Transcriptional Modulation Research Articles

Advances in the Development of Mitochondrial Pyruvate Carrier Inhibitors for Therapeutic Applications

The mitochondrial pyruvate carrier (MPC) is a transmembrane protein complex critical for cellular energy metabolism, enabling the transport of pyruvate from the cytosol into the mitochondria, where it fuels the citric acid cycle. By regulating this essential entry point of carbon into mitochondrial metabolism, MPC is pivotal for maintaining cellular energy balance and metabolic flexibility. Dysregulation of MPC activity has been implicated in several metabolic disorders, including type 2 diabetes, obesity, and cancer, underscoring its potential as a therapeutic target. This review provides an overview of the MPC complex, examining its structural components, regulatory mechanisms, and biological functions. We explore the current understanding of transcriptional, translational, and post-translational modifications that modulate MPC function and highlight the clinical relevance of MPC dysfunction in metabolic and neurodegenerative diseases. Progress in the development of MPC-targeting therapeutics is discussed, with a focus on challenges in designing selective and potent inhibitors. Emphasis is placed on modern approaches for identifying novel inhibitors, particularly virtual screening and computational strategies. This review establishes a foundation for further research into the medicinal chemistry of MPC inhibitors, promoting advances in structure-based drug design to develop therapeutics for metabolic and neurodegenerative diseases.

WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS IDENTIFIES BIOLOGICAL PATHWAYS AND BIOMARKER GENES ASSOCIATED WITH CHICKENS' ADAPTATION TO BOTH LOW AND HIGH ALTITUDES

The main aim of the study was to identify modules, hub genes, and possible pathways linked with hypoxia adaptation in six types of tissues and organs (heart, kidney, liver, lung, muscle, and spleen) at altitudes ranging from 2,300 to 3,500 metersOn a transcription dataset from hypoxia-sensitive tissues, we performed weighted gene co-expression network analysis on 13,940 selected genes, and 10 transcriptional modules in total were detected (Turquoise 196 genes, Purple 27 genes, Blue 196, Brown 182, Yellow 108, Green 79 genes, Red 69 genes, Black 50 genes, Pink 44 genes, and Magenta 37 genes). Furthermore, we discovered that the majority of variable genes were screened by sub-setting 1000 genes; samples belonging to the same tissue clearly clustered together, and the expression in the liver and lung was more associated than in the heart and spleen. Functional enrichment analysis of all genes in 12 selected modules revealed that 9 KEGG pathways were considerably enriched, 13 Gene ontology terms were significantly enriched in the biological process and cellular component pathways, and 15 gene ontology terms were significantly enriched in the molecular function pathway. Through weighted gene co-expression network analysis, the results of this study expand our knowledge of the molecular pathway of catalytic and metabolic activity as a biomarker pathway

Interferon regulatory factor 2 of red-spotted grouper (Epinephelus akaara): Insights into its transcriptional profiling, antiviral potential, and function in macrophage polarization.

Interferon regulatory factor 2 (IRF2) is a member of the IRF family that is specifically involved in diverse immune responses via interferon (IFN)/IRF-dependent signaling pathways. In this study, IRF2 of Epinephelus akaara (EAIRF2) was identified and characterized by evaluating its structural and functional properties. EAIRF2 showed the highest homology with IRF2 of Epinephelus coioides and clustered with teleosts in the phylogenetic tree. The highest level of EAIRF2 mRNA was found in the blood under normal physiological conditions. In the immune challenge experiment, significant transcriptional modulation of EAIRF2 upon lipopolysaccharide (LPS), polyinosinic: polycytidylic acid (poly I:C), and nervous necrosis virus (NNV) challenge were observed. The subcellular localization assay confirmed the role of EAIRF2 as a transcription factor by revealing its specific nuclear localization. To elucidate its functional implications in antiviral defense, EAIRF2 was overexpressed in fathead minnow cells, which were subsequently infected with viral hemorrhagic septicemia virus (VHSV). Notably, cells overexpressing EAIRF2 exhibited a significant reduction in the transcription of VHSV genes. Concurrently, the genes associated with the IFN/IRF signaling pathway were upregulated. Furthermore, the Hoechst and propidium iodide dual staining assay, water-soluble tetrazolium-1 (WST-1) assay, and transcriptional analysis of B-cell lymphoma 2-associated X protein (Bax)/B-cell lymphoma 2 (Bcl-2) indicated that EAIRF2 possesses anti-apoptotic properties during viral infection and poly I:C treatment. Additionally, EAIRF2 overexpression in murine macrophages induced M1 polarization and augmented relative marker gene expression. Collectively, these findings suggest that EAIRF2 is a pivotal immune-related gene, specifically implicated in the IFN/IRF-mediated antiviral defense mechanism, apoptotic signaling pathway, and activation of macrophage-mediated immune responses in Epinephelus akaara. The finding of this study enhances our understanding of IRF2's function in teleost immunity and presents potential avenues for developing therapeutic strategies against viral infections and other immune-related conditions in aquaculture species.

SUMO modified ETV1 promotes M2-polarized tumor-associated macrophage infiltration and cancer progression by facilitating CCL2 transcription in esophageal squamous cell carcinoma cells.

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant tumors with a high metastasis rate and a poor prognosis. ETS variant transcription factor 1 (ETV1) plays an important role in multiple malignancies. However, its function in ESCC progression and tumor microenvironment (TME) remains to be explored. In this study, we characterized the role of ETV1 in ESCC process and TME. Gene expression and immune infiltration in ESCC samples from the Cancer Genome Atlas (TCGA) were analyzed. The expression of ETV1 in clinical samples was detected by real-time PCR, western blot and immunohistochemistry staining. Cell growth was detected by CCK-8 and colony formation assays. Macrophage phenotypes were determined using flow cytometry. Immunofluorescence double staining was used to detect the tumor-associated macrophage (TAM) infiltration. The tumor volume was recorded and weighed. Transcriptional activity was measured using dual-luciferase assay, chromatin immunoprecipitation (ChIP) assay and DNA pull-down assay. In this study, through analysis of ESCC samples from TCGA database and the clinic, we noticed that ETV1 was highly expressed in ESCC tumor tissues and was associated with TAM infiltration. Overexpression of ETV1 promoted ESCC cell proliferation in vitro and xenograft tumor growth in nude mice, while ETV1 knockdown elicited the opposite effects. Furthermore, ETV1 upregulation in tumor tissues was found to drive M2 macrophage infiltration both in vitro (transwell assays) and in vivo (xenograft tumor models). C-C motif chemokine ligand 2 (CCL2), a key factor inducing M2 macrophage polarization, was also found to be elevated in ESCC tumor tissues. Mechanism study demonstrated that ETV1 facilitated M2 macrophage infiltration via the transcriptional modulation of CCL2. In addition, the cause of the changes in ETV1 activity and expression was investigated. The E2 small ubiquitin-like modifier (SUMO) binding enzyme UBC9 increased ETV1 activity and expression, indicating the presence of SUMO modification in ETV1. Our data deciphered the mechanism of ETV1-mediated M2 macrophage infiltration in the TME of ESCC, which has important implications for the development of novel prognostic and therapeutic targets to optimize current therapies against ESCC.

ScRNA seq of an F1 cross of Marek’s disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators

Marek’s disease (MD), a T cell lymphoma disease in chickens, is caused by the Marek’s disease virus (MDV) found ubiquitously in the poultry industry. Genetically resistant Line 63 (L6) and susceptible Line 72 (L7) chickens have been instrumental to research on avian immune system response to MDV infection. In this study we characterized molecular signatures unique to splenic immune cell types across different genetic backgrounds 6 days after infection. Using three populations, L6, L7, and an F1 cross between L6xL7, we evaluated the immune cell transcriptome of responding cell types using single cell RNA sequencing. Several MDV genes were found expressed mainly in cytotoxic T cells while ICP4 and MEQ MDV genes were expressed across infected cell types. Using the F1 we quantified allele specific expression (ASE) of biallelic SNPs and found biased expression of parental alleles specific to immune cell subtypes. We identified 22 SNPs with ASE in response to MDV infection mapped to gene rich regions surrounding 59 genes of critical importance for chromatin remodeling and transcriptional regulation. Histone deacetylase genes (HDAC1 and HDAC8) had increased expression of L6 alleles, while small nuclear RNA genes (SNORA68 and SNORA72) expressed higher levels of L7 alleles with infection in T cell subsets. SNPs with ASE also mapped genes important for an adequate immune response including GNLY (cytotoxic activity) and PDIA3 (component of MHC class I peptide loading complex), and genes known to promote viral replication (MCM5 and EIF3M). These results show that functional variants associated with susceptibility to MD may have a bigger impact in subsets of immune cell types, and by characterizing the transcriptomes of these subtypes we can unravel molecular signatures specific to MD genomic resistance.

An integrative multiparametric approach stratifies putative distinct phenotypes of blast phase chronic myelomonocytic leukemia.

Approximately 30% of patients with chronic myelomonocytic leukemia (CMML) undergo transformation to a chemo-refractory blastic phase (BP-CMML). Seeking novel therapeutic approaches, we profiled blast transcriptomes from 42 BP-CMMLs, observing extensive transcriptional heterogeneity and poor alignment to current acute myeloid leukemia (AML) classifications. BP-CMMLs display distinctive transcriptomic profiles, including enrichment for quiescence and variability in drug response signatures. Integrating clinical, immunophenotype, and transcriptome parameters, Random Forest unsupervised clustering distinguishes immature and mature subtypes characterized by differential expression of transcriptional modules, oncogenes, apoptotic regulators, and patterns of surface marker expression. Subtypes differ in predicted response to AML drugs, validated exvivo in primary samples. Iteratively refined stratification resolves a classification structure comprising five subtypes along a maturation spectrum, predictive of response to novel agents including consistent patterns for receptor tyrosine kinase (RTK), cyclin-dependent kinase (CDK), mechanistic target of rapamycin (MTOR), and mitogen-activated protein kinase (MAPK) inhibitors. Finally, we generate a prototype decision tree to stratify BP-CMML with high specificity and sensitivity, requiring validation but with potential clinical applicability to guide personalized drug selection for improved outcomes.

Global transcriptional modulation and nutritional status of soybean plants following foliar application of zinc borate as a suspension concentrate fertilizer

The management of micronutrients, such as boron (B) and zinc (Zn), is critical for plant growth and crop yields. One method of rapid intervention crop management to mitigate nutritional deficiency is the foliar supply of B and Zn. Our study investigates the effect of foliar-supplied B and Zn availability on the global transcriptional modulation in soybean (Glycine max). The transcriptional response to B was more widespread compared to Zn. RNA-Seq of leaves under different B levels revealed modulated genes with potential roles in nutritional homeostasis and stress response that may be key to controlling B status in the plant. We also identified putative B transporters whose expression levels were significantly affected by B supplementation with foliar fertilization of plants growing under low B conditions. Furthermore, a gene lacking functional annotation (Glyma.03G180300) emerged as a novel potential marker of B status. Two genes (Glyma.16G118000, Glyma.16G199000) were consistently induced by Zn availability, highlighting their potential as biomarkers for assessing its status in soybean plants. This work advances our understanding of nutritional homeostasis in soybean plants and identifies target genes and potential molecular mechanisms involved in nutritional response. Our study informs fertilizer design targeting specific nutrient transporters, thereby enhancing nutrient efficiency in crops.

The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance to irinotecan (CPT-11).

Background. Colorectal carcinomas (CRCs) are seldom eradicated by cytotoxic chemotherapy. Cancer cells with stem-like functional properties, often referred to as "cancer stem cells" (CSCs), display preferential resistance to several anti-tumor agents used in cancer chemotherapy, but the molecular mechanisms underpinning their selective survival remain only partially understood. Methods. In this study, we used Transcription Factor Target Genes (TFTG) enrichment analysis to identify transcriptional regulators (activators or repressors) that undergo preferential activation by chemotherapy in CRC cells with a "bottom-of-the-crypt" phenotype (EPCAM + /CD44 + /CD166 + ; CSC-enriched) as compared to CRC cells with a "top-of-the-crypt" phenotype (EPCAM + /CD44 neg /CD166 neg ; CSC-depleted). The two cell populations were purified in parallel by fluorescence-activated cell sorting (FACS) from a patient-derived xenograft (PDX) line representative of a moderately differentiated human CRC, following in vivo chemotherapy with irinotecan (CPT-11). The transcriptional regulators identified as differentially activated were tested for differential expression in normal vs. cancer tissues, and in cell populations enriched in stem/progenitor cell-types as compared to differentiated lineages (goblet cells, enterocytes) in the mouse colon epithelium. Finally, the top candidate was tested for mechanistic contribution to drug-resistance by selective down-regulation using short-hairpin RNAs (shRNAs). Results. Our analysis identified E2F4 and TFDP1, two core components of the DREAM transcriptional repression complex, as transcriptional modulators preferentially activated by irinotecan in EPCAM + /CD44 + /CD166 + as compared to EPCAM + /CD44 neg /CD166 neg cancer cells. The expression levels of both genes ( E2F4 , TFDP1 ) were found up-regulated in CRCs as compared to human normal colon tissues, and in a sub-population of mouse colon epithelial cells enriched in stem/progenitor elements (Epcam + /Cd44 + /Cd66a low /Kit neg ) as compared to other sub-populations enriched in either goblet cells (Epcam + /Cd44 + /Cd66a low /Kit + ) or enterocytes (Epcam + /Cd44 neg /Cd66a high ). Most importantly, E2F4 down-regulation using shRNAs dramatically enhanced the sensitivity of human CRCs to in vivo treatment with irinotecan , across three independent PDX models. Conclusions. Our data identified E2F4 and the DREAM repressor complex as critical regulators of human CRC resistance to irinotecan , and as candidate targets for the development of chemo-sensitizing agents.

Membrane drug transporters in cancer: From chemoresistance mechanism to therapeutic strategies.

Chemoresistance is a multifactorial phenomenon and the primary cause to the ineffectiveness of oncotherapy and cancer recurrence. Membrane drug transporters are crucial for drug delivery and disposition in cancer cells. Changes in the expression and functionality of these transporters lead to decreased intracellular accumulation and reduced toxicity of antineoplastic drugs. As the mechanism has been better understood and genetic engineering technology progressed quickly in recent years, some novel targeting strategies have come to light. This article summarizes the regulatory mechanisms of membrane drug transporters and provides an extensive review of current approaches to address transporters-mediated chemoresistance. These strategies include the use of chemical inhibitors to block efflux transporters, the development of copper chelators to enhance platinum drug uptake, the delivery of genetic drugs to alter transporter expression, the regulation of transcription and post-translational modifications. Additionally, we provide information of the clinical trial performance of the related targeting strategies, along with the ongoing challenges. Even though some clinical trials failed due to unexpected side effects and limited therapeutic efficacy, the advent of targeting membrane drug transporters still presents a hopeful path for overcoming chemoresistance.

P0197 Comparison of pharmacodynamic and mechanistic response of guselkumab intravenous and subcutaneous induction in moderately to severely active Crohn’s disease: molecular analysis of the GRAVITI and GALAXI Phase 3 studies

Abstract Background Guselkumab (GUS) is a selective dual-acting IL-23p19 subunit inhibitor that potently blocks IL-23 and binds to CD64 demonstrated efficacy with intravenous (IV) induction in patients with moderately to severely active Crohn’s disease (CD) in the GALAXI trials.1 Subcutaneous (SC) induction with GUS evaluated in the Ph3 GRAVITI trial was also efficacious in treating patients with CD.2 Here we present a comparison of the pharmacodynamic and mechanistic response of GUS SC and GUS IV induction therapy in CD. Methods Serum proteins were evaluated from 290 GRAVITI patients randomised to PBO or GUS 400mg SC q4w, and a subset of 292 GALAXI patients randomised to PBO or GUS 200mg IV q4w at Weeks 0 and 12 using a 92-analyte inflammatory protein panel. Transcriptional profiling from each of the five anatomic segments in GRAVITI was conducted with samples from 277 patients at WK0 and WK12 using RNA sequencing. A tissue inflammation score (bMIS3) was used to assess segmental molecular inflammation which correlated with segmental histology scores defined by Global Histologic Activity Score (GHAS), endoscopic scores and subscores defined by Simple Endoscopic Score for CD (SES-CD).3 Analysis of treatment effect was performed using molecularly inflamed samples (defined as bMIS >0) from segments with SES-CD >0 at baseline. Transcriptional gene modules were evaluated for differential expression. Results In serum, protein changes observed with GUS 400mg SC q4w induction at WK12 were highly correlated with those observed with GUS 200mg IV q4w induction at WK12 (R=0.96, p<0.05), including similar reduction of IFNγ, IL-17A, CRP and fecal calprotectin (p<0.05; Figure 1). In tissue, segmental molecular inflammation assessed by bMIS correlated with segmental histological and endoscopic subscores (percent affected tissue and ulceration severity). In each anatomic segment, GUS SC induction reduced key cellular and inflammatory transcriptional modules at WK12 including plasma cell, inflammatory epithelial, neutrophil, and IL-23/Th17 biology consistent with molecular analysis from GUS IV induction in GALAXI Ph2b.4 The decrease in molecular inflammation in 5 anatomic segments corresponded to the segmental endoscopic improvement observed in isolated ileal, ileocolonic and colonic patient subgroups. Conclusion Following SC induction, the protein changes observed in serum at WK12 in GRAVITI were highly correlated with those seen with GUS IV induction from GALAXI Ph3. These data demonstrate similar molecular effects of GUS SC and IV induction doses and are aligned with previously reported similar efficacy results, supporting the flexible choice for patients and healthcare professionals between GUS SC and IV to treat patients with CD.

Targeting hypoxia-induced signaling via HIF-2 inhibition, a promising treatment strategy for intestinal fibrosis?

Abstract Background and aims With this project, we aim to evaluate if targeting hypoxia-induced signalling via hypoxia inducible factor (HIF)-2 inhibition impacts experimental intestinal fibrosis and validate our findings in stenotic fibroblasts from CD patients. Methods Colonic fibroblasts will be sorted from mice with a fibroblast-specific deletion of the oxygen sensitive enzyme prolyl hydroxylase (PHD2) (i.e. PHD2ff- Col1a2-ERT2:Cre) and their wildtype littermate controls, followed by RNA sequencing and pathway analysis. Validation of key fibrotic mediators will be performed via qPCR or immunostainings. Intestinal fibrosis will be induced in PHD2ff Col1a2-ERT2:Cre mice wildtype littermate controls by chronic administration of dextran sodium sulphate in their drinking water, followed by treatment with the oral HIF-2 inhibitor, belzutifan. Translatability of preclinical findings will be confirmed in bio-banked fibrostenotic fibroblasts from CD patients. Anticipated impact Intestinal fibrosis is a debilitating complication of IBD which cannot be fully prevented by current anti-inflammatory therapies, highlighting the unmet clinical need for anti-fibrotic treatment strategies. Our preliminary data demonstrated that genetic deletion of Phd2 in fibroblasts aggravates experimental intestinal fibrosis without affecting inflammation and is most likely mediated via HIF-2. This suggests that signaling induced by this transcriptional modulator plays a crucial role in the fibrotic process. This proposal will identify the molecular mediators driving this fibrosis-promoting effect and validate if HIF-2 targeting could represent a promising novel anti-fibrotic treatment strategy. Data resulting from this project will therefore represent a final preclinical step and provide proof-of-concept data with the perspective to initiate a clinical trial in fibrostenotic IBD with belzutifan (awaiting EMA approval, but recently FDA-approved for advanced renal cell carcinoma).

P0061 Guselkumab induction therapy results in molecular resolution of inflammation in moderately to severely active Ulcerative Colitis: results from the Phase 3 QUASAR induction study

Abstract Background Guselkumab (GUS) is a selective dual-acting IL-23p19 subunit inhibitor that potently neutralises interleukin 23 (IL-23) and binds to CD64, a receptor on cells that produce IL-23.1 GUS is now approved in the United States for treatment of moderately to severely active ulcerative colitis (UC). GUS has demonstrated efficacy in UC based on the results of the QUASAR Phase 2/3 programme.2,3 Mechanistic data from the Phase 2b induction study demonstrated a restoration of intestinal homeostasis and initiation of epithelial repair.4 These findings were confirmed in the larger Phase 3 QUASAR induction study presented here. Methods At induction baseline, 701 patients with moderately to severely active UC were randomized 3:2 to receive GUS 200mg IV induction or placebo (PBO) and clinical efficacy was assessed at Week 12 (WK12). Molecular analysis of the randomised population was performed comparing induction WK12 to baseline (WK0). Transcriptional profiling of colonic biopsies from 593 patients was performed with bulk RNA sequencing and gene modules were evaluated for differential expression. Serum proteomic profiling of 648 patients was conducted using a targeted O-Link Inflammation panel and differential protein abundance was assessed. Results Significantly higher proportions of patients treated with GUS 200mg IV achieved clinical remission, endoscopic improvement, histologic-endoscopic mucosal improvement (HEMI), and endoscopic remission at WK12 compared with PBO. GUS IV induction demonstrated significant downregulation of inflammatory transcriptional modules in colon tissue at WK12, representing Th17, plasma cell, neutrophil and inflammatory fibroblast biology, and an upregulation of healthy epithelium-related gene modules including goblet cells and healthy epithelium (all false discovery rate [FDR]<0.05). This response correlated with changes observed in the GUS 200mg IV arm of the Phase 2b induction study (r=0.97, p<0.0001). GUS treated patients who achieved HEMI at WK12 demonstrated the most robust changes in gene module expression at WK12 (p<0.0001), nearing non-IBD control levels. Inflammatory serum proteins were reduced as early as WK4, and continued to decline through WK12 (IFNγ, IL-17A, OSM, and IL-6, FDR<0.05). Changes in serum proteins were consistent with those observed in the GUS 200mg arm of the Phase 2b induction study (r=0.96, p<0.0001) (Figure 1). Conclusion Mechanistic observations in response to GUS 200mg IV induction were validated in the Phase 3 QUASAR induction study. These data demonstrate GUS IV induction reduced inflammatory biology towards normal while also increasing the healthy epithelium in patients who achieved HEMI at WK12.

Evolutionary lineage-specific genomic imprinting at the ZNF791 locus.

Genomic imprinting is an epigenetic process that results in parent-of-origin effects on mammalian development and growth. Research on genomic imprinting in domesticated animals has lagged due to a primary focus on orthologs of mouse and human imprinted genes. This emphasis has limited the discovery of imprinted genes specific to livestock. To identify genomic imprinting in pigs, we generated parthenogenetic porcine embryos alongside biparental normal embryos, and then performed whole-genome bisulfite sequencing and RNA sequencing on these samples. In our analyses, we discovered a maternally methylated differentially methylated region within the orthologous ZNF791 locus in pigs. Additionally, we identified both a major imprinted isoform of the ZNF791-like gene and an unannotated antisense transcript that has not been previously annotated. Importantly, our comparative analyses of the orthologous ZNF791 gene in various eutherian mammals, including humans, non-human primates, rodents, artiodactyls, and dogs, revealed that this gene is subjected to genomic imprinting exclusively in domesticated animals, thereby highlighting lineage-specific imprinting. Furthermore, we explored the potential mechanisms behind the establishment of maternal DNA methylation imprints in porcine and bovine oocytes, supporting the notion that integration of transposable elements, active transcription, and histone modification may collectively contribute to the methylation of embedded intragenic CpG island promoters. Our findings convey fundamental insights into molecular and evolutionary aspects of livestock species-specific genomic imprinting and provide critical agricultural implications.

Viral diversity and phloem transcriptional changes in grapevine Shiraz disease infected vines

Shiraz disease (SD) is a highly destructive disease of grapevines that is associated with grapevine virus A (GVA) infection of vineyards in Australia and South Africa. However, little is known about the transcriptional modifications in grapevine phloem tissues induced by SD. In this study, we explored the viral diversity and transcriptional changes linked to SD. Vines symptomatic for SD exhibited higher viral abundance and were also shown to be co-infected with both GVA and grapevine leafroll-associated virus (GLRaV-4) strain 9. Differential gene (DE) expression analysis revealed physiological responses of Vitis vinifera to the infection. Similar to other plant pathogen infections, SD upregulated genes associated with the systemic acquired resistance (SAR) mechanism and downregulated genes related to vine immunity. Additionally, upregulated genes suggests that callose deposition and the blocking of phloem sieve elements are likely employed by V. vinifera as a defence strategy to limit the internal spread of SD viruses.

Host-virus interactions during infection with a wild-type ILTV strain or a glycoprotein G deletion mutant ILTV vaccine strain in an ex vivo system.

Previous studies have demonstrated the safety and efficacy of a live-attenuated glycoprotein G (gG) deletion mutant vaccine strain of ILTV (∆gG-ILTV). In the current study, transcriptional profiles of chicken tracheal organ cultures (TOCs), 24 h post inoculation with ∆gG-ILTV or the gG-expressing parent wild-type strain, CSW-1 ILTV were explored and compared with the mock-infected TOCs using RNA-seq analysis. Transcriptomes of the vaccine and wild-type ILTV were also compared with each other. Although no viral genes (except for gG) were differentially regulated between the two ILTV-infected TOCs, pair-wise comparison of the transcriptomes of the ∆gG-ILTV or the CSW-1 ILTV-infected TOCs (each compared with mock-infected TOCs) identified the similarities and differences in host gene transcription between them. Several immune checkpoint inhibitors with likely roles in ILTV-mediated immune augmentation, and gene ontologies indicating cytokine response, and cytokine signaling were upregulated in both TOCs. Additionally, several other biological processes, molecular functions, and cellular components were enriched uniquely in the ∆gG-ILTV-infected TOCs, including those that indicated modifications to tracheal extracellular matrix (ECM) structural components, which may have a role in immune modulation in vivo. This study has revealed that the modifications of transcription of host genes during the early stages of ILTV infection are not limited to changes in cytokine or chemokine gene transcription, but several other immune-related genes and ECM components. Moreover, their differential regulation in the ex vivo system appears to be influenced by gG expression, potentially affecting the outcome of ILTV infection in vivo.IMPORTANCEInfectious laryngotracheitis virus (ILTV) remains a serious threat to poultry industries worldwide, causing significant economic losses. The glycoprotein G (gG) of ILTV is a virulence factor and a chemokine-binding protein with immunoregulatory functions. The influence of gG on the transcription of select host chemokine and cytokine genes has been demonstrated previously. This study extends our understanding of the early and localized host-ILTV interactions using genome-wide transcriptome analysis of ILTV-infected chicken tracheal organ cultures, and the role of gG during the process. Differential regulation of genes encoding immune checkpoint inhibitors observed in this study may have a role in ILTV-induced inhibition of type I interferon response, or negative regulation of T cell responses, bringing clarity to these ILTV immune-evasion mechanisms. Furthermore, differential regulation of genes encoding certain structural components and receptors with roles in cell migration, in the absence of gG, is consistent with the immunomodulatory role of ILTV gG.

Genome-wide association study of varenicline-aided smoking cessation.

Varenicline is an α4β2 nicotinic acetylcholine receptor partial agonist with the highest therapeutic efficacy of any pharmacological smoking cessation aid and a 12-month cessation rate of 26%. Genetic variation may be associated with varenicline response, but to date no genome-wide association studies of varenicline response have been published. In this study, we investigated the genetic contribution to varenicline effectiveness using two electronic health record-derived phenotypes. We defined short-term varenicline effectiveness (SVE) and long-term varenicline effectiveness (LVE) by assessing smoking status at 3 and 12 months, respectively, after initiating varenicline treatment. In Stage 1, comprising five European cohort studies, we tested genome-wide associations with SVE (1,405 cases, 2,074 controls) and LVE (1,576 cases, 2,555 controls), defining sentinel variants (the most strongly associated variant within 1 megabase) with p-value <5×10-6 to follow up in Stage 2. In Stage 2, we tested association between sentinel variants and comparable smoking cessation endpoints in varenicline randomised controlled trials. We subsequently meta-analysed Stages 1 and 2. No variants reached genome-wide significance in the meta-analysis. In Stage 1, 10 sentinel variants were associated with SVE and five with LVE at a suggestive significance threshold (p-value <5×10-6); none of these sentinels were previously implicated in varenicline-aided smoking cessation or in genetic studies of smoking behaviour. We provide initial insights into the biological underpinnings of varenicline-aided smoking cessation, through implicating genes involved in various processes, including gene expression, cilium assembly and early-stage development. Leveraging electronic health records, we undertook the largest genetic study of varenicline-aided smoking cessation to date, and the only such study to test genome-wide associations. We showed distinct genetic variants associated (p-value <5×10-6) with varenicline-aided smoking cessation which implicate diverse cellular functions, including transcriptional regulation, RNA modification and cilium assembly. These provide insights which, if independently corroborated, will improve understanding of varenicline response. The growing availability of biobank resources with genetic and varenicline response data will provide future opportunities for larger studies using the approach we developed.

Transcriptional modulation in Mediterranean Mussel Mytilus galloprovincialis following exposure to four pharmaceuticals widely distributed in coastal areas

Transcriptional modulation in Mediterranean Mussel Mytilus galloprovincialis following exposure to four pharmaceuticals widely distributed in coastal areas

A tripartite transcriptional module regulates protoderm specification during embryogenesis in Arabidopsis.

Protoderm formation is a crucial step in early embryo patterning in plants, separating the precursors of the epidermis and the inner tissues. Although key regulators such as ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2) have been identified in the model plant Arabidopsis thaliana, the genetic pathways controlling protoderm specification remain largely unexplored. Here, we combined genetic, cytological, and molecular approaches to investigate the regulatory mechanisms of protoderm specification in Arabidopsis thaliana. We report a novel role of the β-importin KETCH1 in protoderm specification. KETCH1 loss-of-function leads to aberrant protoderm cell morphology and absent ATML1 transcription in embryos. We further demonstrate that KETCH1 directly interacts with an RNA Polymerase II (Pol-II) cofactor JANUS, mediating its nuclear accumulation. Furthermore, JANUS directly interacts with the WUS HOMEOBOX2 (WOX2) protein, which is critical for WOX2-activated ATML1 expression. Consequently, JANUS, KETCH1, and WOX2 loss-of-function results in similar protoderm defects. Our results identify the tripartite KETCH1/JANUS/WOX2 transcriptional module as a novel regulatory axis in Arabidopsis protoderm specification.

Pseudovibriamides from Pseudovibrio marine sponge bacteria promote flagellar motility via transcriptional modulation.

Pseudovibrio α-Proteobacteria have been repeatedly isolated from marine sponges and proposed to be beneficial to the host. Bacterial motility is known to contribute to host colonization. We have previously identified pseudovibriamides A and B, produced in culture by Pseudovibrio brasiliensis Ab134, and shown that pseudovibriamide A promotes flagellar motility. Pseudovibriamides are encoded in a hybrid nonribosomal peptide synthetase-polyketide synthase gene cluster that also includes several accessory genes. Pseudovibriamide A is a linear heptapeptide and pseudovibriamide B is a nonadepsipeptide derived from pseudovibriamide A. Here, we define the borders of the pseudovibriamides gene cluster, assign function to biosynthetic genes using reverse genetics, and test the hypothesis that pseudovibriamides impact motility by modulating gene transcription. RNA-sequencing transcriptomic analyses of strains having different compositions of pseudovibriamides suggested that both pseudovibriamides A and B affect genes potentially involved in motility, and that a compensatory mechanism is at play in mutants that produce only pseudovibriamide A, resulting in comparable flagellar motility as the wild type. The data gathered suggest that pseudovibriamides A and B have opposite roles in modulating a subset of genes, with pseudovibriamide B having a primary effect in gene activation, and pseudovibriamide A on inhibition. Finally, we observed many differentially expressed genes (up to 29% of the total gene number) indicating that pseudovibriamides have a global effect on transcription that goes beyond motility.IMPORTANCEMarine sponges are found throughout the oceans from tropical coral reefs to polar sea floors, playing crucial roles in marine ecosystems. Pseudovibrio bacteria have been proposed to contribute to sponge health. We have previously shown that pseudovibriamides produced by Pseudovibrio brasiliensis promote bacterial motility, a behavior that is beneficial to bacterial survival and host colonization. The gene cluster that encodes pseudovibriamide biosynthesis is found in two-thirds of Pseudovibrio genomes. This gene cluster is also present in Pseudomonas bacteria that interact with terrestrial plants and animals. Here, we first assign functions to pseudovibriamide biosynthetic genes using reverse genetics. We then show that pseudovibriamides play a major role in transcriptional regulation, affecting up to 29% of P. brasiliensis genes, including motility genes. Thus, this work gives insights into pseudovibriamide biosynthesis and provides evidence that they are signaling molecules relevant to bacterial motility and to other yet-to-be-identified phenotypes.

The Role and Mechanism of TRIM Proteins in Gastric Cancer.

Tripartite motif (TRIM) family proteins, distinguished by their N-terminal region that includes a Really Interesting New Gene (RING) domain with E3 ligase activity, two B-box domains, and a coiled-coil region, have been recognized as significant contributors in carcinogenesis, primarily via the ubiquitin-proteasome system (UPS) for degrading proteins. Mechanistically, these proteins modulate a variety of signaling pathways, including Wnt/β-catenin, PI3K/AKT, and TGF-β/Smad, contributing to cellular regulation, and also impact cellular activities through non-signaling mechanisms, including modulation of gene transcription, protein degradation, and stability via protein-protein interactions. Currently, growing evidence indicates that TRIM proteins emerge as potential regulators in gastric cancer, exhibiting both tumor-suppressive and oncogenic roles. Given their critical involvement in cellular processes and the notable challenges of gastric cancer, exploring the specific contributions of TRIM proteins to this disease is necessary. Consequently, this review elucidates the roles and mechanisms of TRIM proteins in gastric cancer, emphasizing their potential as therapeutic targets and prognostic factors.