Immune Pathways Research Articles

Preparation and immunological study of Ichthyophthirius multifiliis β-tubulin DNA vaccine in grass carp (Ctenopharyngodon idella)

Grass carp, a common aquatic species in China, suffer significant annual losses due to infection by the parasitic ciliate Ichthyophthirius multifiliis (Ich), thus necessitating effective prevention and control measures. In the present study, the Ich β-tubulin gene was cloned and inserted into the eukaryotic expression vector pVAX1 plasmid to construct the Ich β-tubulin DNA vaccine (pVAX1-Bt). After two doses of the pVAX1-Bt vaccine, the relative percentage survival (RPS) reached 70.0 %, whereas the RPS after 2 doses of pVAX1 reached 10.0 %. The β-tubulin antibody, specific antibody IgM, and immune enzymes (MDA, SOD, CAT, ACP, AKP, and cortisol) were tested over13 weeks. The findings revealed a significant enhancement in the vaccinated fish compared to their unvaccinated counterparts, indicating that the vaccine can activate the humoral immune pathway and non-specific immunity in fish, thereby promoting the production of specific antibodies and memory B cells. Collectively, these results indicate that the Ich β-tubulin DNA vaccine has potential in treatment of Ich infection (ichthyophthiriasis).

Activation of PKR by a short-hairpin RNA

Recognition of viral infection often relies on the detection of double-stranded RNA (dsRNA), a process that is conserved in many different organisms. In mammals, proteins such as MDA5, RIG-I, OAS, and PKR detect viral dsRNA, but struggle to differentiate between viral and endogenous dsRNA. This study investigates an shRNA targeting DDX54’s potential to activate PKR, a key player in the immune response to dsRNA. Knockdown of DDX54 by a specific shRNA induced robust PKR activation in human cells, even when DDX54 is overexpressed, suggesting an off-target mechanism. Activation of PKR by the shRNA was enhanced by knockdown of ADAR1, a dsRNA binding protein that suppresses PKR activation, indicating a dsRNA-mediated mechanism. In vitro assays confirmed direct PKR activation by the shRNA. These findings emphasize the need for rigorous controls and alternative methods to validate gene function and minimize unintended immune pathway activation.

Association of RDoC dimensions with post-mortem brain transcriptional profiles in Alzheimer's Disease.

Neuropsychiatric symptoms are common in people with Alzheimer's disease (AD) across all severity stages. Their heterogeneous presentation and variable temporal association with cognitive decline suggest shared and distinct biological mechanisms. We hypothesized that specific patterns of gene expression associate with distinct NIMH Research Domain Criteria (RDoC) domains in AD. Post-mortem bulk RNAseq on the insula and anterior cingulate cortex from 60 brain donors representing the spectrum of canonical AD neuropathology combined with natural language processing approaches based on the RDoC Clinical Domains. Distinct sets of >100 genes (p FDR <0.05) were specifically associated with at least one clinical domain (Cognitive, Social, Negative, Positive, Arousal). In addition, dysregulation of immune response pathways was shared across domains and brain regions. Our findings provide evidence for distinct transcriptional profiles associated with RDoC domains suggesting that each dimension is characterized by specific sets of genes providing insight into the underlying mechanisms.

Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.

Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.

GREM1 may be a biological indicator and potential target of bladder cancer

Gremlin 1 (GREM1) can regulate the development of many cancers. However, a few studies have revealed the role of GREM1 in bladder cancer (BC). To evaluate the expression and potential function of GREM1 in bladder cancer, we used R version 3.6.3 and related packages to analyze the data from common databases. Samples from our institution were assessed by immunohistochemical staining (IHC), which was approved by the Institutional Ethics Committee (K20220830). GREM1 was highly expressed in BC tissues according to the TCGA and IHC data. Data from TCGA, GSE31684, GSE32894, and IHC showed that GREM1 has significant prognostic value for BC patients. GREM1 is involved in immune and metabolism-related pathways. According to the TIDE algorithm, 61.0% of patients with low GREM1 expression responded well to immunotherapy, compared to only 13.3% in the high GREM1 expression group. High GREM1 expression was associated with sensitivity to cisplatin, docetaxel, gemcitabine, and vinblastine. Thus, GREM1 can predict prognosis and responses to immunotherapy and chemotherapy in BC patients, making it a potential biomarker and therapeutic target.

Effect of Moniezia Benedeni infection on ileal transcriptome profile characteristics of sheep

BackgroundThe intestinal mucosal immune system, renowned for its precise and sensitive regulation, can provide comprehensive and effective protection for the body, among which the ileum is a critical induction site for regulating mucosal immune homeostasis. Moniezia benedeni parasitizes the small intestine of sheep and can cause serious pathological damage or even death to the host when the infection is severe. In this study, 5 sheep infected with Moniezia benedeni were selected as the infected group, and 5 uninfected sheep were selected as the control group. The ileal transcriptome profile characteristics of Moniezia benedeni infection were analyzed based on RNA-seq sequencing technology, aiming to lay a foundation for further exploring the perception mechanism of sheep intestines to Moniezia benedeni infection and formulating effective prevention and control strategies.ResultsThe results showed that a total of 3,891 differentially expressed genes (DEGs) were detected in the ileum tissues of sheep between the infected and control groups with 2,429 up-regulated genes and 1,462 down-regulated genes. GO and KEGG pathway enrichment analysis of differential genes, as well as Clue GO analysis showed that differential genes were significantly enriched in immune and metabolic-related biological processes and signaling pathways. Particularly, in immune-related signaling pathways, the B cell receptor signaling pathway was significantly down-regulated, while in metabolic regulation related signaling pathways, Bile secretion, Fat digestion and absorption and Vitamin digestion and absorption were notably up-regulated. On this basis, the differential core genes related to immune metabolism were verified by qRT-PCR method. The results showed that OVAR, CD3E, CD8A, CD4 and CD28 were significantly up-regulated (P < 0.05), while CIITA, BLNK, BCL6 and CD79A were significantly down-regulated (P < 0.05), which were consistent with transcriptome sequencing data.ConclusionsThe results demonstrated that Moniezia benedeni infection significantly affected the immune and metabolic processes in sheep ileum, particularly, it significantly inhibited the activation process of host B cells, and also led to an overactive function of bile acid metabolism. This finding provides a solid foundation for further elucidating the response mechanism of Peyer's patches in sheep ileum to Moniezia tapeworm infection.

Purified Astragalus Polysaccharide Combined with Inactivated Vaccine Markedly Prevents Infectious Haematopoietic Necrosis Virus Infection in Rainbow Trout (Oncorhynchus mykiss).

Rainbow trout (Oncorhynchus mykiss) is experiencing a catastrophic pandemic. In recent years, infectious hematopoietic necrosis virus (IHNV) has spread nationwide, resulting in significant mortality. Currently, there are no available treatments or vaccines for IHNV in China. Here, the Astragalus extract was purified and characterized. Then, we developed an inactivated IHNV vaccine with purified Astragalus polysaccharide (P-APS) as an adjuvant. Safety assays showed that IHNV was successfully inactivated. After a serious IHNV challenge, the cumulative mortality rates were 76.0, 38.0, and 22.1% in control, vaccine, and P-APS + vaccine groups, respectively. P-APS + vaccine was effective at reducing head kidney damage and apoptosis after IHNV challenge by histopathological and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) analyses. The P-APS + vaccine group showed better results in enhancing specific antibodies (IgM) and immune enzyme activities (C3, LZM, GOT, and GPT). RNA-seq revealed that many immune-related pathways were significantly enriched. TLR2, TLR7, C3, IFN-γ, IgM, MHC1, MHC2, MX1, and VIG1 were identified as core genes based on RNA-seq and PPI networks. Mechanistic investigations showed that P-APS + vaccine activates the immune pathway by upregulating the expression of these genes. P-ASP+vaccine induced effective innate and adaptive immune responses that were stronger than single vaccines after vaccination and IHNV challenged. Our findings will provide a promising vaccine candidate against IHNV.

Human keratinocyte response to 4,4’-methylene diphenyl diisocyanate-glutathione conjugate exposure

Workplace exposure to diisocyanates like 4,4’-methylene diphenyl diisocyanate can cause occupational asthma (MDI-OA), and the underlying biological pathways are still being researched. Although uncertainty remains, evidence supports the hypothesis that dermal exposure to MDI plays an important role in the development of MDI-OA. Gene expression, proteomics, and informatics tools were utilised to characterise changes in expression of RNA and protein in cultured human HEKa keratinocyte cells following exposure to conjugates of MDI with glutathione (MDI-GSH). RT-qPCR analysis using a panel of 39 candidate primers demonstrated 9 candidate genes upregulated and 30 unchanged. HPLC-MS/MS analysis of HEKa cell lysate identified 18 540 proteins across all samples 60 proteins demonstrate statistically significant differential expression in exposed cells, some of which suggest activation of immune and inflammatory pathways. The results support the hypothesis that dermal exposures have the potential to play an important role in the development of MDI-OA. Furthermore, proteomic and gene expression data suggest multiple immune (adaptive and innate) and inflammatory pathways may be involved in the development of MDI-OA.

6779 The Diversity of Immune Checkpoint Inhibitor Associated Diabetes

Abstract Disclosure: V.A. Mendpara: None. M. Lansang: None. M. Caromori: None. L. Kennedy: None. K. Zhou: None. Immune checkpoint inhibitor (ICI) treatment has become a first-line therapy for a variety of cancers, including use of nivolumab (a programmed death 1 [PD-1] inhibitor) for metastatic melanoma. Though able to prolong survival, ICIs cause immune-related adverse events (irAE) through down-regulation of immune control pathways. One irAE is diabetes mellitus (DM), referred to as ICI-induced DM. Despite its low incidence (2%), ICI-induced DM carries with it high morbidity, with need for hospitalization in up to 25% of patients, and burden as patients are typically committed to multiple daily insulin injections (MDII). Here we report diverse presentations of four patients treated with ICI for metastatic melanoma who developed ICI-induced DM. The median age at DM presentation was 60.5 years (range 59-78 years). All patients received nivolumab and one patient was also treated with ipilimumab (a cytotoxic T-lymphocyte-associated antigen 4 inhibitor). The median time from start of ICI to development of ICI-induced DM was 32.5 wks, ranging from 27-46 wks. Three of the 4 patients previously developed hypothyroidism at median of 15 wks from starting ICI. Two patients presented in DKA and the other 2 with severe hyperglycemia (glucose &amp;gt;300 mg/dL). Median HbA1c was 7.05% (range 6.4%-7.4%) at presentation. GAD Ab was negative in 3 of 4 patients, including one who had DKA. C-peptide was undetectable (&amp;lt;0.2 ng/mL) in the 2 patients with DKA, 0.4 ng/mL in one other patient, and not measured in the fourth. All patients were immediately started on MDII. However, the two patients without DKA on presentation were eventually initiated on non-insulin agents. One of them was started on a DPP-4 inhibitor and discontinued fast-acting insulin, and the other started a GLP-1 receptor agonist and reduced their fast-acting insulin requirement. The heterogeneity of DM presentation and its clinical course reported here highlights a few important points. The first is that the onset of ICI-induced DM is often much later than that of the most common endocrine irAE, hypothyroidism, which has an onset around 10 weeks in average. Second, DM often presents as severe hyperglycemia incidentally detected on blood work. GAD Ab positivity is relatively less common, suggesting a different underlying etiology than classic type 1 DM. Onset of severe hyperglycemia can occur over many weeks (as indicated by higher HbA1c), making it important to monitor for hyperglycemia in those with no previous history of prediabetes or DM. Finally, it may be possible to use a combination of non-insulin antihyperglycemic agents to provide better glycemic management. No widely validated strategies for the surveillance of irAEs are currently available, and a better understanding in the propensity of patients to develop irAEs is clearly required. Importantly, optimal management of irAEs relies on early recognition and frequently demands a multidisciplinary approach. Presentation: 6/2/2024

A genetic study to identify pathogenic mechanisms and drug targets for benign prostatic hyperplasia: a multi-omics Mendelian randomization study

Benign prostatic hyperplasia (BPH) as a common geriatric disease in urology, the incidence and prevalence are rapidly increasing with the aging society, prompting an urgent need for effective prevention and treatment of BPH. However, limited therapeutic efficacy and higher risk of complications result in the treatment of BPH remaining challenging. The unclear pathogenic mechanism also hampers further exploration of therapeutic approaches for BPH. In this study, we used multi-omics methods to integrate genomics, transcriptomics, immunomics, and metabolomics data and identify biomolecules associated with BPH. We performed transcriptomic imputation, summary data-based Mendelian randomization (SMR), joint/conditional analysis, colocalization analysis, and FOCUS to explore high-confidence genes associated with BPH in blood and prostate tissue. Subsequently, three-step SMR was used to identify the DNA methylation sites regulating high-confidence genes to improve the pathogenic pathways of BPH. We also used cis-instruments of druggable genes to conduct SMR analysis to find potential drug targets for BPH. Finally, we used MR analysis to explore the immune pathways and metabolomics related to BPH. Multiple analytical methods identified BTN3A2 (Blood: TWAS Z score = 5.02912, TWAS P = 4.93 × 10–7; Prostate: TWAS Z score = 4.89, TWAS P = 1.01 × 10–6) and C4A (Blood: TWAS Z score = 4.90754, TWAS P = 9.22 × 10–7; Prostate: TWAS Z score = 5.084, TWAS P = 3.70 × 10–7) as high-confidence genes for BPH and identified the cg14345882-BTN3A2-BPH pathogenic pathway. We also used druggable gene data to identify 30 promising therapeutic target genes, including BTN3A2 and C4A. For MR analysis of immune pathways, we identified immune cell surface molecules as well as the inflammatory factor IL-17 (OR = 1.25, 95% CI = 1.09–1.43, PFDR = 0.12, Maximum likelihood) as risk factors for BPH. In addition, we found that disulfide levels of cysteinylglycine (OR = 1.11, 95% CI = 1.05–1.18, P = 5.18 × 10–4, Weighted median), oxidation levels of cysteinylglycine (OR = 1.09, 95% CI = 1.04–1.14, P = 3.87 × 10–4, Weighted median), and sebacate levels (OR = 1.05, 95% CI = 1.02–1.08, P = 3.0 × 10–4, Maximum likelihood) increase the risk of BPH. This multi-omics study explored biomolecules associated with BPH, improved the pathogenic pathways of BPH, and identified promising therapeutic targets. Our results provide evidence for future studies aimed at developing appropriate therapeutic interventions.

Physiological and molecular responses of juvenile silver crucian carp (Carassius gibelio) to long-term high alkaline stress: Growth performance, histopathology, and transcriptomic analysis

Salty-alkaline waters are widely distributed globally, and how to effectively develop saline-alkaline water to improve the utilization rate of water resources has become a global challenge. This study examined the survival performance of juvenile silver crucian carp (Carassius gibelio) under alkaline gradient acclimation conditions and explored the regulatory mechanisms for their adaptation to high alkalinity. Compared to directly immersing in high concentrations, alkaline gradient acclimation significantly improved the survival rate of juvenile silver crucian carp. Long-term high alkaline stress caused significant reduction in the growth performance of juvenile silver crucian carp. After alkaline stress, the enzyme activities of Na+-K+-ATP (NKA) and Ca2+-Mg2+-ATP (CMA) in the gills were significantly decreased. Meanwhile, histopathology of the gills showed structural changes, indicating that the physiological functions of juvenile silver crucian carp were impaired under alkaline conditions. Transcriptomic analysis found that the expression of genes related to metabolism and immune response pathways in the gill and kidney underwent significant changes. Genes related to carbohydrate metabolism were upregulated while those related to protein metabolism were downregulated, indicating that alkaline stress caused the organism to utilize carbohydrates rather than proteins as much as possible to meet enhanced metabolism. The HIF pathway that maintains the body's survival was significantly up-regulated, at the expense of high energy consumption. Dysregulation of genes related to the formation of neutrophil extracellular traps (NETosis) pathway indicated that the immune function of the fish was suppressed. Overall, this study revealed the physiological and molecular responses of juvenile silver crucian carp to alkaline stress, deepening our understanding of their adaptation strategies and the potential impact of alkaline environments on aquatic life.

Emerging Biologic Therapies for the Treatment of Atopic Dermatitis.

Atopic dermatitis (AD) is a prevalent inflammatory skin disease having a significant impact on patients' quality of life. Conventional treatments, including topical therapies and systemic immunosuppressants, often have limited efficacy and long-term safety concerns. Emerging biologic therapies target specific immune pathways implicated in AD pathogenesis, offering new therapeutic options in a disease known for its complex immune pathomechanisms. This review focuses on novel biologics under investigation, particularly those targeting specific immune pathways such as interleukin-4 (IL-4), IL-13, IL-22, IL-31, thymic stromal lymphopoietin (TSLP), and OX40-OX40L axis. Interleukin-4 and IL-13 inhibitors aim to reduce Th2-driven inflammation, while IL-22 inhibitors focus on restoring skin barrier function. Interleukin-31 inhibitors help alleviate pruritus, a major symptom in AD. OX40-OX40L pathway inhibitors can selectively suppress the activity of pathogenic T cells, without inducing significant immunosuppression. Bispecific antibodies targeting both IL-4 and IL-31 pathways are emerging as potential dual-action treatment for AD. Thymic stromal lymphopoietin inhibitors offer a novel strategy to control inflammation. While many of these therapies offer promising safety and efficacy profiles, long-term studies and real-world data are essential to confirm their lasting impact. This review highlights the potential of these emerging systemic therapies to continue transforming AD management and improve patient outcomes.

Effect of Stocking Density on Stress-Related Gene Expression of Pacific White Shrimp (Litopenaeus vannamei) Infected with Infectious Myonecrosis Virus (IMNV)

The stress level of vannamei shrimp (Litopenaeus vannamei) is affected by increased density and several genes are expressed under the condition. This study aimed to determine the expression of genes encoding white shrimp stress after density treatment and the infectious myonecrosis virus (IMNV) challenge test. A completely randomized design (CRD) was carried out with 6 treatment groups, i.e. 3 different stocking density groups without IMNV infection (100, 200, and 400 shrimp/m2) and 3 different stocking density groups + IMNV infection (100, 200, and 400 shrimp/m2). In addition, a shrimp density of 400 shrimp/m2 reported the fastest rate of developing the IMNV virus as seen from the clinical symptoms. The lowest cumulative number of shrimp deaths was at a density of 100 shrimp/m2 and was caused by the IMNV virus confirmed through RT-PCR. Expression of stress-coding genes was divided into upregulated and downregulated characteristics. The upregulated genes were lectin and translationally controlled tumor protein (TCTP), while the downregulated gene was Toll Receptor. The results showed that the expression of genes related to immunity in L. vannamei was upregulated after pathogen challenges such as lectin and TCTP, meanwhile, the Toll receptor gene was downregulated. Further study should also be performed to measure the expression of the three genes in revealing the immune pathways.

Integrated analysis of metabolomic and transcriptomic profiles elucidates the core role of glycerophospholipid metabolism in hypertension related to metabolic syndrome

BackgroundMetabolic syndrome (MetS) represents a comprehensive framework that encompasses conditions such as diabetes, hypertension (HBP), obesity, and dyslipidemia. MetS without hypertension significantly contributes to the development of refractory hypertension. However, the underlying molecular regulatory mechanisms of hypertension associated with MetS remain incompletely elucidated. The objective of this study was to identify differences in plasma metabolome and leukocyte transcriptome profiles between patients with MetS comorbid HBP compared to those with MetS with hypertension and HBP alone. MethodsIn this study, whole blood samples were collected from 104 participants, including patients with HBP, MetS without hypertension (MS), and MetS with hypertension (MS-HBP). Ultra-high-performance liquid chromatography was employed to perform metabolomic analysis of plasma samples. Comparative analysis was conducted to identify distinct metabolites among the three groups, while MetaboAnalyst 5.0 was utilized for enrichment and pathway analysis. Clinical correlation analysis and receiver operating characteristic analyses were applied to select biomarker metabolites for MS-HBP. Transcriptomic profiling of white blood cells was performed to identify dysregulated genes and KEGG/GO pathways. Integrative analysis of metabolomics and transcriptomics was used to construct molecular interaction networks. Finally, blood pressure was monitored every 2 weeks during the treatment period for experimental validation. ResultsThe metabolomic results indicated that lipid metabolic pathways, particularly glycerophospholipid metabolic pathways, played a crucial role in MS-HBP. The area under the curve of tryptophan-isoleucine for diagnosis in the MS-HBP group was 0.82. Tryptophyl-isoleucine demonstrated a negative correlation with both HbA1c and diastolic blood pressure. Transcriptomic analysis revealed the involvement of MS-HBP in numerous immune and inflammatory pathways. Furthermore, the integrated analysis of metabolomic and transcriptomic data emphasized the importance of glycerophospholipid metabolism in MS-HBP. PPC exhibited a comparable effect on lowering blood pressure in SHR rats. ConclusionThe findings of this study demonstrated that glycerophospholipid metabolism plays a pivotal role in the pathophysiological processes of MS-HBP, providing novel insights into early clinical diagnosis and the optimization of therapeutic strategies.

Age, anticoagulants, hypertension and cardiovascular genetic traits predict cranial ischaemic complications in patients with giant cell arteritis

ObjectivesThis project aimed to determine whether cranial ischaemic complications at the presentation of giant cell arteritis (GCA) were associated with pre-existing cardiovascular (CV) risk factors, CV disease or genetic risk...

Identification of DNA methylation markers for age and Bovine Respiratory Disease in dairy cattle: A pilot study based on Reduced Representation Bisulfite Sequencing

Methylation profiles of animals are known to differ by age and disease status. Bovine respiratory disease (BRD), a complex infectious disease, primarily affects calves and has significant impact on animal welfare and the cattle industry, due to production losses, increased veterinary costs as well as animal losses. BRD susceptibility is multifactorial, influenced by both environmental and genetic factors. We have performed a pilot study to investigate the epigenetic profile of BRD susceptibility in six calves (three healthy versus three diagnosed with BRD) and age-related methylation differences between healthy calves and adult dairy cows (three calves versus four adult cows) using Reduced Representation Bisulfite Sequencing (RRBS). We identified 2537 genes within differentially methylated regions between calves and adults. Functional analysis revealed enrichment of developmental pathways including cell fate commitment and tissue morphogenesis. Between healthy and BRD affected calves, 964 genes were identified within differentially methylated regions. Immune and vasculature regulatory pathways were enriched and key candidates in BRD susceptibility involved in complement cascade regulation, vasoconstriction and respiratory cilia structure and function were identified. Further studies with a greater sample size are needed to validate these findings and formulate integration into breeding programmes aiming to increase animal longevity and disease resistance.

Transcriptomic Analysis of the CNL Gene Family in the Resistant Rice Cultivar IR28 in Response to Ustilaginoidea virens Infection.

Rice false smut, caused by Ustilaginoidea virens, threatens rice production by reducing yields and contaminating grains with harmful ustiloxins. However, studies on resistance genes are scarce. In this study, the resistance level of IR28 (resistant cultivar) to U. virens was validated through artificial inoculation. Notably, a reactivation of resistance genes after transient down-regulation during the first 3 to 5 dpi was observed in IR28 compared to WX98 (susceptible cultivar). Cluster results of a principal component analysis and hierarchical cluster analysis of differentially expressed genes (DEGs) in the transcriptome exhibited longer expression patterns in the early infection phase of IR28, consistent with its sustained resistance response. Results of GO and KEGG enrichment analyses highlighted the suppression of immune pathways when the hyphae first invade stamen filaments at 5 dpi, but sustained up-regulated DEGs were linked to the 'Plant-pathogen interaction' (osa04626) pathway, notably disease-resistant protein RPM1 (K13457, CNLs, coil-coiled NLR). An analysis of CNLs identified 245 proteins containing Rx-CC and NB-ARC domains in the Oryza sativa Indica genome. Partial candidate CNLs were shown to exhibit up-regulation at both 1 and 5 dpi in IR28. This study provides insights into CNLs' responses to U. virens in IR28, potentially informing resistance mechanisms and genetic breeding targets.

Immunotherapy may be more appropriate for ERBB2 low-expressing extramammary paget’s disease patients: a prognosis analysis and exploration of targeted therapy and immunotherapy of extramammary paget’s disease patients

Extramammary Paget’s disease (EMPD) is a rare cutaneous malignancy characterized by its uncertain etiology and metastatic potential. Surgery remains the first-line clinical treatment for EMPD, but the efficacy of radiotherapy and chemotherapy remains to be fully evaluated, and new therapies for EMPD are urgently needed. In this study, we initially screened 815 EMPD patients in the Surveillance, Epidemiology, and End Results (SEER) database and analyzed their clinical features and prognostic factors. Using the dataset from the Genome Sequence Archive (GSA) database, we subsequently conducted weighted gene coexpression network analysis (WGCNA), gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and immune infiltration analyses, grouping the samples based on EMPD disease status and the levels of ERBB2 expression. The prognostic analysis based on the SEER database identified increased age at diagnosis, distant metastasis, and receipt of radiotherapy as independent risk factors for EMPD. Moreover, our results indicated that patients who received chemotherapy had worse prognoses than those who did not, highlighting the urgent need for novel treatment approaches for EMPD. Functional analysis of the GSA-derived dataset revealed that EMPD tissues were significantly enriched in immune-related pathways compared with normal skin tissues. Compared with those with high ERBB2 expression, tissues with low ERBB2 expression displayed greater immunogenicity and enrichment of immune pathways, particularly those related to B cells. These findings suggest that patients with low ERBB2 expression are likely to benefit from immunotherapy, especially B-cell-related immunotherapy.

Unraveling the pathogenic interplay between SARS-CoV-2 and polycystic ovary syndrome using bioinformatics and experimental validation

The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among polycystic ovary syndrome (PCOS) is significantly higher than in the general population. However, the mechanisms underlying this remain obscure. This study aimed to explore the mechanisms by identifying the genetic signature of SARS-CoV-2 infection in PCOS. In the present study, a total of 27 common differentially expressed genes (DEGs) were selected for subsequent analyses. Functional analyses showed that immunity and hormone-related pathways collectively participated in the development and progression of PCOS and SARS-CoV-2 infection. Under these, 7 significant hub genes were identified, including S100A9, MMP9, TLR2, THBD, ITGB2, ICAM1, and CD86 by using the algorithm in Cytoscape. Furthermore, hub gene expression was confirmed in the validation set, PCOS clinical samples, and mouse model. Immune microenvironment analysis with the CIBERSORTx database demonstrated that the hub genes were significantly correlated with T cells, dendritic cells, mast cells, B cells, NK cells, and eosinophils and positively correlated with immune scores. Among the hub genes, S100A9, MMP9, THBD, ITGB2, CD86, and ICAM1 demonstrated potential as possible diagnostic markers for COVID-19 and PCOS. In addition, we established the interaction networks of ovary-specific genes, transcription factors, miRNAs, drugs, and chemical compounds with hub genes with NetworkAnalyst. This work uncovered the common pathogenesis and genetic signature of PCOS and SARS-CoV-2 infection, which might provide a theoretical basis and innovative ideas for further mechanistic research and drug discovery of the comorbidity of the two diseases.

Mechanisms of Berberine in anti-pancreatic ductal adenocarcinoma revealed by integrated multi-omics profiling

This study integrates pharmacology databases with bulk RNA-seq and scRNA-seq to reveal the latent anti-PDAC capacities of BBR. Target genes of BBR were sifted through TargetNet, CTD, SwissTargetPrediction, and Binding Database. Based on the GSE183795 dataset, DEG analysis, GSEA, and WGCNA were sequentially run to build a disease network. Through sub-network filtration acquired PDAC-related hub genes. A PPI network was established using the shared genes. Degree algorithm from cytoHubba screened the key cluster in the network. Analysis of differential mRNA expression and ROC curves gauged the diagnostic performance of clustered genes. CYBERSORT uncovered the potential role of the key cluster on PDAC immunomodulation. ScRNA-seq analysis evaluated the distribution and expression profile of the key cluster at the single-cell level, assessing enrichment within annotated cell subpopulations to delineate the target distribution of BBR in PDAC. We identified 425 drug target genes and 771 disease target genes, using 57 intersecting genes to construct the PPI network. CytoHubba anchored the top 10 highest contributing genes to be the key cluster. mRNA expression levels and ROC curves confirmed that these genes showed good robustness for PDAC. CYBERSORT revealed that the key cluster influenced immune pathways predominantly associated with Macrophages M0, CD8 T cells, and naïve B cells. ScRNA-seq analysis clarified that BBR mainly acted on epithelial cells and macrophages in PDAC tissues. BBR potentially targets CDK1, CCNB1, CTNNB1, CDK2, TOP2A, MCM2, RUNX2, MYC, PLK1, and AURKA to exert therapeutic effects on PDAC. The mechanisms of action appear to significantly involve macrophage polarization-related immunological responses.