Pathway Genes Research Articles

An Oxidative Stress Study on Curcumin and NanoCurcumin against Aluminum Phosphide-induced Kidney Injury in Rats: The Role of SIRT1/FOXO3 Signaling Pathway in Nephrotoxicity.

In this study, we have investigated the aluminium phosphide (ALP) toxicity on Renal Function and oxidative stress in kidney tissue of male rats and the possible protective role of Curcumin and nanoCurcumin against ALP-induced nephrotoxicity. Thirty-six adult male rats were divided into 6 groups (n=6). ALP (2 mg/kg oral administration) and control groups received Curcumin and nanoCurcumin (oral administration 100 mg/kg) or without it. After seven days of treatment, kidney parameters, oxidative stress biomarkers, and expression level of sirtuins1 (SIRT1)/Forkhead box protein O1 (FoxO1) pathway genes were evaluated in kidney tissue. In addition, histopathological changes in the kidney tissues were assayed. In the ALP group, compared to the control group, lipid peroxidation levels, urea, and creatinine were increased, and total antioxidant capacity and thiol groups decreased significantly p < 0.05. In Curcumin and nanoCurcumin groups compared to the ALP group, lipid peroxidation and creatinine decreased significantly p < 0.05. Also, Curcumin and nanoCurcumin improved the tissue damage caused by ALP. NanoCurcumin modulated the effect of ALP on the gene expression levels in SIRT1/FoxO1. The present study showed that ALP intoxication in kidney tissue can induce oxidative damage. Moreover, Curcumin and nanocurcumin, as potential antioxidants, can be effective therapeutics in ALP-induced nephrotoxicity.

From genes to color: Evolutionary insights and mechanistic pathways of the yellow gene in insect pigmentation

Insect pigmentation plays a vital role in ecology and evolution, influencing survival, mate attraction, and communication. This review examines the complex mechanisms governing insect coloration, focusing on the roles of pigments (melanins and carotenoids) and structural colors. Specifically, the yellow gene in Drosophila is highlighted for its critical function in melanin biosynthesis and its evolutionary implications. Variations in the yellow gene's expression and regulation, influenced by both cis- and trans-regulatory elements, contribute to the phenotypic diversity of pigmentation patterns across insect species. The interplay between developmental genes and the yellow gene further illustrates how subtle genetic changes drive morphological diversity. While advances in CRISPR and other genetic tools have enhanced our understanding of pigmentation, challenges remain in deciphering the gene’s complex interactions and the influence of environmental factors. Future research should focus on refining genomic techniques, exploring environmental impacts on pigmentation, and utilizing single-cell omics to gain deeper insights into the regulatory networks governing the yellow gene. This comprehensive understanding of insect pigmentation will not only enrich our knowledge of biodiversity but also inform conservation and biotechnological innovations.

Subset-specific mitochondrial stress and DNA damage shape T cell responses to fever and inflammation

Heat is a cardinal feature of inflammation, yet its impacts on immune cells remain uncertain. We show that moderate-grade fever temperatures (39°C) increased murine CD4 T cell metabolism, proliferation, and inflammatory effector activity while decreasing regulatory T cell suppressive capacity. However, heat-exposed T helper 1 (T H 1) cells selectively developed mitochondrial stress and DNA damage that activated Trp53 and stimulator of interferon genes pathways. Although many T H 1 cells subjected to such temperatures died, surviving T H 1 cells exhibited increased mitochondrial mass and enhanced activity. Electron transport chain complex 1 (ETC1) was rapidly impaired under fever-range temperatures, a phenomenon that was specifically detrimental to T H 1 cells. T H 1 cells with elevated DNA damage and ETC1 signatures were also detected in human chronic inflammation. Thus, fever-relevant temperatures disrupt ETC1 to selectively drive apoptosis or adaptation of T H 1 cells to maintain genomic integrity and enhance effector functions.

Molecular and physiological mechanisms of aging are distinct in the cardiac right and left ventricles

AbstractAging is the primary risk factor for heart disease, the leading global cause of death. Right ventricular (RV) function predicts survival in several age‐related clinical contexts, yet no therapies directly improve RV function, in large part due to a poor mechanistic understanding of RV aging and how it is distinct from the widely studied left ventricle (LV). To address this gap, we comprehensively quantified RV functional and morphological remodeling with age. We further aimed to identify molecular mechanisms of RV aging thus we performed RNAseq on RV and LV from male and female young (4 months) and aged (19–21 months) C57BL6 mice. Contrary to the concentric hypertrophic remodeling and diastolic dysfunction that occurs in the LV, the aging RV underwent eccentric remodeling with significant dilation and impaired systolic function. Transcriptomic data were also consistent with ventricle‐specific aging, with few genes (13%) similarly shared between ventricles with aging. KEGG analysis identified shared aging genes in inflammatory and immune cell pathways that were confirmed by flow cytometry that demonstrated higher percent of GR1+ myeloid cells in both ventricles. Unique RV aging genes enriched in the biosynthesis of saturated fatty acids, PPAR signaling, and butanoate metabolism, and we identified putative novel RV‐specific aging genes. Together, we suggest that the RV and LV are unique cardiac chambers that undergo distinct remodeling with age. These robust differences may explain why therapies designed from LV‐based studies fail to improve RV function and suggest that future efforts emphasizing ventricular differences may elucidate new therapies for healthy cardiac aging.

Transcriptional Patterns in Stages of Alzheimer's Disease are Cell Type Specific and Partially Converge with the Effects of Alcohol Use Disorder in Humans

Advances in single cell technologies have led to the discovery and characterization of new brain cell-types, that in turn lead to a better understanding of the pathogenesis of Alzheimer’s disease (AD). Here, we present a detailed analysis of single nucleus (sn)RNA-seq data for three stages of AD from middle temporal gyrus (MTG) and compare it with snRNA-seq data from the prefrontal cortices from individuals with alcohol use disorder (AUD). We observed a significant decrease in both inhibitory and excitatory neurons, in general agreement with previous reports. We observed several cell-type specific gene expressions and pathways dysregulations that delineate AD stages. Endothelial and VLMCs (vascular leptomeningeal cells) showed the greatest degree of gene expression changes. Cell-type specific evidence of neurodegeneration was seen in multiple neuronal cell-types particularly in SST (somatostatin) and L5 ET (layer-5 extra-telencephalic) neurons, among others. Evidence of inflammatory responses were seen in non-neuronal cells, particularly in intermediate and advanced AD. We observed common perturbations in AD and AUD, particularly in pathways, like transcription, translation, apoptosis, autophagy, calcium signaling, neuroinflammation, and phosphorylation, that imply shared transcriptional pathogenic mechanisms and support a role for excessive alcohol intake in AD progression. Major AUD gene markers form and perturb a network of genes significantly associated with intermediate and advanced AD. Master regulator analysis from AUD gene markers revealed significant correlation with advanced AD of transcription factors that have implications in intellectual disability, neuroinflammation, and other neurodegenerative conditions, further suggesting a shared nexus of transcriptional changes between AD and AUD.Significance StatementThis study holds significant implications for understanding the intricate molecular landscape of Alzheimer's disease (AD) and its intersection with alcohol use disorder (AUD). By profiling transcriptional changes in the neocortex associated with AD progression and comparing them with those in AUD, we shed light on shared gene expression and pathway dysregulations between the two conditions. Our findings corroborate prior research on neuronal depletion and highlight novel insights into cell-type-specific gene expression patterns in AD stages. Moreover, the identification of common genetic signatures suggests a potential exacerbating effect of AUD on AD progression. This comprehensive analysis not only deepens our understanding of AD pathology but also underscores the importance of considering AUD as a potential risk factor for accelerating AD onset or severity.

Screening and identification of susceptibility genes for cervical cancer via bioinformatics analysis and the construction of an mitophagy-related genes diagnostic model

PurposeThis study aims to utilize bioinformatics methods to systematically screen and identify susceptibility genes for cervical cancer, as well as to construct and validate an mitophagy-related genes (MRGs) diagnostic model. The objective is to increase the understanding of the disease’s pathogenesis and improve early diagnosis and treatment.MethodWe initially collected a large amount of genomic data, including gene expression profile and single nucleotide polymorphism (SNP) data, from the control group and Cervical cancer (CC) patients. Through bioinformatics analysis, which employs methods such as differential gene expression analysis and pathway enrichment analysis, we identified a set of candidate susceptibility genes associated with cervical cancer.ResultsMRGs were extracted from single-cell RNA sequencing data, and a network graph was constructed on the basis of intercellular interaction data. Furthermore, using machine learning algorithms, we constructed a clinical prognostic model and validated and optimized it via extensive clinical data. Through bioinformatics analysis, we successfully identified a group of genes whose expression significantly differed during the development of CC and revealed the biological pathways in which these genes are involved. Moreover, our constructed clinical prognostic model demonstrated excellent performance in the validation phase, accurately predicting the clinical prognosis of patients.ConclusionThis study delves into the susceptibility genes of cervical cancer through bioinformatics approaches and successfully builds a reliable clinical prognostic model. This study not only helps uncover potential pathogenic mechanisms of cervical cancer but also provides new directions for early diagnosis and treatment of the disease.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. “Omics” and “Meta-omics” techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

BackgroundDecreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.ResultsWe observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.ConclusionsOur metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.

Astaxanthin Alleviates Hepatic Lipid Metabolic Dysregulation Induced by Microcystin-LR

Microcystin-LR (MC-LR), frequently generated by cyanobacteria, has been demonstrated to raise the likelihood of liver disease. Few previous studies have explored the potential antagonist against MC-LR. Astaxanthin (ASX) has been shown to possess various beneficial effects in regulating lipid metabolism in the liver. However, whether ASX could alleviate MC-LR-induced hepatic lipid metabolic dysregulation is as yet unclear. In this work, the important roles and mechanisms of ASX in countering MC-LR-induced liver damage and lipid metabolic dysregulation were explored for the first time. The findings revealed that ASX not only prevented weight loss but also enhanced liver health after MC-LR exposure. Moreover, ASX effectively decreased triglyceride, total cholesterol, aspartate transaminase, and alanine aminotransferase contents in mice that were elevated by MC-LR. Histological observation showed that ASX significantly alleviated lipid accumulation and inflammation induced by MC-LR. Mechanically, ASX could significantly diminish the expression of genes responsible for lipid generation (Srebp-1c, Fasn, Cd36, Scd1, Dgat1, and Pparg), which probably reduced lipid accumulation induced by MC-LR. Analogously, MC-LR increased intracellular lipid deposition in THLE-3 cells, while ASX decreased these symptoms by down-regulating the expression of key genes in the lipid synthesis pathway. Our results implied that ASX played a crucial part in lipid synthesis and effectively alleviated MC-LR-induced lipid metabolism dysregulation. ASX might be developed as a novel protectant against hepatic impairment and lipid metabolic dysregulation associated with MC-LR. This study offers new insights for further management of MC-LR-related metabolic diseases.

A combined transcriptomics and proteomics approach reveals S100A4 as a potential biomarker for Graves’ orbitopathy

BackgroundThere are no reliable biomarkers to identify Graves’ disease patients who will develop severe Graves’ orbitopathy (GO). We hypothesize that integrating various omics platforms can enhance our understanding of disease mechanisms and uncover potential biomarkers. This study aimed to (1) elucidate the differential gene expression profile of orbital fibroblasts in GO during early adipogenesis to better understand disease mechanisms and (2) compare tear protein profiles from our earlier study and the transcriptome profiles of orbital fibroblasts (OFs) to identify possible biomarkers of the disease.MethodsOFs were grown from orbital adipose tissue obtained from nine GO patients (three for discovery and six for validation experiments). Total RNA was extracted from OFs on day 0 as the baseline for each sample and from differentiated OFs on days 4 and 8. Protein–protein interaction (PPI) analysis and functional enrichment analysis were also carried out. The differentially expressed genes (DEGs) from the RNA sequencing experiments were then compared to the full tear proteome profile from the author’s previous study, which examined the tear protein changes of GO patients based on fold change &amp;gt; 1.6 or &amp;lt; −1.6. FDR &amp;lt; 0.05 was applied within all datasets. Further validation of S100 calcium-binding protein A4 (S100A4) downregulation in GO was performed via quantitative real-time PCR (qPCR).ResultsThe whole transcriptomic analysis revealed 9 upregulated genes and 15 downregulated genes in common between the discovery and validation experiments. From the PPI network analysis, an interaction network containing six identified DEGs (ALDH2, MAP2K6, MT2A, SOCS3, S100A4, and THBD) was observed. The functional enrichment network analysis identified a set of genes related to oxysterol production. S100A4 was found to be consistently downregulated in both our transcriptome studies and the full-tear proteome profile from the author’s previous study.ConclusionOur study identified several DEGs and potential gene pathways in GO patients, which concurred with the results of other studies. Tear S100A4 may serve as a biomarker for the propensity to develop thyroid eye disease (TED) in patients with autoimmune thyroid disease (AITD) before clinical manifestation and should be confirmed in future studies.

Histone deacetylase HDAC3 regulates ergosterol production for oxidative stress tolerance in the entomopathogenic and endophytic fungus Metarhizium robertsii.

Oxidative stress is encountered by fungi in almost all niches, resulting in fungal degeneration or even death. Fungal tolerance to oxidative stress has been extensively studied, but the current understanding of the mechanisms regulating oxidative stress tolerance in fungi remains limited. The entomopathogenic and endophytic fungus Metarhizium robertsii encounters oxidative stress when it infects insects and develops a symbiotic relationship with plants, and we found that host reactive oxygen species (ROSs) greatly limited fungal growth in both insects and plants. We identified a histone H3 deacetylase (HDAC3) that catalyzed the deacetylation of lysine 56 of histone H3. Deleting Hdac3 significantly reduced the tolerance of M. robertsii to oxidative stress from insects and plants, thereby decreasing fungal ability to colonize the insect hemocoel and plant roots. HDAC3 achieved this by regulating the expression of three genes in the ergosterol biosynthesis pathway, which includes the lanosterol synthase gene Las1. The deletion of Hdac3 or Las1 reduced the ergosterol content and impaired cell membrane integrity. This resulted in an increase in ROS accumulation in fungal cells that were thus more sensitive to oxidative stress. We further showed that HDAC3 regulated the expression of the three ergosterol biosynthesis genes in an indirect manner. Our work significantly advances insights into the epigenetic regulation of oxidative stress tolerance and the interactions between M. robertsii and its plant and insect hosts.IMPORTANCEOxidative stress is a common challenge encountered by fungi that have evolved sophisticated mechanisms underlying tolerance to this stress. Although fungal tolerance to oxidative stress has been extensively investigated, the current understanding of the mechanisms for fungi to regulate oxidative stress tolerance remains limited. In the model entomopathogenic and plant symbiotic fungus Metarhizium robertsii, we found that the histone H3 deacetylase HDAC3 regulates the production of ergosterol, an essential cell membrane component. This maintains the cell membrane integrity to resist the oxidative stress derived from the insect and plant hosts for successful infection of insects and development of symbiotic associates with plants. Our work provides significant insights into the regulation of oxidative stress tolerance in M. robertsii and its interactions with insects and plants.

Comparison of B-Cell Lupus and Lymphoma Using a Novel Immune Imbalance Transcriptomics Algorithm Reveals Potential Therapeutic Targets

Background/Objectives: Systemic lupus erythematosus (lupus) and B-cell lymphoma (lymphoma) co-occur at higher-than-expected rates and primarily depend on B cells for their pathology. These observations implicate shared inflammation-related B cell molecular mechanisms as a potential cause of co-occurrence. Methods: We consequently implemented a novel Immune Imbalance Transcriptomics (IIT) algorithm and applied IIT to lupus, lymphoma, and healthy B cell RNA-sequencing (RNA-seq) data to find shared and contrasting mechanisms that are potential therapeutic targets. Results: We observed 7143 significantly dysregulated genes in both lupus and lymphoma. Of those genes, we found 5137 to have a significant immune imbalance, defined as a significant dysregulation by both diseases, as analyzed by IIT. Gene Ontology (GO) term and pathway enrichment of the IIT genes yielded immune-related “Neutrophil Degranulation” and “Adaptive Immune System”, which validates that the IIT algorithm isolates biologically relevant genes in immunity and inflammation. We found that 344 IIT gene products are known targets for established and/or repurposed drugs. Among our results, we found 48 known and 296 novel lupus targets, along with 151 known and 193 novel lymphoma targets. Known disease drug targets in our IIT results further validate that IIT isolates genes with disease-relevant mechanisms. Conclusions: We anticipate the IIT algorithm, together with the shared and contrasting gene mechanisms uncovered here, will contribute to the development of immune-related therapeutic options for lupus and lymphoma patients.

Steroid hormone-deprived sex reversal in cyp11a1 mutant XX tilapia experiences an ovary-like stage at molecular level

Fish sex is largely influenced by steroid hormones, especially sex hormones. Here, we established a steroid hormone-free genetic model by mutation of cyp11a1 in Nile tilapia, which was confirmed by EIA assay. Gonadal phenotype and transcriptome analyses showed that the XX mutants displayed sex reversal from female to male but with defective spermatogenesis. Despite the sex reversal, the aromatase encoding gene cyp19a1a was continuously expressed in the gonads of the XX mutants, which might be caused by androgen deficiency. Whole-mount fluorescence in situ hybridization and transcriptome analysis showed that the gonads of the XX mutants firstly developed towards ovary but shifted to testis between 10 to 15 days after hatching. Detailed expression analysis of key sex differentiation pathway genes foxl3 and dmrt1 combined with apoptosis analysis revealed transdifferentiation of germ cells from female to male during sex reversal. Rescue experiments showed that both P5 and E2 treatment rescued the sex reversal of cyp11a1 mutant XX fish. Overall, our results revealed a transient ovary-like stage and transdifferentiation of germ cells from female to male in the early gonads of the steroid hormone-deprived cyp11a1 mutant XX fish.

A role for germline variants in multiple myeloma?

In Blood Cancer Discovery, Thibaud and colleagues report the incidence of pathogenic germline variants (PGVs) in multiple myeloma patients and that these are associated with DNA repair pathway genes including BRCA1 and BRCA2. They find an association of patients with PGVs and previous family or personal history of cancer and that these patients are diagnosed slightly earlier than those without PGVs. Patients with PGVs had a longer progression free survival than those without PGVs when they received high dose melphalan and autologous stem cell transplant, providing a therapeutic rationale for diagnostic germline testing in myeloma.

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation.

Abstract B082: Oncogenic KRAS-mediated epigenetic reprogramming is altered by loss of Activating Transcription Factor 3

Abstract Introduction: Over 90% of PDAC patients harbor an activating KRAS mutation, the most common form being KRASG12D. However, additional genetic mutations and environmental events, including chronic or hereditary pancreatitis, are needed for KRAS mutations to lead to PDAC. Our laboratory showed Activating Transcription Factor 3 (ATF3) was required for repressing genes that stabilize the mature acinar cell phenotype and for KRASG12D-driven progression to advanced PanIN lesions. However, ATF3 contributes to gene activation and repression and has been linked to numerous transcription factors and epigenetic mediators, and how ATF3 affects PDAC progression remains unknown. We hypothesize that KRASG12D promotes ATF3-driven histone acetylation in precursor PanINs lesions. Methods: C57Bl/6l mice allowing for acinar-inducible KRASG12D combined with (Ptf1acreERTKRASG12D) or without (Ptf1acreERTKRASG12DAtf3-/-; APK) Atf3 deletion were treated with tamoxifen to induce KRASG12D. After 10 days, mice were treated with cerulein to induce injury and PanIN progression. Mice were sacrificed after two weeks and 3D organoid lines developed. RNA-seq and chromatin immunoprecipitation for H3K27 acetylation (H3K27ac) followed by sequencing (ChIP-seq) was performed. Bioinformatic analysis was used to identify differentially enriched pathways. Levels of acetyl-CoA, the substrate for acetylation, was compared between lines along with levels of H3K27ac, H3K4me1, H3K4me3, and H3K9me3 through western blots. Results and Discussion: KRASG12D expression promoted epigenetic reprogramming in PanINs, including dysregulation of H3K27ac enrichment. ChIP-seq results showed the absence of ATF3 reduces H3K27 acetylation preferentially at gene promoters and pathway analysis showed differential enrichment and activation of KRAS signaling. Mechanistically, ATF3-deleted mice have lower acetyl-CoA levels, linking ATF3 to metabolic pathways as a possible mechanism for gene regulation. Comparing genes with an ATF3-dependent acetylation pattern to a curated list of KRAS-targeted genes identified SMARCC2 (BAF170), a SWI/SNF complex subunit, and KDM1B, a histone demethylase affecting H3K4, suggesting a potential role for ATF3 in widespread epigenetic regulation. Public sequencing data from PDAC patients, supports these findings as ATF3 expression is positively correlated with expression of several SWI/SNF complex subunits and demethylases. Conclusion: This study highlights a role for ATF3- mediated epigenetic dysregulatio. In oncogenic KRAS-dependent PDAC. Targeting this ATF3- mediated epigenetic landscape could be a promising new therapeutic avenue. Citation Format: Fatemeh Mousavi, Christopher L Pin, Parisa Shooshtari. Oncogenic KRAS-mediated epigenetic reprogramming is altered by loss of Activating Transcription Factor 3 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B082.

Acute exposure to electronic cigarette components alters mRNA expression of pre-osteoblasts.

The use of traditional nicotine delivery products such as tobacco has long been linked to detrimental health effects. However, little work to date has focused on the emerging market of aerosolized nicotine delivery known as electronic nicotine delivery systems (ENDS) or electronic cigarettes, and their potential for new effects on human health. Challenges studying these devices include heterogeneity in the formulation of the common components of most available ENDS, including nicotine and a carrier (commonly composed of propylene glycol and vegetable glycerin, or PG/VG). In the present study, we report on experiments interrogating the effects of major identified components in e-cigarettes. Specifically, the potential concomitant effects of nicotine and common carrier ingredients in commercial "vape" products are explored invitro to inform the potential health effects on the craniofacial skeleton through novel vectors as compared to traditional tobacco products. MC3T3-E1 murine pre-osteoblast cells were cultured invitro with clinically relevant liquid concentrations of nicotine, propylene glycol (PG), vegetable glycerin (VG), Nicotine+PG/VG, and the vape liquid of a commercial product (Juul). Cells were treated acutely for 24 h and RNA-Seq was utilized to determine segregating alteration in mRNA signaling. Influential gene targets identified with sparse partial least squares discriminant analysis (sPLS-DA) implemented in mixOmics were assessed using the PANTHER Classification system for molecular functions, biological processes, cellular components, and pathways of effect. Additional endpoint functional analyses were used to confirm cell cycle changes. The initial excitatory concentration (EC50) studied defined a target concentration of carrier PG/VG liquid that altered the cell cycle of the calvarial cells. Initial sPLS-DA analysis demonstrated the segregation of nicotine and non-nicotine exposures utilized in our invitro modeling. Pathway analysis suggests a strong influence of nicotine exposures on cellular processes including metabolic processes and response to stimuli including autophagic flux. Further interrogation of the individual treatment conditions demonstrated segregation by treatment modality (Control, Nicotine, Carrier (PG+VG), Nicotine+PG/VG) along three dimensions best characterized by: latent variable 1 (PLSDA-1) showing strong segregation based on nicotine influence on cellular processes associated with cellular adhesion to collagen, osteoblast differentiation, and calcium binding and metabolism; latent variable 2 (PLSDA-2) showing strong segregation of influence based on PG+VG and Control influence on cell migration, survival, and cycle regulation; and latent variable 3 (PLSDA-3) showing strong segregation based on Nicotine and Control exposure influence on cell activity and growth and developmental processes. Further, gene co-expression network analysis implicates targets of the major pathway genes associated with bone growth and development, particularly craniofacial (FGF, Notch, TGFβ, WNT) and analysis of active subnetwork pathways found these additionally overrepresented in the Juul exposure relative to Nicotine+PG/VG. Finally, experimentation confirmed alterations in cell count, and increased evidence of cell stress (markers of autophagy), but no alteration in apoptosis. These data suggest concomitant treatment with Nicotine+PG/VG drives alterations in pre-osteoblast cell cycle signaling, specifically transcriptomic targets related to cell cycle and potentially cell stress. Although we suspected cell stress and well as cytotoxic effects of Nicotine+PG/VG, no great influence on apoptotic factors was observed. Further RNA-Seq analysis allowed for the direct interrogation of molecular targets of major pathways involved in bone and craniofacial development, each demonstrating segregation (altered signaling) due to e-cigarette-type exposure. These data have implications directed toward ENDS formulation as synergistic effects of Nicotine+PG/VG are evidenced here. Thus, future research will continue to interrogate how varied formulation of Nicotine+PG/VG affects overall cell functions in multiple vital systems.

PSI-6 Early life programming of the bovine jejunum function in response to maternal vitamin and mineral supplementation

Abstract Despite the increased appreciation of the involvement of maternal nutrition in fetal development, its effects on jejunum programming remain largely unexplored. Here, we investigated the impact of maternal vitamin and mineral supplementation throughout gestation on the differential gene expression and underlying biological pathways in the jejunum of neonatal calves. For this, beginning 60 d before breeding and continuing throughout gestation, crossbred Angus heifers (n = 14) were fed either a basal diet (CON; n = 7) or the basal diet plus 113 g•heifer-1•d-1 of VTM supplement (VTM; n = 7). All heifers were gestating female calves, which were euthanized 30 h after birth. Samples of jejunum mucosa were collected, stored at -80°C, then subjected to total RNA isolation and RNA sequencing. After quality control, the reads were mapped using STAR aligner and differentially expressed genes (DEGs) were identified using DESeq2. Maternal VTM supplementation did not affect calf organ mass, including jejunum weight. However, high-resolution respirometry analysis revealed greater mitochondrial efficiency in jejunum of calves from VTM supplemented dams. Additionally, we identified 528 DEGs between the VTM and CON calves (P-value ≤ 0.05 and |log2FC| &amp;gt; 0.5). Among them, the genes IGFBP2 and IGFBP6, which are key genes in insulin pathway and involved in regulation of insulin-like growth factors (IGF), IGF transport, and uptake, were upregulated in the VTM group. Additional pathways were identified using ShinyGO, which included the pancreatic secretion pathway, over-represented by genes such as PLCB1, CCK, and SLC26A3. The gene PLCB1 has been associated with feed efficiency, growth, and carcass traits in multiple species. Likewise, the SLC26A3 gene encodes a key intestinal chloride anion exchanger associated with enhanced feed efficiency in cattle. Genes encoding signaling molecules involved with immune response, T cell activation, and defense response were also among the DEGs upregulated in the VTM calves, including the TNFSF18 and TNFRSF4 genes. Our findings suggest that maternal prenatal vitamin and mineral supplementation throughout gestation affects the expression of genes involved in the jejunum function of offspring at a neonatal time point. The long-term consequences of these changes, however, warrant further investigation.

PSIII-2 Exploring differential gene expression and pathways associated with pregnancy outcomes in beef heifers

Abstract Heifer fertility is a key factor in the success of beef production systems, as the reproductive performance of a heifer correlates with her stayability in the breeding herd. However, despite being reproductively mature and physically healthy, 5 to 15% of these heifers fail to conceive within a designated breeding season. The underlying physiological mechanisms preventing these heifers from achieving pregnancy remain elusive. Therefore, this study aimed to determine differentially expressed genes (DEGs) and biological pathways associated with pregnancy outcomes in beef heifers. Angus-Simmental crossbred heifers were subjected to an estrus synchronization and fixed-time artificial insemination (AI) program (7-d CO-Synch + CIDR) and blood samples were collected at the time of AI for isolation of peripheral white blood cells (PWBC). After pregnancy check, heifers were classified as pregnant (P) and non-pregnant (NP). Based on that, 6 animals per group were randomly selected for total RNA isolation from the PWBC samples, and genome-wide expression was measured through RNA sequencing. The RNA-Seq data were analyzed using an in-house bioinformatics pipeline, with filtered reads aligned to the Bos taurus reference genome using STAR. DEGs were identified using DESeq2, followed by functional analysis using ShinyGO. Our approach unveiled 230 DEGs, comprising 102 up and 128 downregulated genes in the NP group (P-value ≤ 0.05 and |log2FC| &amp;gt; 0.5). Upregulated genes included those from the cytochrome P450 superfamily (CYP27B1 and CYP2U1). The genes SCML2, USIG2, and FBP1 were upregulated and have been associated with immune response and increased PWBC counts. This may be related to the over-representation of biological processes involved in cell division based on the upregulated genes. KEGG pathway over-representation analysis of DEGs retrieved allograft rejection, graft-versus-host disease, type I Diabetes Mellitus, insulin signaling pathway, and transcriptional misregulation of cancer. These pathways included genes such as BOLA-DQB, PRKAR1B, CALML4 and JUP, which were reported as downregulated during times of inflammatory response. Another downregulated gene was GZMB, which is needed for proper cell targeting during immune response. This finding may provide a link between immune function and early pregnancy failure. However, the relationship between the immune system and pregnancy warrants further investigation. Our results shed light on the molecular mechanisms underlying reproductive performance in beef heifers and support previous studies associating immune function with pregnancy outcomes. These differentially expressed genes may be further explored as potential avenues for enhancing fertility in beef production systems.

Involvement of Aryl Hydrocarbon Receptor in Longevity and Healthspan: Insights from Humans, Mice, and C. elegans

In previous studies, using transcriptomic analysis, we observed higher levels of aryl hydrocarbon receptor (AHR) gene expression in the peripheral blood cells of centenarians compared to octogenarians. This suggests the potential significance of this receptor in maintaining physiological balance and promoting healthy aging, possibly linked to its critical role in detoxifying xenobiotics. In our current study, we confirmed that AHR expression is indeed higher in centenarians. We employed C. elegans as a model known for its suitability in longevity studies to explore whether the AHR pathway has a significant impact on lifespan and healthspan. Our survival assays revealed that two different mutants of AHR-1 exhibited lower longevity. Additionally, we used a mouse model to examine whether supplementation with pomegranate extract modulates the expression of AHR pathway genes in the liver. Furthermore, we studied a nutritional strategy based on pomegranate extract administration to investigate its potential modulation of life- and healthspan in worms.