Integrated transcriptomic and metabolomic analyses reveal host-metabolite interactions underlying cloacal inflammation in laying Pekin ducks.

To the Editor: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by proliferation of abnormal myeloblasts in the bone marrow. Traditional treatment, such as chemotherapy with or without hematopoietic stem cell transplantation (HSCT), has been used as the first-line therapy in AML. However, the clinical outcome of patients with AML varies greatly due to several factors, such as the tumor immune microenvironment (TME).[1] Immune checkpoint inhibitors (ICIs) have recently gained popularity as therapeutic options for relapsed AML or MRD-positive AML patients.[2] Based on previous studies, immune dysregulation plays an important role in AML relapse, and immune-related genes may provide prognostic information for AML patients. Thus, exploring the immune-related genetic prognostic index (IRGPI) to predict prognosis and therefore provide personalized guidance for ICI therapy is urgently needed. In this study, we developed an immune-related genetic prognostic index for AML that was able to predict overall survival (OS) and ICI immunotherapy benefit. We focused on all immune-related genes in AML transcriptome data and screened immune-related genes associated with prognosis by weighted gene coexpression network analysis (WGCNA) to construct an immune-related gene prognostic index (IRGPI). We then characterized the immune and molecular features of the IRGPI, examined its prognostic ability for AML patients, and compared it with tumor immune dysfunction and exclusion (TIDE) as well as the tumor inflammation signature (TIS).[3,4] The results showed that the IRGPI is a promising prognostic biomarker for AML patients to predict the survival and benefits of ICI immunotherapy. First, transcriptome and clinical information of the cohort The Cancer Genome Atlas (TCGA)-AML and all data for normal tissue samples from 336 whole blood samples in Genotype-Tissue Expression (GTEx) were retrieved via the UCSC Xena platform. RNA-seq data for 104 AML samples (GSE71014) and survival information were downloaded from the Gene Expression Omnibus (GEO). The clinical characteristics of 132 AML patients from TCGA-LAML used for survival analysis are listed in Supplementary Table 1, https://links.lww.com/CM9/B503. Lists of immune-related genes were downloaded from the ImmPort and InnateDB database. A total of 14,672 differentially expressed genes were obtained in differential expression analysis. By intersecting these genes with the lists of immune-related genes obtained from ImmPort and InnateDB, 908 differentially expressed immune-related genes were identified, of which 189 genes were upregulated and 719 downregulated in tumor samples compared with normal samples. WGCNA was carried out on candidate genes to obtain immune-related hub genes (n = 908), revealing the top 117 immune-related hub genes with a threshold degree of >20. Expression of 24 of these immune-related hub genes correlated closely with AML patient OS, as determined by Kaplan–Meier (K–M) analysis (P <0.001). To determine independent prognostic genes, multivariate Cox regression analysis for OS was performed among the 24 immune-related hub genes, and only seven genes (CLEC11A, IL1R2, IL1RL2, TRIM55, TREML2, CAMK2A, and BMP2) were found to significantly affect the OS of AML patients. Then, we constructed a prognostic index for all cancer samples calculated by the following formula: IRGPI = expression level of CLEC11A × (-0.59) + expression level of IL1R2 × 0.37 + expression level of IL1RL2 × 3.63 + expression level of TRIM55 × (4.98) + expression level of TREML2 × (1.25) + expression level of CAMK2A × (2.17) + expression level of BMP2 × (0.83). Taking the median IRGPI as the cut-off value, IRGPI-high patients had a lower OS than IRGPI-low patients (P <0.001) among AML samples from TCGA. Then, the role of the IRGPI was validated using the GSE71014 cohort. The patients in the IRGPI-low subgroup had a significantly better prognosis than those in the IRGPI-high subgroup (P = 0.044, data not shown), which was consistent with the result using the TCGA dataset and indicated the prognostic value of the IRGPI. Multivariate Cox regression analysis confirmed the IRGPI to be an independent prognostic factor after adjusting for other clinicopathologic factors (P <0.001). Next, we explored the relationship between the IRGPI score and CD274 expression as well as CTLA4 and LAG3. The IRGPI score correlated significantly positively with CD274 expression (r = 0.42, P <0.001) and slightly with CTLA4 and LAG3 expression (r =0.3, P <0.001; r = 0.27, P <0.001) (data not shown). To analyze the composition of immune cells in different IRGPI subgroups, we used the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm to evaluate differences in immune cells between the IRGPI-high and IRGPI-low groups. We found that monocytes and eosinophils were more abundant in the IRGPI-high subgroup but that resting mast cells were more abundant in the IRGPI-low subgroup. Further analysis showed that higher monocytes correlated with lower OS ability and that higher resting mast cells were associated with longer OS (data not shown). We then used TIDE to evaluate the potential clinical efficacy of immunotherapy in the two IRGPI groups. Previous studies have shown that a higher TIDE prediction score is related to a higher potential for immune evasion, indicating that such patients are less likely to benefit from ICI therapy.[3] Our results showed that the IRGPI-high group had a higher TIDE score than the IRGPI-low subgroup [Figure 1A], suggesting that IRGPI-low patients may benefit more from ICI therapy than IRGPI-high patients. Moreover, previous studies have shown that a higher TIDE prediction score is associated with a worse outcome. Therefore, IRGPI-low patients with a low TIDE score might have a better prognosis than IRGPI-high patients with a high TIDE score. In addition, the IRGPI-high group had a higher risk of T-cell exclusion and T-cell dysfunction than the IRGPI-low group [Figure 1B, C]. We also performed receiver operating characteristic (ROC) analysis of the IRGPI for OS at 1-year, 2-year, and 3-year follow-up, and Figure 1D shows a robust prediction ability at 3 years (AUC: 0.819). The area under the ROC curve for the IRGPI was higher than that for TIDE or TIS [Figure 1E]. Further analysis revealed a correlation between the IRGPI-high group and lower survival probability in the IMvigor210 cohort[5] [Figure 1F], suggesting a strong prognosis ability compared with TIDE and TIS in AML and a possible indicator for ICI therapy benefit.Figure 1: The benefit of ICI therapy in the two IRGPI subgroups. (A–C) TIDE, T-cell dysfunction, and exclusion score in different IRGPI subgroups. The score between the two IRGPI subgroups was compared through the Wilcoxon test (* P < 0.001, † P <0.01). (D) ROC analysis of IRGPI on overall survival at 12-, 24-, and 36-month follow-up in TCGA cohort. (E) ROC analysis of IRGPI, TIS, and TIDE on overall survival at 36-month follow-up in TCGA cohort. (F) Kaplan–Meier survival analysis of the IRGPI subgroups in the IMvigor210 cohort. ICI: Immune checkpoint inhibitor; IRGPI: Immune-related genetic prognostic index; ROC: Receiver operating characteristic; TCGA: The Cancer Genome Atlas; TIDE: Tumor immune dysfunction and exclusion.By using RNA-seq data of AML, we identified a prognostic biomarker, the IRGPI, for AML. The IRGPI proved to be a valid prognostic immune-related biomarker for AML, with better survival in IRGPI-low patients and worse survival in IRGPI-high patients in both TCGA and GEO cohorts.In our study, the composition of some immune cells differed between the two IRGPI subgroups: the IRGPI-high subgroup had higher levels of monocytes and neutrophils, whereas resting mast cells were significantly enriched in the IRGPI-low subgroup. It has been reported that monocytes can be driven by AML blasts to differentiate into the M2-like phenotype, which promotes a more immunosuppressive microenvironment and is averse to AML clearance.[6] This is in accordance with the result that higher monocytes correlated with lower OS in our study. Therefore, the phenotype and functions of neutrophils in AML should be carefully evaluated in the future. Previous studies have proven that biomarkers, such as TIDE and TIS, can predict patient response to immunotherapy. TIDE can be used to identify two immune escape mechanisms that induce T-cell dysfunction in tumors with high CTL invasion and prevent T-cell invasion in tumors with low CTL levels.[3] In addition, TIS provides both quantitative and qualitative information about the TME, and 18 genes that reflect an ongoing CD8 T-cell response have shown promising results in predicting response to anti-PD-1/PD-L1 agents.[4] However, both TIDE and TIS focus on the immune function of T cells. Since the composition of immune cell subtypes and expression of immunosuppressive molecules were different between the two IRGPI subgroups, the IRGPI might reflect different immune benefits from ICR therapy identified with TIDE. Furthermore, both markers relate to patient response to immunotherapy rather than patient survival time. Encouragingly, the predictive value of the IRGPI in our study was comparable to that of TIDE and TIS, and the IRGPI might be a better predictor of OS at longer follow-up times. We further confirmed the prognostic value of the IRGPI in predicting the survival of patients who receive ICI therapy. Moreover, as the IRGPI is composed of only seven genes, it is easier to implement than TIDE and TIS. In conclusion, the IRGPI is a promising immune-related prognostic biomarker that may help in distinguishing immune and molecular characteristics and predicting AML patient clinical outcomes. The IRGPI might serve as a prognostic indicator for response to ICI immunotherapy; however, our prognostic model was limited to data from public databases and lacked more prospective real-world data. Therefore, more studies are needed to verify our results. Second, as we only considered an index of immune-related genes, many prominent prognostic genes in AML might have been excluded. It is possible that the IRGPI can be applied jointly with other types of biomarkers to achieve higher prediction performance. Finally, it should be emphasized that the association between the risk score and immune activity has not yet been experimentally addressed. Funding This study was supported by grants from the National Natural Science Foundation of China (Nos. 81670166, 81870140, 82070184, and 81621001), Peking University People's Hospital Research and Development Funds (No. RDL2021-01), Beijing Life Oasis Public Service Center (No. CARTFR-01), and CSH Young Scholars and 3SBio Pharmaceutical joint research project (No. KYC2201001). Conflict of Interest None.

e16683 Background: Hepatocellular carcinoma is the most common malignant tumor. Although the treatment of HCC has significantly improved, the 5-year survival rate is still only 18%. There is increasing evidence that tumor immune microenvironment (TIM) plays critical roles during cancer initiation and progression. Based on the comprehensive exploration of the immunogenomic, an immune-related risk model was constructed to predict hepatocellular carcinoma prognosis. Methods: Transcriptomic data of HCC patients were downloaded from the TCGA database, and the differentially expressed immune-related genes (IRGs) (FDR &lt; 0.01, |log2fold change| &gt; 2) were identified. Functional enrichment analysis was performed to explore potential molecular mechanisms of the differentially expressed IRGs. By univariate and multivariate Cox regression analysis, we identified eight prognosis-related IRGs. Based on the expression levels of IRGs, we constructed the immune-related risk model. The Kaplan‐Meier (K‐M) survival curves, ROC curves, univariate and multivariate analysis were used to evaluate the immune-related risk model. According to the risk score, HCC patients were stratified into low and high-risk groups. CIBERSORT was applied to analyze the profiling difference of infiltrating immune cells between the two groups. Results: A total of 113 differentially expressed IRGs were identified, of which nine IRGs were correlated with the prognosis of HCC patients. Functional enrichment analysis showed that these genes were involved in immune response and immune signal pathway. The immune-related risk model consisted of eight IRGs (FABP6, RBP2, MAPT, BIRC5, PLXNA3, CSPG5, IL17D and STC2). The immune risk score was an independent prognostic factor (HR, 2.63 [1.93−3.58]; P = 8.16E−10) and the patients with a high-risk score tended to have a shorter OS than those with a low-risk score. In the TCGA cohort, high-risk patients tended to have an advanced stage. Moreover, we found that the patients in the high-risk group had higher fractions of T follicular cells helper and macrophages M0. The patients with low-risk scores had higher fractions of CD8+ T cells and CD4+ T cells. Conclusions: We have identified the immune-related risk model of hepatocellular carcinoma based on the expression profiles of eight immune-related genes. This model could predict prognosis and reflect the tumor immune microenvironment of HCC patients, which can provide new insights in the individualized treatment of HCC and potential novel targets for immunotherapy.

N-Acylethanolamine Acid Amidase (NAAA) is an N-terminal cysteine hydrolase and plays a vital physiological role in inflammatory response. However, the roles of NAAA in tumor immunity are still unclear. By using a series of bioinformatics approaches, we study combined data from different databases, including the Cancer Genome Atlas, the Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, cBioPortal, Human Protein Atlas, TIMER, and ImmuCellAI to investigate the role of NAAA expression in prognosis and tumor immunity response. We would like to reveal the potential correlations between NAAA expression and gene alterations, tumor mutational burden (TMB), microsatellite instability (MSI), DNA methylation, tumor microenvironment (TME), immune infiltration levels, and various immune-related genes across different cancers. The results show that NAAA displayed abnormal expression within most malignant tumors, and overexpression of NAAA was associated with the poor prognosis of tumor patients. Through gene set enrichment analysis (GSEA), we found that NAAA was significantly associated with cell cycle and immune regulation-related signaling pathways, such as in innate immune system, adaptive immune system, neutrophil degranulation, and Toll-like receptor signaling pathways (TLRs). Further, the expression of NAAA was also confirmed to be correlated with tumor microenvironment and diverse infiltration of immune cells, especially tumor-associated macrophage (TAM). In addition to this, we found that NAAA is co-expressed with genes encoding major histocompatibility complex (MHC), immune activation, immune suppression, chemokine, and chemokine receptors. Meanwhile, we demonstrate that NAAA expression was correlated with TMB in 4 cancers and with MSI in 10 cancers. Our study reveals that NAAA plays an important role in tumorigenesis and cancer immunity, which may be used to function as a prognostic biomarker and potential target for cancer immunotherapy.

BackgroundPneumonia, induced by various bacteria or viruses, is a globally prevalent inflammatory disease that threatens the life of millions of people. Staphylococcus aureus (S. aureus) is a major pathogen of pneumonia and can be inhibited by Diphenyl pyrimidine (DP), while the underlying mechanisms are largely unknown.MethodsIn this study, we conducted the S. aureus-induced rat pneumonia model and then performed DP treatment to inhibit the injury. Meanwhile, whole transcriptome sequencing (RNA-seq) experiment was performed to identify the dysregulated genes with expression and alternative splicing changes, as well as their enriched functions. Hub genes and immune cell proportion changes by DP were also identified to explore the underlying mechanism.ResultsWe identified 2,225 up and 1,257 down DEGs between DP and SA samples, and found they were significantly enriched in immune and inflammatory response pathways, as well as angiogenesis and apoptosis pathways. At the same time, DP treatment also significantly altered the alternative splicing profile, including 3898 AS genes and 416 co-regulated genes with DEGs. Functional analysis of co-regulated genes demonstrated they were enriched in immune response, signal transduction, and apoptosis regulation pathways. Finally, we identified ten hub genes by protein-protein network analysis from DEGs, including CCNA2, TOP2A, CDK1, ESPL1, KIF2C, PBK, UHRF1, RACGAP1, PCLAF, and RAD51 that were totally repressed by DP treatment.ConclusionIn summary, our study demonstrated that DP treatment can profoundly modulate the immune and inflammatory response by regulating the transcriptome profile of peripheral blood monocytes (PBMCs). The identified hub genes by DP treatment are potential therapeutic targets for S. aureus-induced pneumonia in future.

BackgroundThe amplification or mutation of oncogenes and escape from immune surveillance systems promote tumor metastasis. However, subtle changes in the immune microenvironment and signaling pathways are poorly understood during the formation of lymphovascular space involvement (LVSI) and lymph node (LN) metastasis of endometrioid endometrial adenocarcinoma (EEA).Patients and methodsWe detected tumor immunology-related signaling pathways and immunocyte subtypes according to the mRNA levels of 750 oncogenes and genes relating to the tumor microenvironment and immune response using the Nanostring PanCancer IO 360 Panel in 24 paraffin-embedded tissues of EEAs and benign gynecological diseases. Internal reference genes were used for data normalization.ResultsAngiogenesis and immune cell adhesion signaling pathways were activated during LVSI formation of EEA progression. However, during the development of LVSI to LN metastasis, immune system signaling pathways were significantly inhibited, including antigen presentation, cytotoxicity, lymphoid compartment, interferon signaling, and costimulatory signaling pathways. Immune-related genes (CD69, HLA-DOA, ATF3, GBP1, AP2, DTX3L, EGR1, GBP4, TAP1, EIF2AK2, MX1, ISG15, STAT1, and HLA-DRA) were significantly downregulated in EEA with LN metastasis compared to those in EEA with LVSI. Instead, hypoxia, metabolic stress, epigenetic regulation, matrix remodeling, and metastasis signaling pathways were continuously activated in LN metastasis. We also found that neutrophils, macrophages, and mast cells might be involved in LVSI formation and LN metastasis in EEA.ConclusionsEEA with metastatic LNs showed significant immunosuppressive effects. Some oncogenes, matrix remodeling- and hypoxia-related genes, and neutrophil signatures showed higher expression, suggesting their potential as therapeutic targets and offering new immunotherapy strategies in EEA during LN metastasis.

The tumor immune microenvironment (TIME) is now considered as an important factor during gastric cancer (GC) development. This study identified a novel immune-related risk model for predicting prognosis and assessing the immune status of GC patients. Transcriptomic data were obtained from the TCGA database. The differential expressed immune-related genes (IRGs) were identified through the ImmPort portal. Enrichment analysis was performed to explore the potential molecular mechanism of these IRGs. By the Cox regression analysis, we constructed the immune prognostic model. Then, the association between the model and the immune microenvironment was estimated. The model was validated in the GSE84433 dataset. Totally, we identified 222 differentially expressed IRGs. These IRGs were closely correlated with immune response and immune signaling pathways. Through the Cox regression analysis, we developed the immune prognostic model based on the expression of seven IRGs (CXCL3, NOX4, PROC, FAM19A4, RNASE2, IGHD2-15, CGB5). Patients were stratified into two groups according to immune-related risk scores. Survival analysis indicated that the prognosis of high-risk patients was poorer than low-risk patients. Moreover, the immune-related risk score was an independent prognostic biomarker. More importantly, we found that the infiltration level of immunosuppressive cells and the expression of inhibitory immune checkpoints were higher in high-risk patients. The immune microenvironment tended to be a suppressive status in patients with high-risk scores. This study demonstrated that our model had predictive value for prognosis and the TIME in GC. It might be a robust tool to improve personalized patient management.

Growth stagnation or weight loss is prevalent in weaned piglets, with post-weaning diarrhea severely compromising intestinal health, underscoring the criticality of intestinal structural integrity for preventing digestive disorders. Tight junction proteins (TJPs), core components of intestinal intercellular junctions, play indispensable roles in maintaining barrier function, nutrient absorption, and intestinal homeostasis by regulating paracellular permeability and mediating immune defense-related signaling pathways. Dysregulated TJP expression disrupts these processes and impairs piglet growth performance. Despite recent progress in characterizing TJP-mediated regulation of intestinal health in weaned piglets, key knowledge gaps remain regarding the specific regulatory mechanisms by which distinct TJP subtypes modulate intestinal microbiota-immune crosstalk. Future research should prioritize elucidating the effects of nutritional interventions on TJP expression and intestinal health, as well as the molecular mechanisms underlying TJP involvement in intestinal diseases. These efforts will provide theoretical support for developing novel feed additives and nutritional strategies to improve weaned piglet health.

BackgroundMajor depression, bipolar disorder are linked by multiple common genetic and environmental risk factors but the trajectories of these factors to result in the different illnesses is still unknown. Considerable evidence implicates immune dysregulation in mood disorder pathology with involvement of stress response genes suggesting reactions to environmental insults. In addition, neurodevelopmentally linked growth factor systems such as the epidermal growth factor (EGF) system is of interest given its involvement in neural processes such as synaptic plasticity disrupted in these disorders. Therefore, we sought to determine if immune and EGF system genes interacted in mood disorders to mediate the impact of environmental risk factors in the pathology of these disorders.Aims & ObjectivesTo examine if key EGF and immune signalling pathways are differentially expressed in brain in mood disorder patients and if there could be any interactions between them.MethodThe expression of candidate genes from EGF and immune systems and related signalling pathways were examined in post-mortem dorsolateral prefrontal (DLPFC) (n=114 genes) and orbitofrontal cortical (OFC) (n=105 genes) tissues, from mood disorder (n=30), schizophrenia (n=18), and healthy (n=20) subjects, using RT-qPCR. Protein levels of 8 immune molecules were measured by western immunoassay in these brain regions. Data were analysed by ANOVA or corresponding non-parametric tests. General linear modeling (GLM) was used to test for interactions between EGF and immune pathway molecules.ResultsIn DLPFC, there were 64 differentially expressed genes (DEG) between patient and healthy control groups. Of these, 19 were significantly altered in mood disorder predominantly in mTOR, TNF, toll-like receptor (TLR) and complement signalling pathways with minimal changes noted in MAPK-ERK, PI3K-AKT, cytokine signalling and JAK-STAT pathways. ERBB4 was uniquely changed in mood disorder and was the only upregulated gene in a patient cohort. Forty-three of the DEG (67%) were significantly altered between the patient groups, with all of them exhibiting the lowest expression in schizophrenia.In OFC, only three genes were differentially expressed across the groups and IKBKG was significantly downregulated in mood disorder against controls. There were no protein changes in mood disorder patients either in BA46 or BA11. Significant interactions between EGF system molecules BRAF and PIK3CA, and immune signalling through IFNA1 in mood disorder were noted.Discussion & ConclusionsWe found that although there were common changes in the mTOR, TLR and the TNF signalling pathways between the schizophrenia and mood disorder cohorts, expression profiles between them were highly different. Particularly, the unique upregulation of ERBB4 receptor in mood disorder may carry pathological significance and indicate that the ErbB-PI3K-AKT-mTOR signalling axis may be differently regulated from schizophrenia in DLPFC. These findings overall may signify some important pathological differences in EGF and immune system signalling between these disorders. Further, those immune pathways altered in mood disorder indicate attenuation in innate immune response in these disorders suggesting possible association to early environmental insults. There may be regional differences between BA46 and BA11 in EGF and immune system dysfunction in mood disorders.

The incidence and mortality rates of prostate cancer are significantly higher in African-American men when compared to European-American men. We tested the hypothesis that differences in tumor biology contribute to this survival health disparity. Using microarray technology, we obtained gene expression profiles of primary prostate tumors resected from 33 African-American and 36 European-American patients. These tumors were matched on clinical parameters. We also evaluated 18 non-tumor prostate tissues from 7 African-American and 11 European-American patients. The resulting datasets were analyzed for expression differences on the gene and pathway level comparing African-American with European-American patients. Our analysis revealed 162 transcripts to be differentially expressed between African-American and European-American prostate cancer patients at a false discovery rate of 5% or less. Using a disease association analysis, we identified a common relationship of these transcripts with autoimmunity and inflammation. These findings were corroborated on the pathway level with numerous differentially expressed genes clustering in immune response, defense response, antigen presentation, B-cell/T-cell function, cytokine signaling, and inflammatory response pathways. Most commonly, the genes involved in these pathways were more highly expressed in tumors of African-American patients when compared with those of European-American patients. Amongst the immune-specific genes over-expressed by African-American patients was indoleamine 2,3-dioxygenease, HLA-E, and HLA-G. All three of these genes are well-known contributors of immunologic tolerance in tumors. Furthermore, a distinctive interferon signature was identified in the African-American prostate tumors, suggesting the possibility of viral involvement in disease etiology in this African-American population. In conclusion, the gene expression profiles of prostate tumors indicate prominent differences in tumor immunobiology between African-American and European-American men. The profiles portray the existence of a distinct tumor microenvironment in these two patient groups.

The objective of this study was to investigate alterations in nutrient utilization, standardized ileal digestibility of amino acids (SIDAA), and intestinal health in response to heat stress (HS) in Pekin ducks. A total of 240 healthy 28-day-old male Pekin ducks were randomly allocated to three groups: a normal control (NC) group, an HS group, and a pair-fed (PF; provided an amount of feed equal to that consumed by the HS group to eliminate the effects of feed intake) group, each with eight replicate cages of ten birds. The results showed that HS significantly reduced the apparent utilization of dietary energy, ether extract, and crude protein compared to both the NC and PF groups (p < 0.05), but yielded comparable SIDAA to the PF group. The HS group exhibited reduced mRNA levels of EAAT3 and PepT1, along with elevated mRNA levels of CAT1, GLUT5, and FATP6 in the jejunum compared to the NC or PF groups, respectively (p < 0.05). Furthermore, HS resulted in a significant deterioration of jejunal morphology and goblet cell count compared to the NC and PF groups (p < 0.05). Serum fluorescein isothiocyanate-dextran levels were significantly higher in HS ducks than in NC ducks (p < 0.05), but did not differ from PF ducks. At order-level classification of ileal mucosal microbiota, HS markedly increased the relative abundance of Bacillales, Deferribacterales, and Actinomycetales versus NC (p < 0.05), while significantly decreasing Bifidobacteriales abundance relative to PF (p < 0.05). Collectively, HS induces a leaky gut and microbiota dysbiosis that compromises gut health, thereby reducing dietary nutrient utilization in Pekin ducks. The observed reduction in feed intake constitutes a primary driver of intestinal health deterioration in heat-stressed Pekin ducks.

Hypoxia most often occurs in cancer and the occurrence of hypoxia helps the cells in adapting different responses than the normal such as the activation of of those signaling pathways which regulate proliferation, angiogenesis, and cell death. There are large number of genes which are known to be associated with diverse biological processes and their control and coordination and in different cancers, the hypoxia-response differs. In this study our goal is to understand the impact of alteration in expression of hypoxia and immune systems related genes and its survival in breast cancer and analyzed the hallmarks of molecular signatures. For this purpose we have collected the hypoxia-associated genes based on the literature related with diverse biological processes and functions. For all these genes, we have studied the survival analysis, breast cancer gene expression profiling, and relevant hypoxic genes alterations. Based on our study, we conclude that there are 17 critical pathways and 40 genes from hypoxic gene list appear to play the major roles in case of breast cancer and overall we observe that immune signaling pathways and its components are highly altered in case of breast cancer. Among the top raked hallmarks of molecular signatures are apoptosis, hypoxia, DNA repair, E2F targets, MYC targets, androgen and estrogen response, and TNFa signaling.

The lipid composition performs important functions in interaction between macropha-ge and Mycobacterium tuberculosis (MTB)/Mycobacterium bovis (MB). Current understanding regarding the lipid responses of bovine alveolar macrophage (BAM) to MTB/MB is quite limited. The present study conducted lipidomics and transcriptome to assess alterations in BAM lipid compositions upon MB and MTB infection. We found that both MTB and MB induced glycerophospholipids accumulation in BAM, and MTB induced more alterations in lipid composition. MTB could affect the contents of various lipids, especially ceramide phosphocholines, polystyrene (PS) (17:0/0:0), testolic acid and testosterone acetate. Meanwhile, MB particularly induced accumulation of 1-alkyl,2-acylglycerophosphoinositols. Both MB and MTB suppressed the contents of palmitoleamide, N-ethyl arachidonoyl amine, N-(1,1-dimethyl-2-hydroxy-ethyl) arachidonoyll amine, eicosanoyl-EA, and PS (O-18:0/17:0) in BAM. Additionally, transcriptome analysis revealed that only MTB triggered genes involved in immune signaling and lipid related pathways in BAM. And MTB mainly activated genes CXCL2 and CXCL3 relevant to NOD-like receptor, IL-17 and TNF to further induce lipid accumulation in BAM, which in turn promoted the formation of foam cells. Meanwhile, time course RT-qPCR results showed that MTB was recognized by BAM to triggered dramatic immune responses, whereas MB could effectively escape the recognition system of BAM, leading rearrangement of lipid metabolisms in BAM at early infection stage. Altogether, the results of the present study provided evidence for changes in lipid metabolism of MTB/MB attacked BAM and contributed to the detection and treatment of zoonotic tuberculosis.

BackgroundHereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disease with a varying range of phenotypes involving abnormal vasculature primarily manifested as arteriovenous malformations in various organs, including the nose, brain, liver, and lungs. The varied presentation and involvement of different organ systems makes the choice of potential treatment medications difficult.ResultsA patient with a mixed-clinical presentation and presumed diagnosis of HHT, severe exertional dyspnea, and diffuse pulmonary shunting at the microscopic level presented for treatment. We sought to analyze her metabolomic plasma profile to assist with pharmacologic treatment selection. Fasting serum samples from 5 individuals (4 healthy and 1 with HHT) were metabolomically profiled.A global metabolic network reconstruction, Recon 1, was used to help guide the choice of medication via analysis of the differential metabolism between the patient and healthy controls using metabolomic data. Flux Balance Analysis highlighted changes in metabolic pathway activity, notably in nitric oxide synthase (NOS), which suggested a potential link between changes in vascular endothelial function and metabolism. This finding supported the use of an already approved medication, bevacizumab (Avastin). Following 2 months of treatment, the patient's metabolic profile shifted, becoming more similar to the control subject profiles, suggesting that the treatment was addressing at least part of the pathophysiological state.ConclusionsIn this 'individualized case study' of personalized medicine, we carry out untargeted metabolomic profiling of a patient and healthy controls. Rather than filtering the data down to a single value, these data are analyzed in the context of a network model of metabolism, in order to simulate the biochemical phenotypic differences between healthy and disease states; the results then guide the therapy. This presents one approach to achieving the goals of individualized medicine through Systems Biology and causal models analysis.

Avian reovirus (ARV) infection is prevalent in farmed poultry and causes viral arthritis and severe immunosuppression. The spleen plays a very important part in protecting hosts against infectious pathogens. In this research, transcriptome and translatome sequencing technology were combined to investigate the mechanisms of transcriptional and translational regulation in the spleen after ARV infection. On a genome-wide scale, ARV infection can significantly reduce the translation efficiency (TE) of splenic genes. Differentially expressed translational efficiency genes (DTEGs) were identified, including 15 upregulated DTEGs and 396 downregulated DTEGs. These DTEGs were mainly enriched in immune regulation signaling pathways, which indicates that ARV infection reduces the innate immune response in the spleen. In addition, combined analyses revealed that the innate immune response involves the effects of transcriptional and translational regulation. Moreover, we discovered the key gene IL4I1, the most significantly upregulated gene at both the transcriptional and translational levels. Further studies in DF1 cells showed that overexpression of IL4I1 could inhibit the replication of ARV, while inhibiting the expression of endogenous IL4I1 with siRNA promoted the replication of ARV. Overexpression of IL4I1 significantly downregulated the mRNA expression of IFN-β, LGP2, TBK1 and NF-κB; however, the expression of these genes was significantly upregulated after inhibition of IL4I1, suggesting that IL4I1 may be a negative feedback effect of innate immune signaling pathways. In addition, there may be an interaction between IL4I1 and ARV σA protein, and we speculate that the IL4I1 protein plays a regulatory role by interacting with the σA protein. This study not only provides a new perspective on the regulatory mechanisms of the innate immune response after ARV infection but also enriches the knowledge of the host defense mechanisms against ARV invasion and the outcome of ARV evasion of the host’s innate immune response.

Testicular transcriptomes were analyzed to characterize thedifferentially expressed genes between mulard and Pekin ducks, which willhelp establish gene expression datasets to assist in further determinationof the mechanisms of genetic sterility in mulard ducks. Paraffin sectionswere made to compare the developmental differences in testis tissue betweenmulard and Pekin ducks. Comparative transcriptome sequencing of testistissues was performed, and the expression of candidate genes was verified byquantitative reverse transcription-polymerase chain reaction (qRT-PCR). Inmulard ducks, spermatogonia and spermatocytes were arranged in a disorderedmanner, and no mature sperm were observed in the testis tissue. However,different stages of development of sperm were observed in seminiferoustubules in the testis tissue of Pekin ducks. A total of 43.84 Gb of cleanreads were assembled into 193 535 UniGenes. Of these, 2131 transcriptsexhibited differential expression (false discover rate andfold change ), including 997 upregulated and 1134 downregulatedtranscripts in mulard ducks as compared to those in Pekin duck testistissues. Several upregulated genes were related to reproductive functions,including ryanodine receptor 2 (RYR2), calmodulin (CALM), argininosuccinatesynthase and delta-1-pyrroline-5-carboxylate synthetase ALDH18A1 (P5CS).Downregulated transcripts included the testis-specificserine/threonine-protein kinase 3, aquaporin-7 (AQP7) and glycerol kinaseGlpK (GK). The 10 related transcripts involved in the developmental biologicalprocess were identified by GO (Gene Ontology) annotation. The KEGG (KyotoEncyclopedia of Genes and Genomes) pathways indicated that peroxisomeproliferator-activated receptors (PPARs) and calcium signaling pathways weresignificantly () associated with normal testis physiology.The differential expression of select genes implicated in reproductiveprocesses was verified by qRT-PCR, which was consistent with the expressiontrend of transcriptome sequencing (RNA-seq). Differentially expressed candidate genes RYR2, CALM, P5CS,AQP7 and GK were identified by transcriptional analysis in mulard and Pekinduck testes. These were important for the normal development of the maleduck reproductive system. These data provide a framework for the furtherexploration of the molecular and genetic mechanisms of sterility in mulardducks.Highlights. The mulard duck is an intergeneric sterile hybridoffspring resulting from mating between Muscovy and Pekin ducks. Thetranscriptomes of testis tissue from mulard and Pekin ducks weresystematically characterized, and differentially expressed genes were screened, inorder to gain insights into potential gonad gene expression mechanismscontributing to genetic sterility in mulard ducks.