Immune Gene Expression Patterns Research Articles

Integrative analysis of ferroptosis-related genes reveals that ABHD12 is a novel prognostic biomarker and facilitates hepatocellular carcinoma tumorigenesis

Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, making the prognostic prediction challenging. Ferroptosis, an iron-dependent form of cell death, is a key regulator in the initiation, progression, and metastasis of HCC. However, the expression and function of ferroptosis-related genes (FRGs) in HCC remained largely unclear. In this study, we analyzed TCGA datasets and identified 58 survival-related deferentially expressed FRGs (DE-FRGs). Then, based on the results of LASSO analysis, we developed a novel prognostic model based on 12 survival-related DE-FRGs. Survival assays indicated a strong prognostic ability of this new model in predicting clinical prognosis of HCC patients. In addition, we conducted an exploration of molecular subtypes related to HCC and delved into the associated immune characteristics and gene expression patterns. Among the 12 survival-related DE-FRGs, our attention focused on ABHD12 (abhydrolase domain containing 12) which was highly expressed in HCC and associated with advanced clinical stages. Multivariate assays confirmed that ABHD12 was a significant prognostic factor for HCC patients. Immune analysis revealed that ABHD12 may play an important role in tumor microenvironment. Finally, we performed RT-PCR and confirmed that ABHD12 was highly expressed in HCC cells. Functional experiments revealed that ABHD12 knockdown may suppress the proliferation and migration of HCC cells. These findings emphasized the significance of ABHD12 as a potential prognostic marker for HCC and its crucial role in the field of tumor biology. Additionally, the study introduces a novel survival model that holds promise for enhancing prognostic predictions in HCC patients. Overall, this research provided valuable insights for a deeper comprehension of the complexity of HCC and the development of personalized treatment strategies.

In vitro analysis of the expression of inflammasome, antiviral, and immune genes in an Oreochromis niloticus liver cell line following stimulation with bacterial ligands and infection with tilapia lake virus.

The inflammasome is a multimeric protein complex that plays a vital role in the defence against pathogens and is therefore considered an essential component of the innate immune system. In this study, the expression patterns of inflammasome genes (NLRC3, ASC, and CAS-1), antiviral genes (IFNγ and MX), and immune genes (IL-1β and IL-18) were analysed in Oreochromis niloticus liver (ONIL) cells following stimulation with the bacterial ligands peptidoglycan (PGN) and lipopolysaccharide (LPS) and infection with TiLV. The cells were stimulated with PGN and LPS at concentrations of 10, 25, and 50 µg/ml. For viral infection, 106 TCID50 of TiLV per ml was used. After LPS stimulation, all seven genes were found to be expressed at specific time points at each of the three doses tested. However, at even higher doses of LPS, NLRC3 levels decreased. Following TiLV infection, all of the genes showed significant upregulation, especially at early time points. However, the gene expression pattern was found to be unique in PGN-treated cells. For instance, NLRC3 and ASC did not show any response to PGN stimulation, and the expression of IFNγ was downregulated at 25 and 50 µg of PGN per ml. CAS-1 and IL-18 expression was downregulated at 25 µg of PGN per ml. At a higher dose (50 µg/ml), IL-1β showed downregulation. Overall, our results indicate that these genes are involved in the immune response to viral and bacterial infection and that the degree of response is ligand- and dose-dependent.

Investigating gene signatures associated with immunity in colon adenocarcinoma to predict the immunotherapy effectiveness using NFM and WGCNA algorithms.

Colon adenocarcinoma (COAD), a frequently encountered and highly lethal malignancy of the digestive system, has been the focus of intensive research regarding its prognosis. The intricate immune microenvironment plays a pivotal role in the pathological progression of COAD; nevertheless, the underlying molecular mechanisms remain incompletely understood. This study aims to explore the immune gene expression patterns in COAD, construct a robust prognostic model, and delve into the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby providing critical support for individualized treatment strategies and prognostic evaluation. Initially, we curated a comprehensive dataset by screening 2600 immune-related genes (IRGs) from the ImmPort and InnateDB databases, successfully obtaining a rich data resource. Subsequently, the COAD patient cohort was classified using the non-negative matrix factorization (NMF) algorithm, enabling accurate categorization. Continuing on, utilizing the weighted gene co-expression network analysis (WGCNA) method, we analyzed the top 5000 genes with the smallest p-values among the differentially expressed genes (DEGs) between immune subtypes. Through this rigorous screening process, we identified the gene modules with the strongest correlation to the COAD subpopulation, and the intersection of genes in these modules with DEGs (COAD vs COAD vs Normal colon tissue) is referred to as Differentially Expressed Immune Genes Associated with COAD (DEIGRC). Employing diverse bioinformatics methodologies, we successfully developed a prognostic model (DPM) consisting of six genes derived from the DEIGRC, which was further validated across multiple independent datasets. Not only does this predictive model accurately forecast the prognosis of COAD patients, but it also provides valuable insights for formulating personalized treatment regimens. Within the constructed DPM, we observed a downregulation of CALB2 expression levels in COAD tissues, whereas NOXA1, KDF1, LARS2, GSR, and TIMP1 exhibited upregulated expression levels. These genes likely play indispensable roles in the initiation and progression of COAD and thus represent potential therapeutic targets for patient management. Furthermore, our investigation into the molecular mechanisms and therapeutic targets for COAD liver metastasis revealed associations with relevant processes such as fat digestion and absorption, cancer gene protein polysaccharides, and nitrogen metabolism. Consequently, genes including CAV1, ANXA1, CPS1, EDNRA, and GC emerge as promising candidates as therapeutic targets for COAD liver metastasis, thereby providing crucial insights for future clinical practices and drug development. In summary, this study uncovers the immune gene expression patterns in COAD, establishes a robust prognostic model, and elucidates the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby possessing significant theoretical and clinical implications. These findings are anticipated to offer substantial support for both the treatment and prognosis management of COAD patients.

Population-level immunologic variation in wild threespine stickleback (Gasterosteusaculeatus)

Wild organisms are regularly exposed to a wide range of parasites, requiring the management of an effective immune response while avoiding immunopathology. Currently, our knowledge of immunoparasitology primarily derives from controlled laboratory studies, neglecting the genetic and environmental diversity that contribute to immune phenotypes observed in wild populations. To gain insight into the immunologic variability in natural settings, we examined differences in immune gene expression of two Alaskan stickleback (Gasterosteus aculeatus) populations with varying susceptibility to infection by the cestode Schistocephalus solidus. Between these two populations, we found distinct immune gene expression patterns at the population level in response to infection with fish from the high-infection population displaying signs of parasite-driven immune manipulation. Further, we found significant differences in baseline immune gene profiles between the populations, with uninfected low-infection population fish showing signatures of inflammation compared to uninfected high-infection population fish. These results shed light on divergent responses of wild populations to the same parasite, providing valuable insights into host-parasite interactions in natural ecosystems.

Complex associations between cancer progression and immune gene expression reveals early influence of transmissible cancer on Tasmanian devils.

The world's largest extant carnivorous marsupial, the Tasmanian devil, is challenged by Devil Facial Tumor Disease (DFTD), a fatal, clonally transmitted cancer. In two decades, DFTD has spread across 95% of the species distributional range. A previous study has shown that factors such as season, geographic location, and infection with DFTD can impact the expression of immune genes in Tasmanian devils. To date, no study has investigated within-individual immune gene expression changes prior to and throughout the course of DFTD infection. To explore possible changes in immune response, we investigated four locations across Tasmania that differed in DFTD exposure history, ranging between 2 and >30 years. Our study demonstrated considerable complexity in the immune responses to DFTD. The same factors (sex, age, season, location and DFTD infection) affected immune gene expression both across and within devils, although seasonal and location specific variations were diminished in DFTD affected devils. We also found that expression of both adaptive and innate immune genes starts to alter early in DFTD infection and continues to change as DFTD progresses. A novel finding was that the lower expression of immune genes MHC-II, NKG2D and CD8 may predict susceptibility to earlier DFTD infection. A case study of a single devil with regressed tumor showed opposite/contrasting immune gene expression patterns compared to the general trends observed across devils with DFTD infection. Our study highlights the complexity of DFTD's interactions with the host immune system and the need for long-term studies to fully understand how DFTD alters the evolutionary trajectory of devil immunity.

Single-centre, randomised clinical trial of the immunomodulatory mechanisms of daily supplementation of palm tocotrienol-rich fraction in healthy human volunteers following influenza vaccination.

Vitamin E from palm oil, known as the tocotrienol-rich fraction (TRF), has been shown to have immune-enhancing activity. To date, only one dose of TRF (400 mg daily) has been tested in a clinical trial. The proposed study will evaluate the immune-enhancing activity effects of lower doses (200, 100 and 50 mg) in a clinical trial using an influenza vaccine as the immunological challenge. A single-centre, randomised, parallel, double-blinded, placebo-controlled clinical trial with balance allocation involving five arms will be conducted. The healthy volunteers recruited will be randomly assigned to one of the arms, and they will be asked to take the respective supplements (400 mg, 200 mg, 100 mg, 50 mg of TRF or placebo) daily with their dinner. The volunteers will receive the influenza vaccine after four weeks. They will be asked to return to the study site four weeks later. A blood sample will be taken for the study at baseline, four and eight weeks. Primary outcome measures will be antibody levels to influenza, blood leucocyte profile and cytokine production. Secondary outcomes will be correlating plasma vitamin E levels with immune responses, plasma proteins and gene expression patterns. The findings from this study will be published in relevant peer-reviewed journals and presented at relevant national and international scientific meetings. The recent world events have created the awareness of having a healthy and functional immune system. Nutrition plays an important role in helping the immune system to function optimally. This study will show the effects of lower doses of TRF in boosting the immune response of healthy individuals and also elucidate the mechanisms through which TRF exerts its immune-enhancing effects. Australian New Zealand Clinical Trials Registry (ANZCTR) [ ACTRN12622000844741] dated 15 June 2022. 2.

Comprehensive characterization of adipogenesis-related genes in colorectal cancer for clinical significance and immunogenomic landscape analyses

ObjectiveColorectal cancer (CRC) is a major global health concern, necessitating the identification of biomarkers and molecular subtypes for improved clinical management. This study aims to evaluate the clinical value of adipogenesis-related genes and molecular subtypes in CRC.MethodsA comprehensive analysis of adipogenesis-related genes in CRC was performed using publicly available datasets (TCGA and GEO database) and bioinformatics tools. Unsupervised cluster analysis was employed to identify the molecular subtypes of CRC, while LASSO regression analysis was utilized to develop a risk prognostic model. The immunogenomic patterns and immunotherapy analysis were used to predict patient response to immunotherapy. Furthermore, qPCR analysis was conducted to confirm the expression of the identified key genes in vitro.ResultsThrough the analysis of RNAseq data from normal and tumor tissues, we identified 50 differentially expressed genes. Unsupervised cluster analysis identified two subtypes (Cluster A and Cluster B) with significantly different survival outcomes. Cluster A and B displayed differential immune cell compositions and enrichment in specific biological pathways, providing insights into potential therapeutic targets. A risk-scoring model was developed using five ARGs, which successfully classified patients into high and low-risk groups, showing distinct survival outcomes. The model was validated and showed robust predictive performance. High-risk patients exhibited altered immune cell proportions and gene expression patterns compared to low-risk patients. In qPCR validation, four out of the five key genes were consistent with the results of bioinformatics analysis.ConclusionOverall, the findings of our investigation offer valuable understanding regarding the clinical relevance of ARGs and molecular subtypes in CRC, laying the groundwork for improved precision medicine applications and personalized treatment modalities.

Deciphering Transcriptomic and (Epi)Genetic Signatures of Central Nervous System Infiltration in Patients Diagnosed with Diffuse Large B-Cell Lymphoma

Introduction Central Nervous System (CNS) involvement in Diffuse Large B Cell Lymphoma (DLBCL) is a rare complication with bad prognosis. The CNS Prognostic Index is employed to categorize patients at a high risk of CNS relapse; however, its effectiveness is not accurate. The discovery of precise biomarkers for predicting CNS involvement in DLBCL patients remains unmet. Our objective was to characterize the immune, transcriptomic, genomic and epigenomic hallmarks of systemic tumors at diagnosis of patients who later experienced relapse in the CNS. By exploring these biological profiles, we sought to gain valuable insights into the underlying mechanisms and potential biomarkers associated with CNS relapse in DLBCL. Methods We conducted a retrospective study including 38 patients diagnosed with nodal DLBCL who experienced relapse within the first two years after diagnosis. Among these patients, 12 individuals relapsed specifically in the CNS, while 26 relapsed in systemic sites. As a control group, we included 21 patients who did not relapse. DNA and RNA were extracted from FFPE tumor samples collected at diagnosis. To evaluate immune cell infiltration, we utilized the nCounter PanCancer Immune Profiling Panel (Nanostring); cell-of-origin (COO) was determined using the Lymph2Cx assay. Transcriptomic profiles were generated by bulk RNA sequencing and mutational analysis was performed using a custom targeted NGS panel, which included the most frequently mutated genes observed in lymphoid neoplasms. Methylation profiles were obtained using the Illumina Infinium MethylationEPIC Array 850K. Results Immune profiling analysis showed cell composition was not significantly different between groups; however, we observed distinct immune gene expression patterns at diagnosis in patients who experienced CNS relapse. Multiple genes were overexpressed in the CNS-relapsed group compared to non-relapsed group, which encompassed various functional categories including chemokine signaling such as IL7R (FC=2; P=0.05) and CCR6 (FC=3.4; P=0.01); adhesion like VCAM1 (FC=1.6; P=0.03) and ITGA4 (FC=2.2; P=0.006); and immune regulation such as CD1A (FC=4.8; P=0.001), LTB (FC=3.3; P=0.009) and BTLA (FC=2.3; P=0.02) (Fig.1A). The ITGA4 gene also presented higher expression levels in the CNS-relapsed group when compared to both systemic-relapsed and non-relapsed groups combined (FC=1.7; P=0.03). No significant differences were observed in the COO classification between groups. Whole-genome transcriptomic data revealed enrichment in gene sets associated with proliferation and survival in the CNS-relapsed group (Fig.1B). Analysis of genetic alterations indicated that patients with CNS relapse exhibited an increased mutation load and frequency in PIM1, IGLL5, and KMT2D genes. Finally, analysis of the CNS relapse-related epigenome showed 343 differentially hypomethylated CpG sites compared to both systemic and non-relapsed groups together, affecting a total of 211 genes. Pathway enrichment analysis of these genes revealed a link between CNS infiltration and cell migration and locomotion. Conclusions Tumors from DLBCL patients that will relapse in the CNS present a higher chemokine, adhesion and proliferation signatures at diagnosis. Of notice, BTLA, CCR6 and IL7R proteins have been previously reported to be implicated in B cell entry into the CNS in B-cell malignancies. Interestingly, patients with CNS relapse demonstrated significant overexpression of the ITGA4 gene, which encodes the integrin α4 subunit (CD49d) of the Very Late Antigen-4. Engagement between CD49d on B cells and its endothelial ligand VCAM-1 is required for migration of these cells across the blood-brain barrier. In fact, Natalizumab (anti-CD49d mAb) is administered in multiple sclerosis to impede entrance and accumulation of B cells in the brain. Initial experiments in mice have shown increased expression of CD49d in lymphoma B cells that have infiltrated the brain, compared to those in the spleen. Herein, we have demonstrated that DLBCL cells at diagnosis already own specific transcriptomic and (epi)genetic hallmarks that could confer a higher capacity to infiltrate the CNS. Validation of these findings in larger cohorts of patients could improve selection of patients with an increased risk of CNS involvement in need of prophylactic CNS-directed therapies at diagnosis.

Cannabis smoke suppresses antiviral immune responses to influenza A in mice.

Despite its increasingly widespread use, little is known about the impact of cannabis smoking on the response to viral infections like influenza A virus (IAV). Many assume that cannabis smoking will disrupt antiviral responses in a manner similar to cigarette smoking; however, since cannabinoids exhibit anti-inflammatory effects, cannabis smoke exposure may impact viral infection in distinct ways. Male and female BALB/c mice were exposed daily to cannabis smoke and concurrently intranasally instilled with IAV. Viral burden, inflammatory mediator levels (multiplex ELISA), lung immune cells populations (flow cytometry) and gene expression patterns (RNA sequencing) were assessed in the lungs. Plasma IAV-specific antibodies were measured via ELISA. We found that cannabis smoke exposure increased pulmonary viral burden while decreasing total leukocytes, including macrophages, monocytes and dendritic cell populations in the lungs. Furthermore, infection-induced upregulation of certain inflammatory mediators (interferon-γ and C-C motif chemokine ligand 5) was blunted by cannabis smoke exposure, which in females was linked to the transcriptional downregulation of pathways involved in innate and adaptive immune responses. Finally, plasma levels of IAV-specific IgM and IgG1 were significantly decreased in cannabis smoke-exposed, infected mice compared to infected controls, only in female mice. Overall, cannabis smoke exposure disrupted host-defence processes, leading to increased viral burden and dampened inflammatory signalling. These results suggest that cannabis smoking is detrimental to the maintenance of pulmonary homeostasis during viral infection and highlight the need for data regarding the impact on immune competency in humans.

The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection.

Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0h, 20h, 60h and 100h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.

Gene expression signatures in conjunctival fornix aspirates of patients with dry eye disease associated with Meibomian gland dysfunction. A proof-of-concept study

BackgroundMeibomian gland dysfunction (MGD) is one of the most common conditions in ophthalmic practice and the most frequent cause of evaporative dry eye disease (DED). However, the immune mechanisms leading to this pathology are not fully understood and the diagnostic tests available are limited. Here, we used the nCounter technology to analyze immune gene expression in DED-MGD that can be used for developing diagnostic signatures for DED. MethodsConjunctival cell samples were obtained by aspiration from patients with DED-MGD (n = 27) and asymptomatic controls (n = 22). RNA was purified, converted to cDNA, preamplified and analyzed using the Gene Expression Human Immune V2 panel (NanoString), which includes 579 target and 15 housekeeping genes. A machine learning (ML) algorithm was applied to design a signature associated with DED-MGD. ResultsForty-five immune genes were found upregulated in DED-MGD vs. controls, involved in eight signaling pathways, IFN I/II, MHC class I/II, immunometabolism, B cell receptor, T Cell receptor, and T helper-17 (Th-17) differentiation. Additionally, statistically significant correlations were found between 31 genes and clinical characteristics of the disease such as lid margin or tear osmolarity (Pearson's r < 0.05). ML analysis using a recursive feature elimination (RFE) algorithm selected a 4-gene mRNA signature that discriminated DED-MGD from control samples with an area under the ROC curve (AUC ROC) of 0.86 and an accuracy of 77.5%. ConclusionsMultiplexed mRNA analysis of conjunctival cells can be used to analyze immune gene expression patterns in patients with DED-MGD and to generate diagnostic signatures.

Cecropin P1 antimicrobial peptide modulates differential expression of immune relevant genes in rainbow trout (Oncorhynchus mykiss) gill cell line, RTgill-W1

Accumulated evidence indicates that antimicrobial peptides modulate immune activities in fish. In this study, we profiled the differential expression patterns of representative immune relevant genes in an epithelial-like cell line of rainbow trout gill, RTgill-W1, in response to exposure of cecropin P1 antimicrobial peptide. RTgill-W1 cells were treated with synthetic cecropin P1 over time (0, 2, 4 and 24 h) with or without the present of lipopolysaccharide (LPS) or polyinosinic polycytidylic acid (PolyI:C). The relative abundances of each mRNA were measured by real-time quantitative PCR. The dose-response study revealed significant perturbations of mRNA levels of genes related to pro-inflammation, acute phase, surface proteins and transcription factors at 30 μM of cecropin P1. In addition, cecropin P1 altered the differential expression patterns that were induced by LPS or PolyI:C, at different time points in RTgill-W1. Overall, our results indicate that cecropin P1 exhibits pro-inflammation activity, modulate cell-cell interaction and cytokine signal transduction in rainbow trout gill cell, and may suggest a potential application of this peptide as an immune adjuvant for disease control in aquaculture.

Abstract 6115: Comprehensive DNA repair landscape analysis reveals novel small cell lung cancer biology

Abstract Background: Small cell lung cancer (SCLC) is the most lethal form of lung cancer. The five-year overall survival rate for SCLC patients is only ~7%, a statistic that has not improved for decades. Compared to non-small cell lung cancers, SCLCs highly express DNA repair proteins. Despite this acknowledgement, a comprehensive analysis of the DNA repair machinery within SCLC has not been completed. This study was performed to study the SCLC DNA repair landscape. Methods: We applied a novel DNA repair analysis method to IMPOWER133 (n = 271) and MD Anderson GEMINI (n = 85) clinical SCLC datasets. This single-sample weighted expression (ssWE) method uses transcriptomic data to assess regulation of ten single-strand break repair, double-strand break repair, translesion synthesis, and damage sensing pathways within individual tumors. Importantly, this method considers all pathway effectors and applies a scaling factor to capture effector essentiality to repair completion. Unsupervised k-means clustering was used to group samples following ssWE analysis. Chi-square tests were used to test for significant enrichment patterns between DNA repair and established SCLC transcription factor (TF) subtypes assignments. Results: Unsupervised clustering demonstrated that IMPOWER133 and GEMINI SCLCs were robustly split into three clusters as defined by their DNA repair phenotypes (DNA Damage Response (DDR) High, Intermediate, Low). We found that expression of DNA damage responsive transcription factors (E2F1, MYBL2, FOXM1) and the intra-S and G2/M checkpoint machinery significantly increased across DDR clusters (High&amp;gt;Intermediate&amp;gt;Low). Also, we found that SCLC TF subtypes showed statistically significant enrichment patterns across DDR clusters (IMPOWER133, MDACC Χ2 p&amp;lt;0.001). Most notably, inflamed SCLC (SCLC-I) were significantly under-represented in the DDR High cluster. Given this, we hypothesized that DDR Low tumors exhibited a more “inflamed” phenotype. To test this hypothesis, we isolated ASCL1+ SCLC (SCLC-A) tumors, which are considered “immune cold” compared to other subtypes, stratified them by their DDR status, and analyzed expression patterns of key immune genes. Strikingly, we found that splitting treatment naïve SCLC-A tumors by their DDR status identified tumors that appeared more “inflamed” (DDR Low). DDR Low SCLC-A showed increased expression of MHC Class I and inflammatory cytokine genes. Conversely, DDR High SCLC-A tumors exhibited an immune evasive profile. Conclusions: We provide the first evidence that SCLCs exhibit a spectrum of DNA repair machinery and cell cycle checkpoint pathway expression within TF subtypes. Additionally, we find that DDR status may be a key determinant of “inflamed” biology in treatment naïve SCLC-A—the predominant form of SCLC—independent of the SCLC-I subtype. Moving forward, our results have important implications for SCLC treatment and clinical trial design. Citation Format: Benjamin B. Morris, Barzin Nabet, David Shames, Simon Heeke, Carl M. Gay, Jing Wang, Jianjun Zhang, John V. Heymach, Lauren A. Byers. Comprehensive DNA repair landscape analysis reveals novel small cell lung cancer biology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6115.

Cellular and Molecular Atlas of Peripheral Blood Mononuclear Cells from a Pregnant Woman After Recovery from COVID-19

Abstract Objective This study aimed to investigate the immune response of a pregnant woman who recovered from the coronavirus disease 2019 (COVID_RS) by using single-cell transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) and to analyze the properties of different immune cell subsets. Methods PBMCs were collected from the COVID_RS patient at 28 weeks of gestation, before a cesarean section. The PBMCs were then analyzed using single-cell RNA sequencing. The transcriptional profiles of myeloid, T, and natural killer (NK) cell subsets were systematically analyzed and compared with those of healthy pregnant controls from a published single-cell RNA sequencing data set. Results We identified major cell types such as T cells, B cells, NK cells, and myeloid cells in the PBMCs of our COVID_RS patient. The increase of myeloid and B cells and decrease of T cells and NK cells in the PBMCs in this patient were quite distinct compared with that in the control subjects. After reclustering and Augur analysis, we found that CD16 monocytes and mucosal-associated invariant T (MAIT) cells were mostly affected within different myeloid, T, and NK cell subtypes in our COVID_RS patient. The proportion of CD16 monocytes in the total myeloid population was increased, and the frequency of MAIT cells in the total T and NK cells was significantly decreased in the COVID-RS patient. We also observed significant enrichment of gene sets related to antigen processing and presentation, T-cell activation, T-cell differentiation, and tumor necrosis factor superfamily cytokine production in CD16 monocytes, and enrichment of gene sets related to antigen processing and presentation, response to type II interferon, and response to virus in MAIT cells. Conclusion Our study provides a single-cell resolution atlas of the immune gene expression patterns in PBMCs from a COVID_RS patient. Our findings suggest that CD16-positive monocytes and MAIT cells likely play crucial roles in the maternal immune response against severe acute respiratory syndrome coronavirus 2 infection. These results contribute to a better understanding of the maternal immune response to severe acute respiratory syndrome coronavirus 2 infection and may have implications for the development of effective treatments and preventive strategies for the coronavirus disease 2019 in pregnant women.

Identification of immune-related molecular clusters and diagnostic markers in chronic kidney disease based on cluster analysis.

Background: Chronic kidney disease (CKD) is a heterogeneous disease with multiple etiologies, risk factors, clinical manifestations, and prognosis. The aim of this study was to identify different immune-related molecular clusters in CKD, their functional immunological properties, and to screen for promising diagnostic markers. Methods: Datasets of 440 CKD patients were obtained from the comprehensive gene expression database. The core immune-related genes (IRGs) were identified by weighted gene co-expression network analysis. We used unsupervised clustering to divide CKD samples into two immune-related subclusters. Then, functional enrichment analysis was performed for differentially expressed genes (DEGs) between clusters. Three machine learning methods (LASSO, RF, and SVM-RFE) and Venn diagrams were applied to filter out 5 significant IRGs with distinguished subtypes. A nomogram diagnostic model was developed, and the prediction effect was verified using calibration curve, decision curve analysis. CIBERSORT was applied to assess the variation in immune cell infiltration among clusters. The expression levels, immune characteristics and immune cell correlation of core diagnostic markers were investigated. Finally, the Nephroseq V5 was used to assess the correlation among core diagnostic markers and renal function. Results: The 15 core IRGs screened were differentially expressed in normal and CKD samples. CKD was classified into two immune-related molecular clusters. Cluster 2 is significantly enriched in biological functions such as leukocyte adhesion and regulation as well as immune activation, and has a severe immune prognosis compared to cluster 1. A nomogram diagnostic model with reliable prediction of immune-related clusters was developed based on five signature genes. The core diagnostic markers LYZ, CTSS, and ISG20 were identified as playing an important role in the immune microenvironment and were shown to correlate meaningfully with immune cell infiltration and renal function. Conclusion: Our study identifies two subtypes of CKD with distinct immune gene expression patterns and provides promising predictive models. Along with the exploration of the role of three promising diagnostic markers in the immune microenvironment of CKD, it is anticipated to provide novel breakthroughs in potential targets for disease treatment.

Comparison of the Pathogenicity of SARS-CoV-2 Delta and Omicron Variants by Analyzing the Expression Patterns of Immune Response Genes in K18-hACE2 Transgenic Mice.

The recently emerged variants of the severe acute respiratory coronavirus 2 (SARS-CoV-2) pose a threat to public health. Understanding the pathogenicity of these variants is a salient factor in the development of effective SARS-CoV-2 therapeutics. This study aimed to compare the expression patterns of genes involved in immune responses in K18-hACE2 mice infected with the wild-type, Delta, and Omicron SARS-CoV-2 variants. K18-hACE2 mice were intranasally infected with either wild-type (B.1), Delta (B.1.617.2), or Omicron (B.1.1.529) variants. On day 6 post-infection, lung, brain, and kidney tissues were collected from each variant-infected group. The mRNA expression levels of 39 immune response genes in all three groups were compared by RT-qPCR. Viral titers were measured using the median tissue culture infectious dose (TCID50) assay and expressed as Log10 TCID50/0.1 g. The statistical significance of the differences in gene expression was determined by one-way analysis of variance (ANOVA) (alpha = 0.05). The expression of toll-like receptors (TLRs) was upregulated in the lung and brain tissues of the wild-type- and Delta-infected groups but not in those of the Omicron-infected group. The highest expression of cytokines, including interleukin (IL)-1α, IL-1β, IL-17α, interferon, and tumor necrosis factors, was observed in the lungs of mice infected with the wild-type variant. Additionally, CCL4, CCL11, CXCL9, and CXCL10 were upregulated (>3-fold) in wild-type-infected mice, with markedly higher expressions in the brain than in the lungs. Most of the apoptotic factors were mainly expressed in the brain tissues of Omicron-infected mice (caspase 8, caspase 9, p53, Bax, Bak, BCL-2, and Bcl-XL), whereas neither the lung nor kidney showed more than 3-fold upregulation of these apoptotic factors. Collectively, our findings revealed that the wild-type SARS-CoV-2 variant exhibited the highest pathogenicity, followed by the Delta variant, then the Omicron variant.

Increased tumor glycolysis is associated with decreased immune infiltration across human solid tumors.

Response to immunotherapy across multiple cancer types is approximately 25%, with some tumor types showing increased response rates compared to others (i.e. response rates in melanoma and non-small cell lung cancer (NSCLC) are typically 30-60%). Patients whose tumors are resistant to immunotherapy often lack high levels of pre-existing inflammation in the tumor microenvironment. Increased tumor glycolysis, acting through glucose deprivation and lactic acid accumulation, has been shown to have pleiotropic immune suppressive effects using in-vitro and in-vivo models of disease. To determine whether the immune suppressive effect of tumor glycolysis is observed across human solid tumors, we analyzed glycolytic and immune gene expression patterns in multiple solid malignancies. We found that increased expression of a glycolytic signature was associated with decreased immune infiltration and a more aggressive disease across multiple tumor types. Radiologic and pathologic analysis of untreated estrogen receptor (ER)-negative breast cancers corroborated these observations, and demonstrated that protein expression of glycolytic enzymes correlates positively with glucose uptake and negatively with infiltration of CD3+ and CD8+ lymphocytes. This study reveals an inverse relationship between tumor glycolysis and immune infiltration in a large cohort of multiple solid tumor types.

Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis

BackgroundEnhancers are cis-regulatory elements present in eukaryote genomes, which constitute indispensable determinants of gene regulation by governing the spatiotemporal and quantitative expression dynamics of target genes, and are involved in multiple life processes, for instance during development and disease states. The importance of enhancer activity has additionally been highlighted for immune responses in animals and plants; however, the dynamics of enhancer activities and molecular functions in plant innate immunity are largely unknown. Here, we investigated the involvement of distal enhancers in early innate immunity in Arabidopsis thaliana.ResultsA group of putative distal enhancers producing low-abundance transcripts either unidirectionally or bidirectionally are identified. We show that enhancer transcripts are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns and are strongly correlated with open chromatin, low levels of methylated DNA, and increases in RNA polymerase II targeting and acetylated histone marks. Dynamic enhancer transcription is correlated with target early immune gene expression patterns. Cis motifs that are bound by immune-related transcription factors, such as WRKYs and SARD1, are highly enriched within upregulated enhancers. Moreover, a subset of core pattern-induced enhancers are upregulated by multiple patterns from diverse pathogens. The expression dynamics of putative immunity-related enhancers and the importance of WRKY binding motifs for enhancer function were also validated.ConclusionsOur study demonstrates the general occurrence of enhancer transcription in plants and provides novel information on the distal regulatory landscape during early plant innate immunity, providing new insights into immune gene regulation and ultimately improving the mechanistic understanding of the plant immune system.

Treatment with a VEGFR-2 antibody results in intra-tumor immune modulation and enhances anti-tumor efficacy of PD-L1 blockade in syngeneic murine tumor models.

Prolonged activation of vascular endothelial growth factor receptor-2 (VEGFR-2) due to mis-regulation of the VEGF pathway induces aberrant blood vessel expansion, which supports growth and survival of solid tumors. Therapeutic interventions that inhibit the VEGFR-2 pathway have therefore become a mainstay of cancer treatment. Non-clinical studies have recently revealed that blockade of angiogenesis can modulate the tumor microenvironment and enhance the efficacy of concurrent immune therapies. Ramucirumab is an FDA-approved anti-angiogenic antibody that inhibits VEGFR-2 and is currently being evaluated in clinical studies in combination with anti-programmed cell death (PD-1) axis checkpoint inhibitors (pembrolizumab, durvalumab, or sintilimab) across several cancer types. The purpose of this study is to establish a mechanistic basis for the enhanced activity observed in the combined blockade of VEGFR-2 and PD-1-axis pathways. Pre-clinical studies were conducted in murine tumor models known to be responsive to anti-PD-1 axis therapy, using monoclonal antibodies that block mouse VEGFR-2 and programmed death-ligand 1 (PD-L1). Combination therapy resulted in enhanced anti-tumor activity compared to anti-PD-L1 monotherapy. VEGFR-2 blockade at early timepoints post-anti-PD-L1 therapy resulted in a dose-dependent and transient enhanced infiltration of T cells, and establishment of immunological memory. VEGFR-2 blockade at later timepoints resulted in enhancement of anti-PD-L1-driven immune cell infiltration. VEGFR-2 and PD-L1 monotherapies induced both unique and overlapping patterns of immune gene expression, and combination therapy resulted in an enhanced immune activation signature. Collectively, these results provide new and actionable insights into the mechanisms by which concurrent VEGFR-2 and PD-L1 antibody therapy leads to enhanced anti-tumor efficacy.

Redclaw crayfish (Cherax quadricarinatus) responds to Vibrio parahaemolyticus infection by activating toll and immune deficiency signaling pathways and transcription of associated immune response genes

In invertebrates, several genes controlled by the Toll and immunodeficiency (IMD) signaling cascade are altered during microbial infection. However, little is known about the expression patterns of innate immune response genes in red-clawed crayfish (Cherax quadricarinatus). In the present study, the transcription of five genes was assessed in C. quadricarinatus challenged with Vibrio parahaemolyticus (V. parahaemolyticus). The expression of Relish, Toll-like receptor (TLR), tumor necrosis factor receptor-related factor 6 (TRAF6), Akirin, and IMD in different tissues and at different time points after infection were assessed. In addition, the Relish gene was amplified, the protein conformation of the Relish gene was predicted, and gene expression changes associated with antimicrobial peptide production in C. quadricarinatus were analyzed using RNA interference (RNAi). During V. parahaemolyticus infection, the transcripts of the above five genes were significantly increased in the hepatopancreas of C. quadricarinatus (P < 0.05). In contrast, TLR was significantly downregulated in muscle tissue at the initial stage of infection (P < 0.05); TRAF6 and IMD were significantly down-regulated throughout infection (P < 0.05); Akirin transcripts had the lowest abundance at 24 h post-infection; Relish, IMD and Akirin genes were significantly up-regulated in gill tissue at the early stage of infection (P < 0.05); only TRAF6 was significantly up-regulated at 6, 24 and 48 h after infection. The Relish gene of C. quadricarinatus is closely related to the Exopalaemon carinicauda. When the Relish gene was knocked down by RNAi, the V. parahaemolyticus challenge showed that the mortality rate of the RANi group was significantly higher than that of the NC group; pathological sections showed that the hepatopancreatic tissue damage was the most severe 12 h after the interference; and the interference significantly inhibited IRF4, NF-κB, ALF, laccase, SOD1, and lectin genes. Therefore, it can be hypothesized that the Toll and IMD pathways are activated in C. quadricarinatus in response to bacterial infection and that genes associated with these pathways are differentially transcribed in different tissues. This study provides insights into the Toll and IMD signaling pathways and the spatiotemporal expression of key genes regulating bacterial infection resistance in C. quadricarinatus.