Specific Set Of Genes Research Articles

Neutrophil prime unique transcriptional responses in intestinal organoids during infection with nontyphoidal Salmonella enterica serovars.

Nontyphoidal strains of Salmonella enterica are a major cause of foodborne illnesses, and infection with these bacteria results in inflammatory gastroenteritis. Polymorphonuclear leukocytes (PMNs), also known as neutrophils, are a dominant immune cell type found at the site of infection in Salmonella-infected individuals, but how they regulate infection outcome is not well understood. Here, we used a co-culture model of primary human PMNs and human intestinal organoids to probe the role of PMNs during infection with two of the most prevalent Salmonella serovars: Salmonella enterica serovar Enteritidis and Typhimurium. Using a transcriptomics approach, we identified a dominant role for PMNs in mounting differential immune responses including production of pro-inflammatory cytokines, chemokines, and antimicrobial peptides. We also identified specific gene sets that were induced by PMNs in response to Enteritidis or Typhimurium infection. By comparing host responses to these serovars, we uncovered differential regulation of host metabolic pathways particularly induction of cholesterol biosynthetic pathways during Typhimurium infection and suppression of RNA metabolism during Enteritidis infection. Together, these findings provide insight into the role of human PMNs in modulating different host responses to pathogens that cause similar disease in humans.IMPORTANCENontyphoidal serovars of Salmonella enterica are known to induce robust recruitment of polymorphonuclear leukocytes (PMNs) in the gut during early stages of infection, but the specific role of PMNs in regulating infection outcome of different serovars is poorly understood. Due to differences in human infection progression compared to small animal models, characterizing the role of PMNs during infection has been challenging. Here, we used a co-culture model of human intestinal organoids with human primary PMNs to study the role of PMNs during infection of human intestinal epithelium. Using a transcriptomics approach, we define PMN-dependent reprogramming of the host response to Salmonella, establishing a clear role in amplifying pro-inflammatory gene expression. Additionally, the host response driven by PMNs differed between two similar nontyphoidal Salmonella serovars. These findings highlight the importance of building more physiological infection models to replicate human infection conditions to study host responses specific to individual pathogens.

GADD45β-MTK1 signaling axis mediates oncogenic stress-induced activation of the p38 and JNK pathways.

The ERK pathway governs essential biological processes such as cell proliferation and survival, and its hyperactivation by various oncogenes ultimately drives carcinogenesis. However, normal mammalian cells typically recognize aberrant ERK signaling as oncogenic stress and respond by inducing cell cycle arrest or apoptosis through activation of the p38 and JNK pathways. Despite the critical role of this response in preventing carcinogenesis, the precise molecular mechanisms underlying oncogene-induced, ERK-dependent activation of p38/JNK and its tumor-suppressive effects remain unclear. Here, we demonstrate that MAP three kinase 1 (MTK1), a stress-responsive MAPKKK, serves as a key mediator of p38/JNK activation induced by oncogenic ERK signaling. Mechanistically, aberrant ERK signaling induces sustained expression of the transcription factor early growth response protein 1 (EGR1), which promotes the production of the MTK1 activator GADD45β, leading to persistent activation of MTK1-p38/JNK signaling. Gene knockout and transcriptome analyses revealed that this GADD45β/MTK1-mediated cross-talk between the ERK and p38/JNK pathways preferentially upregulates a specific set of genes involved in apoptosis and the immune response. Notably, the expression of EGR1, GADD45β, and MTK1 is frequently downregulated in many cancers with high ERK activity, resulting in the disruption of the tumor-suppressive ERK-p38/JNK cross-talk. Restoring GADD45β expression in cancer cells reactivates p38/JNK signaling and suppresses tumorigenesis. Our findings delineate a molecular mechanism by which normal cells sense and respond to oncogenic stress to prevent abnormal growth, and highlight the significance of its dysregulation in cancer.

Identification of miR-451 target genes as prognostic markers in diffuse large B-cell lymphoma

ABSTRACT Background B-cell lymphoma, a diverse malignancy, is intricately regulated by multiple factors. MicroRNAs (miRNAs) have been demonstrated to be important regulators of the initiation and progression of human B-cell lymphoma, but their functions need to be further explored. Research design and methods Two B-cell lymphoma cell lines, Romas and HBL-1, were engineered to overexpress miR-451, with cell proliferation assessed via cell counting assays. Flow cytometry was used to study the effects of miR-451 on cell cycle and apoptosis. Bioinformatics analyses were performed using GEO datasets (GSE181063, GSE32918, GSE56315) to identify DEGs, and potential miR-451 target genes were predicted using tools like ENCORI, TargetScan, and R packages. A risk model for DLBCL prognosis was developed using Cox and LASSO regression. qRT-PCR validated the expression of these target genes. Results This study revealed that miR-451 inhibited cell proliferation, arrested the cell cycle, and induced apoptosis in human DLBCL cell lines. Bioinformatics analysis identified 9 target genes (MMP9, AQP9, RIN2, EOMES, LCP2, SELPLG, MAL, SOCS5, S1PR3) significantly associated with DLBCL prognosis, suggesting a potential mechanism by which miR-451 suppresses DLBCL development. Conclusions Our study indicates that a specific set of miR-451 target genes may significantly influence DLBCL patient outcomes.

The Role of the Bone Morphogenetic Protein Antagonist Noggin in Nucleus Pulposus Intervertebral Disc Cells.

Low back pain (LBP) is a significant global health issue, contributing to disability and socioeconomic burdens worldwide. The degeneration of the human intervertebral disc (IVD) is a critical factor in the pathogenesis of LBP. Recent studies have emphasized the significance of a specific set of genes and extracellular matrix (ECM) in IVD health. In particular, Noggin has emerged as a critical gene due to its high expression levels in healthy nucleus pulposus cells (NPCs) observed in our previous research. In this study, it was hypothesized that decreased Noggin expression in NPCs is associated with IVD degeneration and contributes to LBP development. A lentivirus-mediated RNAi was applied to knock down Noggin expression in primary NPCs from six human donors. The NPCs after transduction were evaluated through cell viability analysis, XTT assay, and cell apoptosis analyses. After two weeks, a colony formation assay was used to examine the anchor-independent growth ability of transduced cells. At the transcript level, anabolic and catabolic markers were quantified using RT-qPCR. The results demonstrated that lentivirus-mediated downregulation of Noggin significantly inhibited cell proliferation, reduced cell viability, and suppressed colony formation, while inducing apoptosis in human NPCs in vitro. Notably, it disrupted cellular anabolic processes and promoted catabolic activity in human NPCs post-transduction. Our findings indicated that the degeneration of human IVD is possibly related to decreased Noggin expression in NPCs. This research provides valuable insights into the role of Noggin in IVD homeostasis and its implications in LBP treatment.

An unexpected role of Nogo-A as regulator of tooth enamel formation

Neurite outgrowth inhibitor A (Nogo-A) is a major player in neural development and regeneration and the target of clinical trials aiming at promoting the regeneration of the central nervous system upon traumatic and ischemic injury. In this work, we investigated the functions of Nogo-A during tooth development to determine its role in dental physiology and pathology. Using immunohistochemistry and in situ hybridization techniques, we showed that Nogo-A is highly expressed in the developing mouse teeth and, most specifically, in the ameloblasts that are responsible for the formation of enamel. Using both Nogo-A knockout and K14-Cre;Nogo-A fl/fl transgenic mice, we showed that Nogo-A deletion in the dental epithelium leads to the formation of defective enamel. This phenotype is associated with overexpression of a set of specific genes involved in ameloblast differentiation and enamel matrix production, such as amelogenin, ameloblastin and enamelin. By characterising the interactome of Nogo-A in the dental epithelium of wild-type and mutant animals, we found that Nogo-A directly interacts with molecules important for regulating gene expression, and its deletion disturbs their cellular localisation. Furthermore, we demonstrated that inhibition of the intracellular, but not cell-surface, Nogo-A is responsible for gene expression modulation in ameloblasts. Taken together, these results reveal an unexpected function for Nogo-A in tooth enamel formation by regulating gene expression and cytodifferentiation events.

JunB is required for CD8+ T cell responses to acute infections.

Basic-leucine zipper transcription factor ATF-like (BATF) and interferon regulatory factor 4 (IRF4) are crucial transcription factors for generation of cytotoxic effector and memory CD8+ T cells. JunB is required for expression of genes controlled by BATF and IRF4 in CD4+ T cell responses, but the role of JunB in CD8+ T cells remains unknown. Here, we demonstrate that JunB is essential for cytotoxic CD8+ T cell responses. JunB expression is transiently induced, depending on T cell receptor (TCR) signal strength. JunB deficiency severely impairs clonal expansion of effector CD8+ T cells in response to acute infection with Listeria monocytogenes. Junb-deficient CD8+ T cells fail to control transcription and chromatin accessibility of a specific set of genes regulated by BATF and IRF4, resulting in impaired cell survival, glycolysis, and cytotoxic CD8+ T cell differentiation. Furthermore, JunB deficiency enhances expression of coinhibitory receptors, including programmed death receptor 1 (PD-1) and T-cell immunoglobulin mucin-3 (TIM3) upon activation of naïve CD8+ T cells. These results indicate that JunB, in collaboration with BATF and IRF4, promotes multiple key events in the early stage of cytotoxic CD8+ T cell responses.

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.

Practical application of heterosis on yield evidence and fruits biochemical composition for tomato (Solanum lycopersicum L.) in open ground

Relevance. The research is devoted to studying the peculiarities of the high-parent heterosis manifestation which connected with yield traits and the biochemical composition of tomato fruits.Materials and Methods. The work was carried out in 2021–2023 in open field conditions on the experimental plot of the Belarusian State Agricultural Academy (Mogilev region, Belarus). The objects of research were 30 F1 hybrids and 11 parental forms with different levels of economically valuable traits and with the specific set of genes for pathogen resistance and lycopene accumulation. The aim of the research was to create high-yield heterotic F1 tomato hybrids, adapted to open field conditions in Belarus, with a valuable biochemical composition of fruits.Results. The best hybrid combinations showed an early yield of 0.90–2.49 kg/m2, a marketable yield of 7.50–11.40 kg/m2, and a total yield of 8.22–13.12 kg/m2. High heterosis effect was established for early (88.9–291.0%), marketable (36.0–111.2%), and total (28.6–97.8%) yield in some hybrids. Significant differences in the accumulation of dry matter, carotene, and soluble carbohydrates were ascertained between the hybrids. Hybrid combinations with the highest value of true heterosis on accumulation of dry matter (18.3–21.6%), carotene (20.2–22.9%), and soluble carbohydrates (15.7–38.9%) were identified. Inheritance of early, marketable and total yield, dry matter content, carotene and soluble carbohydrates predominantly took place according to the positive overdominance, fruit weight – according to the intermediate inheritance, vitamin C content – according to the negative overdominance. Hybrids Brusnichny F1, Mansiata F1, Rada F1 were transferred to the State Inspection for Testing and Protection of Plant Varieties of the Republic of Belarus and successfully passed the testing stage in 2023.

8109 Cancer-Associated Fibroblasts Correlate with Aggressive Thyroid Cancer Behavior: Insights from Four Large Patient Cohorts

Abstract Disclosure: M.A. Loberg: None. X. George: None. P.J. Courtney: None. H.C. Eric: None. A. Golding: None. B. David: None. M. Alshalalfa: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. Y. Hao: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. J.P. Klopper: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. R.T. Kloos: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc.. V. Weiss: None. Thyroid tumor molecular analysis often utilizes fine-needle aspirate (FNA) samples to predict malignancy with high sensitivity. An outstanding question is if molecular sequencing can provide prognostic information to predict disease aggression, potentially informing management. Recently, the composition of the tumor microenvironment, in particular the presence of tumor-promoting fibroblasts, has been associated with aggressive thyroid cancer. However, fibroblast gene expression has not previously been analyzed in thyroid tumor FNA samples. In this work, we detect cancer-associated fibroblast (CAF) gene signatures across 4 distinct bulk RNA sequencing cohorts and confirm detection in FNA samples. Associations between CAF gene signatures and tumor characteristics were explored in: Afirma Genomic Sequencing Classifier (GSC) cohort from FNA (n=47,695), a Memorial Healthcare System (MHS) retrospective FNA cohort with pathology outcome data (n=318), TCGA papillary thyroid cancers (n=496), and a Vanderbilt University Medical Center-University of Washington (VUMC-UW) resection cohort (n=312). Published breast CAF gene sets were used to generate normal fibroblast and CAF subtype scores. Novel thyroid cancer specific CAF gene sets were generated from thyroid cancer single-cell RNA sequencing data. Scores for each gene set were calculated as the average Z-score. Across all cohorts, multiple CAF subsets were enriched in samples with BRAFV600E and papillary histology. The strongest enrichment was in an SFRP2+ CAF subset identified in thyroid cancer single-cell sequencing data. In Afirma GSC FNA samples, SFRP2+ CAFs were enriched in GSC-suspicious and Bethesda V/VI relative to GSC-benign nodules (Wilcoxon p value &amp;lt; 2e-[1]6 for all). In TCGA, SFRP2+ CAFs were associated with extrathyroidal extension, advanced disease stage, and aggressive histology. In the MHS cohort of 318 malignant FNA samples, SFRP2+ CAFs were significantly higher in patients with vascular invasion or lymph node metastasis (LNM) (OR:2.75 [95% CI 1.63-4.75], p=4e-5). In the VUMC-UW cohort, SFRP2+ CAFs were associated with shorter progression-free survival (PFS) (p=0.0033). In summary we created a novel thyroid cancer-specific CAF gene signature that is elevated in BRAFV600E+ and aggressive thyroid cancers across multiple large patient cohorts. We also demonstrated the ability to detect these CAF signatures in thyroid FNAs using the Afirma GSC molecular testing platform, with enrichment in suspicious and malignant samples. Amongst the CAF scores tested, thyroid-specific CAF subsets had the highest prognostic potential, and SFRP2+ CAFs, specifically, were associated with shorter PFS, tumor invasion and LNM. Together, these results highlight the potential of interrogating the thyroid tumor stroma in FNA using RNA-based assays to inform prognosis and possibly management. Presentation: 6/3/2024

Sex-dependent differences in the ability of nicotine to modulate discrimination learning and cognitive flexibility in mice.

Nicotine, an addictive compound found in tobacco, functions as an agonist of nicotinic acetylcholine receptors (nAChRs) in the brain. Interestingly, nicotine has been reported to act as a cognitive enhancer in both human subjects and experimental animals. However, its effects in animal studies have not always been consistent, and sex differences have been identified in the effects of nicotine on several behaviors. Specifically, the role that sex plays in modulating the effects of nicotine on discrimination learning and cognitive flexibility in rodents is still unclear. Here, we evaluated sex-dependent differences in the effect of daily nicotine intraperitoneal (i.p.) administration at various doses (0.125, 0.25, and 0.5 mg/kg) on visual discrimination (VD) learning and reversal (VDR) learning in mice. In male mice, 0.5 mg/kg nicotine significantly improved performance in the VDR, but not the VD, task, while 0.5 mg/kg nicotine significantly worsened performance in the VD, but not VDR task in female mice. Furthermore, 0.25 mg/kg nicotine significantly worsened performance in the VD and VDR task only in female mice. Next, to investigate the cellular mechanisms that underlie the sex difference in the effects of nicotine on cognition, transcriptomic analyses were performed focusing on the medial prefrontal cortex tissue samples from male and female mice that had received continuous administration of nicotine for 3 or 18 days. As a result of pathway enrichment analysis and protein-protein interaction analysis using gene sets of differentially expressed genes, decreased expression of postsynaptic-related genes in males and increased expression of innate immunity-related genes in females were identified as possible molecular mechanisms related to sex differences in the effects of nicotine on cognition in discrimination learning and cognitive flexibility. Our result suggests that nicotine modulates cognitive function in a sex-dependent manner by alternating the expression of specific gene sets in the medial prefrontal cortex.

GsQTL: Associating genetic risk variants with gene sets by exploiting their shared variability.

To investigate the functional significance of genetic risk loci identified through genome-wide association studies (GWASs), genetic loci are linked to genes based on their capacity to account for variation in gene expression, resulting in expression quantitative trait loci (eQTL). Following this, gene set analyses are commonly used to gain insights into functionality. However, the efficacy of this approach is hampered by small effect sizes and the burden of multiple testing. We propose an alternative approach: instead of examining the cumulative associations of individual genes within a gene set, we consider the collective variation of the entire gene set. We introduce the concept of gene set QTL (gsQTL), and show it to be more adept at identifying links between genetic risk variants and specific gene sets. Notably, gsQTL experiences less susceptibility to inflation or deflation of significant enrichments compared with conventional methods. Furthermore, we demonstrate the broader applicability of shared variability within gene sets. This is evident in scenarios such as the coordinated regulation of genes by a transcription factor or coordinated differential expression.

A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet.

Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance; however, the molecular mechanisms governing stalk development in pearl millet remain to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined four developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that two co-expression modules together with candidate genes were involved in stalk elongation and the thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement in pearl millet.

TCellSI: A novel method for T cell state assessment and its applications in immune environment prediction.

T cell is an indispensable component of the immune system and its multifaceted functions are shaped by the distinct T cell types and their various states. Although multiple computational models exist for predicting the abundance of diverse T cell types, tools for assessing their states to characterize their degree of resting, activation, and suppression are lacking. To address this gap, a robust and nuanced scoring tool called T cell state identifier (TCellSI) leveraging Mann-Whitney U statistics is established. The TCellSI methodology enables the evaluation of eight distinct T cell states-Quiescence, Regulating, Proliferation, Helper, Cytotoxicity, Progenitor exhaustion, Terminal exhaustion, and Senescence-from transcriptome data, providing T cell state scores (TCSS) for samples through specific marker gene sets and a compiled reference spectrum. Validated against sizeable pseudo-bulk and actual bulk RNA-seq data across a range of T cell types, TCellSI not only accurately characterizes T cell states but also surpasses existing well-discovered signatures in reflecting the nature of T cells. Significantly, the tool demonstrates predictive value in the immune environment, correlating T cell states with patient prognosis and responses to immunotherapy. For better utilization, the TCellSI is readily accessible through user-friendly R package and web server (https://guolab.wchscu.cn/TCellSI/). By offering insights into personalized cancer therapies, TCellSI has the potential to improve treatment outcomes and efficacy.

Multiplex PCR-based genotyping of Salmonella Enteritidis and Salmonella Typhimurium from food sources and assessment of their antimicrobial resistance profiles in Egypt.

Salmonellosis is a widespread zoonotic disease that poses a significant threat to livestock and public health. This study aimed to serotype 20 Salmonella isolates obtained from sixty retail chicken meats, assess Salmonella contamination from eggs, and evaluate antibiotic resistance profiles. Twenty eggs were randomly collected in the new Borg El Arab market. Bacterial isolation was carried out utilizing both traditional culture, biochemical, and PCR methods. Among the twenty eggs analyzed, three (15%) tested positive for Salmonella, while the remaining seventeen (85%) were confirmed as negative. Genotyping through multiplex PCR revealed the presence of two S. Enteritidis and other serovar, with the use of three specific gene sets: a random sequence for Salmonella spp., sdfI gene for S. Enteritidis, and flagellin (fliC gene) for S. Typhimurium. Out of the 20 isolates obtained from chicken meat, five (25%) were identified as S. Typhimurium, and three (15%) were classified as S. Enteritidis. All isolates sourced from chicken meat exhibited resistance to Rifampicin and Amoxicillin, with 90% displaying sensitivity to cefotaxime, gemifloxacin, and Erythromycin. Importantly, S. Blegdam, identified via serological methods, displayed resistance to all tested antibiotics. For the three isolates obtained from eggs, 66.6% showed sensitivity to cefotaxime, erythromycin, cefuraxime, and cefaclor, while displaying complete resistance (100%) to Amoxicillin, rifampicin, clarithromycin, and cefadroxil. Notably, one serovar exhibited absolute resistance to all tested drugs. Stakeholders must implement strict control measures and rationalize antibiotic use in veterinary and human medicine due to the rise of antibiotic-resistant strains.

Unsupervised Analysis Reveals the Involvement of Key Immune Response Genes and the Matrisome in Resistance to BRAF and MEK Inhibitors in Melanoma.

Melanoma tumors exhibit a wide range of heterogeneity in genomics even with shared mutations in the MAPK pathway, including BRAF mutations. Consistently, adaptive drug resistance to BRAF inhibitors and/or BRAF plus MEK inhibitors also exhibits a wide range of heterogeneous responses, which poses an obstacle for discovering common genes and pathways that can be used in clinic for overcoming drug resistance. This study objectively analyzed two sets of previously published tumor genomics data comparing pre-treated melanoma tumors and BRAFi- and/or MEKi-resistant tumors. Heterogeneity in response to BRAFi and BRAFi/MEKi was evident because the pre-treated tumors and resistant tumors did not exhibit a tendency of clustering together. Differentially expressed gene (DEG) analysis revealed eight genes and two related enriched signature gene sets (matrisome and matrisome-associated signature gene sets) shared by both sets of data. The matrisome was closely related to the tumor microenvironment and immune response, and five out of the eight shared genes were also related to immune response. The PLXNC1 gene links the shared gene set and the enriched signature gene sets as it presented in all analysis results. As the PLXNC1 gene was up-regulated in the resistant tumors, we validated the up-regulation of this gene in a laboratory using vemurafenib-resistant cell lines. Given its role in promoting inflammation, this study suggests that resistant tumors exhibit an inflammatory tumor microenvironment. The involvement of the matrisome and the specific set of immune genes identified in this study may provide new opportunities for developing future therapeutic methods.

A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201.

Cryptococcus is a fungal pathogen whose virulence relies on proliferation in and dissemination to host sites, and on synthesis of a defensive yet metabolically costly polysaccharide capsule. Regulatory pathways required for Cryptococcus virulence include a GATA-like transcription factor, Gat201, that regulates Cryptococcal virulence in both capsule-dependent and capsule-independent ways. Here we show that Gat201 is part of a negative regulatory pathway that limits fungal survival at alkaline pH. RNA-seq analysis found strong induction of GAT201 expression within minutes of transfer to RPMI media at alkaline pH. Microscopy, growth curves, and colony forming unit assays show that in RPMI at alkaline pH wild-type Cryptococcus neoformans yeast cells produce capsule but do not bud or maintain viability, while gat201Δ cells make buds and maintain viability, yet fail to produce capsule. GAT201 is required for transcriptional upregulation of a specific set of genes, the majority of which are direct Gat201 targets. Evolutionary analysis shows that Gat201 is in a subfamily of GATA-like transcription factors that is conserved within pathogenic fungi but absent in model yeasts. This work identifies the Gat201 pathway as controlling a trade-off between proliferation and production of defensive capsule. The assays established here will allow characterisation of the mechanisms of action of the Gat201 pathway. Together, our findings urge improved understanding of the regulation of proliferation as a driver of fungal pathogenesis.

A spatial portrait of the human sebaceous gland transcriptional program

Sebaceous glands (SG) and their oily secretion (sebum) are indispensable for maintaining skin structure and function, and their deregulation causes skin disorders including but not limited to acne. Recent studies also indicate that sebum may have important immunomodulatory activities and may influence whole-body energy metabolism. However, the progressive transcriptional changes of sebocytes that lead to sebum production have never been characterized in detail. Here, we exploited the high cellular resolution provided by sebaceous hyperplasia and integrated spatial transcriptomics, pseudotime analysis, RNA velocity, and functional enrichment to map the landscape of sebaceous differentiation by employing spatial transcriptomics. Our results were validated by comparison with published SG transcriptome data and further corroborated by assessing the protein expression pattern of a subset of the transcripts in the public repository Human Protein Atlas. Departing from four sebocyte differentiation stages generated by unsupervised clustering, we demonstrate consecutive modulation of cellular functions associable with specific gene sets, from cell proliferation and oxidative phosphorylation via lipid synthesis to cell death. Both validation methods confirmed the biological significance of our results. Our report is complemented by a freely available and browsable online tool. Our data provide the first high-resolution spatial portrait of the SG transcriptional landscape and deliver starting points for experimentally assessing novel candidate molecules for regulating SG homeostasis in health and disease.

CancerHallmarks.com: A tool for the enrichment analysis of the cancer hallmarks.

e15079 Background: The "Hallmarks of Cancer" concept is a useful framework for understanding the fundamental principles that are shared among different types of cancers. However, the lack of agreement on a specific set of genes for these hallmarks makes it difficult to compare and integrate data, leading to varying interpretations of the biological processes involved in cancer across different studies. In this study, we created a consensus set of cancer hallmark genes by combining data from multiple mapping resources and the scientific literature. Methods: We identified 6,763 candidate cancer hallmark genes associated with ten cancer hallmarks by consolidating information from seven studies. There was a considerable variation in the number of genes within the available resources, ranging between 91 and 7,779. We observed a sizable variation in the number of genes connected to each hallmark. The number of genes across cancer hallmarks ranges between 574 („enabling replicative immortality”) and 3,574 ("sustaining proliferative signaling"). The least number of genes are associated with the more recent hallmarks, published in 2011, and the hallmarks „enabling replicative immortality” and „sustaining angiogenesis”. We identified six genes linked to each of the ten cancer hallmarks: TP53, AKT1, MAP2K1, CTNNB1, HRAS, and PIK3CB. Results: As a practical utility of the hallmark concept, we analyzed the enrichment of cancer hallmarks by evaluating genes associated with overall survival. Only genes with a false discovery rate below 0.01, a hazard rate over 1, and a cutoff value over 100 were analyzed to ensure sufficient robustness of the gene sets. The hallmark "genome instability" was most prominent in liver (p=1.0E-05), lung (p=1.0E-05), and pancreatic cancers (p=0.00164). Renal cancer had higher “invasion and metastasis” (p=0.002). Both pancreatic cancer and lung adenocarcinomas were enriched for “resisting cell death” (p=0.00096 and p=0.037, respectively). Overall, while eight cancer types had no significant hallmark enrichment among druggable genes, pancreatic cancers had the most enriched hallmarks (5 out of 10), emphasizing the disease's complexity. These results highlight the usefulness of the hallmark concept as a valuable tool for organizing information, especially in establishing a direct link between genes and biological functions. Conclusions: We have created a unified list of genes linked to cancer hallmarks. We integrated the data into an easily accessible online tool (accessible at www.cancerhallmarks.com) that enables users to identify the most pertinent cancer-associated “candidate hallmark genes” in their own datasets.

Improved functional mapping of complex trait heritability with GSA-MiXeR implicates biologically specific gene sets.

While genome-wide association studies are increasingly successful in discovering genomic loci associated with complex human traits and disorders, the biological interpretation of these findings remains challenging. Here we developed the GSA-MiXeR analytical tool for gene set analysis (GSA), which fits a model for the heritability of individual genes, accounting for linkage disequilibrium across variants and allowing the quantification of partitioned heritability and fold enrichment for small gene sets. We validated the method using extensive simulations and sensitivity analyses. When applied to a diverse selection of complex traits and disorders, including schizophrenia, GSA-MiXeR prioritizes gene sets with greater biological specificity compared to standard GSA approaches, implicating voltage-gated calcium channel function and dopaminergic signaling for schizophrenia. Such biologically relevant gene sets, often with fewer than ten genes, are more likely to provide insights into the pathobiology of complex diseases and highlight potential drug targets.

HMGA1 regulates trabectedin sensitivity in advanced soft-tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study

HMGA1 is a structural epigenetic chromatin factor that has been associated with tumor progression and drug resistance. Here, we reported the prognostic/predictive value of HMGA1 for trabectedin in advanced soft-tissue sarcoma (STS) and the effect of inhibiting HMGA1 or the mTOR downstream pathway in trabectedin activity. The prognostic/predictive value of HMGA1 expression was assessed in a cohort of 301 STS patients at mRNA (n = 133) and protein level (n = 272), by HTG EdgeSeq transcriptomics and immunohistochemistry, respectively. The effect of HMGA1 silencing on trabectedin activity and gene expression profiling was measured in leiomyosarcoma cells. The effect of combining mTOR inhibitors with trabectedin was assessed on cell viability in vitro studies, whereas in vivo studies tested the activity of this combination. HMGA1 mRNA and protein expression were significantly associated with worse progression-free survival of trabectedin and worse overall survival in STS. HMGA1 silencing sensitized leiomyosarcoma cells for trabectedin treatment, reducing the spheroid area and increasing cell death. The downregulation of HGMA1 significantly decreased the enrichment of some specific gene sets, including the PI3K/AKT/mTOR pathway. The inhibition of mTOR, sensitized leiomyosarcoma cultures for trabectedin treatment, increasing cell death. In in vivo studies, the combination of rapamycin with trabectedin downregulated HMGA1 expression and stabilized tumor growth of 3-methylcholantrene-induced sarcoma-like models. HMGA1 is an adverse prognostic factor for trabectedin treatment in advanced STS. HMGA1 silencing increases trabectedin efficacy, in part by modulating the mTOR signaling pathway. Trabectedin plus mTOR inhibitors are active in preclinical models of sarcoma, downregulating HMGA1 expression levels and stabilizing tumor growth.