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Liquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost‐effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine‐learning techniques are increasingly gaining attention in sample analysis, especially for multidimensional data such as RNA expression profiles. Yet, there is no agreement in the community on which methods are the most effective or how to process the data. To circumvent this, we performed a large‐scale study using various machine‐learning techniques. First, we took a closer look at existing datasets and filtered out some patients to assert data collection quality. The final data collection included platelet RNA samples acquired from 1397 cancer patients (17 types of cancer) and 354 asymptomatic, presumed healthy, donors. Then, we assessed an array of different machine‐learning models and techniques (e.g., feature selection of RNA transcripts) in pan‐cancer detection and multiclass classification. Our results show that simple logistic regression performs the best, reaching a 68% cancer detection rate at a 99% specificity level, and multiclass classification accuracy of 79.38% when distinguishing between five cancer types. In summary, by revisiting classical machine‐learning models, we have exceeded the previously used method by 5% and 9.65% in cancer detection and multiclass classification, respectively. To ease further research, we open‐source our code and data processing pipelines (https://gitlab.com/jopekmaksym/improving‐platelet‐rna‐based‐diagnostics), which we hope will serve the community as a strong baseline.

White adipocytes store energy, while brown and brite adipocytes release heat via nonshivering thermogenesis. In this study, we characterized two murine embryonic clonal preadipocyte lines, EB5 and EB7, each displaying unique gene marker expression profiles. EB5 cells differentiate into brown adipocytes, whereas EB7 cells into brite (also known as beige) adipocytes. To draw a comprehensive comparison, we contrasted the gene expression patterns, adipogenic capacity, as well as carbohydrate and lipid metabolism of these cells to that of F442A, a well‐known white preadipocyte and adipocyte model. We found that commitment to differentiation in both EB5 and EB7 cells can be induced by 3‐Isobutyl‐1‐methylxanthine/dexamethasone (Mix/Dex) and staurosporine/dexamethasone (St/Dex) treatments. Additionally, the administration of rosiglitazone significantly enhances the brown and brite adipocyte phenotypes. Our data also reveal the involvement of a series of genes in the transcriptional cascade guiding adipogenesis, pinpointing GSK3β as a critical regulator for both EB5 and EB7 adipogenesis. In a developmental context, we observe that, akin to brown fat progenitors, brite fat progenitors make their appearance in murine development by 11–12 days of gestation or potentially earlier. This result contributes to our understanding of adipocyte lineage specification during embryonic development. In conclusion, EB5 and EB7 cell lines are valuable for research into adipocyte biology, providing insights into the differentiation and development of brown and beige adipocytes. Furthermore, they could be useful for the characterization of drugs targeting energy balance for the treatment of obesity and metabolic diseases.

Abstract Given the extensive heterogeneity and variability, understanding cellular functions and regulatory mechanisms through the analysis of multi‐omics datasets becomes extremely challenging. Here, a comprehensive modeling framework of multi‐omics machine learning and metabolic network models are proposed that covers various cellular biological processes across multiple scales. This model on an extensive normalized compendium of Bacillus subtilis is validated, which encompasses gene expression data from environmental perturbations, transcriptional regulation, signal transduction, protein translation, and growth measurements. Comparison with high‐throughput experimental data shows that EM_iBsu1209‐ME, constructed on this basis, can accurately predict the expression of 605 genes and the synthesis of 23 metabolites under different conditions. This study paves the way for the construction of comprehensive biological databases and high‐performance multi‐omics metabolic models to achieve accurate predictive analysis in exploring complex mechanisms of cell genotypes and phenotypes.

ABSTRACT Background Quail is an efficient poultry species known for many years, and its productivity is highly affected by gastrointestinal function, health, digestion and commensal bacteria. Specific histological parameters and nutrient absorption–related genes could be used to study intestinal functionality and efficiency. Objectives This study aimed to evaluate the mRNA abundance of nutrient absorption–related genes and intestinal histology changes in laying Japanese quail during productive lifespan. Methods A total of 135 quails from a commercial flock at different egg production periods (early production [EP, 6 weeks of age], pick production [PP, 21 weeks of age] and post pick production [PPP, 40 weeks of age]) were randomly selected (n = 45/group) and kept for 6 weeks. Production performance was evaluated during last 2 weeks of the experimental period, and tissue samples were taken from the duodenum, jejunum and ileum for histological analysis and mRNA abundance purposes at the end of the experiment. The mRNA abundance of the CALB1, SGLT1, SGLT5, EAAT3 and NaPi‐IIb genes were compared among groups. Results Production period did not affect the eggshell thickness, goblet cell number and mRNA abundance of CALB1, EAAT3 and NaPi‐IIb (p > 0.05). The PPP quails had the highest egg weight and FCR compared to EP and PP quails (p

ABSTRACT Background The inclusion of synthetic amino acids in poultry nutrition plays a crucial role in both enhancing the synthesis of immunoglobulins and elevating the overall comprehensiveness of the amino acid profile. Objectives This research examined the effects of consuming threonine (Thr) in various forms levels with low or high oil on broiler chickens' growth and immunity. Methods We investigate the growth performance, feed efficiency, immune response, intestinal morphology, absorptive capacity, and expression of some genes related to the feed intake (Pro‐opiomelanocortin [POMC]), fatty acid synthesis (Acetyl‐CoA Carboxylase [ACC]), immunity (lipopolysaccharide‐induced tumour necrosis like alpha factor [LITAF]), and heat shock protein 70 (HSP70). Eight groups of chicks were used, including four dietary Thr levels (100%, 115%, 130%, or 145%) with two oil levels (mixture of sunflower 50% and soybean oils 50%): (control) and high. Results The higher dietary Thr level (145%) with high oil inclusion significantly increased ACC and POMC gene expression, resulting in the lowest feed intake, body weight gain (BWG), and liver fat content. Combining high oil with 115% Thr was the optimum for the broilers. The birds have significant (p ≤ .05) growth performance, immune parameters, and intestinal health, as well as the lowest expression of ACC, POMC, HSP70, and LITAF, which was reflected in better feed conversion ratio and lower incidence of fatty liver, thermo‐resistance, and immune status of the birds. Conclusions The combination of high oil and 115% Thr levels optimises broiler health and productivity, enhancing growth, immune function, and gut health. This diet lowers the expression of genes associated with fatty liver and stress, leading to better feed efficiency, thermo‐resistance, and overall well‐being. Adopting these dietary adjustments can improve broiler performance and economic viability in poultry farming by enhancing essential productivity metrics.

ABSTRACT Navigation is crucial for central‐place foragers to locate food and return to the nest. Cataglyphis ants are renowned for their advanced navigation abilities, relying on landmark cues and path integration. This study aims to uncover the transcriptomic basis of exceptional spatial learning in the central nervous system of Cataglyphis niger. Ants navigated a maze with a food reward, and we examined expression changes linked to correct decisions in subsequent runs. Correct decisions correlated with expression changes in the optic lobes, but not the central brain, showing a downregulation of genes associated with sucrose response and Creb3l1. The latter gene is homologous to Drosophila crebA, which is essential for long‐term memory formation. To understand how ants use distance information during path integration, we analyzed expression shifts associated with the last distance traveled. We uncovered a transcriptomic footprint in the central brain, but not in the optic lobes, with genes enriched for energy consumption and neurological functions, including neuronal projection development, synaptic target inhibition, and recognition processes. This suggests that transcriptional activity in the central brain is necessary for estimating distance traveled, which is crucial for path integration. Our study supports the distinct roles of different brain parts for navigation in Cataglyphis ants.

ABSTRACT Triploid oysters are commonly used as the basis for production in the aquaculture of eastern oysters along the USA East and Gulf of Mexico coasts. While they are valued for their rapid growth, incidents of triploid mortality during summer months have been well documented in eastern oysters, especially at low salinity sites. We compared global transcriptomic responses of diploid and triploid oysters bred from the same three maternal source populations at two different hatcheries and outplanted to a high (annual mean salinity = 19.4 ± 6.7) and low (annual mean salinity = 9.3 ± 5.0) salinity site. Oysters were sampled for gene expression at the onset of a mortality event in the summer of 2021 to identify triploid‐specific gene expression patterns associated with low salinity sites, which ultimately experienced greater triploid mortality. We also examined chromosome‐specific gene expression to test for instances of aneuploidy in experimental triploid oyster lines, another possible contributor to elevated mortality in triploids. We observed a strong effect of hatchery conditions (cohort) on triploid‐specific mortality (field data) and a strong interactive effect of hatchery, ploidy, and outplant site on gene expression. At the low salinity site where triploid oysters experienced high mortality, we observed downregulation of transcripts related to calcium signaling, ciliary activity, and cell cycle checkpoints in triploids relative to diploids. These transcripts suggest dampening of the salinity stress response and problems during cell division as key cellular processes associated with elevated mortality risk in triploid oysters. No instances of aneuploidy were detected in our triploid oyster lines. Our results suggest that triploid oysters may be fundamentally less tolerant of rapid decreases in salinity, indicating that oyster farmers may need to limit the use of triploid oysters to sites with more stable salinity conditions.

Abstract Clostridioides difficile is an anaerobic, spore‐forming, Gram‐positive pathogenic bacterium. This study aimed to analyze the effect of two samples of healthy fecal microbiota on C. difficile gene expression and growth using an in vitro coculture model. The inner compartment was cocultured with spores of the C. difficile polymerase chain reaction (PCR)‐ribotype 078, while the outer compartment contained fecal samples from donors to mimic the microbiota (FD1 and FD2). A fecal‐free plate served as a control (CT). RNA‐Seq and quantitative PCR confirmation were performed on the inner compartment sample. Similarities in gene expression were observed in the presence of the microbiota. After 12 h, the expression of genes associated with germination, sporulation, toxin production, and growth was downregulated in the presence of the microbiota. At 24 h, in an iron‐deficient environment, C. difficile activated several genes to counteract iron deficiency. The expression of genes associated with germination and sporulation was upregulated at 24 h compared with 12 h in the presence of microbiota from donor 1 (FD1). This study confirmed previous findings that C. difficile can use ethanolamine as a primary nutrient source. To further investigate this interaction, future studies will use a simplified coculture model with an artificial bacterial consortium instead of fecal samples.

Abstract Immunotherapy shows great promise for treating advanced cancers, but its effectiveness varies widely among different patients and cancer types. Identifying biomarkers and developing robust predictive models to discern which patients are most likely to benefit from immunotherapy is of great importance. In this context, we have developed the tumor immunotherapy gene expression R package (tigeR 1.0) to address the increasing need for effective tools to explore biomarkers and construct predictive models. tigeR encompasses four distinct yet closely interconnected modules. The Biomarker Evaluation module enables researchers to evaluate whether the biomarkers of interest are associated with immunotherapy response via built‐in or custom immunotherapy gene expression data. The Tumor Microenvironment Deconvolution module integrates 10 open‐source algorithms to obtain the proportions of different cell types within the tumor microenvironment, facilitating the investigation of the association between immune cell populations and immunotherapy response. The Prediction Model Construction module equips users with the ability to construct sophisticated prediction models using a range of built‐in machine‐learning algorithms. The Response Prediction module predicts the immunotherapy response for the patients from gene expression data using our pretrained machine learning models or public gene expression signatures. By providing these diverse functionalities, tigeR aims to simplify the process of analyzing immunotherapy gene expression data, thus making it accessible to researchers without advanced programming skills. The source code and example for the tigeR project can be accessed at http://github.com/YuLab-SMU/tigeR.

ABSTRACT Amaranthus dubius, an African leafy vegetable (ALV), is an easy‐to‐grow, annual shrub and a highly nutritious food source, containing elevated levels of essential nutrients in the leaves. Many ALVs, including A. dubius, can tolerate salinity stress, enabling their cultivation on marginal land. However, the widespread propagation of A. dubius as a stable food source has thus far not been realised due partially to the high frequency at which hybridisation occurs, resulting in high genotypic and phenotypic variability. Therefore, to increase the agricultural output capacity of this species on salt‐affected marginal lands, it is important to screen, select and then clonally propagate the identified salinity‐tolerant genotypes to ensure true‐to‐type fidelity in the regenerated population. It is also important, thereafter, to elucidate their underlying gene expression of the stress response. The present study exposed 4‐week‐old A. dubius seedlings to 100, 200 and 400 mM NaCl to determine their degree of salt tolerance. Genotypes were then screened, selected and clonally propagated through cuttings, based on high growth rates and biomass, and salt tolerance. Generally, growth and physiological parameters decreased as substrate salinity increased. However, individual salt‐stressed genotypes demonstrated similar vigour to nonstressed plants and were able to maintain total protein and chlorophyll concentrations despite increasing salinity. The relative expression of an NHX1‐like transcript was quantified in 15 genotypes using degenerately primed real‐time qPCR. The relative expression of the putative NHX1 gene was 6.7 times greater in root tissues of seedlings treated with 400 mM NaCl (10.7 ± 1.8) compared to the roots of untreated seedlings (1.6 ± 1.3), and 2.8‐fold more than leaf tissues harvested from seedlings treated with 400 mM NaCl. Furthermore, the relative electrical conductivity (EC) of root tissues was 10 times greater than the EC of leaf tissues from the same 400 mM NaCl treatment. Numerous genotypes yielded similar chlorophyll content between 200 and 400 mM NaCl treatments, with genotypes salinity‐1 (S1) (3.5 ± 0.2 μg/cm2) and S34 (4.0 ± 0.4 μg/cm2) having the highest concentrations of chlorophyll in the 400 mM group, which was positively correlated with total protein content. Following micropropagation through direct organogenesis, selected clones maintained true‐to‐type traits such as similar chlorophyll, protein and NHX1‐like expression as their parent plants when exposed to 400 mM NaCl. This study revealed that some genotypes demonstrated salt stress tolerance capabilities rivalling established halophytes by regulating the constitutive or inducible expression of an NHX1‐like protein in roots and leaves. The correlation between protein content and NHX1‐like expression was nonlinear and nonproportional, demonstrating the complexity of this response and necessitating further exploration of specific protein families or functional groups conferring salinity tolerance in this species.

ABSTRACT The impact of global changes on populations may not be necessarily uniform across a species' range. Here, we aim at comparing the phenotypic and transcriptomic response to warming and an invasive predator cue in populations across different geographic scales in the damselfly Ischnura elegans. We collected adult females in two ponds in southern Poland (central latitude) and two ponds in southern Sweden (high latitude). We raised their larvae in growth chambers and exposed them to combination of temperature and a predator cue released by the crayfish Orconectes limosus. When larvae reached the prefinal larval stage, they were phenotyped for traits related to growth and size and collected for a gene expression analysis. High‐latitude populations exhibited greater phenotypic and transcriptomic variation than central‐latitude populations. Across latitudes and ponds, temperature generally increased growth rate and the predator cue decreased mass, but the effects of temperature were also pond‐specific. Comparison of the transcriptomic profiles revealed a greater overlap in the response to temperature across latitudes and ponds, especially for pathway‐related oxidative stress and sugar and lipid metabolism. The transcriptomic response to a predator cue and to the interaction temperature × predator cue was more pond‐specific and overlapped only for few genes and pathways related to cuticle, development and signal transduction. We demonstrated that central‐ and high‐latitude populations may partially respond through similar mechanisms to warming and, to a lower extent to a predator cue and to the interaction temperature × predator cue. For the predator cue and the interaction, the large fraction of ponds‐specific genes suggests local adaptation. We show that high‐latitude populations were generally more plastic at the phenotypic and transcriptomic level and may be more capable to cope with environmental changes than their central‐latitude counterparts.

Abstract Background The tumoricidal complex alpha1‐oleate targets bladder cancer cells, triggering rapid, apoptosis‐like tumor cell death. Clinical effects of alpha1‐oleate were recently observed in patients with non‐muscle invasive bladder cancer (NMIBC), using a randomized, placebo‐controlled study protocol. Aims To investigate if there are dose‐dependent effects of alpha1‐oleate. Materials and Methods Here, patients with NMIBC were treated by intravesical instillation of increasing concentrations of alpha1‐oleate (1.7, 8.5, or 17 mM) and the treatment response was defined relative to a placebo group. Results Strong, dose‐dependent anti‐tumor effects were detected in alpha1‐oleate treated patients for a combination of molecular and clinical indicators; a complete or partial response was detected in 88% of tumors treated with 8.5 mM compared to 47% of tumors treated with 1.7 mM of alpha1‐oleate. Uptake of alpha1‐oleate by the tumor triggered rapid shedding of tumor cells into the urine and cell death by an apoptosis‐like mechanism. RNA sequencing of tissue biopsies confirmed the activation of apoptotic cell death and strong inhibition of cancer gene networks, including bladder cancer related genes. Drug‐related side effects were not recorded, except for local irritation at the site of instillation. Discussion and Conclusions These dose‐dependent anti‐tumor effects of alpha1‐oleate are promising and support the potential of alpha1‐oleate treatment in patients with NMIBC.

Abstract In this paper, we explored the influence of lipase on cuticle wax and anthocyanin metabolism in blueberries. The results demonstrated a progressive alteration in wax crystal structure, transitions from rod‐like to short rod‐like and flaky, and even disappearance of the cuticle wax. Gas chromatography–mass spectrometry analysis revealed a reduction in esters, aldehydes, long‐chain alkanes, and total wax content following lipase treatment of blueberry fruits. Additionally, ultra high performance liquid chromatography–mass spectrometry analysis showed significant decreases in peonidin, petunidin, cyanidin, and delphinidin, accompanied by an increase in malvidin content due to lipase treatment. Subsequent investigations uncovered that lipase treatment inhibited the activities of key anthocyanin synthetic enzymes, namely phenylalanine ammonia‐lyase (PAL), chalcone isomerase (CHI), and dihydroflavonol reductase (DFR). Moreover, lipase treatment downregulated the expression of synthesis‐related genes, including PAL, 4‐coumarate: CoA ligase, chalcone synthase (CHS), CHI, and DFR. In summary, our findings indicate that lipase disrupts the integrity of cuticle wax structure, inhibits anthocyanin synthesis, and reduces anthocyanin content. Accordingly, our studies suggest that inhibiting lipase could offer a novel approach to preserving the freshness and anthocyanin concentration of blueberries.

The coupling of transcription and translation enables prokaryotes to regulate mRNA stability and reduce nonfunctional transcripts. Eukaryotes evolved other means to perform these functions. Here, we quantify the disparity between gene expression and protein levels and attempt to explain its origins. We collected publicly available simultaneous measurements of gene expression, protein level, division rate, and growth inhibition of breast cancer cells under drug perturbation. We used the cell lines as entities with shared origin, different evolutionary trajectories, and cancer hallmarks to define tasks subject to specializing and trading‐off. We observed varying average mRNA and protein correlation across cell lines, and it was consistently higher for the gene products in the cancer hallmarks. The enrichment of hallmark gene products signifies the resources invested in it as a task. Enrichment based on mRNA or protein abundance corresponds to the relative resources dedicated to transcription and translation. The differences in gene‐ and protein‐based enrichment correlated with nominal division rates but not growth inhibition under drug perturbations. Comparing the range of enrichment scores of the hallmarks within each cell signifies the resources dedicated to each. Cells appear to have a wider range of enrichment in protein synthesis relative to gene transcription. The difference and range of enrichment of the hallmark genes and proteins correlated with cell division and inhibition in response to drug treatments. We posit that cancer cells may express the genes coding for seemingly nonspecialized tasks but do not translate them to the corresponding proteins. This trade‐off may cost the cells under normal conditions but confer benefits during stress.

Abstract Solute carriers (SLCs) regulate transfer of a wide range of molecules across cell membranes using facilitative or secondary active transport. In pregnancy, these transporters, expressed at the placental barrier, are important for delivery of nutrients to the fetus, whilst also limiting entry of potentially harmful substances, such as drugs. In the present study, RNA‐sequencing analysis was used to investigate expression of SLCs in the fetal (embryonic day 19) rat brain, choroid plexus and placenta in untreated control animals and following maternal paracetamol treatment. In the treated group, paracetamol (15 mg/kg) was administered to dams twice daily for 5 days (from embryonic day 15 to 19). In untreated animals, overall expression of SLCs was highest in the placenta. In the paracetamol treatment group, expression of several SLCs was significantly different compared with control animals, with ion, amino acid, neurotransmitter and sugar transporters most affected. The number of SLC transcripts that changed significantly following treatment was the highest in the choroid plexus and lowest in the brain. All SLC transcripts that changed in the placenta following paracetamol treatment were downregulated. These results suggest that administration of paracetamol during pregnancy could potentially disrupt fetal nutrient homeostasis and affect brain development, resulting in major consequences for the neonate and extending into childhood.

Abstract Background Current diagnostic tools are unable to distinguish low‐grade indolent prostate cancer (PrCa) from that with a propensity to become metastatic and/or lethal. Recent evidence suggests that reprogramming of the transcriptome may drive the metastatic phenotype, and that this reprogramming is controlled, at least in part, by epigenetic changes to the DNA of cancer cells, including methylation. These changes, referred to as ‘epigenetic drivers,’ have previously been associated with cancer cell survival. Methods Here, using Illumina Methylation EPIC array data of paired primary PrCa and metastatic bone samples, we identified WNT5A as a putative epi‐driver of PrCa metastasis to the bone, which was further validated in vitro. Results Significantly higher WNT5A methylation was observed in primary PrCa samples and 22Rv1 cells compared to metastatic bone samples and PC‐3 cells. This higher methylation was associated with significantly lower WNT5A gene expression. Conclusion Given the limited effective therapies available for metastatic cancer sufferers, particularly those whose disease has metastasised to the bone, WNT5A presents as a potential putative target for therapy.

Abstract The lotus seed embryo, known as “Plumula nelumbinis,” holds significance in Chinese culture as a traditional medicinal and edible herb rich in beneficial bioactive compounds like flavonoids, alkaloids, and polyphenols. Using ultrahigh‐performance liquid chromatography‐quadrupole‐exactive Orbitrap mass spectrometry, we meticulously analyzed the total flavonoids in Plumula nelumbinis (PNF) sourced from Hangzhou's West Lake. Our investigation preliminarily identified 29 flavonoid compounds, including 21 flavonoid O‐glycosides, five flavonoid C‐glycosides, and three aglycones, through comparisons with standards and literature references. Subsequent cellular anti‐inflammatory experiments using lipopolysaccharide (LPS)‐induced RAW264.7 cells demonstrated that treatment with 300 μg/mL of lotus seed flavonoids significantly reduced inflammatory factors' production, such as nitric oxide, prostaglandin E2, tumor necrosis factor, interleukin‐6, and interleukin‐1β. Additionally, PNF effectively lowered intracellular reactive oxygen species levels, mitigated LPS‐induced cell apoptosis, and nuclear translocation of nuclear factor‐κB (NF‐κB) p65 protein, collectively suppressing the NF‐κB p65 inflammatory pathway and demonstrating potent anti‐inflammatory properties. Crucially, the observed gene expression patterns of inflammatory factors aligned with their respective protein secretion levels. This study provides a comprehensive exploration of lotus seed flavonoids' anti‐inflammatory potential, highlighting their significance in potential therapeutic applications and laying the groundwork for future advancements in related functional foods.

Abstract Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species are poorly understood. We studied two corals, Montipora capitata and Pocillopora acuta, that inhabit the sheltered Kāne'ohe Bay, Hawai'i. M. capitata colonies in the bay are outbreeding diploids, whereas P. acuta is a mixture of clonal diploids and triploids. Populations were sampled from six reefs and subjected to either control (no stress), thermal stress, pH stress, or combined pH and thermal stress treatments. RNA‐seq data were generated to test two competing hypotheses: (1) gene expression is largely independent of genotype, reflecting a shared treatment‐driven response (TDE) or, (2) genotype dominates gene expression, regardless of treatment (GDE). Our results strongly support the GDE model, even under severe stress. We suggest that post‐transcriptional processes (e.g., control of translation, protein turnover) modify the signal from the transcriptome, and may underlie the observed differences in coral bleaching sensitivity via the downstream proteome and metabolome.

Abstract Parental age impacts offspring quantity and quality. Most prior research focused on maternal age. Since in most organisms the mother produces the costly eggs plus provides all or most parental care, it is difficult to distinguish maternal effects mediated via the egg from later maternal care. Here, we addressed the effects of parental age on offspring in Syngnathus typhle, a pipefish with male pregnancy. The divide between one parent producing the eggs and the second parent being the exclusive provider of parental care facilitates a distinction between the effects of parental age on egg quality versus parental age on early development. We fully reciprocally crossed young and old mothers and young and old fathers and assessed impact of parental age combination on offspring number, offspring size, and offspring gene expression patterns. Neither parental combination significantly influenced offspring size or male gestation duration; however, they influenced the number of offspring. Paternal, but not maternal, age strongly affected the offspring gene expression. Offspring from old fathers exhibited substantial changes in the expression of genes related to cell cycle regulation, protein synthesis, DNA repair, and neurogenesis. Our findings thus highlight the importance of gestation, as opposed to gamete production, in shaping the parental contribution to offspring development.

Abstract Phenotype plasticity and evolution adaptations are the two main ways in which allow populations to deal with environmental changes, but the potential relationship between them remains controversial. Using a reciprocal transplant approach with cattle adapted to the Tibetan Plateau and adjacent lowlands, we aim to investigate the relative contributions of evolutionary processes and phenotypic plasticity in driving both phenotypic and transcriptomic changes under natural conditions. We observed that while numerous genetic transcriptomic changes were evident during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes with ancestral plasticity are generally reversed by evolutionary adaptations and show a closer expression level to the ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotypes level, with a majority of biochemical and hemorheology phenotypes showing a tendency to revert to their ancestral patterns, suggesting the restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. The findings of our study contribute to the debate regarding the relative contributions of plasticity and genetic changes in mammal environment adaptation. Furthermore, we highlight that the restoration of ancestral phenotypes represents a general pattern in cattle new environment adaptation.

Abstract Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full‐length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression‐modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra‐transcribed region scale. The expMotif‐transcribed region combination is the most predominant contributor to the expression‐modulating effect of SSRs, and some intra‐transcribed regions are critical for this effect. Genes containing the same type of expMotif‐SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.

Abstract Background We previously reported that metastases are generally characterized by a core program of gene expression that activates tissue remodeling/vascularization, alters ion homeostasis, induces the oxidative metabolism, and silences extracellular matrix interactions. This core program distinguishes metastases from their originating primary tumors as well as from their destination host tissues. Therefore, the gene products involved are potential targets for anti‐metastasis drug treatment. Methods Because the silencing of extracellular matrix interactions predisposes to anoiks in the absence of active survival mechanisms, we tested inhibitors against the other three components. Results Individually, the low‐specificity VEGFR blocker pazopanib (in vivo combined with marimastat), the antioxidant dimethyl sulfoxide (or the substitute atovaquone, which is approved for internal administration), and the ionic modulators bumetanide and tetrathiomolybdate inhibited soft agar colony formation by breast and pancreatic cancer cell lines. The individual candidate agents have a record of use in humans (with limited efficacy when administered individually) and are available for repurposing. In combination, the effects of these drugs were additive or synergistic. In two mouse models of cancer (utilizing 4T1 cells or B16‐F10 cells), the combination treatment with these medications, applied immediately (to prevent metastasis formation) or after a delay (to suppress established metastases), dramatically reduced the occurrence of disseminated foci. Conclusions The combination of tissue remodeling inhibitors, suppressors of the oxidative metabolism, and ion homeostasis modulators has very strong promise for the treatment of metastases by multiple cancers.

Endometriosis and endometrial cancer are closely related to oxidative stress. However, the direct relationship between copper and zinc levels and oxidative stress in the extracellular and intracellular space remains unclear. The presented study is focused on the determination of serum Zn and Cu levels, glutathione concentration and enzyme activity in three groups: patients diagnosed with endometrial cancer (EC), patients diagnosed with endometriosis (EM), and a healthy control group. Spectrophotometric determination of trace elements revealed that levels of zinc and copper were lower in blood plasma of patients with endometriosis as compared with the other groups; however, there were no significant differences in the Cu/Zn ratio. Furthermore, significantly increased blood serum glutathione levels were detected in both EM and EC groups compared with the control group. While the activity of superoxide dismutase (SOD) was similar across the studied groups, we observed differences in the activity of other enzymes associated with oxidative stress, including glutathione peroxidase (GPx), glutathione reductase (GR) and glutathione S‐transferase (GST), between the control group and the EM and EC patients. Additionally, analysis of gene expression based on free circulating mRNA indicated significant differences in the expression of SOD isoenzymes between the patient groups and the control group; expression of GPx isoenzymes was also altered. Obtained results may have potential application in diagnostics as well as monitoring of endometriosis and endometrial cancer.

Abstract Hyperuricemia (HUA) is a metabolic disease caused by excessive uric acid in patients. Flavonoids have attracted extensive attention due to their safety, effectiveness, and little side effects in the treatment of HUA and inhibition of xanthine oxidase (XO) activity. In this paper, the studies on the treatment of HUA and the inhibition of XO activity by flavonoids (including flavones, flavonols, flavanones, flavanols, isoflavonoids, anthocyanins, and chalcones) were comprehensively reviewed from the aspects of structure–activity relationship and animal experiments. Results showed that hydrogen bonds and hydrophobic interactions were the two most important forces involved in the interaction between flavonoids and XO. Flavonoids could combine with the hydrophobic cavity of XO to cause changes in XO structure and influence the action of enzyme and substrate, thereby decreasing the catalytic activity of XO. Moreover, flavonoids undergo a series of metabolic reactions in the organism, which plays a role in alleviating HUA by affecting the expression of related genes and proteins (e.g., glucose transporter 9, urate transporter 1, and organic anion transporter 1) in the kidneys, liver, and intestinal tract of the organism and changing the internal environment in organs. In addition, this paper provides new perspectives on the shortcomings of the current research, to promote the in‐depth development and application of flavonoids.

Abstract Introduction Pearl millet (Pennisetum glaucum) plays a crucial role as a cereal crop in arid and semi‐arid regions, where it confronts the formidable challenge of salt stress. Materials and Methods To unravel the underlying molecular mechanisms that underpin its salt stress resilience, we subjected 14‐day‐old seedlings to three distinct groups: Control, 75 mM NaCl and 150 mM NaCl. These pots received daily irrigation with their respective treatment solutions for a duration of 7 days. Following this week‐long treatment, we measured plant chlorophyll content, as well as the fresh and dry weights of shoots and roots. It became evident that the saline treatment, particularly in the 150 mM NaCl group, had a more pronounced impact on both weight and chlorophyll content in comparison to the control group, surpassing the effects observed in the 75 mM NaCl group. Subsequently, we conducted RNA sequence analysis on the leaves of Pearl millet from both the control and 150 mM NaCl‐treated groups. Results The results revealed that 27.6% of Pennisetum glaucum genes exhibited differential expression, with 3246 genes being upregulated and 7408 genes downregulated when compared to the control group. Principal component analysis underscored distinct variations in gene expression patterns between the control and salt‐stressed groups. Pathway analysis sheds light on the upregulated differentially expressed genes (DEGs), highlighting their involvement in crucial pathways such as phytyl‐PP biosynthesis, lysine degradation, glutamate biosynthesis, nitrate assimilation and DLO biosynthesis. Conversely, the downregulated DEGs were associated with pathways like coumarins biosynthesis, pinobanksin biosynthesis, UDP‐ d‐glucuronate biosynthesis and cholesterol biosynthesis, among others. Furthermore, our transcription factor analysis unveiled specific families associated with the salt stress response, including bHLH, ERF, NAC, WRKY, bZIP, MYB and HD‐ZIP. Conclusions These findings represent a significant advancement in our comprehension of Pearl millet's capacity to withstand salt stress and provide potential targets for the development of salt‐resistant crops, contributing to the advancement of sustainable agriculture in regions affected by salinity.

Abstract A feeding trial with Macrobrachium acanthurus juveniles was performed to determine growth performance and utilization of diets varying in protein, lipid, and carbohydrate level. Twelve diets were formulated with three levels of protein (P) and supplemented with different proportions of lipids (L) and carbohydrates (C): P30‐L20‐C8, P30‐L15‐C19, P30‐L12‐C25, P30‐L10‐C31, P35‐L20‐C3, P35‐L15‐C15, P35‐L10‐C26, P35‐L5‐C38, P40‐L15‐C8, P40‐L10‐C19, P40‐L5‐C31, and P40‐L1‐C40. Lipids and carbohydrates were added allowing an overall energy content limit of 400 kcal per 100 g of diet. Each diet was fed to triplicate groups of juveniles with an initial weight of 60.9 ± 10.9 mg (mean ± SD) for 60 days. Overall growth performance and gene expression of fatty acid synthase (FAS), carnitine palmitoyltransferase 1 (CPT1), glucose‐6‐phosphatase (G6P), and hexokinase (HK) in the hepatopancreas were assessed. Highest weight gain values and specific growth rates were observed in prawns fed diets with 35% of protein inclusion. Expression of FAS was downregulated when fed 30% of protein. Results indicate M. acanthurus use protein as their primary source of energy and when this is low in the diet, lipids are used to spare the energy from proteins. Suggested inclusion of protein, lipids, and carbohydrates in diets for M. acanthurus should be 35%, 15%, and 15%, respectively.

Abstract Tetraselmis helgolandica var. Tsingtaoensis is a marine microalga. It can produce a large amount of starch, especially amylose, with addition of carbon source and specific circadian rhythm. The mechanism behind this phenomenon is still unclear. Analysis of this mechanism can help to develop T. helgolandica into a new green bioengineering chassis organism. We explained how circadian rhythm and glucose affect the rate of starch accumulation and starch structure in T. helgolandica based on the transcriptome. The glucose inhibited the photosynthetic system of T. helgolandica, while the circadian rhythm can alleviate the inhibition. Circadian rhythm induced the upregulation of Embden–Meyerhof–Parnas pathway and pentose phosphate pathway (PPP) in T. helgolandica, but had little effect on the tricarboxylic acid cycle. PPP pathway provides Ribulose‐1,5‐bisphosphate, which may be beneficial for dark reactions and nucleotide synthesis. And PPP pathway provides Nicotinamide adenine dinucleotide phosphate, which facilitates energy substance synthesis. This will further upregulate the starch metabolic pathway. The transcript level of the key gene ADP‐Glucose pyrophosphorylase is mainly regulated by glucose. The granule‐bound starch synthase (gbss), a key gene for amylose synthesis, is mainly influenced by circadian rhythm. In general, the increase of starch synthesis and amylose ratio requires both glucose addition and circadian rhythm. We report the first referenced transcriptome of T. helgolandica. Differences between transcripts reveal how circadian rhythm and glucose addition affected the rate of starch synthesis and structural variation. It provides a reference for an in‐depth study of starch synthesis in green algae.

Abstract Synthetic biology aims to engineer transgene switches for precise therapeutic protein control in cell‐based gene therapies. However, off‐the‐shelf trigger‐inducible gene circuits are usually switched on by single or structurally similar molecules. This study presents a mammalian gene‐switch platform that controls therapeutic gene expression by a wide range of molecules generating low, non‐toxic levels of reactive oxygen species (ROS). In this system, KEAP1 (Kelch‐like ECH‐associated protein 1) serves as ROS sensor, regulating the translocation of NRF2 (nuclear factor erythroid 2‐related factor 2) to the nucleus, where NRF2 binds to antioxidant response elements (ARE) to activate the expression of a gene of interest. It is found that a promoter containing eight‐tandem ARE repeats is highly sensitive to the low ROS levels generated by the soluble and volatile molecules, which include food preservatives, food additives, pharmaceuticals, and signal transduction inducers. In a proof‐of‐concept study, it is shown that many of these compounds can independently trigger microencapsulated engineered cells to produce sufficient insulin to restore normoglycemia in experimental type‐1 diabetic mice. It is believed that this system greatly extends the variety of small‐molecule inducers available to drive therapeutic gene switches.

Abstract Macrophages regulate essential aspects of innate immunity against pathogens. In response to microbial components, macrophages activate primary and secondary inflammatory gene programs crucial for host defense. The liver X receptors (LXRα, LXRβ) are ligand‐dependent nuclear receptors that direct gene expression important for cholesterol metabolism and inflammation, but little is known about the individual roles of LXRα and LXRβ in antimicrobial responses. Here, the results demonstrate that induction of LXRα transcription by prolonged exposure to lipopolysaccharide (LPS) supports inflammatory gene expression in macrophages. LXRα transcription is induced by NF‐κB and type‐I interferon downstream of TLR4 activation. Moreover, LPS triggers a reprogramming of the LXRα cistrome that promotes cytokine and chemokine gene expression through direct LXRα binding to DNA consensus sequences within cis‐regulatory regions including enhancers. LXRα‐deficient macrophages present fewer binding of p65 NF‐κB and reduced histone H3K27 acetylation at enhancers of secondary inflammatory response genes. Mice lacking LXRα in the hematopoietic compartment show impaired responses to bacterial endotoxin in peritonitis models, exhibiting reduced neutrophil infiltration and decreased expansion and inflammatory activation of recruited F4/80lo‐MHC‐IIhi peritoneal macrophages. Together, these results uncover a previously unrecognized function for LXRα‐dependent transcriptional cis‐activation of secondary inflammatory gene expression in macrophages and the host response to microbial ligands.

Abstract Background One of the main problems in the poultry industry is excess body fat, and the anti‐fat effect of Cratagus extract has been confirmed in several studies. Objectives The present study was carried out to investigate the effects of hawthorn extract (Crataegus oxyacantha) on growth performance, haematological variables and hepatic gene expression in broiler chickens reared at high altitude (2100 m). Methods A total of 225‐day‐old chicks (Ross 308) were randomly distributed into three treatments. Experimental treatments were prepared by adding 0.0, 0.2 and 0.4 mL of hawthorn extract per litre of consumption of water. Results The results showed that weight gain and feed conversion ratio were significantly improved and abdominal fat decreased by consumption of two levels of Crateagus extract when compared to the control (p

Abstract HMG (high mobility group) proteins are a diverse family of nonhistone chromosomal proteins that interact with DNA and a wide range of transcriptional regulators to regulate the structural architecture of DNA. HMGXB4 (also known as HMG2L1) is an HMG protein family member that contains a single HMG box domain. Our previous studies have demonstrated that HMGXB4 suppresses smooth muscle differentiation and exacerbates endotoxemia by promoting a systemic inflammatory response in mice. However, the expression of Hmgxb4 in vivo has not fully examined. Herein, we generated a mouse model that harbors a gene trap in the form of a lacZ gene insertion into the Hmgxb4 gene. This mouse enables the visualization of endogenous HMGXB4 expression in different tissues via staining for the β‐galactosidase activity of LacZ which is under the control of the endogenous Hmgxb4 gene promoter. We found that HMGXB4 is widely expressed in mouse tissues and is a nuclear protein. Furthermore, the Hmgxb4 gene trap mice exhibit normal cardiac function and blood pressure. Measurement of β‐galactosidase activity in the Hmgxb4 gene trap mice demonstrated that the arterial injury significantly induces Hmgxb4 expression. In summary, the Hmgxb4 gene trap reporter mouse described here provides a valuable tool to examine the expression level of endogenous Hmgxb4 in both physiological and pathological settings in vivo.

Abstract In July 2016, East Bank of Flower Garden Banks (FGB) National Marine Sanctuary experienced a localized mortality event (LME) of multiple invertebrate species that ultimately led to reductions in coral cover. Abiotic data taken directly after the event suggested that acute deoxygenation contributed to the mortality. Despite the large impact of this event on the coral community, there was no direct evidence that this LME was driven by acute deoxygenation, and thus we explored whether gene expression responses of corals to the LME would indicate what abiotic factors may have contributed to the LME. Gene expression of affected and unaffected corals sampled during the mortality event revealed evidence of the physiological consequences of the LME on coral hosts and their algal symbionts from two congeneric species (Orbicella franksi and Orbicella faveolata). Affected colonies of both species differentially regulated genes involved in mitochondrial regulation and oxidative stress. To further test the hypothesis that deoxygenation led to the LME, we measured coral host and algal symbiont gene expression in response to ex situ experimental deoxygenation (control = 6.9 ± 0.08 mg L−1, anoxic = 0.083 ± 0.017 mg L−1) in healthy O. faveolata colonies from the FGB. However, this deoxygenation experiment revealed divergent gene expression patterns compared to the corals sampled during the LME and was more similar to a generalized coral environmental stress response. It is therefore likely that while the LME was connected to low oxygen, it was a series of interconnected stressors that elicited the unique gene expression responses observed here. These in situ and ex situ data highlight how field responses to stressors are unique from those in controlled laboratory conditions, and that the complexities of deoxygenation events in the field likely arise from interactions between multiple environmental factors simultaneously.

Abstract The major carp Rohu (Labeo rohita) is a prime freshwater aquaculture species across the Indian subcontinent that faces various production‐related issues associated with water quality parameters. The present study examined the effects of three different doses of NH3 (T1 = 1 mg/L, T2 = 2 mg/L and T3 = 3 mg/L) on cellular (gill ultrastructure), physiological (growth and oxygen consumption rate), biochemical (blood cell counts, blood cortisol and glucose levels) and genetic (expression of five genes involved in growth, immunity and metabolism) traits of Rohu. The experimental ammonia dose significantly affected the tested biological parameters (p

Abstract Rubisco activase (Rca) is an essential photosynthetic enzyme that removes inhibitors from the catalytic sites of the carboxylating enzyme Rubisco. In wheat, Rca is composed of one longer 46 kDa α‐isoform and two shorter 42 kDa β‐isoforms encoded by the genes TaRca1 and TaRca2. TaRca1 produces a single transcript from which a short 1β‐isoform is expressed, whereas two alternative transcripts are generated from TaRca2 directing expression of either a long 2α‐isoform or a short 2β‐isoform. The 2β isoform is similar but not identical to 1β. Here, virus‐induced gene silencing (VIGS) was used to silence the different TaRca transcripts. Abundance of the transcripts and the respective protein isoforms was then evaluated in the VIGS‐treated and control plants. Remarkably, treatment with the construct specifically targeting TaRca1 efficiently decreased expression not only of TaRca1 but also of the two alternative TaRca2 transcripts. Similarly, specific targeting of the TaRca2 transcript encoding a long isoform TaRca2α resulted in silencing of both TaRca2 alternative transcripts. The corresponding protein isoforms decreased in abundance. These findings indicate concomitant down‐regulation of TaRca1 and TaRca2 at both transcript and protein levels and may impact the feasibility of altering the relative abundance of Rca isoforms in wheat.

Abstract With climate change, selection for water efficiency and heat resilience are vitally important. We undertook this study to determine the effect of chronic cyclic heat stress (HS) on the hypothalamic expression profile of water homeostasis‐associated markers in high (HWE)‐ and low (LWE)‐water efficient chicken lines. HS significantly elevated core body temperatures of both lines. However, the amplitude was higher by 0.5–1°C in HWE compared to their LWE counterparts. HWE line drank significantly less water than LWE during both thermoneutral (TN) and HS conditions, and HS increased water intake in both lines with pronounced magnitude in LWE birds. HWE had better feed conversion ratio (FCR), water conversion ratio (WCR), and water to feed intake ratio. At the molecular level, the overall hypothalamic expression of aquaporins (AQP8 and AQP12), arginine vasopressin (AVP) and its related receptor AVP2R, angiotensinogen (AGT), angiotensin II receptor type 1 (AT1), and calbindin 2 (CALB2) were significantly lower; however, CALB1 mRNA and AQP2 protein levels were higher in HWE compared to LWE line. Compared to TN conditions, HS exposure significantly increased mRNA abundances of AQPs (8, 12), AVPR1a, natriuretic peptide A (NPPA), angiotensin I‐converting enzyme (ACE), CALB1 and 2, and transient receptor potential cation channel subfamily V member 1 and 4 (TRPV1 and TRPV4) as well as the protein levels of AQP2, however it decreased that of AQP4 gene expression. A significant line by environment interaction was observed in several hypothalamic genes. Heat stress significantly upregulated AQP2 and SCT at mRNA levels and AQP1 and AQP3 at both mRNA and protein levels, but it downregulated that of AQP4 protein only in LWE birds. In HWE broilers, however, HS upregulated the hypothalamic expression of renin (REN) and AVPR1b genes and AQP5 proteins, but it downregulated that of AQP3 protein. The hypothalamic expression of AQP (5, 7, 10, and 11) genes was increased by HS in both chicken lines. In summary, this is the first report showing improvement of growth performances in HWE birds. The hypothalamic expression of several genes was affected in a line‐ and/or environment‐dependent manner, revealing potential molecular signatures for water efficiency and/or heat tolerance in chickens.

Abstract Background Aspirin use has been associated with reduced ovarian cancer risk, yet the underlying biological mechanisms are not fully understood. To gain mechanistic insights, we assessed the association between prediagnosis low and regular‐dose aspirin use and gene expression profiles in ovarian tumors. Methods RNA sequencing was performed on high‐grade serous, poorly differentiated, and high‐grade endometrioid ovarian cancer tumors from the Nurses' Health Study (NHS), NHSII, and New England Case–Control Study (n = 92 cases for low, 153 cases for regular‐dose aspirin). Linear regression identified differentially expressed genes associated with aspirin use, adjusted for birth decade and cohort. False discovery rates (FDR) were used to account for multiple testing and gene set enrichment analysis was used to identify biological pathways. Results No individual genes were significantly differentially expressed in ovarian tumors in low or regular‐dose aspirin users accounting for multiple comparisons. However, current versus never use of low‐dose aspirin was associated with upregulation of immune pathways (e.g., allograft rejection, FDR = 5.8 × 10−10; interferon‐gamma response, FDR = 2.0 × 10−4) and downregulation of estrogen response pathways (e.g., estrogen response late, FDR = 4.9 × 10−8). Ovarian tumors from current regular aspirin users versus never users were also associated with upregulation in interferon pathways (FDR

Abstract Background Iron deficiency can impair immune function, increasing tuberculosis (TB) susceptibility and severity. The research aimed to investigate iron deficiency anemia in TB patients and household contacts and its association with natural resistance‐associated macrophage protein 1 (NRAMP1) polymorphism and expression. Methods The levels of iron, ferritin, and transferrin were measured in the serum by ELISA (Enzyme‐Linked Immunosorbent Assay). NRAMP1 polymorphisms were determined by polymerase chain reaction (PCR) and sequencing. NRAMP1 gene expression was measured by real‐time PCR. Interferon‐gamma release assay (IGRA) checked on household contacts to screen household contacts with positive IGRA as the control. Results This study involved 35 TB cases and 35 TB contacts. The results showed that the serum Fe levels were found to be lower in the TB case group (median 149.6 μmol/L) than in the positive IGRA household contacts group (median 628.53 μmol/L) with a p‐value

Glioblastoma (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of patients with GBM has led to an improved categorization into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome‐wide multi‐omic approaches to identify potential molecular vulnerabilities existing in patients with GBM. Integration of gene expression and DNA methylation data from both bulk GBM and patient‐derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype‐specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP‐1, SMAD3 and RUNX1/RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype‐specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal‐like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.

Abstract Background Amongst healthy older people, a number of correlates of impaired skeletal muscle mass and function have been defined. Although the prevalence of obesity is increasing markedly in this age group, information is sparse about the particular impacts of obesity on ageing skeletal muscle or the molecular mechanisms that underlie this and associated disease risk. Methods Here, we examined genome‐wide transcriptional changes using RNA sequencing in muscle biopsies from 40 older community‐dwelling men from the Hertfordshire Sarcopenia Study with regard to obesity (body mass index [BMI] >30 kg/m2, n = 7), overweight (BMI 25–30, n = 19), normal weight (BMI

Abstract Background Shivers in horses is characterized by abnormal hindlimb movement when walking backward and is proposed to be caused by a Purkinje cell (PC) axonopathy based on histopathology. Objectives Define region‐specific differences in gene expression within the lateral cerebellar hemisphere and compare cerebellar protein expression between Shivers horses and controls. Animals Case‐control study of 5 Shivers and 4 control geldings ≥16.2 hands in height. Methods Using spatial transcriptomics, gene expression was compared between Shivers and control horses in PC soma and lateral cerebellar hemisphere white matter, consisting primarily of axons. Tandem‐mass‐tag (TMT‐11) proteomic analysis was performed on lateral cerebellar hemisphere homogenates. Results Differences in gene expression between Shivers and control horses were evident in principal component analysis of axon‐containing white matter but not PC soma. In white matter, there were 455/1846 differentially expressed genes (DEG; 350 ↓DEG, 105 ↑DEG) between Shivers and controls, with significant gene set enrichment of the Toll‐Like Receptor 4 (TLR4) cascade, highlighting neuroinflammation. There were 50/936 differentially expressed proteins (DEP). The 27 ↓DEP highlighted loss of axonal proteins including intermediate filaments (5), myelin (3), cytoskeleton (2), neurite outgrowth (2), and Na/K ATPase (1). The 23 ↑DEP were involved in the extracellular matrix (7), cytoskeleton (7), redox balance (2), neurite outgrowth (1), signal transduction (1), and others. Conclusion and Clinical Importance Our findings support axonal degeneration as a characteristic feature of Shivers. Combined with histopathology, these findings are consistent with the known distinctive response of PC to injury where axonal changes occur without a substantial impact on PC soma.

Abstract Background In the modern broiler industry, leg and gait disorders are considerable problems. Fast‐growing broilers are especially susceptible to bone abnormalities, causing major problems for broiler producers. Strontium ranelate (SrR) has been used successfully for the treatment of osteoporosis in humans. In addition, cerium oxide (CeO) is an anti‐stress agent applied in the biological system. Methods This study was conducted to investigate the effect of SrR, CeO, and their combinations on tibia quality in broilers. A total of 384 one‐day‐old Ross chicks were divided into six treatments, with four replicates per treatment (16 birds per replicate). The control group was fed a standard diet, and other groups were fed SrR at levels 450, 900 mg/kg feed, CeO at levels 300 and 600 mg/kg feed and a combination of 450 SrR + 300 CeO mg/kg feed. Bone mineral density (BMD), bone mineral content (BMC), bone strength (BS), tibia area, tibia weight, bone Length, bone diameter, minerals in tibia bone of male broilers, alkaline phosphatase gene (ALP) and osteocalcin gene (OC) in male broilers were analysed. Results The results showed that the addition of SrR and CeO had no significant influence (p > 0.01) on BMD, BMC, BS, bone weight, bone length and bone diameter. While there was a significant interaction between sex and treatments, especially in the combination group, BS in females significantly (p < 0.01) increased compared to the control group. Generally, females were found to be more responsive to treatments than males. Significant increases in gene expression were noticed in OC with the addition of low levels of SrR and CeO and mixed group compared to the control. The gene expression of ALP was increased significantly only in a combination group compared to the control group. Conclusion It is concluded that SrR and CeO can be used as beneficial additives in the feed to improve the tibia quality of broilers.

Transcription factors (TFs) are key players in the regulation of gene transcription in mammalian cells. Although high‐throughput screening can be used to identify differentially expressed genes between comparable groups, the precision of the corresponding datasets is far from optimal. Here, we establish Target Finder of Transcription Factor (TFoTF), a method for the prediction of TF‐targeted genes from genomic and cancer‐related transcriptomic data. TFoTF can identify potential TF‐targeted genes in large cancer datasets and efficiently estimate correlations between TFs and their targeted genes with a significant level of specificity, sensitivity, and precision. Overall, TFoTF is an easy‐to‐use tool that can be utilized to generate testable hypotheses in the context of cancer research projects.

Abstract Background TP53 is the most commonly mutated gene across all cancer types. R175H mutation was considered structural mutation where the mutation causes misfolding of the protein and leads to a significant conformational alterations within p53's DNA binding domain. The aim of this study was to explain the reason why R175H worse the response to immunotherapy by analyzing tumor immune microenvironment through the expression of immune cells and PD‐1. Materials and Methods Patients diagnosed with metastatic carcinoma, including colorectal cancer (CRC), breast cancer (BRCA), gastric cancer (GC), non‐small cell lung cancer (NSCLC), and 20 other cancer types, treated in a palliative setting at Samsung Medical Center between October 2019 and April 2021, were enrolled. Of these patients, those who underwent TDS analysis (TruSight™ Oncology 500 assay [TSO 500]) were finally analyzed. Results Of 1770 patients, 1012 (57.2%) harbored genetic alterations in TP53. All mutations were single nucleotide variants (SNVs), and the most frequent SNV was R175H (n = 84, 7.5%) which was known as one of the most common hotspot TP53 mutation. The overall survival of patients with TP53 R175H mutations was significantly worse following chemotherapy (606 vs. 456 days, p

Abstract Background PTGS2 encodes cyclooxygenase‐2 (COX‐2), which catalyses the committed step in prostaglandin synthesis. Various in vivo and in vitro data suggest that COX‐2 mediates the VEGF signalling pathway. In silico analysis performed in TCGA, PanCancer Atlas for head and neck cancers, demonstrated significant expression and co‐expression of PTGS2 and genes that regulate VEGF signalling. This study was designed to elucidate the expression pattern of PTGS2 and genes regulating VEGF signalling in patients with locally advanced oral squamous cell carcinoma (OSCC). Methodology Tumour and normal tissue samples were collected from patients with locally advanced OSCC. RNA was isolated from tissue samples, followed by cDNA synthesis. The cDNA was used for gene expression analysis (RT‐PCR) using target‐specific primers. The results obtained were compared with the in silico gene expression of the target genes in the TCGA datasets. Co‐expression analysis was performed to establish an association between PTGS2 and VEGF signalling genes. Results Tumour and normal tissue samples were collected from 24 OSCC patients. Significant upregulation of PTGS2 expression was observed. Furthermore, VEGFA, KDR, CXCR1 and CXCR2 were significantly upregulated in tumour samples compared with paired normal samples, except for VEGFB, whose expression was not statistically significant. A similar expression pattern was observed in silico, except for CXCR2 which was highly expressed in the normal samples. Co‐expression analysis showed a significant positive correlation between PTGS2 and VEGF signalling genes, except for VEGFB which showed a negative correlation. Conclusion PTGS2 and VEGF signalling genes are upregulated in OSCC, which has a profound impact on clinical outcomes.

Abstract Background Breast cancer is a metabolically heterogeneous disease, and although the concept of heterogeneous cancer metabolism is known, its precise role in human breast cancer is yet to be fully elucidated. Methods We investigated in an explorative approach a cohort of 42 primary mamma carcinoma patients with positron emission tomography/magnetic resonance imaging (PET/MR) prior to surgery, followed by histopathology and molecular diagnosis. From a subset of patients, which showed high metabolic heterogeneity based on tracer uptake and pathology classification, tumour centre and periphery specimen tissue samples were further investigated by a targeted breast cancer gene expression panel and quantitative metabolomics by nuclear magnetic resonance (NMR) spectroscopy. All data were analysed in a combinatory approach. Results [18F]FDG (2‐deoxy‐2‐[fluorine‐18]fluoro‐d‐glucose) tracer uptake confirmed dominance of glucose metabolism in the breast tumour centre, with lower levels in the periphery. Additionally, we observed differences in lipid and proliferation related genes between luminal A and B subtypes in the centre and periphery. Tumour periphery showed elevated acetate levels and enrichment in lipid metabolic pathways genes especially in luminal B. Furthermore, serine was increased in the periphery and higher expression of thymidylate synthase (TYMS) indicated one‐carbon metabolism increased in tumour periphery. The overall metabolic activity based on [18F]FDG uptake of luminal B subtype was higher than that of luminal A and the difference between the periphery and centre increased with tumour grade. Conclusion Our analysis indicates variations in metabolism among different breast cancer subtypes and sampling locations which details the heterogeneity of the breast tumours. Correlation analysis of [18F]FDG tracer uptake, transcriptome and tumour metabolites like acetate and serine facilitate the search for new candidates for metabolic tracers and permit distinguishing luminal A and B. This knowledge may help to differentiate subtypes preclinically or to provide patients guide for neoadjuvant therapy and optimised surgical protocols based on individual tumour metabolism.

Abstract Macaques (genus Macaca) are the most widely distributed non‐human primates, and their evolutionary history, gene expression profiles, and genetic differences have been extensively studied. However, the DNA methylomes of macaque species are not available in public databases, which hampers understanding of epigenetic differences among macaque species. Epigenetic modifications can potentially affect development, physiology, behavior, and evolution. Here, we investigated the methylation patterns of the Tibetan macaque (M. thibetana; TM), Chinese rhesus macaque (M. mulatta lasiota; CR), and crab‐eating macaque (M. fascicularis; CE) through whole‐genome bisulfite sequencing from peripheral blood. We compared genome‐wide methylation site information for the three species. We identified 12,128 (CR vs. CE), 59,165 (CR vs. TM), and 39,751 (CE vs. TM) differentially methylated regions (DMRs) in the three macaques. Furthermore, we obtained the differentially expressed genes (DEGs) among the three macaque species. The differences between CR and CE were smaller at both the methylome and transcriptome levels than compared with TM (CR vs. TM and CE vs. TM). We also found a change in the density of single nucleotide mutations in DMRs relative to their flanking regions, indicating a potential mechanism through which genomic alterations may modulate methylation landscapes, thereby influencing the transcriptome. Functional enrichment analyses showed the DMR‐related genes were enriched in developmental processes and neurological functions, such as the growth hormone‐related pathway, insulin secretion pathway, thyroid hormone synthesis pathway, morphine addiction, and GABAergic synapses. These differences may be associated with variations in physiology and habitat among the macaques. Our study provides one of the first genome‐wide comparisons of genetic, gene expression, and epigenetic variations across different macaques. Our results should facilitate further research on comparative genomic and genetic differences in macaque species.

Abstract Depression is a highly prevalent and disabling mental disorder, involving numerous genetic changes that are associated with abnormal functions in multiple regions of the brain. However, there is little transcriptomic‐wide characterization of chronic social defeat stress (CSDS) to comprehensively compare the transcriptional changes in multiple brain regions. Spatial transcriptomics (ST) was used to reveal the spatial difference of gene expression in the control, resilient (RES) and susceptible (SUS) mouse brains, and annotated eight anatomical brain regions and six cell types. The gene expression profiles uncovered that CSDS leads to gene synchrony changes in different brain regions. Then it was identified that inhibitory neurons and synaptic functions in multiple regions were primarily affected by CSDS. The brain regions Hippocampus (HIP), Isocortex, and Amygdala (AMY) present more pronounced transcriptional changes in genes associated with depressive psychiatric disorders than other regions. Signalling communication between these three brain regions may play a critical role in susceptibility to CSDS. Taken together, this study provides important new insights into CSDS susceptibility at the ST level, which offers a new approach for understanding and treating depression.

Abstract UDP‐glucuronosyltransferases (UGTs) are phase II drug metabolizing enzymes that play important roles in the detoxification of endogenous and exogenous substrates. The 22 human UGTs belong to four families (UGT1, UGT2, UGT3, and UGT8) and differ in their expression, substrate specificity, UDP‐sugar preference, and physiological functions. Differential expression/activity of the UGTs contributes to interperson variability in drug responses and toxicity, hormone homeostasis, and disease/cancer risks. However, in normal tissues, the tissue‐specific expression profiles and transcriptional regulation of the UGTs are still not fully understood. In this study, we comprehensively analyzed the transcriptome of 22 UGTs in 54 human tissues/regions using RNAseq data from GTEx. We then validated the findings in the liver and small intestine samples using real‐time PCR. Our results showed large interindividual variability across tissues in the expression of each UGT and the overall composition of UGT pools, consisting of different UGTs and their splice isoforms. Our results also revealed coexpression of the UGTs, Cytochrome P450s, and many transcription factors in the liver, suggesting potential coregulation or functional coordination. Our results provide the groundwork for future studies to detail further the regulation of the expression and activity of the UGTs.

Abstract Background Small intestine carcinoma (SIC) cases in Japan have recently been treated with chemotherapy according to colorectal carcinoma classification, while papilla of Vater carcinoma (PVC) cases according to cholangiocarcinoma (CHC) classification. However, few research reports support the molecular genetic validity of these therapeutic choices. Patients and methods Here, we investigated the clinicopathological and molecular genetic factors of SIC and PVC. We used the data from the Japanese version of The Cancer Genome Atlas. Additionally, molecular genetic data on gastric adenocarcinoma (GAD), colorectal adenocarcinoma (CRAD), pancreatic ductal adenocarcinoma (PDAC), and CHC were also referred to. Results This study consisted of tumor samples from 12 patients of SIC and three patients of PVC treated from January 2014 to March 2019. Among them, six patients had pancreatic invasion. t‐Distributed stochastic neighbor embedding analysis showed that the gene expression pattern of SIC was similar not only to those of GAD and CRAD, but also to that of PDAC in the pancreatic invasion patients. In addition, PVC resembled the GAD, CRAD, and PDAC, rather than the CHC. The molecular genetic characteristics of the six patients with pancreatic invasion were: one had high microsatellite instability, two had a TP53 driver mutation, and three had tumor mutation burden values

Abstract Snd1 is an evolutionarily conserved RNA‐binding protein implicated in several regulatory processes in gene expression including activation of transcription, mRNA splicing, and microRNA decay. Here, we have investigated the outcome of Snd1 gene deletion in the mouse. The knockout mice are viable showing no gross abnormalities apart from decreased fertility, organ and body size, and decreased number of myeloid cells concomitant with decreased expression of granule protein genes. Deletion of Snd1 affected the expression of relatively small number of genes in spleen and liver. However, mRNA expression changes in the knockout mouse liver showed high similarity to expression profile in adaptation to hypoxia. MicroRNA expression in liver showed upregulation of the hypoxia‐induced microRNAs miR‐96 and ‐182. Similar to Snd1 deletion, mimics of miR‐96/182 enhanced hypoxia‐responsive reporter activity. To further elucidate the function of SND1, BioID biotin proximity ligation assay was performed in HEK‐293T cells to identify interacting proteins. Over 50% of the identified interactors were RNA‐binding proteins, including stress granule proteins. Taken together, our results show that in normal growth conditions, Snd1 is not a critical factor for mRNA transcription in the mouse, and describe a function for Snd1 in hypoxia adaptation through negatively regulating hypoxia‐related miRNAs and hypoxia‐induced transcription consistent with a role as stress response regulator.