcC- infection in glecrk-i.2–1 and glecrk-i.2–2. The GUS reporter system also revealed that G-LecRK-I.2 was expressed only in guard cells. We also found that G-LecRK-I.2 could interact H+-ATPase AHA1 to regulate H+-ATPase activity in the guard cells. Taken together, our results show that G-LecRK-I.2 plays an important role in regulating stomatal closure under flg22 and Pst DC3000 treatments and in ROS and NO signaling specifically in guard cells.

Immunomodulation Evidence of Nanostructured Recombinant Proteins in Salmonid Cells.

Recent studies have demonstrated that immune-related recombinant proteins can enhance immune function, increasing host survival against infectious diseases in salmonids. This research evaluated inclusion bodies (IBs) of antimicrobial peptides (CAMPIB and HAMPIB) and a cytokine (IL1βIB and TNFαIB) as potential immunostimulants in farmed salmonids. For this purpose, we produced five IBs (including iRFPIB as a control), and we evaluated their ability to modulate immune marker gene expression of three IBs in the RTS11 cell line by RT-qPCR. Additionally, we characterized the scale-up of IBs production by comparing two different scale systems. The results showed that CAMPIB can increase the upregulation of tnfα, il1β, il8, and il10, HAMPIB significantly increases the upregulation of tnfα, inos, and il10, and IL1βIB significantly upregulated the expression of tnfα, il1β, and cox2. A comparison of IL1βIB production showed that the yield was greater in shake flasks than in bioreactors (39 ± 1.15 mg/L and 14.5 ± 4.08 mg/L), and larger nanoparticles were produced in shake flasks (540 ± 129 nm and 427 ± 134 nm, p < 0.0001, respectively). However, compared with its shake flask counterpart, the IL1βIB produced in a bioreactor has an increased immunomodulatory ability. Further studies are needed to understand the immune response pathways activated by IBs and the optimal production conditions in bioreactors, such as a defined medium, fed-batch production, and mechanical bacterial lysis, to increase yield.

Oligogalacturonide application increases resistance to Fusarium head blight in durum wheat.

Fusariosis causes substantial yield losses in the wheat crop worldwide and compromises food safety because of the presence of toxins associated with the fungal disease. Among the current approaches to crop protection, the use of elicitors able to activate natural defense mechanisms in plants is a strategy gaining increasing attention. Several studies indicate that applications of plant cell-wall-derived elicitors, such as oligogalacturonides (OGs) derived from partial degradation of pectin, induce local and systemic resistance against plant pathogens. The aim of this study was to establish the efficacy of OGs in protecting durum wheat (Triticum turgidum subsp. durum), which is characterized by an extreme susceptibility to Fusarium graminearum. To evaluate the functionality of OGs, spikes and seedlings of cv. Svevo were inoculated with OGs, F. graminearum spores, and a co-treatment of both. Results demonstrated that OGs are active elicitors of wheat defenses, triggering typical immune marker genes and determining regulation of fungal genes. Moreover, bioassays on spikes and transcriptomic analyses on seedlings showed that OGs can regulate relevant physiological processes in Svevo with dose-dependent specificity. Thus, the OG sensing system plays an important role in fine tuning immune signaling pathways in durum wheat.

Chronic Inflammation Disrupts Circadian Rhythms in Splenic CD4+ and CD8+ T Cells in Mice.

Internal circadian clocks coordinate 24 h rhythms in behavior and physiology. Many immune functions show daily oscillations, and cellular circadian clocks can impact immune functions and disease outcome. Inflammation may disrupt circadian clocks in peripheral tissues and innate immune cells. However, it remains elusive if chronic inflammation impacts adaptive immune cell clock, e.g., in CD4+ and CD8+ T lymphocytes. We studied this in the experimental autoimmune encephalomyelitis (EAE), a mouse model for multiple sclerosis, as an established experimental paradigm for chronic inflammation. We analyzed splenic T cell circadian clock and immune gene expression rhythms in mice with late-stage EAE, CFA/PTx-treated, and untreated mice. In both treatment groups, clock gene expression rhythms were altered with differential effects for baseline expression and peak phase compared with control mice. Most immune cell marker genes tested in this study did not show circadian oscillations in either of the three groups, but time-of-day- independent alterations were observed in EAE and CFA/PTx compared to control mice. Notably, T cell effects were likely independent of central clock function as circadian behavioral rhythms in EAE mice remained intact. Together, chronic inflammation induced by CFA/PTx treatment and EAE immunization has lasting effects on circadian rhythms in peripheral immune cells.

Systemic resistance induced in tomato plants by Beauveria bassiana-derived proteins against tomato yellow leaf curl virus and aphid Myzus persicae.

Tomato (Solanum lycopersicum L.) is an economically important vegetable crop around the globe. Tomato yellow leaf curling (TYLC) is the most devastating viral disease posing a serious threat to tomato production throughout the tropical and subtropical world. Induction of microbe-mediated systemic resistance in plants has been of great interest in recent years as a novel microbiological tool in disease and insect pest management. This in-vitro study aimed to determine the effectiveness of different strains (BB252, BB72 and ARSEF-2860) of a hypocreal fungus Beauveria bassiana against TYLCV disease and aphid Myzus persicae. Potted tomato plants exogenously treated with conidial and filtrate suspensions of B. bassiana strains and of their partially purified or purified proteins were exposed to TYLCV inoculum and aphid M. persicae. Results showed a significant suppression of TYLCV disease severity index by the exogenous application of conidial, filtrate and protein treatments of all B. bassiana strains and this response was directly proportional to the treatment concentration. Similarly, mean fecundity rate of M. persicae was also significantly reduced by the highest concentration of ARSEF-2860-derived elicitor protein PeBb1, followed by the highest concentrations of BB252- and BB72-derived partially purified proteins. Moreover, these B. bassiana-derived proteins also caused a significant upregulation of most of the plant immune marker genes associated with plant defense. Overall, the study findings suggest that these B. bassiana strains and their partially purified or purified elicitor proteins could be effective biological tools for the management of TYLCV and aphid infestation on tomato plants. © 2023 Society of Chemical Industry.

Predictable regulation of survival by intratumoral microbe-immune crosstalk in patients with lung adenocarcinoma.

Intratumoral microbiota can regulate the tumor immune microenvironment (TIME) and mediate tumor prognosis by promoting inflammatory response or inhibiting anti-tumor effects. Recent studies have elucidated the potential role of local tumor microbiota in the development and progression of lung adenocarcinoma (LUAD). However, whether intratumoral microbes are involved in the TIME that mediates the prognosis of LUAD remains unknown. Here, we obtained the matched tumor microbiome and host transcriptome and survival data of 478 patients with LUAD in The Cancer Genome Atlas (TCGA). Machine learning models based on immune cell marker genes can predict 1- to 5-year survival with relative accuracy. Patients were stratified into high- and low-survival-risk groups based on immune cell marker genes, with significant differences in intratumoral microbial communities. Specifically, patients in the high-risk group had significantly higher alpha diversity (p < 0.05) and were characterized by an enrichment of lung cancer-related genera such as Streptococcus. However, network analysis highlighted a more active pattern of dominant bacteria and immune cell crosstalk in TIME in the low-risk group compared to the high-risk group. Our study demonstrated that intratumoral microbiota-immune crosstalk was strongly associated with prognosis in LUAD patients, which would provide new targets for the development of precise therapeutic strategies.

Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images.

Immune-based therapy is a promising type of treatment for hepatocellular carcinoma (HCC) but has only been partially successful due to the high heterogeneity in HCC tumor. The differences in the degree of tumor cell progression and in the activity of tumor immune microenvironment could lead to varied clinical outcome. Accurate subgrouping for recurrence risk is an approach to address the issue of such heterogeneity. It remains under investigation as whether integrating quantitative whole slide image (WSI) features with the expression profile of immune marker genes can improve the risk stratification, and whether clinical outcome prediction can assist in understanding molecular biology that drives the outcome. We included a total of 231 patients from the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) project. For each patient, we extracted 18 statistical metrics corresponding to a global region of interest and 135 features regarding nucleus shape from WSI. A risk score was developed using these image features with high-dimensional survival modeling. We also introduced into the model the expression profile of 66 representative marker genes relevant to currently available immunotherapies. We stratified all patients into higher and lower-risk subgroup based on the final risk score selected from multiple models generated, and further investigated underlying molecular mechanisms associated with the risk stratification. One WSI feature and three immune marker genes were selected into the final recurrence-free survival (RFS) prediction model following the best integrated modeling framework. The resultant score showed a significantly improved prediction performance on the test dataset (mean time-dependent AUCs = 0.707) as compared to those of other types (e.g: mean time-dependent AUCs of AJCC tumor stage = 0.525) of input data integration. To assess that the risk score could provide a higher-resolution risk stratification, a lower-risk subgroup (or a higher-risk subgroup) was arbitrarily assigned according to score falling below (or above) the median score. The lower risk subgroup had significantly longer median RFS time than that of the higher-risk patients (median RFS = 903 vs. 265 days, log-rank test p-value< 0.0001). Additionally, the higher-risk subgroup, in contrast to the lower-risk patients were characterized with a significant downregulation of immune checkpoint genes, suppressive signal in tumor immune response pathways, and depletion of CD8 T cells. These observations for the higher-risk subgroup suggest that new targets for adoptive or checkpoint-based combined systemic therapies may be useful. We developed a novel prognostic model to predict RFS for HCC patients, using one feature that can be automatically extracted from routine histopathological images, as well as the expression profiles of three immune marker genes. The methodology used in this paper demonstrates the feasibility of developing prognostic models that provide both useful risk stratification along with valuable biological insights into the underlying characteristics of the subgroups identified.

Molecular subtyping based on immune cell marker genes predicts prognosis and therapeutic response in patients with lung adenocarcinoma

ObjectiveLung adenocarcinoma (LA) is one of the most common malignancies and is responsible for the greatest number of tumor-related deaths. Our research aimed to explore the molecular subtype signatures of LA to clarify the correlation among the immune microenvironment, clinical outcomes, and therapeutic response.MethodsThe LA immune cell marker genes (LICMGs) identified by single-cell RNA sequencing (scRNA-seq) analysis were used to discriminate the molecular subtypes and homologous immune and metabolic traits of GSE72094 LA cases. In addition, the model-building genes were identified from 1441 LICMGs by Cox-regression analysis, and a LA immune difference score (LIDscore) was developed to quantify individual differences in each patient, thereby predicting prognosis and susceptibility to immunotherapy and chemotherapy of LA patients.ResultsPatients of the GSE72094 cohort were divided into two distinct molecular subtypes based on LICMGs: immune activating subtype (Cluster-C1) and metabolically activating subtype (cluster-C2). The two molecular subtypes have distinct characteristics regarding prognosis, clinicopathology, genomics, immune microenvironment, and response to immunotherapy. Among the LICMGs, LGR4, GOLM1, CYP24A1, SFTPB, COL1A1, HLA-DQA1, MS4A7, PPARG, and IL7R were enrolled to construct a LIDscore model. Low-LIDscore patients had a higher survival rate due to abundant immune cell infiltration, activated immunity, and lower genetic variation, but probably the higher levels of Treg cells in the immune microenvironment lead to immune cell dysfunction and promote tumor immune escape, thus decreasing the responsiveness to immunotherapy compared with that of the high-LIDscore patients. Overall, high-LIDscore patients had a higher responsiveness to immunotherapy and a higher sensitivity to chemotherapy than the low-LIDscore group.ConclusionsMolecular subtypes based on LICMGs provided a promising strategy for predicting patient prognosis, biological characteristics, and immune microenvironment features. In addition, they helped identify the patients most likely to benefit from immunotherapy and chemotherapy.

Identification the immune related marker genes and transcription-factor network in ruptured cerebral aneurysms using bioinformatics analysis and machine-learning strategies

BackgroundAs a high level of mortality and morbidity disease, ruptured cerebral aneurysms (RCA) is the most common cause of intracranial hemorrhage. MethodsThe expression profiles of GSE13353, GSE26969 were downloaded from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs) between RCA and unruptured cerebral aneurysms (URCA). The Least Absolute Shrinkage Selection Operator (LASSO) and the SVM-RFE (SVM-RFE) analysis were used to screen the potential diagnostic genes for RCA, which were further tested in the validation cohort (GSE54083). The TRRUST database was used to predict transcription factors (TF) and the JASPAR database was used to validate the marker genes and STAT1 binding sites. Finally, the CMAP database was used to predict RCA-associated drugs for clinical transformation. ResultsA total of 120 DEGs were identified. The functional enrichment analysis revealed that NF-kappa B signaling pathway, tuberculosis, rheumatoid arthritis were enriched in the RCA group. NANS, NTRK3, OLFML2A were identified as diagnostic biomarkers of RCA. Transcription of all three marker genes is regulated by the predicted transcription factor STAT1, the CMAP database was eventually used to screen 10 most promising drugs for the treatment of RCA. ConclusionNANS, NTRK3, OLFML2A may become new candidate biomarkers of RCA, moreover, STAT1 plays an important role in the development of RCA. The mentioned immune cells may play a key role in the development and progression of RCA. MEK and MAP kinase inhibitors are the most likely drug mechanisms for RCA therapy.