Differences In Gene Expression Research Articles

Sink strength, nutrient allocation, cannabinoid yield and associated transcript profiles vary in two drug-type Cannabis chemovars.

Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response SPX DOMAIN GENE3, nitrate reductase and two nitrate transporters. Altered nutrient sensing, acquisition or distribution are likely a consequence of adaption to growth on marginal, low-nutrient input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments.

Nutritional condition drives spatial variation in physiology of Antarctic lipid-storing copepods.

Lipid-rich copepods form an essential link between primary producers and higher trophic levels in high-latitude oceans. These zooplankton can take advantage of ephemeral phytoplankton blooms to fuel development and reproduction. However, we have limited understanding of how the physiological condition of these animals varies in relation to environmental factors such as food availability. Due to high advection, it is likely that physiological plasticity, rather than local adaptation, is primarily responsible for physiological differences within a region. We use transcriptomics and other physiological metrics to understand how two species of copepods (Calanoides acutus and Calanus propinquus) vary across environmental gradients along the West Antarctic Peninsula. For the primarily herbivorous C. acutus, physiological separation between sampling locations appears to be driven by feeding status, and gene expression differences indicate differential expression of genes regulating lipid metabolism, reproduction, aerobic metabolism, and protein translation. For the more omnivorous C. propinquus, physiology and gene expression did not segregate as clearly by location, showed minimal signs of food deprivation at any location, and had a weaker relationship with chlorophyll compared to C. acutus. By comparing these results with concurrent starvation experiments, we find that spatial variation in gene expression reflects short-term differences in food availability (particularly for C. acutus), and we identify genes whose expression indicates recent feeding status. Further examination of the relationships between food availability, copepod physiology, and population dynamics will ultimately improve our capacity to predict how copepod populations will respond to rapidly changing environmental conditions in the West Antarctic Peninsula ecosystem.

Ancestry and Fetal Sex Differences in Hofbauer Cell Gene Expression and Cell Communications in Mid-Gestation Human Placenta

Ancestry and Fetal Sex Differences in Hofbauer Cell Gene Expression and Cell Communications in Mid-Gestation Human Placenta

Sex differences in placental gene expression and intraplacental variation in normotensive versus hypertensive pregnancies

Sex differences in placental gene expression and intraplacental variation in normotensive versus hypertensive pregnancies

Interactions at the Oviposition Scar: Molecular and Metabolic Insights into Elaeagnus angustifolia’s Resistance Response to Anoplophora glabripennis

The Russian olive (Elaeagnus angustifolia), which functions as a “dead-end trap tree” for the Asian long-horned beetle (Anoplophora glabripennis) in mixed plantations, can successfully attract Asian long-horned beetles for oviposition and subsequently kill the eggs by gum. This study aimed to investigate gum secretion differences by comparing molecular and metabolic features across three conditions—an oviposition scar, a mechanical scar, and a healthy branch—using high-performance liquid chromatography and high-throughput RNA sequencing methods. Our findings indicated that the gum mass secreted by an oviposition scar was 1.65 times greater than that secreted by a mechanical scar. Significant differences in gene expression and metabolism were observed among the three comparison groups. A Kyoto Encyclopedia of Genes and Genomes annotation and enrichment analysis showed that an oviposition scar significantly affected starch and sucrose metabolism, leading to the discovery of 52 differentially expressed genes and 7 differentially accumulated metabolites. A network interaction analysis of differentially expressed metabolites and genes showed that EaSUS1, EaYfcE1, and EaPGM1 regulate sucrose, uridine diphosphate glucose, α-D-glucose-1P, and D-glucose-6P. Although the polysaccharide content in the OSs was 2.22 times higher than that in the MSs, the sucrose content was lower. The results indicated that the Asian long-horned beetle causes Russian olive sucrose degradation and D-glucose-6P formation. Therefore, we hypothesized that damage caused by the Asian long-horned beetle could enhance tree gum secretions through hydrolyzed sucrose and stimulate the Russian olive’s specific immune response. Our study focused on the first pair of a dead-end trap tree and an invasive borer pest in forestry, potentially offering valuable insights into the ecological self-regulation of Asian long-horned beetle outbreaks.

Isolation and Identification of Highly Sb-Resistant Rhodotorula glutinis Strain J5 and its Mechanism of Resistance to Sb(III).

Sb-resistant strains can detoxify antimony through metabolic mechanisms such as oxidation and affect the migration, transformation, and ultimate fate of antimony in the environment. In this study, a strain of Sb-resistant fungi, Rhodotorula glutinis sp. Strain J5, was isolated from Xikuangshan mine and its growth characteristics, gene expression differences, and functional annotation under Sb(III) stress were further investigated to reveal the mechanism of resistance to Sb(III). We identified strain J5 as belonging to the Rhodotorula glutinis species optimally growing at pH 5.0 and at 28°C of temperature. According to gene annotation and differential expression, the resistance mechanism of Strain J5 includes: reducing the endocytosis of antimony by aquaporin AQP8 and transmembrane transporter pst, enhancing the efflux of Sb(III) by the gene expression of acr2, acr3 and ABC, improving the oxidation of Sb(III) by iron-sulfur protein and Superoxide dismutase (SOD), glutathione (GSH) and cysteine (Cys) chelation, methylation of methyltransferase and N-methyltransferase, accelerating cell damage repair and EPS synthesis and other biochemical reaction mechanisms. FT-IR analysis shows that the -OH, -COOH, -NH, -PO, C-O, and other active groups of Strain J5 can be complexed with Sb(III), resulting in chemical adsorption. Strain J5 displays significant resistance to Sb(III) with the MIC of 1300mg/L, playing a crucial role in the global biochemical transformation of antimony and its potential application in soil microbial remediation.

Cells and molecules underpinning cannabis-related variations in cortical thickness during adolescence.

During adolescence, cannabis experimentation is common, and its association with inter-individual variations in brain maturation well studied. Cellular and molecular underpinnings of these system-level relationships are, however, unclear. We thus conducted a three-step study. First, we exposed adolescent male mice to Δ-9-tetrahydrocannabinol (THC) or a synthetic cannabinoid WIN 55,212-2 (WIN) and assessed differentially expressed genes (DEGs), spine numbers and dendritic complexity in their frontal cortex. Second, in human (male) adolescents, we examined group differences in cortical thickness in 34 brain regions, using magnetic resonance imaging, between those who experimented with cannabis before age 16 (n=140) and those who did not (n=327). Finally, we correlated spatially these group differences with gene expression of human homologs of the mouse-identified DEGs. The spatial expression of 13 THC-related human homologs of DEGs correlated with cannabis-related variations in cortical thickness, and virtual histology revealed co-expression patterns of these 13 genes with cell-specific markers of astrocytes, microglia and a type of pyramidal cells enriched in dendrite-regulating genes. Similarly, the spatial expression of 18 WIN-related human homologs of DEGs correlated with group differences in cortical thickness, and showed co-expression patterns with the same three cell types. Gene ontology analysis indicated that 37 THC-related human homologs are enriched in neuron-projection development, while 33 WIN-related homologs are enriched in processes associated with learning and memory. In mice, we observed spine loss and lower dendritic complexity in pyramidal cells of THC-exposed animals (vs. controls). Experimentation with cannabis during adolescence may influence cortical thickness by impacting glutamatergic synapses and dendritic arborization.Significance Statement Cells and molecular underpinning of cannabis-related variations in cortical thickness observed in adolescents are poorly understood. We assessed differences in gene expression in the frontal cortex of adolescent mice exposed (or not) to Δ-9-tetra-hydrocannabinol (THC) or WIN 55,212-2 (WIN). THC preferentially targeted glial cells, while WIN affected pyramidal neurons; both modified nuclear-coded subunits in mitochondrial respiratory complexes and excitatory synapse genes. In humans, we evaluated a spatial correlation between group differences in cortical thickness and the expression of human homologs of the cannabinoid-sensitive genes in mice. These genes co-expressed with those specific to astrocytes, microglia and a type of pyramidal cells enriched in dendrite-regulating genes. Experimentation with cannabis during adolescence may influence cortical thickness via synaptic processes and dendritic arborization.

Identification of autophagy-related signatures in doxorubicin-induced cardiotoxicity

PurposeDoxorubicin is an antibiotic drug used clinically to treat infectious diseases and tumors. Unfortunately, it is cardiotoxic. Autophagy is a cellular self-decomposition process that is essential for maintaining homeostasis in the internal environment. Accordingly, the present study was proposed to characterize the autophagy-related signatures of doxorubicin-induced cardiotoxicity. MethodsDatasets related to doxorubicin-induced cardiotoxicity were retrieved by searching the GEO database and differentially expressed genes (DEGs) were identified. DEGs were taken to intersect with autophagy-related genes to obtain autophagy-related signatures, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein-protein interaction (PPI) network were performed on them. Further, construction of miRNA-hub gene networks and identification of target drugs to reveal potential molecular mechanisms and therapeutic strategies. Animal models of doxorubicin-induced cardiotoxicity were constructed to validate differences in gene expression for autophagy-related signatures. ResultsPBMC and heart samples from the GSE37260 dataset were selected for analysis. There were 995 and 2357 DEGs in PBMC and heart samples, respectively, and they had 23 intersecting genes with autophagy-related genes. RT-qPCR confirmed the differential expression of 23 intersecting genes in doxorubicin-induced cardiotoxicity animal models in general agreement with the bioinformatics results. An autophagy-related signatures consisting of 23 intersecting genes is involved in mediating processes and pathways such as autophagy, oxidative stress, apoptosis, protein ubiquitination and phosphorylation. Moreover, Akt1, Hif1a and Mapk3 are hub genes in autophagy-associated signatures and their upstream miRNAs are mainly rno-miR-1188-5p, rno-miR-150-3p and rno-miR-326-3p, and their drugs are mainly CHEMBL55802, Carboxyamidotriazole and 3-methyladenine. ConclusionThis study identifies for the first-time autophagy-related signatures in doxorubicin's cardiotoxicity, which could provide potential molecular mechanisms and therapeutic strategies for doxorubicin-induced cardiotoxicity.

Therapeutic Potential of PLK1, KIF4A, CDCA5, UBE2C, CDT1, SKA3, AURKB, and PTTG1 Genes in Triple-Negative Breast Cancer: Correlating Their Expression with Sensitivity to GSK 461364 and IKK 16 Drugs.

The treatment of triple-negative breast cancer (TNBC) has been associated with challenges due to the lack of expression of ER, PR, and HER2 receptors in tumor cells. This study aimed to identify genes with potential therapeutic targets in TNBC. Data from the cancer genome atlas regarding breast cancer (BC) were downloaded. After initial preprocessing, cancer samples were categorized into four groups: TNBC, HER2-positive, luminal A, and luminal B. Gene expression differences between these groups were calculated, focusing on genes that showed differential expression in TNBC. A protein-protein interaction network was conducted to identify hub genes among the candidate genes related to TNBC. The protein expression of candidate genes was assessed using immunohistochemistry data from the human protein atlas. Drug resistance and sensitivity associated with hub genes were identified using data from PharmacoDB. TNBC samples and the RT-qPCR method were used to confirm the results. Our findings revealed that eight genes, namely PLK1, KIF4A, CDCA5, UBE2C, CDT1, SKA3, AURKB, and PTTG1, had significant upregulation at the RNA level in TNBC subgroup compared to other subgroups and could be considered hub genes in TNBC. Compared to other subgroups, their expression level in TNBC samples had high sensitivity and specificity. RT-qPCR results also demonstrated a significant increase in levels of SKA3 and PTTG1 in the TNBC compared to healthy tissue and other subgroups. The protein expression of these genes was notably high in some BC samples. PharmacoDB data showed that some candidate genes were closely linked to drug sensitivity of GSK 461364 and IKK 16. The results of this study showed a significant increase in the expression level of PLK1, KIF4A, CDCA5, UBE2C, CDT1, SKA3, AURKB, and PTTG1 in TNBC compared to other BC subgroups. These genes show considerable promise as therapeutic targets for the TNBC subgroup.

Unveiling the power of optimism: Exploring behavioral and neuromolecular correlates of alcohol seeking and drinking in rats with biased judgement

Alcohol use disorder (AUD) is a common psychiatric condition with substantial global mortality. Despite extensive research into its pathophysiology, the cognitive predispositions driving alcohol dependence are less understood. This study explores whether biased cognition, specifically traits of optimism and pessimism, predicts susceptibility to alcohol-seeking behaviors using an animal model.Rats were initially tested for judgement bias through Ambiguous Cue Interpretation tests. Those identified as ‘optimistic' or ‘pessimistic' were further examined for their tendency to escalate alcohol intake using the intermittent access 2-bottle choice (2BC) paradigm. Additionally, we assessed how judgement bias influenced the development of compulsive alcohol-seeking behavior in a Seeking-Taking (ST) and Seeking-Taking Punishment tasks, alcohol-seeking motivation in the Progressive Ratio Schedule of Reinforcement paradigm, the speed of extinction, and reinstatement after abstinence. Neurochemical analyses were conducted to investigate trait-specific differences in neurotransmitter-related gene expression and receptor densities in the brain. We used TaqMan Gene Expression Array Cards to analyze expression levels of genes linked to serotonergic, dopaminergic, glutamatergic, and GABAergic pathways, and alcohol metabolism in various brain regions. Receptor densities for 5-HT1A, 5-HT2A, and D2 were measured using autoradiography analysis.Behaviorally, ‘optimistic' rats showed significantly lower alcohol consumption in the 2BC paradigm compared to ‘pessimistic' rats. This lowered intake correlated with decreased monoamine oxidase-A (Maoa) expression in the medial prefrontal cortex (mPFC) and increased metabotropic glutamate receptor 2 (Grm2) expression in the amygdala (Amy). Additionally, we observed significant interactions between judgement bias and alcohol intake in the expression of several genes in the mPFC, nucleus accumbens (Nacc), orbitofrontal cortex (OFC), and Amy, as well as in 5-HT2A receptor binding in the Nacc.Overall, these results suggest that optimism is linked to lower alcohol consumption and related neurochemical changes, indicating a potential cognitive mechanism in AUD risk.

CytoKernel: Robust kernel embeddings for assessing differential expression of single cell data.

High-throughput sequencing of single-cell data can be used to rigorously evlauate cell specification and enable intricate variations between groups or conditions. Many popular existing methods for differential expression target differences in aggregate measurements (mean, median, sum) and limit their approaches to detect only global differential changes. We present a robust method for differential expression of single-cell data using a kernel-based score test, cytoKernel. cytoKernel is specifically designed to assess the differential expression of single cell RNA sequencing and high-dimensional flow or mass cytometry data using the full probability distribution pattern. cytoKernel is based on kernel embeddings which employs the probability distributions of the single cell data, by calculating the pairwise divergence/distance between distributions of subjects. It can detect both patterns involving aggregate changes, as well as more elusive variations that are often overlooked due to the multimodal characteristics of single cell data. We performed extensive benchmarks across both simulated and real data sets from mass cytometry data and single-cell RNA sequencing. The cytoKernel procedure effectively controls the False Discovery Rate (FDR) and shows favourable performance compared to existing methods. The method is able to identify more differential patterns than existing approaches. We apply cytoKernel to assess gene expression and protein marker expression differences from cell subpopulations in various publicly available single-cell RNAseq and mass cytometry data sets. The methods described in this paper are implemented in the open-source R package cytoKernel, which is freely available from Bioconductor at \url{http://bioconductor.org/packages/cytoKernel}.

Placental homogeneity: Characterizing transcriptional variation among equine chorioallantoic locations

The proper function of the placenta is essential for the health and growth of the fetus and the mother. The placenta relies on dynamic gene expression for its correct and timely development and function. Although numerous studies have identified genes vital for placental functions, equine placental molecular research has primarily focused on single placental locations, in sharp contrast with the broader approach in human studies. Here, we hypothesized that the molecular differences across different regions of the equine placenta are negligible because of its diffuse placental type with a macroscopic homogenous distribution of villi across the placental surface. We compared the transcriptome and stereological findings of the body, pregnant horn, and non-pregnant horn within the equine chorioallantois. Our transcriptomic analysis indicates that the variation between regions of the placenta within individuals is less than the variation observed between individuals. A low number of differentially expressed genes (DEGs) (n = 8) was identified when comparing pregnant and non-pregnant horns within the same placenta, suggesting a remarkable molecular uniformity. A higher number of DEGs was identified when comparing each horn to the body (193 DEGs comparing pregnant horn with body and 207 DEGs comparing non-pregnant horn with body). Genes with a higher expression in the body were associated with processes such as extracellular matrix synthesis and remodeling, which is relevant for placental maturation and placenta-endometrial separation at term and implies asynchrony of these processes across locations. The stereological analysis showed no differences in microcotyledonary density, and width between the locations. However, we observed a greater chorioallantoic thickness in the body and pregnant horn compared to the non-pregnant horn. Overall, our findings reveal a uniform transcriptomic profile across the placental horns, alongside a more distinct gene expression pattern between the uterine body and horns. These regional differences in gene expression suggest a different pace in the placental maturation and detachment among the placental locations.

In Situ Analyses of Placental Inflammatory Response to SARS-CoV-2 Infection in Cases of Mother-Fetus Vertical Transmission.

It has been shown that vertical transmission of the SARS-CoV-2 strain is relatively rare, and there is still limited information on the specific impact of maternal SARS-CoV-2 infection on vertical transmission. The current study focuses on a transcriptomics analysis aimed at examining differences in gene expression between placentas from mother-newborn pairs affected by COVID-19 and those from unaffected controls. Additionally, it investigates the in situ expression of molecules involved in placental inflammation. The Papa Giovanni XXIII Hospital in Bergamo, Italy, has recorded three instances of intrauterine transmission of SARS-CoV-2. The first two cases occurred early in the pandemic and involved pregnant women in their third trimester who were diagnosed with SARS-CoV-2. The third case involved an asymptomatic woman in her second trimester with a twin pregnancy, who unfortunately delivered two stillborn fetuses due to the premature rupture of membranes. Transcriptomic analysis revealed significant differences in gene expression between the placentae of COVID-19-affected mother/newborn pairs and two matched controls. The infected and control placentae were matched for gestational age. According to the Benjamani-Hochberg method, 305 genes met the criterion of an adjusted p-value of less than 0.05, and 219 genes met the criterion of less than 0.01. Up-regulated genes involved in cell signaling (e.g., CCL20, C3, MARCO) and immune response (e.g., LILRA3, CXCL10, CD48, CD86, IL1RN, IL-18R1) suggest their potential role in the inflammatory response to SARS-CoV-2. RNAscope® technology, coupled with image analysis, was utilized to quantify the surface area covered by SARS-CoV-2, ACE2, IL-1β, IL-6, IL-8, IL-10, and TNF-α on both the maternal and fetal sides of the placenta. A non-statistically significant gradient for SARS-CoV-2 was observed, with a higher surface coverage on the fetal side (2.42 ± 3.71%) compared to the maternal side (0.74 ± 1.19%) of the placenta. Although not statistically significant, the surface area covered by ACE2 mRNA was higher on the maternal side (0.02 ± 0.04%) compared to the fetal side (0.01 ± 0.01%) of the placenta. IL-6 and IL-8 were more prevalent on the fetal side (0.03 ± 0.04% and 0.06 ± 0.08%, respectively) compared to the maternal side (0.02 ± 0.01% and 0.02 ± 0.02%, respectively). The mean surface areas of IL-1β and IL-10 were found to be equal on both the fetal (0.04 ± 0.04% and 0.01 ± 0.01%, respectively) and maternal sides of the placenta (0.04 ± 0.05% and 0.01 ± 0.01%, respectively). The mean surface area of TNF-α was found to be equal on both the fetal and maternal sides of the placenta (0.02 ± 0.02% and 0.02 ± 0.02%, respectively). On the maternal side, ACE-2 and all examined interleukins, but not TNF-α, exhibited an inverse mRNA amount compared to SARS-CoV-2. On the fetal side, ACE-2, IL-6 and IL-8 were inversely correlated with SARS-CoV-2 (r = -0.3, r = -0.1 and r = -0.4, respectively), while IL-1β and IL-10 showed positive correlations (r = 0.9, p = 0.005 and r = 0.5, respectively). TNF-α exhibited a positive correlation with SARS-CoV-2 on both maternal (r = 0.4) and fetal sides (r = 0.9) of the placenta. Further research is needed to evaluate the correlation between cell signaling and immune response genes in the placenta and the vertical transmission of SARS-CoV-2. Nonetheless, the current study extends our comprehension of the molecular and immunological factors involved in SARS-CoV-2 placental infection underlying maternal-fetal transmission.

Influence of incubation temperature on embryonic Days 4–7 on gene expression, M. pectoralis and M. gastrocnemius microstructure, and tibia characteristics in Ross 308 Broilers

ABSTRACT The incubation temperature can influence chicken bone and muscle development, and breast and leg muscles may respond differently to changes therein. Ross 308 broiler eggs were incubated at 36.5°C, 37.5°C (control), 38.5°C and 39.0°C on embryonic days 4–7. M. pectoralis and M. gastrocnemius were sampled at hatching and 5 weeks post-hatching, and differences in gene expression, microstructure and energy metabolism were examined. Tibia strength was tested, and gait scoring was performed. Broiler performance was similar at slaughter age, but initial growth was slowed by the 36.5°C treatment. The 38.5°C treatment reduced the M. gastrocnemius weight and shifted the M. pectoralis/M. gastrocnemius ratio. All treatments reduced M. gastrocnemius glycogen content relative to the control. The expression of single myogenesis-related genes was altered in the M. pectoralis by 36.5°C. The results indicate that the incubation temperature influences broiler muscle energy metabolism, and that the temperature of 38.5°C hampers leg muscle development.

Tyrosine-protein kinase SYK-related gene signature in baseline immune cells associated with adjuvant immunotherapy-induced immune-related adverse events in melanoma.

Immune checkpoint inhibition (ICI) shows benefits in adjuvant (AT) and neoadjuvant (NAT) melanoma treatments. However, ICI frequently induces severe immune-related adverse events (irAEs). Unlike metastatic disease, where irAEs are a clinical trade-off for treatment that improves survival, the toxicity burden from ICI in AT is a substantial clinical problem urging for irAE-predictive biomarkers. We assessed post-surgical, pre-ICI treatment peripheral CD4+ and CD8+ T cells from clinical trial patients (CheckMate-915) treated with AT nivolumab (NIVO, n=130) or ipilimumab/nivolumab (COMBO, n=82). Performing RNA-seq differential gene expression analysis we tested baseline differences associated with severe (grade 3-5) irAEs and constructed an irAE-predictive model using LASSO-regularized logistic regression. The analysis of predicted protein-protein interactions among differentially expressed genes (DEGs) in peripheral CD4+ cells revealed significant enrichment of the spleen tyrosine kinase (SYK) pathway, associated with severe irAEs in COMBO-treated patients. This gene-expression signature predicted severe-irAE COMBO patients (chi-square p-value=0.001) with 73% accuracy and was independent of disease recurrence (p=0.79). The irAE-predictive model incorporating this gene-expression signature demonstrated 82% accuracy (chi-square p-value=8.91E-06). We identified baseline gene-expression differences in key immune pathways of peripheral blood T cells from COMBO-treated patients with grade 3-5 irAEs, and defined a SYK-related gene signature correctly identifying ~60% of COMBO-treated patients with grade 3-5 irAE. This finding aligns with our previous work linking anti-CTLA-4 irAEs with a germline variant associated with high SYK expression. This gene signature may serve as a baseline biomarker of severe grade 3-5 irAE risk, which is especially important in AT.

Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling.

Merkel cell polyomavirus (MCPyV) is the causative agent of the majority of Merkel cell carcinomas (MCC). The virus has limited coding capacity, with its early viral proteins, large T (LT) and small T (sT), being multifunctional and contributing to infection and transformation. A fundamental difference in early viral gene expression between infection and MCPyV-driven tumorigenesis is the expression of a truncated LT (LTtr) in the tumor. In contrast, sT is expressed in both conditions and contributes significantly to oncogenesis. Here, we identified novel functions of early viral proteins by performing genome-wide transcriptome and chromatin studies in primary human fibroblasts. Due to current limitations in infection and tumorigenesis models, we mimic these conditions by ectopically expressing sT, LT or LTtr, individually or in combination, at different time points. In addition to its known function in cell cycle and inflammation modulation, we reveal a fundamentally new function of sT. We show that sT regulates the type I interferon (IFN) response downstream of the type I interferon receptor (IFNAR) by interfering with the interferon-stimulated gene factor 3 (ISGF3)-induced interferon-stimulated gene (ISG) response. Expression of sT leads to a reduction in the expression of interferon regulatory factor 9 (IRF9) which is a central component of the ISGF3 complex. We further show that this function of sT is conserved in BKPyV. We provide a first mechanistic understanding of which early viral proteins trigger and control the type I IFN response, which may influence MCPyV infection, persistence and, during MCC progression, regulation of the tumor microenvironment.

74 Unraveling the Complexities of Obesity in Clear Cell Renal Cell Carcinoma Carcinogenesis

Abstract Background Obesity has been identified as an established risk factor in the development of clear cell renal cell carcinoma (ccRCC). ccRCC arises from the proximal convoluted tubule (PCT) of the kidney which is also the site of obesity-associated chronic kidney disease. Obesity can lead to chronic cellular insults which may lead to DNA injury and whether these mechanisms are critical to cancer initiation in the kidney is unclear. One potential way that obesity can lead to cancer is by altering lipid metabolism, including increasing circulating saturated fatty acids. In particular, palmitic acid is known to be lipotoxic to proximal tubules of the kidney. Understanding how free fatty acids initiate cancer is critical to understanding the role of obesity in cancer initiation and development. We hypothesize that chronic injury and repair due to excess FFA exposure could lead to ccRCC carcinogenesis and aim to define the metabolic phenotype of obesity associated ccRCC. Methods Using publicly available data from The KIRC Cancer Genome Atlas Program (TCGA) and clinicopathologic data, we compared the RNAseq profiles of obese (BMI >= 30) to normal weight (BMI =< 25) sample origins. Of the 337, a total of 333 had BMI available for analysis. We evaluated differences in Hallmark and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Using DESeq, we adjusted for age and sex. In vitro, HK PCT cells were cultured in DMEM+10%FBS treated with bovine serum albumin (BSA)-palmitic acid complex for 48 hrs. We measured cell viability using Alamar Blue. Results were normalized to controls with BSA only. We extracted protein and performed western blots to identify DNA damage (pATM, H2AX) and endoplasmic reticulum stress (ATF4, eFI2alpha). Results Most of the patients in our clinical data cohort are male (64.4%), while 45.4% of patients are categorized by BMI as obese and 33.2% are categorized as normal. We utilized 333 individuals from the Kyoto Encyclopedia of Genes and Genomes (KEGG) to link genomic information to pathways associated with fatty acid metabolism as well as other cancer-associated hallmark metabolic pathways. We confirmed that excess free fatty acid supplementation leads to decreased cell viability in renal proximal tubule cells and renal embryonal cells and aim to assess differences in gene expression and metabolomic variation with fatty acid supplementation. Conclusions Through the investigation of these questions, we hope to improve understanding of obesity associated ccRCC and ultimately impact oncological outcomes for patients with this cancer. Understanding changes in lipid metabolism around ccRCC initiation will help identify novel pathways for pharmacologic intervention at earlier stages of the disease. DOD CDMRP Funding: yes

Identification and validation of genes associated with prognosis of cisplatin-resistant ovarian cancer

PurposeTo investigate the role of prognostic genes related to cisplatin resistance in ovarian cancer during disease progression.MethodThe gene expression profile of the NCI-60 cell line was acquired through comprehensive analysis of the GEO database accession GSE116439. We performed a thorough analysis of gene expression differences in samples from seven individuals exposed to cisplatin concentrations of 0 nM compared to seven samples exposed to 15000 nM over a 24-h period. Key genes were initially identified through LASSO regression, followed by their enrichment through differential gene function analysis (GO) and pathway enrichment analysis (KEGG). Subsequently, a prognostic risk model was established for these key genes. The prognostic model's performance was assessed through K-M survival curves and ROC curves. To examine the variance in immune cell infiltration between the high and low-risk groups, CIBERSORTx analysis was employed. Finally, validation of prognostic gene expression in cisplatin-resistant ovarian cancer was carried out using clinical samples, employing RT-qPCR and Western Blot techniques.ResultsA total of 132 differential genes were found between cisplatin resistance and control group, and 8 key prognostic genes were selected by analysis, namely VPS13B, PLGRKT, CDKAL1, TBC1D22A, TAP1, PPP3CA, CUX1 and PPP1R15A. The efficacy of the risk assessment model derived from prognostic biomarkers, as indicated by favorable performance on both Kaplan–Meier survival curves and ROC curves. Significant variations in the abundance of Macrophages M1, T cells CD4 memory resting, T cells follicular helper, and T cells gamma delta were observed between the high and low-risk groups. To further validate our findings, RT-qPCR and Western Blot analyses were employed, confirming differential expression of the identified eight key genes between the two groups.ConclusionVPS13B, TBC1D22A, PPP3CA, CUX1 and PPP1R15A were identified as poor prognostic genes of cisplatin resistance in ovarian cancer, while PLGRKT, CDKAL1 and TAP1 were identified as good prognostic genes. This offers a novel perspective for future advancements in ovarian cancer treatment, suggesting potential avenues for the development of new therapeutic targets.

Bespoke strategies of Paxillus involutus to extract potassium from diverse phyllosilicates

Phyllosilicates provide a primary source of minerals used by microorganisms and plants, particularly clay minerals, i.e., phyllosilicates of very small particle size. Fungi can actively break down (or “weather”) minerals to extract nutrients, but whether they use identical mechanisms when accessing different clay minerals is unclear. In addition, it is yet to be understood whether starvation stresses due to the limited availability of a mineral-nutrient would result in different weathering behaviours of microbes.Here, we performed a microcosm experiment to address these questions. We used the ectomycorrhizal basidiomycete Paxillus involutus and the phyllosilicates K-vermiculite, muscovite and phlogopite. These silicates have different degrees of recalcitrance to the removal of K cations from the mineral, and each was provided in the microscosm experiment as the sole potassium (K) source. The type of potassium "extraction-assimilation" was tested against a potassium-availability gradient, with a situation of maximum starvation stress (no potassium availability) and one of maximum availability (potassium provided as a solute in the culture medium). Our study revealed that different phyllosilicate minerals stimulated different patterns of fungal gene expression, which indicated bespoke weathering mechanisms for different phyllosilicates. The potassium uptake capacity of the fungus was highest with K-vermiculite compared to phlogopite and muscovite. Interestingly, the assimilation of phosphorus by the fungus was reduced in K-depleted conditions.Moreover, the potassium deprivation condition prompted the fungus to assimilate sodium instead. Also, in the presence of the minerals, the fungus showed significant differences in gene expression compared with the negative and positive control conditions, suggesting that the mineral environment modulates the starvation stress levels. The nutrients assimilated by the mycelium from both the minerals and the culture medium also varied according to the type of silicate added and the K starvation level to which the fungus was subjected. Based on what has been observed here, many geochemical processes could depend on fungi's genetic and functional plasticity, which would have considerable environmental consequences with a direct link between the evolution of fungi and that of the Earth's crust.

Sex differences in gene expression of nutrient transporters in the placenta of rats subjected to high-intensity resistance training associated with an obesogenic diet

Sex differences in gene expression of nutrient transporters in the placenta of rats subjected to high-intensity resistance training associated with an obesogenic diet