Expression Profiles Of Immune-related Genes Research Articles

Unravelling the ontogeny and tissue-specific expression profiles of immune-related genes in the near-threatened endemic catfish, Clarias dussumieri

Clarias dussumieri, an air breathing catfish endemic to the Western Ghats in India, is categorized as 'Near Threatened' by the IUCN. This species is of high regional consumer demand and is one of the prioritized candidate species for aquaculture diversification and conservation. Despite its ecological and commercial significance, comprehensive studies on its immune system are lacking. This study elucidates the ontogenetic development and tissue-specific (brain, anterior kidney, gill, spleen, muscle, liver, hindgut and skin) expression profiles of key immune-related genes in C. dussumieri. Larvae were sampled at various developmental stages post-fertilization, and tissues from adult fish were analyzed for expression patterns of genes associated with inflammation (IL-1β, TNF-α, iNOS), antimicrobial defense (LYS, HAMP), stress response (HSP70), complement system (C3), cell-mediated immunity (MHC-IIβ, CD4-1), and adaptive immunity (IgM). The expression of IL-1β was highest at 60 days post-fertilization (60D), while TNF-α expression peaked at 25D before dropping notably by 60D. iNOS showed a peak at 7D, underscoring its importance in early immune defence. LYS exhibited a high expression at 10D, while HAMP peaked at 60D, highlighting their roles in antimicrobial defence. Stress marker HSP70 increased from 15D onwards and complement component C3 was consistently expressed at low levels throughout development. MHC-IIβ and CD4-1 showed significant increase since 10D and 7D respectively, suggesting the establishment of cell-mediated immunity. IgM expression increased notably from 15 days, indicating the development of adaptive immunity. In adult fish tissues, IL-1β, TNF-α, LYS and HSP70 showed highest expression in the hindgut, while C3 was predominantly expressed in the liver. MHC-IIβ and CD4-1 were highly expressed in the spleen and anterior kidney respectively. IgM was abundant in the anterior kidney and spleen. This study provides crucial baseline data on the immune competence of different developmental stages of C. dussumieri, informing strategies for effective vaccination and disease management in aquaculture, and enhancing our understanding of fish immunology for conservation efforts.

Wnt/B-catenin activation and TP53 mutations associate with distinct immune profiles in advanced thyroid cancer.

Anaplastic thyroid carcinomas (ATCs) and poorly differentiated thyroid carcinomas (PDTCs) exhibit distinct immune-related gene expression profiles. Most ATCs are characterized by active immune interactions (hot or altered immunosuppressed immunophenotypes), while PDTCs are largely immunologically inert (cold immunophenotypes). This study aimed to elucidate the mechanisms driving these divergent immunological fates, focusing on the Wnt/β-catenin pathway and TP53 mutations. Our data reveal that ATCs frequently harbor TP53 mutations (83.3%), which correlate with a hot immunophenotype, characterized by high expression of β-catenin-regulated cytokine CCL4 and recruitment of CD103+ dendritic cells. Conversely, PDTCs, with a lower incidence of TP53 mutations (12.5%), often exhibit a cold immunophenotype. In cold cancers and PDTCs, β-catenin is overexpressed suggesting that Wnt/β-catenin pathway activation drives immune exclusion through CCL4 downregulation.Further analysis indicated that loss of p53 function is inversely correlated with β-catenin expression. P53-mutated cancers showed significantly higher expression of CCL4 and densities of CD103+ dendritic cells compared to their p53-wild-type counterparts. Additionally, p53-mutated ATCs expressed a higher number of immune-related genes, supporting the role of p53 loss in activating immune responses in cancer. Our study indicates a potential correlation between the activation of the Wnt/β-catenin pathway and the development of cold thyroid cancers, which may be mediated by the suppression of CCL4 expression. Concurrently, mutations in the p53 gene appear to be linked with the occurrence of hot thyroid cancers. While these associations are compelling, they are based on observational data. Experimental research is necessary to determine the causal relationships underlying these findings.

Immune response and protection efficacy of formalin-killed vaccines against Streptococcus iniae in four-finger threadfin Eleutheronema tetradactylum.

Four-finger threadfin, Eleutheronema tetradactylum farming in southern Taiwan has been facing disease problems caused by Streptococcus iniae since 2018. The development of a vaccine against infectious S. iniae in the cultured threadfin industry is necessary. Thus, this study aimed to examine the efficacy of threadfin immunized formalin-killed cells (FKC) from S. iniae GSI-111 for 42 days post-vaccination (dpv) using two doses of FKC alone (a booster at 14 dpv) as group A, and FKC mixed with ISA763A adjuvant using a single dose as group B or double doses as group C. Immunoglobulin (Ig)-M was purified from threadfin, and rabbit anti-threadfin IgM polyclonal antibodies were used to detect antibody level in immunized fish; the vaccinated group A displayed higher levels at 3 dpv and all vaccinated treatments demonstrated high antibody levels between 14 and 42 dpv. All vaccine groups showed significantly higher values of lysozyme activity at 42 dpv compared with the control group; the vaccinated A group peaked at 14 dpv. The expression profiles of pro-inflammatory and immune-related genes, TNF-α, IL-12A, and C2 were upregulated at 3 dpv, while CD8A and chemokine receptor CXCR4 were upregulated at 42 dpv. Finally, the threadfins were challenged with S. iniae at 42 dpv. The average relative percent survival was 96% for vaccination A and B treatments, and 100% for vaccination C treatment. In summary, this study demonstrated that FKC vaccines whether formulated with an adjuvant could stimulate immune response and effective protect threadfins against S. iniae infection.

The Immune Microenvironment Landscape of Pituitary NeuroEndocrine Tumors, a Transcriptomic Approach.

Pituitary neuroendocrine tumors (PitNET) are known to be variably infiltrated by different immune cells. Nonetheless, their role in pituitary oncogenesis has only begun to be unveiled. The immune microenvironment could determine the biological and clinical behavior of a neoplasm and may have prognostic implications. To evaluate the expression of immune-related genes and to correlate such expression with the presence of infiltrating immune cells in forty-two PitNETs of different lineages, we performed whole transcriptome analysis and RT-qPCR. Deconvolution analysis was carried out to infer the immune cell types present in each tumor and the presence of immune cells was confirmed by immunofluorescence. We found characteristic expression profiles of immune-related genes including those encoding interleukins and chemokines for each tumor lineage. Genes such as IL4-I1, IL-36A, TIRAP, IL-17REL, and CCL5 were upregulated in all PitNETS, whereas IL34, IL20RA, and IL-2RB characterize the NR5A1-, TBX19-, and POU1F1-derived tumors, respectively. Transcriptome deconvolution analysis showed that M2 macrophages, CD4+ T cells, CD8+ T cells, NK cells, and neutrophils can potentially infiltrate PitNET. Furthermore, CD4+ and CD8+ T cells and NK cells infiltration was validated by immunofluorescence. Expression of CCL18, IL-5RA, and HLA-B as well as macrophage tumor infiltration could identify patients who can potentially benefit from treatment with immune checkpoint inhibitors.

Expression of immune-related genes and breast cancer recurrence in women with ductal carcinoma in situ

Background and aimDuctal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer with highly variable clinical behavior, but risk stratification is still challenging. We sought to identify immune-related gene expression signatures of pure DCIS associated with different risks of breast cancer recurrence. MethodsA retrospective nested case-control study of 143 pure DCIS was performed including 70 women with subsequent ipsilateral breast event (IBE, in situ or invasive; cases) and 73 DCIS women with no IBE and matched for age, tumor size, treatment, hormone receptors/HER2 status, and follow-up time (controls). RNA was extracted from DCIS samples and subjected to next-generation sequencing gene expression analysis of 395 immune-related genes. Correlations between DCIS immune-related gene expression and IBE were analyzed using weighted Cox regression for nested case-control data. ResultsEight immune-related genes were differentially expressed between cases and controls. MAGEA10 expression (present vs. absent) and high expression levels of IFNA17 and CBLB (Q4 vs. Q1) were observed more frequently in DCIS of women with subsequent IBE, mainly invasive (p-valueFDR < 0.05). Conversely, expression of IL3RA1, TAGAP, TNFAIP8, and high expression levels of CCL2 and LRP1 were associated with a lower risk of IBE (p-valueFDR < 0.05). ConclusionThis exploratory analysis of pure DCIS showed significant differences in immune-related gene expression profiles between women with and with no subsequent IBE, particularly as invasive IBE. These results, after additional validation, could improve risk stratification and management of DCIS patients.

Pathogenicity of Aeromonas veronii Isolated from Diseased Macrobrachium rosenbergii and Host Immune-Related Gene Expression Profiles.

Aeromonas veronii is widespread in aquatic environments and is responsible for infecting various aquatic animals. In this study, a dominant strain was isolated from the hepatopancreas of diseased Macrobrachium rosenbergii and was named JDM1-1. According to its morphological, physiological, and biochemical characteristics and molecular identification, isolate JDM1-1 was identified as A. veronii. The results of artificial challenge showed isolate JDM1-1 had high pathogenicity to M. rosenbergii with an LD50 value of 8.35 × 105 CFU/mL during the challenge test. Histopathological analysis revealed severe damage in the hepatopancreas and gills of the diseased prawns, characterized by the enlargement of the hepatic tubule lumen and gaps between the tubules as well as clubbing and degeneration observed at the distal end of the gill filament. Eight virulence-related genes, namely aer, ompA, lip, tapA, hlyA, flgA, flgM, and flgN, were screened by PCR assay. In addition, virulence factor detection showed that the JDM1-1 isolate produced lipase, lecithinase, gelatinase, and hemolysin. Furthermore, the mRNA expression profiles of immune-related genes of M. rosenbergii following A. veronii infection, including ALF1, ALF2, Crustin, C-lectin, and Lysozyme, were assessed, and the results revealed a significant upregulation in the hepatopancreas and intestines at different hours post infection. This study demonstrates that A. veronii is a causative agent associated with massive die-offs of M. rosenbergii and contributes valuable insights into the pathogenesis and host defense mechanisms of A. veronii invasion.

Lymph node metastasis regulation by peritumoral tonsillar tissue mitochondria-related pathway activation in oropharyngeal cancer.

Immune-related gene expression profiles of peritumoral tonsillar tissues are modified by oropharyngeal cancer (OPC) nodal status. This study explored immunometabolism and immune cell count alterations in peritumoral tonsillar tissue according to OPC nodal status. Microarray data analysis of 27 peritumoral tonsillar tissue samples, using a newly generated mitochondrial metabolism-related gene set comprised of 948 genes, detected 228 differentially expressed genes (DEGs) (206 up- and 22 downregulated) in metastasis-negative cases compared to metastasis-positive ones. REACTOME pathway analysis of the 206 upregulated genes revealed the Toll-like receptor 4 cascade were most enriched. Immune cell proportion analysis using the CIBERSORTx algorithm revealed a significantly higher rate of naïve B cells, but lower rates of regulatory T cells and resting natural killer cells in metastasis-negative cases. Digital spatial profiling of the 6 OPC tissues detected 9 DEGs in the lymphoid regions, in contrast, no DEGs were identified in tumor regions according to nodal status. Cancer cell nests and pair matched normal epithelia mitochondrial DNA (mtDNA) from 5 OPC tissues were analyzed by next generation sequencing for variant detection. However, no significant mtDNA variation was found. This study identified mitochondria-related immune cell transcriptional programs and immune cell profiles associated with OPC lymphatic spread in peritumoral tonsil tissue, further evaluation of which will elucidate targetable immune mechanisms associated with OPC lymphatic dissemination.

High hypoxia status in pancreatic cancer is associated with multiple hallmarks of an immunosuppressive tumor microenvironment.

Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is a particularly lethal disease that is often diagnosed late and is refractory to most forms of treatment. Tumour hypoxia is a key hallmark of PDAC and is purported to contribute to multiple facets of disease progression such as treatment resistance, increased invasiveness, metabolic reprogramming, and immunosuppression. We used the Buffa gene signature as a hypoxia score to profile transcriptomics datasets from PDAC cases. We performed cell-type deconvolution and gene expression profiling approaches to compare the immunological phenotypes of cases with low and high hypoxia scores. We further supported our findings by qPCR analyses in PDAC cell lines cultured in hypoxic conditions. First, we demonstrated that this hypoxia score is associated with increased tumour grade and reduced survival suggesting that this score is correlated to disease progression. Subsequently, we compared the immune phenotypes of cases with high versus low hypoxia score expression (HypoxiaHI vs. HypoxiaLOW) to show that high hypoxia is associated with reduced levels of T cells, NK cells and dendritic cells (DC), including the crucial cDC1 subset. Concomitantly, immune-related gene expression profiling revealed that compared to HypoxiaLOW tumours, mRNA levels for multiple immunosuppressive molecules were notably elevated in HypoxiaHI cases. Using a Random Forest machine learning approach for variable selection, we identified LGALS3 (Galectin-3) as the top gene associated with high hypoxia status and confirmed its expression in hypoxic PDAC cell lines. In summary, we demonstrated novel associations between hypoxia and multiple immunosuppressive mediators in PDAC, highlighting avenues for improving PDAC immunotherapy by targeting these immune molecules in combination with hypoxia-targeted drugs.

4P Immune exoproteome, soluble proteome and immune-related gene expression profiles of anti-PD-1 therapy in stage IIIB/IV non-small cell lung cancer: Relevance of immunosuppressive factors

4P Immune exoproteome, soluble proteome and immune-related gene expression profiles of anti-PD-1 therapy in stage IIIB/IV non-small cell lung cancer: Relevance of immunosuppressive factors

Spatial Technologies Reveal the Immune Landscape of Pediatric Acute Myeloid Leukemia

Pediatric acute myeloid leukemia (AML) is a cancer with a particularly low mutational burden in comparison to other pediatric and adult cancers and therefore, thought to be a poor candidate for T cell-engaging immunotherapies (Gröbner et al., 2018; Pfister et al., 2022). However, little is known about the composition and function of T cells in the bone marrow (BM) of pediatric AML patients. Insight into the frequency and function of BM T cells in children with AML is relevant for naturally occurring AML immune defenses, as well as for T cell-engaging immunotherapies (Koedijk et al., 2021). Here, we performed a multidimensional characterization of the tumor immune microenvironment in children with newly diagnosed AML. We obtained 82 formalin-fixed and paraffin-embedded (FFPE) diagnostic bone biopsies from a representative cohort of pediatric patients with treatment-naïve de novo AML (N=72) and from age- and sex-matched pediatric patients with treatment-naïve early-stage rhabdomyosarcoma without malignant BM infiltration (non-leukemic controls, N=10). We employed immunohistochemistry (IHC) alongside immune-related gene expression profiling (NanoString PanCancer IO 360 TM Panel) and spatial transcriptomics (NanoString GeoMx TM Whole Transcriptome Atlas). Moreover, we acquired an additional dataset of pre-treatment immune-related gene expression profiling obtained from the BM of 30 flotetuzumab-treated (CD3 x CD123 bispecific antibody) refractory/relapsed (R/R) adult AML patients (NCT02152956; Vadakekolathu et al., 2020) for TIDE-based immune deconvolution (Jiang et al., 2018). Using IHC, we identified (a trend towards) a decreased abundance of the overall number of T cells ( P=0.09) and CD8 + T cells ( P=0.011; Panel A) in the BM of pediatric AML patients in comparison to non-leukemic controls, respectively. Notably, the extent of overall T cell and CD8 + T cell infiltration could differ up to 180-fold between individual AML patients. In general, this difference in T cell infiltration was not associated with the abundance of leukemic blasts or patient's cytogenetic alterations. Nevertheless, children with complex karyotype AML had higher numbers of BM T cells compared to children with normal karyotype AML ( P=0.03).Using differential gene expression analysis, we identified genes related to T cell-attracting chemokines, cytotoxicity, and immune checkpoints to be significantly upregulated in T cell-infiltrated- compared to T cell-depleted samples. Moreover, the ratio of anti- to pro-inflammatory macrophages (M2/M1-ratio) was significantly lower in T cell-infiltrated- compared to T cell-depleted pediatric AML samples ( P&amp;lt;0.001). Interestingly, this M2/M1-ratio was also significantly lower in R/R adults that responded to flotetuzumab immunotherapy in comparison to non-responders ( P&amp;lt;0.001). In fact, this M2/M1-ratio outperformed several other known predictors of response to flotetuzumab immunotherapy (AUROC: 0.852 (95% CI: 0.71-0.99), P=0.001; Jiang et al., 2018; Ayers et al., 2017). In addition, IHC revealed that 9 immune-infiltrated samples, including 6 KMT2A-rearranged AML samples, harbored large networks of T- and B cells (representative image of B cell-networks shown in panel B). Using spatial transcriptomics, we dissected the composition of these lymphoid aggregates and revealed localized anti-tumor immunity in the BM of AML. In comparison to tumor areas, these aggregates showed a higher abundance of activated cytotoxic T cells ( P&amp;lt;0.001), memory B cells ( P&amp;lt;0.001), and plasma cells ( P&amp;lt;0.001), suggesting the presence of tertiary lymphoid structure-like (TLS-like) aggregates in the BM of AML. In conclusion, we identified a subset of pediatric AML patients with relatively high T cell infiltration and a relatively low abundance of anti-inflammatory macrophages in the BM at diagnosis. Furthermore, we found that the BM M2/M1-ratio may be informative of response to T-cell engaging immunotherapies in adult AML, which needs to be validated in pediatric AML. Lastly, for the first time, we identified TLS-like aggregates in the BM of AML patients, which have been associated with immunotherapy response in many cancers (Schumacher &amp; Thommen, 2022). Additional studies to further characterize the function and relevance of these lymphoid aggregates are ongoing.

Establishment and characterization of an intestinal epithelial cell line from Japanese flounder (Paralichthys olivaceus)

The Japanese flounder Paralichthys olivaceus is a high-value mariculture species. However, the aquaculture industry worldwide faces significant challenges due to flounder ascites, a serious disease caused by gram-negative bacterium Edwardsiella infection of fish cultures. Studies have confirmed that Edwardsiella tarda infection of flounder causes intestinal inflammatory disease. The recognition of pathogenic microorganisms by intestinal epithelial cells is the primary cause of inflammatory responses. In this study, a new cell line derived from the distal intestine (mainly the mid and posterior intestine) of Japanese flounder was established and characterized. This cell line, designated as the PoIEC line, was maintained in DMEM with 15% fetal bovine serum at 24 °C for >1 year, and subcultured >55 times. The PoIECs were epithelial-like cells with cobblestone-like shapes. Microvilli were observed on the surface of the PoIECs through transmission electron microscopy and the existence of epithelial markers was confirmed. PoIECs transfected with a pEGFP-N3 plasmid emitted an intense green fluorescence signal. Transfection efficiency of these cells was calculated to be approximately 37%, making this cell line a potential tool for future exogenous gene function research. Furthermore, PoIECs were stimulated by LPS and live E. tarda, and the expression profiles of immune-related genes (MHC Iα, MHC IIα, TNFα, IL-8, and IL-1β) confirmed that these cells recognized antigens and activated immune responses. In conclusion, a new cell line derived from the intestine of Japanese flounder was established, and this cell line was an ideal cellular platform for the study of mucosal immunity, probiotic flora and nutrient metabolism in the fish gut.

Identification of immune-related hub genes contributing to the pathogenesis, diagnosis, and remission of ulcerative colitis by integrated bioinformatic analyses.

The inflammatory disease ulcerative colitis (UC) is multifaceted, immune-mediated, chronic, and relapsing, which is considered to be mainly driven by dysregulated mucosal immune response. The remission of the inflammatory response is a marker of mucosal healing, relating to the low risk of hospitalizations, colorectal cancer, and colectomy. In spite of this, it is still unclear what the key immunological mechanism is which contributes to UC. Here, we explored the immune mechanism and related key genes underlying the state of inflammation in UC. Co-expression networks were constructed based on the expression profiles of immune-related genes in GSE179285. Using Weighted Gene Co-expression Network Analysis and Protein-protein interactions analysis, common hub genes were identified in the module of interest. Then, screening of real hub genes, significantly differentially expressing in inflamed UC, was carried out by Differential Expression Genes Analysis of GSE75214, GSE53306, and GSE6731datasets and immunohistochemistry of clinical samples. The diagnosis Capacity of the hub gene was identified by "glm" function in R. The potential key immune-related mechanisms were investigated using functional enrichment analysis and gene set enrichment analysis (GSEA). Bioinformatics tools were used to predict potential upstream transcription factors (TF), including the UCSC genome browser, correlation analyses, and JASPAR browser. The analysis revealed the blue module, consisting of 227 immune-related genes, showed the highest correlation with inflamed UC. And then, forty-three common candidates were distinguished. S100A9 was identified within the key module as a real hub gene with good diagnostic performance. The immune genes in the blue module were markedly enriched in the Cytokine-Cytokine receptor interaction. S100A9 most likely gets involved NOD-like receptor (NLR) signaling pathway. SPI1 showed the strongest likelihood to be the regulator. S100A9 was identified as the real immune-related hub gene for inflamed UC. Both diagnosis and remission may be aided by its high expression in the inflamed UC.

Immune-Related Gene Expression Profile at Peritumoral Tonsillar Tissue Is Modified by Oropharyngeal Cancer Nodal Status

Secondary lymphoid organs, such as lymph nodes and tonsils, serve as an interface between the immune system and tumor cells as an initial antigen-presentation site, crucial in antitumor immune response and disease progression. In oropharyngeal cancers originating from palatine tonsils, it was hypothesized that characterizing the immunologic process occurring in the peritumoral tonsil tissue would elucidate immune mechanisms of the lymphatic spread of the disease. A total of 33 patients were enrolled and divided into two cohorts. In Cohort 1 (6 patients), gene expression profiles at the peritumoral lymph regions and tumor regions were analyzed using the whole-transcriptome atlas. In the peritumoral lymph regions, 237 genes were up-regulated in metastasis-negative cases compared with metastasis-positive ones, but only 1 gene was up-regulated in tumor regions. In Cohort 2 (27 patients), microarray analysis of peritumoral tonsil tissue revealed 192 up-regulated genes. Gene ontology analysis revealed the significantly enriched Gene Ontology terms associated with T-cell activation; top 10 hub genes, as ranked by degree, were PTPRC, TLR4, CD80, CD40, STAT3, CD28, CD40LG, CD44, CCR7, and IL7R. Gene set enrichment analysis combined with principal component analysis were used to effectively classify patients as lymph node metastasis positive or negative. These findings suggest peritumoral tonsils as a potential target for investigating the immune mechanisms associated with the lymphatic spread of the disease in oropharyngeal cancers.

Comparative study of the impact of dietary supplementation with different types of CpG oligodeoxynucleotides (CpG ODNs) on enhancing intestinal microbiota diversity, antioxidant capacity, and immune-related gene expression profiles in Pacific white shrimp (Litopenaeus vannamei).

The CpG oligodeoxynucleotides (CpG ODNs) reportedly possess the capacity to strengthen immunity in mammals. This experiment was conducted to evaluate the impact of dietary supplementation with 17 types of CpG ODNs on intestinal microbiota diversity, antioxidant capacity, and immune-related gene expression profiles of the shrimp Litopenaeus vannamei. Diets including 50 mg kg-1 CpG ODNs wrapped in egg whites were prepared and divided into 17 different groups, with 2 control groups (normal feed and feed with egg whites). These CpG ODNs supplemented diets and the control diets were fed to L. vannamei (5.15 ± 0.54 g) three times daily at 5%-8% shrimp body weight for three weeks. The results of consecutive detection of intestinal microbiota by 16S rDNA sequencing indicated that 11 of the 17 types of CpG ODNs significantly enhanced intestinal microbiota diversity, increased the populations of several probiotic bacteria, and activated possible mechanisms relevant to diseases. The immune-related genes expression and antioxidant capacity in hepatopancreas further demonstrated that the 11 types of CpG ODNs effectively improved the innate immunity of shrimp. Additionally, histology results showed that the CpG ODNs in the experiment did not damage the tissue structure of hepatopancreas. The results suggest that CpG ODNs could be used as a trace supplement to improve the intestinal health and immunity of shrimp.

Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes.

The aim of this study is to determine immune-related biomarkers to predict effective antitumor immunity in myelodysplastic syndrome (MDS) during immunotherapy (IMT, αCTLA-4, and/or αPD-1 antibodies) and/or hypomethylating agent (HMA). Peripheral blood samples from 55 patients with MDS were assessed for immune subsets, T-cell receptor (TCR) repertoire, mutations in 295 acute myeloid leukemia (AML)/MDS-related genes, and immune-related gene expression profiling before and after the first treatment. Clinical responders treated with IMT ± HMA but not HMA alone showed a significant expansion of central memory (CM) CD8+ T cells, diverse TCRβ repertoire pretreatment with increased clonality and emergence of novel clones after the initial treatment, and a higher mutation burden pretreatment with subsequent reduction posttreatment. Autophagy, TGFβ, and Th1 differentiation pathways were the most downregulated in nonresponders after treatment, while upregulated in responders. Finally, CTLA-4 but not PD-1 blockade attributed to favorable changes in immune landscape. Analysis of tumor-immune landscape in MDS during immunotherapy provides clinical response biomarkers.

Spatial genomics reveals a high number and specific location of B cells in the pancreatic ductal adenocarcinoma microenvironment of long-term survivors.

Only 10% of pancreatic ductal adenocarcinoma (PDAC) patients survive longer than five years. Factors underlining long-term survivorship in PDAC are not well understood. Therefore, we aimed to identify the key players in the tumor immune microenvironment (TIME) associated with long-term survivorship in PDAC patients. The immune-related gene expression profiles of resected PDAC tumors of patients who survived and remained recurrence-free of disease for ≥36 months (long-term survivors, n=10) were compared to patients who had survived ≤6 months (short-term survivors, n=10) due to tumor recurrence. Validation was performed by the spatial protein expression profile of immune cells using the GeoMx™ Digital Spatial Profiler. An independent cohort of samples consisting of 12 long-term survivors and 10 short-term survivors, was used for additional validation. The independent validation was performed by combining qualitative immunohistochemistry and quantitative protein expression profiling. B cells were found to be significantly increased in the TIME of long-term survivors by gene expression profiling (p=0.018). The high tumor infiltration of B cells was confirmed by spatial protein profiling in the discovery and the validation cohorts (p=0.002 and p=0.01, respectively). The higher number of infiltrated B cells was found mainly in the stromal compartments of PDAC samples and was exclusively found within tumor cells in long-term survivors. This is the first comprehensive study that connects the immune landscape of gene expression profiles and protein spatial infiltration with the survivorship of PDAC patients. We found a higher number and a specific location of B cells in TIME of long-term survivors which emphasizes the importance of B cells and B cell-based therapy for future personalized immunotherapy in PDAC patients.

Dietary Supplement of Grape Wastes Enhances Honeybee Immune System and Reduces Deformed Wing Virus (DWV) Load.

Ingredients rich in phenolic compounds and antioxidants of winemaking wastes, which play an important role in the prevention of various diseases and the control of viruses, are being explored. Currently, there is a concern about honeybee population loss, with deformed wing virus (DWV) being the most common virus infecting apiaries and one of the main causes of honeybee decline. Hence, the effect of grape pomace powder (GPP) as a dietary supplement to enhance the immune system of honeybees affected by DWV was evaluated. The characteristics of the ingredient GPP, obtained by spray-drying, revealed a high anthocyanin content (1102.45 mg 100 g-1), and it was applied at doses of 0.5, 1, 2.5 and 5% as a dietary supplement for bees infected by DWV. The results showed that the GPP treatments strengthened the immune response of honeybees against DWV. Moreover, the expression of the Relish gene was significantly higher in bees fed with GPP compared to the infected control. This study, which is framed in the search of food waste valorization for environmental sustainability, proves the feasibility of using grape wastes as dietary supplements for pollinators, and provides knowledge of the influence of polyphenols on the expression profiles of immune-related genes in honeybees.

Systematic Analysis of Molecular Subtypes Based on the Expression Profile of Immune-Related Genes in Pancreatic Cancer.

Immunotherapy has a good therapeutic effect and provides a new approach for cancer treatment. However, only limited studies have focused on the use of molecular typing to construct an immune characteristic index for gene expression in pancreatic adenocarcinoma (PAAD) and to assess the effectiveness of immunotherapy in patients with PAAD. Clinical follow-up data and gene expression profile of PAAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Based on 184 immune features, molecular subtypes of pancreatic cancer were found by the "ConsensusClusterPlus" package, and the association between clinical features and immune cell subtype distribution was analysed. In addition, the relationship between the proportion of immune subtypes and the expression of immune checkpoints was analysed. The CIBERSORT algorithm was introduced to evaluate the immune scores of different molecular subtypes. We used the tumor immune dysfunction and exclusion (TIDE) algorithm to assess the potential clinical effect of immunotherapy interventions on single-molecule subtypes. In addition, the oxidative stress index was constructed by linear discriminant analysis DNA (LDA), and weighted correlation network analysis was performed to identify the core module of the index and its characteristic genes. Expression of hub genes was verified by immunohistochemical analysis in an independent PAAD cohort. Pancreatic cancer is divided into three molecular subtypes (IS1, IS2, and IS3), with significant differences in prognosis between multiple cohorts. Expression of immune checkpoint-associated genes was significantly reduced in IS3 and higher in IS1 and IS2, suggesting that the three subgroups have different responsiveness to immunotherapy interventions. The results of the CIBERSORT analysis showed that IS1 exhibited the highest levels of immune infiltration, whereas the results of the TIDE analysis showed that the T-cell dysfunction score of IS1 was higher than that of IS2 and IS3. Furthermore, IS3 was found to be more sensitive to 5-FU and to have a higher immune signature index than IS1 and IS2. Based on WGCNA analysis, 10 potential gene markers were identified, and their expression at the protein level was verified by immunohistochemical analysis. Specific molecular expression patterns in pancreatic cancer can predict the efficacy of immunotherapy and influence the prognosis of patients.

Embryo-Uterine Cross-Talk: Exploration of the Immunomodulatory Mechanism in Buffalo.

Understanding the molecular cross-talk between the embryo and uterine endometrium is crucial for the improvement of IVF outcomes. The present work was undertaken to investigate the effect of pre-implantation embryo on the expression profile of immune-related genes in uterine epithelial cells (UECs) and PBMCs in buffalo. UECs were isolated from slaughterhouse-derived non-gravid uteri, cultured ex vivo and characterized, and buffalo embryos were produced in vitro from slaughterhouse-derived ovaries. Embryos co-cultured with steroid-treated UECs significantly stimulated (p &lt; 0.05) the relative mRNA abundance of PTGS2, ISG15, OAS1, MX2, IFNAR1 and IFNAR2 in UECs while they significantly suppressed the mRNA expression of NFkβIA, NFkβ2, TNFα and IL1B, with no significant change in TGFβ1 and IL10 in the co-culture of embryos with UECs. In vitro treatment of PBMCs with conditioned media (CM) derived from embryos as well as UEC-embryo co-culture upregulated the mRNA abundance of ISG15, TGFβ1, PTGS2OAS1, MX2 and STAT1 while it downregulated IL17 and TNFα expression. The expression of IFNAR1 and IFNAR2 was elevated in PBMCs cultured in embryo-derived CM, but there was no significant change in PBMCs cultured in UEC-embryo co-culture CM. Thus, it can be concluded that the developing embryo and its secretions modulate the expression of immune responses by inducing an anti-inflammatory action in uterine epithelial cells for acceptance of the semi-allogenic embryo in the uterus to sustain pregnancy in buffalo.

Expression Profiles of Immune-Related Genes and Apoptosis Study of Avian Intraepithelial-Natural Killer Cells in Chickens Inoculated with Vaccine Strain of Newcastle Disease Virus (NDV) and Challenged with Virulent NDV.

In spite of the available information on the role of natural killer (NK) cells in several viral infections, the interactions between chicken intraepithelial-NK (IEL-NK) cells and Newcastle disease virus (NDV) are poorly understood. In this study, we investigated these interactions following the inoculation of chickens with NDV vaccine strain LaSota and subsequent challenge with velogenic NDV (vNDV) genotype VII (GVII) and VIII (GVIII), through quantification of IEL-NK cell's apoptosis and expression profiling of its surface receptors. Specific-pathogen-free chickens were randomly divided into six groups, as follows: one group of an uninfected control, one group infected with NDV LaSota, two groups each infected with either GVII or GVIII, and two groups inoculated with NDV LaSota and challenged with either GVII (LaSota-genotype VII [LSGVII]) or GVIII (LaSota-genotype VIII [LSGVIII]). Avian intraepithelial lymphocytes (IEL) were isolated from the duodenal loops, and CD3- cells were characterized. Immunophenotyping and apoptosis analysis of CD3-/CD25+/CD45+IEL NK cells were conducted using a flow cytometer. In addition, a gene expression study was conducted using real-time quantitative PCR. Data were analyzed using two-way analysis of variance. The results showed that vNDV GVII or GVIII caused apoptosis of IEL-NK cells; however, following inoculation of LSGVII or LSGVIII, the effect of vNDV GVII and GVIII to cause a reduction in the population of viable IEL-NK cells was significantly reduced. Furthermore, the expression profiles of activating receptors CD69, NK-lysin, and IFN-γ, were generally upregulated in chickens inoculated with LSGVII or LSGVIII. In contrast, B-NK, an inhibitory receptor, was downregulated in these treatment groups. In NDV GVII- and GVIII-challenged groups, however, B-NK was upregulated, whereas the other receptors were generally downregulated. The findings of this study showed that NDV vaccine strain LaSota may prevent apoptosis and cause upregulation of activating receptors of chicken IEL-NK cells in velogenic virus-challenged settings.