ShinyGO: a graphical gene-set enrichment tool for animals and plants

Chemical Carbonylation of Arginine in Peptides and Proteins

The chemoselective incorporation of arginine carbonylation post-translational modification (PTM) within proteins represents an underexplored frontier. This is largely due to the poor nucleophilicity and resistance to chemical oxidation of arginine. Drawing inspiration from the metal catalyzed oxidation (MCO) processes of arginine, we introduce a chemical methodology aimed at generating glutamate-5-semialdehyde from arginine residues within peptides and proteins. This innovative chemical approach capitalizes on the inherent weak nucleophilicity and oxidative properties of arginine. We also demonstrate the application of this strategy to selectively introduce both natural and unnatural post-translational modifications (PTMs) in a targeted manner. Our chemical approach offers a rapid, robust, and highly selective technique, facilitating chemoproteomic profiling of arginine sites prone to forming glutamate-5-semialdehyde PTM within the human proteome. Additionally, this methodology serves as a versatile platform for uncovering microenvironments that are susceptible to undergoing arginine carbonylation PTM, enabling the understanding of the effect of oxidative stress on arginine in proteins and the impact of these PTMs on cellular processes.

Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production

Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.

Limited Diversity of Thermal Adaptation to a Critical Temperature in Zymomonas mobilis: Evidence from Multiple-Parallel Laboratory Evolution Experiments

Laboratory evolution is an effective means of understanding microbial adaptation to the environment. We previously isolated four thermoadapted Zymomonas mobilis mutants, which showed a 2 °C rise in the critical high temperature (CHT), by performing multiple-parallel adaptation experiments. In the present study, the individual mutations in these mutants were intensively analyzed. Two mutations in each adapted mutant were found to primarily contribute to the increase in the upper temperature limit. RNA sequencing (RNA-seq) analysis revealed that the two mutations led to the upregulation of 79-185 genes and the downregulation of 242-311 genes. The findings from transcriptomic and physiological experiments suggest two common and primary mechanisms for thermal resistance: a decrease in the activity of diacylglycerol kinase, which may change the structure of lipopolysaccharide (LPS) probably to strengthen the membrane structure, and an increase in the expression of genes for GroEL/GroES or cell wall hydrolase to repair the protein or membrane damage that occurs at such critical temperatures. Additionally, transporters including efflux pumps may contribute to intracellular homeostasis by expelling toxic compounds such as ethanol and acetate or by maintaining the K+ concentration. The results of this study on four independently thermoadapted mutants led to the conclusion that the mutants have almost the same thermal adaptation strategies and thus their molecular diversity is limited.

Bisphosphonates Trigger Anti-Ageing Effects Across Multiple Cell Types and Protect Against Senescence

Bisphosphonates (BPs) have been the major class of medicines used to treat disorders of excessive bone loss for over five decades. Recently it has been recognized that BPs may also have additional significant beneficial extra-skeletal effects. These include a reduction of all-cause mortality and of conditions commonly linked to ageing, such as cancer and cardiovascular disease. Here we show that bisphosphonates co-localize with lysosomal and endosomal organelles in non-skeletal cells and stimulate cell growth at low doses. In vivo spatial transcriptomic analysis revealed differentially expressed senescence markers in multiple organs of aged BP-treated mice, and a shift in cellular composition toward those of young counterparts. Similarly, a 5000-plex plasma proteome analysis from osteopenic patients before and after BP-treatment showed significant alterations in ~400 proteins including GTPase regulators and markers of senescence, autophagy, apoptosis, and inflammatory responses. Furthermore, treatment with BPs protected against the onset of senescence in vitro. Proteome-wide target deconvolution using 2D thermal profiling revealed novel BP-binding targets (PHB2, ASAH1), and combined with RNA- and ATAC-seq of BP-treated cells and patient data, suggests downstream regulation of the MEF2A transcription factor within the heart. Collectively, these results indicate how BPs may beneficially modify the human plasma proteome, and directly impact multiple non-skeletal cell types through previously unidentified proteins, thereby influencing a range of pathways related to senescence and ageing.

tet2 and tet3 regulate cell fate specification and differentiation events during retinal development

Tet family methylcytosine dioxygenases recognize and oxidize 5-methyl-cytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Previous work demonstrated the requirement for Tet and 5hmC during zebrafish retinogenesis. tet2-/-;tet3-/- mutants possessed defects in the formation of differentiated retinal neurons, but the mechanisms underlying these defects are unknown. Here, we leveraged scRNAseq technologies to better understand cell type-specific deficits and molecular signatures underlying the tet2-/-;tet3-/- retinal phenotype. Our results identified defects in tet2-/-;tet3-/- retinae that included delayed specification of several retinal cell types, reduced maturity across late-stage cones, expansions of immature subpopulations of horizontal and bipolar cells, and altered biases of bipolar cell subtype fates at late differentiation stages. Together, these data highlight the critical role that tet2 and tet3 play as regulators of cell fate specification and terminal differentiation events during retinal development.

Transposon mutagenesis identifies acid resistance and biofilm genes as Shigella sonnei virulence factors in Caenorhabditis elegans infection

Identifying essential genes in bacterial pathogens during infection can enhance knowledge and provide novel targets for antimicrobial agents' development. Currently, only Shigella flexneri essential genes during in vitro growth have been experimentally identified. This study used transposon insertion sequencing (TIS) to identify Shigella sonnei essential genes during Caenorhabditis elegans infection. 498 genes were predicted to be essential in S. sonnei during growth on nutrient-rich media. Some genes previously predicted to be essential in Shigella were found non-essential in S. sonnei, such as acetyl metabolism genes (aceEF, lpdA) and sulphate transport genes (cysA, cyst, cysW). Finally, 217 genes were predicted as S. sonnei virulence genes during infection, including acid resistance and biofilm formation genes which was not linked to S. sonnei virulence previously.

Transcriptional signatures of hippocampal tau pathology in primary age-related tauopathy and Alzheimer's disease

In primary age-related tauopathy (PART) and Alzheimer's disease (AD), tau aggregates share a similar structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, transcriptional similarities between PART and AD and gene expression changes within tau-pathology-bearing neurons are largely unknown. Using GeoMx spatial transcriptomics, mRNA was quantified in hippocampal neurons with and without tau pathology in PART and AD. Synaptic genes were down-regulated in disease overall but up-regulated in tau-pathology-positive neurons. Two transcriptional signatures were associated with intraneuronal tau, both validated in a cortical AD dataset. Genes in the up-regulated signature were enriched in calcium regulation and synaptic function. Notably, transcriptional changes associated with intraneuronal tau in PART and AD were similar, suggesting a possible mechanistic relationship. These findings highlight the power of molecular analysis stratified by pathology and provide insight into common pathways associated with tau pathology in PART and AD.

Unveiling the fitness of Saccharomyces cerevisiae strains for lignocellulosic bioethanol: a genomic exploration through fermentation stress tests

Lignocellulosic biomass holds significant promise as a substrate for bioethanol production, yet the financial viability of lignocellulosic fermentation poses challenges. The pre-treatment step needed for lignocellulosic substrates generates inhibitors that impede Saccharomyces cerevisiae growth, affecting the fermentation process and overall yield. In modern sugarcane-to-ethanol plants, a rapid succession of yeast strains occurs, with dominant strains prevailing. Therefore, yeast strains with both dominance potential and inhibitor tolerance are crucial towards the development of superior strains with industrial fitness. This study adopted a hybrid approach combining biotechnology and bioinformatics to explore a cluster of 20 S. cerevisiae strains, including industrial and oenological strains exhibiting diverse phenotypic features. In-depth genomic analyses focusing on gene copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) were conducted and compared with results from fermentation tests once inoculated in multiple strains kinetics under stressing conditions such as low nitrogen availability and high formic or acetic acid levels. Some strains showed high resistance to biotic stress and acetic acid. Moreover, four out of 20 strains - namely S. cerevisiae YI30, Fp89, Fp90 and CESPLG05 - displayed promising resistance also to formic acid, the most impactful weak acids in pre-treated lignocellulosic biomass. These strains have the potential to be used for the development of superior S. cerevisiae strains tailored for lignocellulosic bioethanol production.

SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome

Type 1 diabetes (T1D) is linked to an altered gut microbiota characterized by reduced short-chain fatty acid (SCFA) production. Oral delivery of a SCFA-yielding biotherapy in adults with T1D was followed by increased SCFAs, altered gut microbiota and immunoregulation, as well as delaying diabetes in preclinical models. Here, we show that SCFA-biotherapy in humans is accompanied by remodeling of the gut proteome and mucosal immune homeostasis. Metabolomics showed arginine, glutamate, nucleotide and tryptophan metabolism were enriched following the SCFA-biotherapy, and found metabolites that correlated with glycemic control. Fecal microbiota transfer demonstrated that the microbiota of SCFA-responders delayed diabetes progression in humanized gnotobiotic mice. The protected mice increased similar metabolite pathways to the humans including producing aryl-hydrocarbon receptor ligands and reducing inflammatory mucosal immunity and increasing IgA production in the gut. These data demonstrate that a potent SCFA immunomodulator promotes multiple beneficial pathways and supports targeting the microbiota as an approach against T1D. Trial registration: Australia New Zealand Clinical Trials Registry ACTRN12618001391268.

Radiation exposure induces genome-wide alternative splicing events in Aedes aegypti mosquitoes

Sterile insect technique is a method to control insect pest populations by sterilizing males with ionizing radiation. However, radiation sickness lowers the fitness of sterilized males. In this study, we investigate impacts of ionizing radiation on gene transcription, specifically alternative splicing events in irradiated male Aedes aegypti mosquitoes. We compared RNA sequencing data from mosquitoes irradiated with a single standard X-ray dose of 50 Grey and un-irradiated control mosquitoes using the Multivariate Analysis of Transcript Splicing computational tool. We found that radiation exposure caused alternative splicing events in 197 genes that are involved in a variety of biological processes including the Hippo and Notch cell signaling pathways. Our results suggest that radiation damage produced by ionizing radiation can alter the splicing of genes involved in important biological functions in male Ae. aegypti mosquitoes. These findings identify several new leads for new projects aimed at understanding the impact of radiation-induced alternative splicing on mosquito fitness and improving sterile insect technique by the development of radio-resistant mosquito strains.

Evaluating sample normalization methods for MS-based multi-omics and the application to a neurodegenerative mouse model

Mass spectrometry (MS)-based omics methods have transformed biomedical research with accurate and high-throughput analysis of diverse molecules in biological systems. Recent technological advances also enabled multi-omics to be achieved from the same sample or on a single analytical platform. Sample normalization is a critical step in MS-omics studies but is usually conducted independently for each omics experiment. To bridge this technical gap, we evaluated different sample normalization methods suitable for analyzing proteins, lipids, and metabolites from the same sample for multi-omics analysis. We found that normalizing samples based on tissue weight or protein concentration before or after extraction generated distinct quantitative results. Normalizing samples first by tissue weight before extraction and then by protein concentration after extraction resulted in the lowest sample variation to reveal true biological differences. We then applied this two-step normalization method to investigate multi-omics profiles of mouse brains lacking the GRN gene. Loss-of-function mutations in the GRN gene lead to the deficiency of the progranulin protein and eventually cause neurodegeneration. Comparing the proteomics, lipidomics, and metabolomics profiles of GRN KO and WT mouse brains revealed molecular changes and pathways related to lysosomal dysfunction and neuroinflammation. In summary, we demonstrated the importance of selecting an appropriate normalization method during multi-omics sample preparation. Our normalization method is applicable to all tissue-based multi-omics studies, ensuring reliable and accurate biomolecule quantification for biological comparisons.

Divergent responses to SARS-CoV-2 infection in bronchial epithelium with pre-existing respiratory diseases

Pre-existing respiratory diseases may influence coronavirus disease (COVID-19) susceptibility and severity. However, the molecular mechanisms underlying the airway epithelial response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection severity in patients with chronic respiratory diseases remain unelucidated. Using an in vitro model of differentiated primary bronchial epithelial cells, we aimed to investigate the molecular mechanisms of SARS-CoV-2 infection in pre-existing cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). Our study revealed reduced susceptibility of CF and COPD airway epithelia to SARS-CoV-2, relative to that in healthy controls. Mechanistically, reduced transmembrane serine protease 2 (TMPRSS2) activity potentially contributed to this resistance of CF epithelium. Upregulated complement and inflammatory pathways in CF and COPD epithelia potentially primed the antiviral state prior to infection. Analysis of a COVID-19 patient cohort validated our findings, correlating specific inflammatory markers (IP-10, SERPINA1, and CFB) with COVID-19 severity. This study elucidates SARS-CoV-2 pathogenesis and identifies potential biomarkers for clinical monitoring.

Citrus flavonoids for overcoming breast cancer resistance to methotrexate: identification of potential targets of nobiletin and sinensetin

Breast cancer is a potentially fatal illness that affects millions of women worldwide. Methotrexate (MTX) may be beneficial for treating breast cancer; however, high doses and prolonged use can cause drug resistance. Although certain citrus flavonoids-nobiletin, sinensetin, tangeretin, hesperidin, hesperetin, and naringenin-may overcome resistance to chemotherapy, no study has investigated MTX resistance. This study investigated the potential of natural chemicals, specifically nobiletin and sinensetin, to overcome MTX resistance in breast cancer cells using MTX-resistant MCF-7 (MCF-7/MTX) and MCF-7 cells. Protein targets of citrus flavonoids were identified from multiple databases and were collected using Venny 2.1. Microarray data of MCF-7 and MCF-7/MTX cells were acquired from the Gene Expression Omnibus. Subsequently, we constructed a protein-protein interaction network and selected the hub proteins. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, drug- and disease-gene enrichment analyses, genetic alteration examination, receiver operating characteristic curve analysis, mRNA levels analysis, prognostic value analysis, and molecular docking analysis were performed along with in vitro experiments. Cytotoxicity of citrus flavonoids (individually and combined) was assessed in MCF-7/MTX cells. Nobiletin and sinensetin significantly enhanced the cytotoxicity of MTX in MCF-7/MTX cells. BCL2L1, CDK1, EGFR, PTGS2, PLK1, MMP2, ACHE, ABCG2, and KIT genes were enriched in cholinesterase activity, cell cycle regulation, and the PI3K/Akt signaling pathway. Nobiletin and sinensetin impeded PLK1, CDK1, and ACHE activities based on molecular docking. Nobiletin and sinensetin in combination with MTX may overcome breast cancer cell resistance to MTX.

ArfGAP2 promotes STING proton channel activity, cytokine transit, and autoinflammation

Stimulator of interferon genes (STING) transmits signals downstream of the cytosolic DNA sensor cyclic guanosine monophosphate-AMP synthase (cGAS), leading to transcriptional upregulation of cytokines. However, components of the STING signaling pathway, such as IRF3 and IFNAR1, are not essential for autoinflammatory disease in STING gain-of-function (STING-associated vasculopathy with onset in infancy [SAVI]) mice. Recent discoveries revealed that STING also functions as a proton channel that deacidifies the Golgi apparatus. Because pH impacts Golgi enzyme activity, protein maturation, and trafficking, we hypothesized that STING proton channel activity influences multiple Golgi functions. Here, we show that STING-mediated proton efflux non-transcriptionally regulates Golgi trafficking of protein cargos. This process requires the Golgi-associated protein ArfGAP2, a cell-type-specific dual regulator of STING-mediated proton efflux and signaling. Deletion of ArfGAP2 in hematopoietic and endothelial cells markedly reduces STING-mediated cytokine and chemokine secretion, immune cell activation, and autoinflammatory pathology in SAVI mice. Thus, ArfGAP2 facilitates STING-mediated signaling and cytokine release in hematopoietic cells, significantly contributing to autoinflammatory disease pathogenesis.

A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences

Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression of recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result in higher expression levels and can lead to protein misfolding and reduced expression. Here, we aimed to develop a novel deep learning (DL) tool using a recurrent neural network (RNN) to define cell type-dependent codon biases. Using gene expression data from three different tissue types (brain, liver, and muscle) and all secretory genes, we trained DL models to predict optimal codon usage. Codon-optimized sequences for test reporter genes exhibited enhanced protein expression compared to their original sequences and those optimized using a publicly available tool. Interestingly, DL models trained on genes expressed in liver cells (hepatocytes) resulted in the highest levels of expression when tested in vitro, irrespective of the cell type. Our findings also demonstrate that DL-based codon optimization algorithms can significantly enhance protein translation, particularly for secretory proteins, which are crucial for therapeutic applications. This research represents a novel approach to codon optimization with broader implications for protein-based pharmaceuticals, vaccine manufacturing, gene therapy, and other recombinant DNA products.

Brainstem neuropeptidergic neurons link a neurohumoral axis to satiation

Hunger is evolutionarily hardwired to ensure that an animal has sufficient energy to survive and reproduce. Just as important as knowing when to start eating is knowing when to stop eating. Here, using spatially resolved single-cell phenotyping, we characterize a population of neuropeptidergic neurons in the brainstem's dorsal raphe nucleus (DRN) and describe how they regulate satiation. These neurons track food from sensory presentation through ingestion, integrate these signals with slower-acting humoral cues, and express cholecystokinin (CCK). These CCK neurons bidirectionally regulate meal size, driving a sustained meal termination signal with a built-in delay. They are also well positioned to sense and respond to ingestion: they express a host of metabolic signaling factors and are integrated into an extended network known to regulate feeding. Together, this work demonstrates how DRN CCK neurons regulate satiation and identifies a likely conserved cellular mechanism that transforms diverse neurohumoral signals into a key behavioral output.

Computational molecular insights into ibrutinib as a potent inhibitor of HER2-L755S mutant in breast cancer: gene expression studies, virtual screening, docking, and molecular dynamics analysis

Background

The proposed study integrates several advanced computational techniques to unravel the molecular mechanisms underlying breast cancer progression and drug resistance.

Methods

We investigated HER2-L755S mutation through a multi-step approach, including gene expression analysis, molecular docking, and molecular dynamics simulations.

Results and Discussion

By conducting a network-based analysis of gene expression data from breast cancer samples, key hub genes such as MYC, EGFR, CDKN2A, ERBB2, CDK1, E2F1, TOP2A, MDM2, TGFB1, and FOXM1 were identified, all of which are critical in tumor growth and metastasis. The study mainly focuses on the ERBB2 gene, which encodes the HER2 protein, and its common mutation HER2-L755S, associated with breast cancer and resistance to the drug lapatinib. The HER2-L755S mutation contributes to both tumorigenesis and therapeutic failure. To address this, alternative therapeutic strategies were investigated using combinatorial computational approaches. The stability and flexibility of the HER2-L755S mutation were evaluated through comparative molecular dynamics simulations over 1000 ns using Gromacs in the unbound (Apo) state. Virtual screening with Schrodinger Glide identified ibrutinib as a promising alternative to lapatinib for targeting the HER2-L755S mutant. Detailed docking and molecular dynamics simulations in the bound (Holo) state demonstrated that the HER2-L755S-ibrutinib complex exhibited higher binding affinity and lower binding energy, indicating more stable interactions compared to other complexes. MM-PBSA analysis revealed that the HER2-L755S-ibrutinib complex had more negative binding energy than the HER2-L755S-afatinib, HER2-L755S-lapatinib, and HER2-L755S-neratinib complexes, suggesting that ibrutinib forms the most stable complex with favorable binding interactions.

Conclusion

These results provide in-depth atomic-level insights into the binding mechanisms of these inhibitors, highlighting ibrutinib as a potentially effective inhibitor for the clinical treatment of breast cancer.

Subtractive genomics and drug repurposing strategies for targeting Streptococcus pneumoniae: insights from molecular docking and dynamics simulations

Introduction

Streptococcus pneumoniae is a Gram-positive bacterium responsible for severe infections such as meningitis and pneumonia. The increasing prevalence of antibiotic resistance necessitates the identification of new therapeutic targets. This study aimed to discover potential drug targets against S. pneumoniae using an in silico subtractive genomics approach.

Methods

The S. pneumoniae genome was compared to the human genome to identify non-homologous sequences using CD-HIT and BLASTp. Essential genes were identified using the Database of Essential Genes (DEG), with consideration for human gut microflora. Protein-protein interaction analyses were conducted to identify key hub genes, and gene ontology (GO) studies were performed to explore associated pathways. Due to the lack of crystal structure data, a potential target was modeled in silico and subjected to structure-based virtual screening.

Results

Approximately 2,000 of the 2,027 proteins from the S. pneumoniae genome were identified as non-homologous to humans. The DEG identified 48 essential genes, which was reduced to 21 after considering human gut microflora. Key hub genes included gpi, fba, rpoD, and trpS, associated with 20 pathways. Virtual screening of 2,509 FDA-approved compounds identified Bromfenac as a leading candidate, exhibiting a binding energy of -26.335 ± 29.105 kJ/mol.

Discussion

Bromfenac, particularly when conjugated with AuAgCu2O nanoparticles, has demonstrated antibacterial and anti-inflammatory properties against Staphylococcus aureus. This suggests that Bromfenac could be repurposed as a potential therapeutic agent against S. pneumoniae, pending further experimental validation. The approach highlights the potential for drug repurposing by targeting proteins essential in pathogens but absent in the host.

Functional analysis of HvSNAC1 in stomatal dynamics and drought adaptation

Drought stress can damage crop growth and lead to a decline in yield, thereby affecting food security, especially in regions vulnerable to climate change. SNAC1 (stress-responsive NAC1), the NAC transcription factor family member, plays a crucial role in stomatal movement regulation. Effective regulation of stomatal movement is essential for protecting plants from water loss during adverse conditions. Our hypothesis revolves around altering HvSNAC1 activity by introducing a point mutation in its encoding gene, thereby influencing stomatal dynamics in barley. Two TILLING mutants, each harboring missense mutations in the NAC domain, exhibited higher stomatal density after drought stress compared to the parent cultivar 'Sebastian'. These mutants also demonstrated distinct patterns of ABA-induced stomatal movement compared to the wild-type (WT). To delve deeper, we conducted a comprehensive analysis of the transcriptomes of these mutants and the parent cultivar 'Sebastian' under both optimal watering conditions and 10 days of drought stress treatment. We identified differentially expressed genes (DEGs) between the mutants and WT plants under control and drought conditions. Furthermore, we pinpointed DEGs specifically expressed in both mutants under drought conditions. Our experiments revealed that the cis-regulatory motif CACG, previously identified in Arabidopsis and rice, is recognized by HvSNAC1 in vitro. Enrichment analysis led to the identification of the cell wall organization category and potential target genes, such as HvEXPA8 (expansin 8), HvXTH (xyloglucan endotransglucosylase/hydrolase), and HvPAE9 (pectin acetylesterase 9), suggesting their regulation by HvSNAC1. These findings suggest that HvSNAC1 may play a role in regulating genes associated with stomatal density, size and reopening.

The proteomic landscape of Toxoplasma gondii extracellular vesicles across diverse host cell types

Introduction

Extracellular vesicles (EVs) are emerging as powerful tools used by pathogens to manipulate host cells, delivering molecular cargo that rewires cellular processes and the immune response. Toxoplasma gondii, a globally distributed parasite capable of infecting nearly all nucleated animal cells, uses this strategy to thrive in diverse host species and tissue environments.

Methods

Here, we reveal the adaptability of T. gondii EVs through proteomic analysis of vesicles released from tachyzoites cultured in four different host cell types: human fibroblasts, green monkey kidney epithelial cells, mouse myoblasts and porcine intestinal epithelial cells.

Results

A core set of 1,244 proteins was consistently identified across TgEVs, defining a conserved signature. Beyond this conserved cargo, host-cell specific variation revealed how T. gondii fine-tunes EV content to exploit different cellular environments. Functional enrichment analyses revealed roles for TgEVs in targeting host protein synthesis and stress response pathways, with implications for immune evasion and infection spread.

Discussion

These findings provide insight into the potential role of EVs in host-pathogen interactions and help us understand the adaptive strategies used by T. gondii to survive and spread.

The gain-of-function UBE3AQ588E variant causes Angelman-like neurodevelopmental phenotypes in mice

Mutations in the E3 ubiquitin ligase UBE3A that cause enzymatic gain-of-function result in disease phenotypes which differ from classic Angelman syndrome. However, these phenotypes are highly heterogeneous raising questions about the mechanistic basis of such phenotypic diversity. Here, we characterize a mouse model harboring a Ube3aQ606E gain of function variant (UBE3AQ588E in humans). Extensive behavioral phenotyping showed that animals possessing a maternally inherited mutation (Ube3amQ606E) paradoxically show many behavioral deficits indicative of overall UBE3A loss-of-function. These included pronounced motor deficits, hypoactivity, and reduced stereotypic behaviors. Moreover, brain weights and MRI analysis revealed global microcephaly with a postnatal onset, consistent with phenotypes described in Angelman syndrome model mice. Additional biochemical analyses demonstrated an increased abundance of UBE3A substrates in brain tissue and immunofluorescence analyses showed that microcephaly is not caused by increased apoptotic cell death. Together, our results strongly suggest a novel mechanism by which the Ube3amQ606E mutation leads to enhanced self-targeted degradation of UBE3A, leading to an overall loss of enzyme activity, resulting in Angelman-like phenotypes in vivo.

A Promising Resveratrol Analogue Suppresses CSCs in Non-Small-Cell Lung Cancer via Inhibition of the ErbB2 Signaling Pathway

The ErbB2 signaling pathway plays a crucial role in cancer stem cells (CSCs), governing cancer aggressiveness and proliferation. Targeting ErbB2 holds promise for advancing cancer therapeutics. Resveratrol (RES) and its derivatives have been noted for their ability to target proteins that are involved in CSCs. In this investigation, we synthesize novel derivatives of RES, aim at elucidating structure-activity relationships (SARs) that could enhance the anticancer properties of the RES analogues, and explore their capacities to suppress CSCs. YI-12, an O-benzyl-substituted 1,3-diphenylpropane, demonstrated the most potent anticancer activity against lung cancer cells (A549 and H460), showing high potential inhibiting cancer colony formation. Interestingly, not only does YI-12 suppress CSCs-related proteins, indicated by decreased expression of CSC-enhancing molecules such as CD133-, OCT4-, and CSC-related protein β-catenin, but it also induces apoptosis in CSC-rich spheroids after treatment. Additionally, molecular docking and bioinformatic analysis suggest ErbB2 as a potential target of the compound with a strong binding affinity (-6.709 kcal/mol) compared to the reference compound TAK-285 (-5.563 kcal/mol). YI-12's capability to bind and inhibit ErbB2 leads to the suppression of PI3K and AKT. In conclusion, we highlight the novel resveratrol derivative YI-12 for its ability to inhibit CSCs through the ErbB2 signaling pathway. This compound represents a promising structure that should be further developed for potential use in anticancer therapy.

Itaconate targets the ERK2 signal to suppress estrogen receptor-positive breast cancer cell growth

Over 70% of breast cancers are estrogen receptor (ER)-positive, with Tamoxifen (Tam) being a standard treatment. However, around 40% of these cancers develop resistance to Tam, which poses a significant clinical challenge. The ACOD1/itaconate (ITA) axis, a metabolic pathway that produces itaconate, has shown promise in inhibiting the growth of ER-positive breast cancer cells. Nonetheless, it remains unclear how effective ITA is against Tam-resistant breast cancer cells and the underlying mechanisms involved. The current report found that Tam-resistant cells exhibit increased sensitivity to ITA compared to their parental cells and show a synergetic effect in combination treatment with Tam. An unbiased proteomic analysis revealed that upregulating the ERK2 signaling pathway contributes to the sensitivity of ER-positive breast cancer cells to ITA. ITA treatment increases ERK2 phosphorylation at T185/Y187 sites by directly alkylating cysteine 254, leading to ERK2 activation and subsequent cell growth inhibition. These effects were abolished in ITA allylation-resistant cells when a cysteine residue was replaced with serine. Additionally, itaconate-induced ERK2 phosphorylation and activation inhibits the growth of Tam-resistant breast cancer cells, which effect is advanced in phosphorylation-mimic ERK2_T185E-expressing cells but blocked in those expressing non-phosphorylation-mimic ERK2_T185A. Furthermore, activated ERK2 interacts physically with API5 to disrupt API5's localization to the nucleus speckle, where API5 may interact with other molecules critical in regulating cell growth-related genes. Our findings clarify the mechanism through which ITA exerts its effects on tamoxifen-sensitive and resistant breast cancer cells and highlight the potential of itaconate as an alternative treatment strategy against breast cancer.

The PPAR-α agonist oleoyethanolamide (OEA) ameliorates valproic acid-induced steatohepatitis in rats via suppressing Wnt3a/β-catenin and activating PGC-1α: Involvement of network pharmacology and molecular docking

Liver damage is one of the most severe side effects of valproic acid (VPA) therapy. Research indicates that PPAR-α prevents Wnt3a/β-catenin-induced PGC-1α dysregulation, which is linked to liver injury. Although PPAR-α activation has hepatoprotective effects, its role in preventing VPA-induced liver injury remains unclear. Our research used network analysis, molecular docking, and in-vivo validation to predict and assess targets and pathways associated with the hepatoprotective effects of oleoylethanolamide (OEA), a PPAR-α agonist, on VPA-induced steatohepatitis. For in-vivo experiments, 24 rats were assigned to V, OEA, VPA, and OEA + VPA. Liver functions, TGs, cholesterol, and LDL were tested. Hepatic levels of PPAR-α, ACO, TNF-α, IL-1β, HO-1, MDA, and TAC, along with Wnt3a/β-catenin, PGC-1α, and Nrf2 expression were assessed. Further, NF-κB, Bax, Bcl-2, and caspase-3 expression were detected immunohistochemically. Network pharmacology identified 258 targets for OEA-steatohepatitis connection, including NFKB1, PPARA, and NFE2L2, in addition to TNF, non-alcoholic fatty liver, NF-κB, PPAR, and WNT signaling, as contributing to steatohepatitis pathogenesis. The docking revealed a strong affinity between OEA and Wnt3a, β-catenin, and PGC-1α. Therefore, we postulated that the hepatoprotective effect of OEA may be due to Wnt3a/β-catenin-mediated inactivation of PGC1-α pathway. In vivo, OEA inhibited Wnt3a/β-catenin and increased PGC1-α by activating PPAR-α. Hence, PGC1-α reduced fat cell β-oxidation and NF-κB-mediated inflammation. OEA lessened MDA and raised TAC to mitigate oxidative damage. OEA additionally reduced apoptosis by lowering Bax/Bcl-2 ratio and caspase-3. In summary, PPAR-α involvement in the protective effects of OEA against VPA-induced steatohepatitis can be confirmed by suppressing Wnt3a/β-catenin and activating PGC-1α signaling.

Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway

In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.

Stabilization of Transcription Factor, HIF-1α by Prolylhydroxylase 1 Knockout Reduces Cardiac Injury After Myocardial Infarction in Mice

Inhibition of HIF-prolyl hydroxylases (PHD1, PHD2, and PHD3) causes the stabilization of hypoxia-inducible factor-1α and -2α (HIF-1α and HIF-2α) to regulate various cell signaling pathways. Hypoxia-inducible factor (HIF) is crucial in regulating signal responses mediated by hypoxia. HIF regulates the transcription of many genes involved in the response to hypoxia and ischemic insult. Our current work investigates the protective effects of PHD1 knockout in mice against myocardial infarction. Study Design: Myocardial infarction (MI) was induced by left anterior descending coronary artery (LAD) ligation (8-12-week-old mice) in both wild-type (WT) and PHD1 knockout (PHD1-/-) mice. WT sham (S) and PHD1-/-S group mice underwent surgery without LAD ligation. Thirty days post-surgery, cardiac functions were measured by echocardiogram. Mice in all the groups were euthanized at various time points for tissue collection post-MI 8 h (gel shift and microarray analysis), 4 days (Western blot analysis), 7 days (blood vessel density), or 30 days (histological analysis). For microarray analysis, WTMI and PHD1-/-MI group mices' heart tissue was used for RNA isolation, then hybridization to a GeneChip™ Mouse Gene 1.0 ST Array as per the manufacturer's instructions. Bioinformatic analysis was performed using the transcriptome analysis console (TAC) to generate a list of differentially regulated genes, followed by ingenuity pathway analysis. Results: The study findings revealed a significant increase in vessel density (capillary and arteriolar density) in the PHD1-/-MI mice compared to those with WTMI. The echocardiographic examination demonstrated that the PHD1-/-MI mice group had an increased ejection fraction and fractional shortening than the WT mice 30 days post-MI. HIF-1α DNA binding activity was higher in PHD1-/-MI mice than in WTMI. The Western blot analysis showed a significant increase in the expression of HSPA12B in the PHD1-/-MI compared to WTMI mice. Bioinformatic analysis using TAC software, Version 4.0.2.15 (1.5 fold, p < 0.05) showed 174 differentially regulated genes. Conclusions: In conclusion, our study showed PHD1 knockout activates several important molecules and signaling pathways, resulting in increased angiogenesis and cardioprotection against myocardial infarction.

Derivation of functional neurons from induced pluripotent stem cells using a simple neuromesodermal progenitor generation and rapid spinal cord neuron differentiation process

To generate spinal cord neurons from pluripotent stem cells via neuromesodermal progenitors (NMPs) is not only an important step for regenerative purposes but also required for human developmental research. This study describes a protocol to obtain spinal cord neurons in culture using induced pluripotent stem-cell-derived NMPs. The protocol starts with a 3D culture of NMPs and continues with the transfer of 3D NMPs to monolayer culture in which retinoic acid and sonic hedgehog pathways were triggered sequentially. The established protocol enabled generation of spinal cord neurons with active calcium signaling, electrophysiological activity, axon elongation capacity, and synaptic vesicle trafficking. The expression profile of marker proteins, including β-Tubulin, NeuroD1, Pax6, NeuN, Mnx-1, Isl1, Isl2, Map2, NF, Sox2 was detected to explore the production of developmental regulatory transcription factors and terminal differentiation markers in a time-dependent manner. Cells during differentiation process acquired a fully neural phenotype, which was confirmed by RNA sequencing at the molecular level. The protein expression profile showed neural differentiation induction pathways based on LS-MS/MS analysis. Since NMPs differentiate into spinal cord neuron cells at the developmental stage, the results of this study highlight the further potential of NMP-derived spinal cord neurons in disease modeling and treatment in the clinics.

Dapagliflozin in Chronic Kidney Disease: Insights from Network Pharmacology and Molecular Docking Simulation

Chronic kidney disease (CKD) involves inflammation, oxidative stress, and fibrosis, leading to renal dysfunction. Dapagliflozin, an SGLT2 inhibitor, shows renoprotective effects beyond glucose control, but its precise molecular mechanisms remain unclear. This study utilizes network pharmacology and molecular docking to elucidate its multi-target effects in CKD. Dapagliflozin's SMILES structure was analyzed for ADMET properties. Potential targets were identified via SwissTargetPrediction, GeneCards, and SEA, and common CKD-related targets were determined. A protein-protein interaction (PPI) network was constructed, and key pathways were identified using GO and KEGG enrichment analyses. Molecular docking was conducted to validate dapagliflozin's binding affinities with hub proteins. A total of 208 common targets were identified, including EGFR, GSK3β, and IL-6. GO and KEGG analyses highlighted key pathways, such as PI3K-Akt, MAPK, and AGE-RAGE, involved in inflammation, oxidative stress, and metabolic regulation. Molecular docking confirmed strong binding affinities with EGFR (-8.42 kcal/mol), GSK3β (-7.70 kcal/mol), and IL-6 (-6.83 kcal/mol). Dapagliflozin exhibits multi-target therapeutic potential in CKD by modulating inflammation, oxidative stress, and metabolic pathways. This integrative approach enhances the understanding of its mechanisms, supporting future experimental validation and clinical application in CKD management.

Draft whole genome sequence of Alternaria alternata strain P02PL2, an endophytic fungal species isolated from Sclerocarya birrea

Here, we report the draft whole genome sequence of an endophytic fungal species, Alternaria alternata P02PL2 isolated from Sclerocarya birrea. The genome of this isolate was sequenced using the MGISEQ 2000RS platform. The estimated genome size for A. alternata P02PL2 was 32.0 Mb with a GC content of 50.56%.

NAD+ prevents chronic kidney disease by activating renal tubular metabolism

Chronic kidney disease (CKD) is associated with renal metabolic disturbances, including impaired fatty acid oxidation (FAO). Nicotinamide adenine dinucleotide (NAD+) is a small molecule that participates in hundreds of metabolism-related reactions. NAD+ levels are decreased in CKD, and NAD+ supplementation is protective. However, both the mechanism of how NAD+ supplementation protects from CKD, as well as the cell types involved, are poorly understood. Using a mouse model of Alport syndrome, we show that nicotinamide riboside (NR), an NAD+ precursor, stimulated renal PPARα signaling and restored FAO in the proximal tubules, thereby protecting from CKD in both sexes. Bulk RNA-sequencing showed that renal metabolic pathways were impaired in Alport mice and activated by NR in both sexes. These transcriptional changes were confirmed by orthogonal imaging techniques and biochemical assays. Single-nuclei RNA sequencing and spatial transcriptomics, both the first of their kind to our knowledge from Alport mice, showed that NAD+ supplementation restored FAO in proximal tubule cells. Finally, we also report, for the first time to our knowledge, sex differences at the transcriptional level in this Alport model. In summary, the data herein identify a nephroprotective mechanism of NAD+ supplementation in CKD, and they demonstrate that this benefit localizes to the proximal tubule cells.

Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage

MAIN CONCLUSION

High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

The most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 and donor lung tissue with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage. We identify changes in cellular composition across progressive damage, including waves of molecularly distinct macrophages and depletion of epithelial and endothelial populations. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early damage, and fibrosis-related collagens in late damage. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation of SERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derived SPP1/osteopontin signalling as a key regulator during early steps of alveolar damage. These results provide a comprehensive, spatially resolved atlas of alveolar damage progression in COVID-19, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways in severe disease.

Mining yeast diversity unveils novel targets for improved heterologous laccase production in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a widely utilized host cell for recombinant protein production due to its well studied and annotated genome, its ability to secrete large and post-translationally modified proteins, fast growth and cost-effective culturing. However, recombinant protein yields from S. cerevisiae often fall behind that of other host systems. To address this, we developed a high-throughput screen of wild, industrial and laboratory S. cerevisiae isolates to identify strains with a natural propensity for greater recombinant protein production, specifically focussing on laccase multicopper oxidases from the fungi Trametes trogii and Myceliophthora thermophila. Using this method, we identified 20 non-laboratory strains with higher capacity to produce active laccase. Interestingly, lower levels of laccase mRNA were measured in most cases, indicating that the drivers of elevated protein production capacity lie beyond the regulation of recombinant gene expression. We characterized the identified strains using complementary genomic and proteomic approaches to reveal several potential pathways driving the improved expression phenotype. Gene ontology analysis suggests broad changes in cellular metabolism, specifically in genes/proteins involved in carbohydrate catabolism, thiamine biosynthesis, transmembrane transport and vacuolar degradation. Targeted deletions of the hexose transporter HXT11 and the Coat protein complex II interacting paralogs PRM8 and 9, involved in ER to Golgi transport, resulted in significantly improved laccase production from the S288C laboratory strain. Whereas the deletion of the Hsp110 SSE1 gene, guided by our proteomic analysis, also led to higher laccase activity, we did not observe major changes of the protein homeostasis network within the strains with higher laccase activity. This study opens new avenues to leverage the vast diversity of Saccharomyces cerevisiae for recombinant protein production, as well as offers new strategies and insights to enhance recombinant protein yields of current strains.

Short Exposures to Phosphine Trigger Differential Gene Expression in Phosphine-Susceptible and -Resistant Strains of Tribolium castaneum

BACKGROUND/OBJECTIVES

Phosphine resistance in insects involves a complex interplay of genetic and physiological factors, which are often poorly understood. Resistance to high concentrations of phosphine worldwide poses a formidable challenge for stored-product pest management and affects global food security. Understanding the genetic basis of phosphine resistance in the red flour beetle, Tribolium castaneum, is urgent because of the species' status as a notorious insect pest of stored grains and their resistance to major classes of insecticides. In this study, we take advantage of T. castaneum as a model species for biological and genetic studies.

METHODS

To tease apart genetic mutations and the differential expression of genes responding to phosphine intoxication, we set up 16 different exposure tests to compare the effects of phosphine dose, exposure time, and sampling time on gene expression in phosphine-susceptible and -resistant T. castaneum adults.

RESULTS

We examined the enrichment of gene ontology terms in genes that were differentially expressed and found that the data further distinguished differences in gene expression by insect strain, phosphine dose, exposure time, and recovery from phosphine exposure. The gene-encoding cytochrome P450 9e2 was expressed more in phosphine-resistant compared to phosphine-susceptible insects under all treatment conditions and was significantly higher in expression in resistant insects that were sampled after short or long phosphine exposures. Therefore, this gene may serve as a new phosphine resistance marker in T. castaneum and can further be utilized as a diagnostic tool for resistance detection.

CONCLUSIONS

These data are important to understand the complex molecular changes in insects that have reduced sensitivity to phosphine to develop new monitoring and resistance prevention strategies.

GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance

The growth of breast tumors is driven and controlled by a subpopulation of cancer cells resembling adult stem cells, which are called cancer stem-like cells (CSCs). In breast cancer, the function and maintenance of CSCs are influenced by protein O-GlcNAcylation and the enzyme responsible for this post-translational modification, O-GlcNAc transferase (OGT). However, the mechanism of CSCs regulation by OGT and O-GlcNAc cycling in breast cancer is still unclear. Analysis of the proteome and O-GlcNAcome, revealed GATAD2B, a component of the Nucleosome Remodeling and Deacetylase (NuRD) complex, as a substrate regulated by OGT. Reducing GATAD2B genetically impairs mammosphere formation, decreases expression of self-renewal factors and CSCs population. O-GlcNAcylation of GATAD2B at the C-terminus protects GATAD2B from ubiquitination and proteasomal degradation in breast cancer cells. We identify ITCH as a novel E3 ligase for GATAD2B and show that targeting ITCH genetically increases GATAD2B levels and increases CSCs phenotypes. Lastly, we show that overexpression of wild-type GATAD2B, but not the mutant lacking C-terminal O-GlcNAc sites, promotes mammosphere formation, expression of CSCs factors and drug resistance. Together, we identify a key role of GATAD2B and ITCH in regulating CSCs in breast cancer and GATAD2B O-GlcNAcylation as a mechanism regulating breast cancer stem-like populations and promoting chemoresistance.

Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle

During mitochondrial damage, information is relayed between the mitochondria and nucleus to coordinate precise responses to preserve cellular health. One such pathway is the mitochondrial integrated stress response (mtISR), which is known to be activated by mitochondrial DNA (mtDNA) damage. However, the causal molecular signals responsible for activation of the mtISR remain mostly unknown. A gene often associated with mtDNA mutations/deletions is Polg1, which encodes the mitochondrial DNA Polymerase γ (PolG). Here, we describe an inducible, tissue specific model of PolG mutation, which in muscle specific animals leads to rapid development of mitochondrial dysfunction and muscular degeneration in male animals from ~5 months of age. Detailed molecular profiling demonstrated robust activation of the mtISR in muscles from these animals. This was accompanied by striking alterations to enzymes in the mitochondrial folate cycle that was likely driven by a specific depletion in the folate cycle metabolite 5,10 methenyl-THF, strongly implying imbalanced folate intermediates as a previously unrecognised pathology linking the mtISR and mitochondrial disease.

Substance P Augments Chemokine Production by Staphylococcus aureus Infected Murine Osteoclasts

Staphylococcal osteomyelitis is a serious infection of the bone and joints characterized by progressive inflammatory tissue damage and leukocyte recruitment leading to net bone loss. Resident bone cells are capable of recognizing Staphylococcus aureus and initiating an inflammatory immune response that recruits leukocytes and alters bone homeostasis. Importantly, bone tissue is richly innervated with substance P containing nerve fibers and we have previously shown that this neuropeptide can augment the inflammatory responses of both osteoblasts and osteoclasts to S. aureus infection via neurokinin-1 receptors (NK-1R). Here, we have extended these studies by demonstrating that pharmacological inhibition of NK-1R ameliorates disease severity in a mouse model of staphylococcal osteomyelitis. This effect was associated with a significant reduction in leukocyte-attracting chemokine production following infection and reduced local levels of osteoclast and neutrophil activity. We then assessed the effect of S. aureus infection on bone-marrow derived osteoclast gene expression in the absence or presence of substance P. We determined that infection upregulates osteoclast expression of mRNAs encoding inflammatory mediators that include the neutrophil-attracting chemokines identified in vivo. Importantly, we found that, while substance P has no effect on chemokine mRNA expression in infected cells, this neuropeptide significantly increases the release of these chemokines by S. aureus challenged osteoclasts but not osteoblasts. Together, these data further support the ability of substance P to exacerbate inflammatory damage in staphylococcal osteomyelitis and indicate that this effect may be due, in part, to an augmentation of osteoclast immune responses that promote leukocyte recruitment.

Immunomodulatory role of the stem cell circadian clock in muscle repair

Circadian rhythms orchestrate physiological processes such as metabolism, immune function, and tissue regeneration, aligning them with the optimal time of day (TOD). This study identifies an interplay between the circadian clock within muscle stem cells (SCs) and their capacity to modulate the immune microenvironment during muscle regeneration. We reveal that the SC clock triggers TOD-dependent inflammatory gene transcription after injury, particularly genes related to neutrophil activity and chemotaxis. These responses are driven by cytosolic regeneration of the signaling metabolite nicotinamide adenine dinucleotide (oxidized form) (NAD+), as enhancing cytosolic NAD+ regeneration in SCs is sufficient to induce inflammatory responses that influence muscle regeneration. Mononuclear single-cell sequencing of the regenerating muscle niche further implicates the cytokine CCL2 in mediating SC-neutrophil cross-talk in a TOD-dependent manner. Our findings highlight the intersection between SC metabolic shifts and immune responses within the muscle microenvironment, dictated by circadian rhythms, and underscore the potential for targeting circadian and metabolic pathways to enhance tissue regeneration.

Divergent B-cell and cytotoxic TNK cell activation signatures in HLA-B27-associated ankylosing spondylitis and acute anterior uveitis

Ankylosing spondylitis (AS), also known as radiographic axial spondyloarthritis (r-axSpA), is an immune-mediated inflammatory disorder frequently associated with acute anterior uveitis (AAU). Both conditions share a strong association with the genetic risk factor, human leukocyte antigen (HLA)-B27. However, the immunophenotype underlying HLA-B27-associated AS and/or AAU pathophysiology remains known. Using cellular indexing of transcriptomes and epitopes (CITE-Seq) in a well-characterized cohort of 25 subjects-including AS (HLA-B27pos), AS+AAU (HLA-B27pos), AAU (HLA-B27pos), HCs (HLA-B27pos), and HCs (HLA-B27neg); N = 5/group-we identified transcriptomic differences at the single-cell level, along with differentially expressed cell surface markers. Our study elucidates both shared and distinct immune alterations linked to HLA-B27 and disease. Furthermore, we employed sparse decomposition of arrays (SDA) analysis, an unsupervised machine learning method, to examine the high-dimensional transcriptional landscape of our data and identify complex and nonlinear relationships. Our study identified HLA-B27- and disease-specific transcriptomic differences in AS and AAU. The immune profiles of AS+AAU closely resembled those of AS, suggesting AS plays a dominant role in immune dysregulation. SDA analysis further revealed dysregulated B-cell maturation and activation in AS subjects, whereas AAU subjects exhibited an enrichment of cytotoxic effector function in T and NK cells. However, both AS and AAU exhibited myeloid cell activation, a key process in initiating and sustaining inflammation. Additionally, both AS and AAU subjects showed a dampening in homeostatic function, i.e., the balance between identifying and actively eliminating foreign pathogens while preventing an immune response against self-antigens, suggesting that inflammation may arise from immune dysregulation. In conclusion, our results highlight overlapping myeloid effector involvement, along with distinct immunophenotypic responses, such as a decrease in naive B cells in AS subjects and a reduction in the CD8/NK cell population in AAU subjects. These results highlight a distinct set of immune mediators driving AS and AAU pathogenesis. Future studies incorporating HLA-B27-negative AS and AAU patients, along with validation of B-cell and myeloid dysfunction in these diseases, may provide novel biomarkers and therapeutic targets.

TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in patient-derived neurons

Monogenic pediatric neurodegenerative disorders can reveal fundamental cellular mechanisms that underlie selective neuronal vulnerability. TBCK-Encephaloneuronopathy (TBCKE) is a rare autosomal recessive disorder caused by stop-gain variants in the TBCK gene. Clinically, patients show evidence of profound neurodevelopmental delays, but also symptoms of progressive encephalopathy and motor neuron disease. Yet, the physiological role of TBCK protein remains unclear. We report a human neuronal TBCKE model, derived from iPSCs homozygous for the Boricua variant (p.R126X). Using unbiased proteomic analyses of human neurons, we find TBCK interacts with PPP1R21, C12orf4, and Cryzl1, consistent with TBCK being part of the FERRY mRNA transport complex. Loss of TBCK leads to depletion of C12ORF4 protein levels across multiple cell types, suggesting TBCK may also play a role regulating at least some members of the FERRY complex. We find that TBCK preferentially, but not exclusively, localizes to the surface of endolysosomal vesicles and can colocalize with mRNA in lysosomes. Furthermore, TBCK-deficient neurons have reduced mRNA content in the axonal compartment relative to the soma. TBCK-deficient neurons show reduced levels of the lysosomal dynein/dynactin adapter protein JIP4, which functionally leads to TBCK-deficient neurons exhibiting striking lysosomal axonal retrograde trafficking defects. Hence, our work reveals that TBCK can mediate endolysosomal trafficking of mRNA, particularly along lysosomes in human axonal compartments. TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in neurons, which likely contribute to the preferential susceptibility to neurodegeneration.

Leandro A, Leandro M, Peralta J, Williams-Blangero S, Sanchez EE, Galan JA, Blangero J, Curran JE. Neurocellular Stress Response to Mojave Type A Rattlesnake Venom: Study of Molecular Mechanisms Using Human iPSC-Derived Neural Stem Cell Model

The Mojave rattlesnake venom shows significant geographical variability. The venom of Type A animals primarily contains β-neurotoxin referred to as Mojave Toxin (MTX), which makes bites from this snake particularly feared. We performed a genome-wide transcriptomic analysis of the neurocellular response to Mojave Type A rattlesnake venom using induced pluripotent stem cell-derived neural stem cells to unveil the molecular mechanisms underlying the damage caused by this snake's envenomation. Our results suggest that snake venom metalloproteases, although having a limited repertoire in Type A venom, facilitate venom spread by digesting the tissue's extracellular matrix. The MTX, which is composed of heterodimers of basic and acidic phospholipase-A2, co-opts the host arachidonic acid and Ca2+ second messenger mechanisms and triggers multiple signaling cascades, such as the activation of MAPKs and NF-κB-regulated proinflammatory genes; the neurotransmitter overload in excitatory synapses leading to a presynaptic blockade of nerve signals; and the upregulation of unfolded protein response (UPR) due to the depletion of Ca2+ from the endoplasmic reticulum. The upregulated UPR and the oxidative stress caused by reactive oxygen species generated in cytochromeP4501A1-mediated hydroxylation of arachidonic acid contribute to mitochondrial toxicity. The activation of UPR, mitochondrial toxicity, and oxidative stress synergistically contributed to apoptotic and ferroptotic cell death.

Transcriptome analysis of wild olive (Olea Europaea L. subsp. europaea var. sylvestris) clone AC18 provides insight into the role of lignin as a constitutive defense mechanism underlying resistance to Verticillium wilt

Host resistance is the most effective and practical control method for the management of Verticillium wilt in olive caused by Verticillium dahliae, which remains as one of the major current threats to this crop. Regrettably, most olive cultivars of agronomic and commercial interest are susceptible to V. dahliae. We previously demonstrated that wild olive (Olea europaea L. subsp. europaea var. sylvestris) clone AC18 harbours resistance to the highly virulent defoliating (D) V. dahliae pathotype, which may be valuable as rootstock and for breeding new, resistant olive cultivars. Mechanisms underlying disease resistance may be of constitutive or induced nature. In this work we aim to unravel constitutive defences that may be involved in AC18 resistance, by comparing the transcriptome from uninfected stems, of AC18 with that of the highly susceptible wild olive clone AC15, GO-term enrichment analysis revealed terms related to systemic acquired resistance, plant cell wall biogenesis and assembly, and phenylpropanoid and lignin metabolism. qRT-PCR analysis of phenylpropanoid and lignin metabolism-related genes showed differences in their expression between the two wild olive clones. Phenolic content of stem cell walls was higher in the resistant AC18. The total lignin content was similar in resistant and susceptible clones, but they differed in monolignol composition. Results from this work identifies putative key genes in wild olive that could aid in breeding olive cultivars resistant, to D. V. dahliae. The research highlights the constitutive defence mechanisms that are effective in protecting against pathogens and our findings may contribute to the deciphering the molecular basis of VW resistance in olive and the conservation and utilization of wild olive genetic resources to tackle future agricultural challenges towards.

Protective targets of PfSPZ vaccines identified from whole-genome sieve analysis of isolates from malaria vaccine efficacy trials in West Africa

Identification of antigens targeted by a protective response is a central quest in malaria vaccinology. Whole-genome sieve analysis (SAWG) in samples collected from placebo-controlled field trials of Plasmodium falciparum (Pf) sporozoite (SPZ) vaccines may enable identification of Pf pre-erythrocytic antigens. We applied SAWG to genomic data generated from Pf isolates collected during two field trials measuring the efficacy, in malaria-exposed African adults, of two PfSPZ vaccines. These randomized, double-blind, placebo-controlled trials were conducted in regions of Mali and Burkina Faso characterized by high seasonal transmission, where parasite genetic diversity is high. Genomic sites in which the vaccine allelic state was significantly underrepresented among breakthrough infections in vaccinees relative to placebo recipients were termed "target sites". Protein-coding loci containing target sites that changed amino acids were termed "target loci". The SAWG conducted on clinical trial samples from the Burkina Faso and Mali trials identified 138 and 80 single-copy protein-coding target loci in the Burkinabe and Malian data sets, respectively, with twelve common to both, a number significantly higher than expected (E = 3.9; 99%CI = [0, 9]). Among these was the thrombospondin-related anonymous protein locus, which encodes PfSSP2|TRAP, one of the most abundant and well-characterized pre-erythrocytic stage antigen as well as other genes encoding membrane-associated proteins of unknown function. These results identify SAWG as a potentially powerful tool for identifying protective vaccine antigens in recombining pathogens with large genome size and reveals potential new protective Pf antigens.

Single-cell transcriptomics of clinical grade adipose-derived regenerative cells reveals consistency between donors independent of gender and BMI

Adipose-derived regenerative cells (ADRCs) also referred to as the stromal vascular fraction, provide an ample source of stem cells with widespread regenerative therapeutic use. Being heterogenous in nature, possibly affecting the clinical outcome after stem cell treatment, the ADRC- donor, -BMI, and -gender may have a large impact on ADRC composition and quality but this remains largely unexplored. Herein, we provide a comprehensive single-cell RNA sequencing ADRC mapping across two cell trial intervention studies but found no gender- or BMI-related variations, except for a minor female increase in PI16/CD55-expressing stem cells. Indeed, ADRC heterogeneity was surprisingly minimal between donors. This provides important decision-making support on adipose stem cell donor selection for stem cell treatments, and suggest that donor, gender and BMI should be regarded as less influential.

Novel De Novo BRCA2 Variant in an Early-Onset Ovarian Cancer Reveals a Unique Tumor Evolution Pathway

Ovarian cancer (OC) is a highly heterogeneous malignancy, often characterized by complex genomic alterations that drive tumor progression and therapy resistance. In this paper, we report a novel de novo BRCA2 germline variant NM_000059.3:c.(8693_8695delinsGT) associated with early-onset OC that featured two regions with differential MMR (Mismatch Repair) gene expression. To date, only six cases of de novo BRCA2 variants have been reported, none of which were associated with early-onset high-grade serous OC. The immunohistochemical analysis of MMR genes revealed two distinct tumor areas, separated by a clear topographic boundary, with the heterogeneous expression of MLH1 and PMS2 proteins. Seventy-five percent of the tumor tissue showed positivity, while the remaining 25% exhibited a complete absence of expression, underscoring the spatial variability in MMR gene expression within the tumor. Integrated comparative spatial genomic profiling identified several tumor features associated with the genetic variant as regions of loss of heterozygosity (LOH) that involved BRCA2 and MLH1 genes, along with a significantly higher mutational tumor burden in the tumor area that lacked MLH1 and PMS2 expression, indicating its further molecular evolution. The following variants were acquired: c.6572C>T in NOTCH2, c.1852C>T in BCL6, c.191A>T in INHBA, c.749C>T in CUX1, c.898C>A in FANCG, and c.1712G>C in KDM6A. Integrated comparative spatial proteomic profiles revealed defects in the DNA repair pathways, as well as significant alterations in the extracellular matrix (ECM). The differential expression of proteins involved in DNA repair, particularly those associated with MMR and Base Excision Repair (BER), highlights the critical role of defective repair mechanisms in driving genomic instability. Furthermore, ECM components, such as collagen isoforms, Fibrillin-1, EMILIN-1, Prolargin, and Lumican, were found to be highly expressed in the MLH1/PMS2-deficient tumor area, suggesting a connection between DNA repair deficiencies, ECM remodeling, and tumor progression. Thus, the identification of the BRCA2 variant sheds light on the poorly understood interplay between DNA repair deficiencies and ECM remodeling in OC, providing new insights into their dual role in shaping tumor evolution and suggesting potential targets for novel therapeutic strategies.

Network pharmacology exploring the mechanistic role of indirubin phytoconstituent from Indigo naturalis targeting GSK-3β in Alzheimer's disease

One of the most common causes of dementia in older adults is Alzheimer's disease (AD). Numerous mechanisms, including acetylcholine breakdown, amyloid beta buildup, neurofibrillary tangle accumulation, and inflammation, are involved in the pathogenesis of AD. Different targets have been demonstrated in studies to alleviate the cognitive impairment in AD. In AD, amyloid β impairs phosphatidylinositol-3 (PI3)/Akt signaling, activating GSK-3β. This sequence leads to an increase in the phosphorylation of tau, the creation of neurofibrillary tangles, neuronal death, loss of synapses, and memory impairments, all of which are typical symptoms seen in the brains of individuals with AD. Using network pharmacology, molecular docking, and MD simulations, we have determined that indirubin can selectively interact with glycogen synthase kinase 3 beta (GSK-3β). Traditional Chinese Medicine, including Indigo naturalis, is known to have the ability to control chronic diseases having indirubin as the main phytoconstituent. The binding energy of indirubin was -10.9 kcal/mol, which was better than that of the reference ligand with -9.4 kcal/mol. According to MD simulations, the indirubin-GSK-3β complex remained stable during the simulation, exhibiting an RMSD of 1.90 in comparison to the 2.01 and 2.34 for reference-GSK-3β complex and free protein, respectively. According to our study, indirubin phytoconstituent from Indigo naturalis, targets GSK-3β in AD, additional investigation in the quest for inhibitors of this crucial biological target required further in-vitro/in-vivo experimental validations.

Deciphering age-related transcriptomic changes in the mouse retinal pigment epithelium

Aging of the retinal pigment epithelium (RPE) leads to a gradual decline in RPE homeostasis over time, significantly impacting retinal health. Understanding the mechanisms underlying RPE aging is crucial for elucidating the background in which many age-related retinal pathologies develop. In this study, we compared the transcriptomes of young and aged mouse RPE and observed a marked upregulation of immunogenic, proinflammatory, and oxidative stress genes in aging RPE. Additionally, aging RPE exhibited dysregulation of pathways associated with visual perception and extracellular matrix production. Research on aging in post-natal quiescent RPE is hindered by the absence of relevant in vitro models. Here, we evaluated an in vitro model of chronologically aged primary human RPE to address this gap and observed gene expression patterns comparable to native-aged RPE. Gene expression profiling in this model highlighted its potential utility in investigating cellular and molecular mechanisms of RPE aging and in screening of therapeutic compounds. In conclusion, our findings underscore the pivotal role of inflammation, immune activation, and oxidative stress in the aging RPE landscape and provide insights into why age increases the risk of retinal pathologies.

Transcriptional Profiling of Abomasal Mucosa from Young Calves Experimentally Infected with Ostertagia ostertagi

Ostertagia ostertagi, also known as the brown stomach worm, causes significant pathology in the abomasum, resulting in production and nutritional losses in cattle. Alternative control measures, such as vaccination, are urgently needed because of rapidly growing anthelmintic drug resistance. There is a need to understand host responses to the infection, especially immune responses, to advance vaccine discovery and design. Therefore, the present study investigated comprehensive changes in gene transcription in the abomasal mucosa of cattle infected with O. ostertagi at 0, 3-5, 7-9, 10, and 21 days post-infection (dpi) using RNA sequencing (RNA-seq). Compared to uninfected controls, infected animals exhibited significant increases in differentially expressed genes (DEGs) throughout the infection period. Infection induced more upregulated than downregulated genes in the abomasal fundic mucosa (FUN) when compared to the abomasal pyloric mucosa (PYL). The largest transcriptional changes occurred between 7-9 and 10 dpi during the final development of the L4 and their emergence from the gastric glands. Most DEGs are associated with host immunity, cellular reorganization, cell migration, and proliferation. Tuft/epithelial cell response to the infection was atypical, lacking an anticipated increase in key alarmin cytokine genes. Numerous genes associated with T helper (Th) 1, Th2, and Th17 responses and T cell exhaustion were upregulated, suggesting altered immune regulation. The data collectively indicate that O. ostertagi infection elicits massive host responses, particularly immune responses, which are intertwined with the parasite's disruption of abomasal function, which likely impairs the nutrient utilization of the host. The infection is characterized by the absence of a dominant Th response and displaying a mixed activation of Th1, Th2, and Th17 pathways. Elevated expression of T cell exhaustion genes and lack of increase in epithelial alarmin cytokine genes suggest a downregulation of, or a deficiency in initiating, effective host immunity to the infection. Understanding mechanisms of parasite-mediated immune evasion and their nutritional consequences will facilitate the rational design of protective vaccines against infections of complex nematode parasites.

Selenoprotein O Promotes Melanoma Metastasis and Regulates Mitochondrial Complex II Activity

Evolutionarily conserved selenoprotein O (SELENOO) catalyzes a posttranslational protein modification known as AMPylation that is essential for the oxidative stress response in bacteria and yeast. Given that oxidative stress experienced in the blood limits survival of metastasizing melanoma cells, SELENOO might be able to affect metastatic potential. However, further work is needed to elucidate the substrates and functional relevance of the mammalian homolog of SELENOO. In this study, we revealed that SELENOO promotes cancer metastasis and identified substrates of SELENOO in mammalian mitochondria. In patients with melanoma, high SELENOO expression was correlated with metastasis and poor overall survival. In a murine model of spontaneous melanoma metastasis, SELENOO deficiency significantly reduced metastasis to distant visceral organs, which could be rescued by treatment with the antioxidant N-acetylcysteine. Mechanistically, SELENOO AMPylated multiple mitochondrial substrates, including succinate dehydrogenase subunit A, one of the four key subunits of mitochondrial complex II. Consistently, SELENOO-deficient cells featured increased mitochondrial complex II activity. Together, these findings demonstrate that SELENOO deficiency limits melanoma metastasis by modulating mitochondrial function and oxidative stress. Significance: SELENOO alters mitochondrial function and supports metastasis in melanoma, highlighting the impact of SELENOO-mediated posttranslational modification of mitochondrial substrates and selenoproteins in cancer progression.

Genome-wide discovery of underlying genetic factors associated with fresh and frozen-thawed semen traits in composite ram breeds exhibiting different cryotolerance

Fewer studies investigate the effects of underlying genetic factors related to semen characteristics, significantly affecting sheep farm profitability. This study aimed to identify single nucleotide polymorphisms (SNP) and genomic regions associated with fresh and frozen-thawed semen traits in rams with low (Hasak) and high (Hasmer) cryotolerance. Semen collected from 11 (5 Hasak with low and 6 Hasmer with high cryotolerance) rams cryopreserved in 0.25 ml straws in the breeding season. Quality characteristics were determined in fresh, equilibrated, and frozen-thawed semen. A Genome-Wide Association Study (GWAS) was conducted to unveil the genetic structure that might be attributed to cryotolerance in low and high cryotoleranced rams. Fresh (regarding total and progressive motility) and equilibrated semen quality were similar in Hasak and Hasmer rams (p > 0.6). However, the freeze-thawing process had a more pronounced negative effect on ram semen traits in Hasak than in Hasmer (p < 0.05). GWAS revealed 27 SNPs correlated with post-thaw semen parameters. Moreover, network analyses revealed pathways related to sperm ion channels and their activities, providing insights into the intricate molecular mechanisms underlying sperm physiology and emphasizing their role in potentially impacting sperm cryotolerance. The functional significance of detected SNPs and the associated pathways require further exploration.