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

Photoperiod-driven testicular DNA methylation in gonadotropin and sex steroid receptor promoters in Siberian hamsters

Seasonal cycles in breeding, often orchestrated by annual changes in photoperiod, are common in nature. Here, we studied how change in photoperiod affects DNA methylation in the testes of a highly seasonal breeder: the Siberian hamster (Phodopus sungorus). We hypothesized that DNA methylation in promoter regions associated with key reproductive genes such as follicle-stimulating hormone receptor in the testes is linked to breeding and non-breeding states. Using Oxford Nanopore sequencing, we identified more than 10 million (10,151,742) differentially methylated cytosine-guanine (CpG) sites in the genome between breeding long photoperiod and non-breeding short photoperiod conditions. ShinyGo enrichment analyses identified biological pathways consisting of reproductive system, hormone-mediated signalling and gonad development. We found that short photoperiod induced DNA methylation in the promoter regions for androgen receptor (Ar), estrogen receptors (Esr1, Esr2), kisspeptin1 receptor (kiss1r) and follicle-stimulating hormone receptor (Fshr). Long photoperiods were observed to have higher DNA methylation in promoters for basic helix-loop-helix ARNT-like 1 (Bmal1), progesterone receptor (Pgr) and thyroid-stimulating hormone receptor (Tshr). Our findings provide insights into the epigenetic mechanisms underlying seasonal adaptations in timing reproduction in Siberian hamsters and could be informative for understanding male fertility and reproductive disorders in mammals.

Normative aging results in degradation of gene networks in a zebra finch basal ganglia nucleus dedicated to vocal behavior

Aging increases brain susceptibility to neurodegenerative diseases, but the mechanisms are not clear. Vocal behavior provides an accessible, reliable, and sensitive biomarker to address this because voice changes in middle age can be early indicators of neurodegenerative diseases. The adult male zebra finch is an excellent model organism for these studies due to well-characterized vocal brain circuitry and strong homology to human brain centers. We performed RNA sequencing of song-dedicated basal ganglia nucleus Area X followed by weighted gene co-expression network analyses to examine changes in gene patterns across younger adult, middle, and older ages. Song-correlated gene networks degrade with age, with modules losing their coherence and migrating to different sets of genes, and changes in connection strength particularly for hub genes including those associated with human speech, Parkinson's, and Alzheimer's diseases. Gene pathway enrichment analyses reveal a lack of ongoing metabolic and biogenic processes in older finches. Our findings provide a robust platform for targeting network hubs in the treatment of neurologically driven human vocal disorders.

HaloPROTAC3 treatment activates the unfolded protein response of the endoplasmic reticulum in nonengineered mammalian cell lines

Proteins fused to HaloTag, an engineered haloalkane dehalogenase, can be depleted by a heterobifunctional degrader compound HaloPROTAC3. The binding of HaloPROTAC3 to both the HaloTag and the E3 ligase von Hippel-Lindau (VHL) brings them into proximity and mediates the degradation of the HaloTag fusion proteins. Here, we generated a colon cancer cell line HCT116 expressing HaloTag fused to the RNA-binding protein IGF2BP3 to study its function. HaloPROTAC3 treatment depleted 75% of HaloTag-IGF2BP3 in 5 h. Transcriptomics revealed that HaloPROTAC3 treatment resulted in the destabilization of IGF2BP3 target mRNAs and activated the unfolded protein response (UPR). Surprisingly, we found that HaloPROTAC3 results in UPR activation in nonengineered mammalian cells. Our data demonstrate that HaloPROTAC3 causes mild endoplasmic reticulum stress independent of IGF2BP3 function and shall guide future studies using the HaloPROTAC3 protein depletion strategy.

Proteome Reprogramming and Acquired Stress Tolerance in Potato Cells Exposed to Acute or Stepwise Water Deficit

Water deficit negatively impacts crop productivity and quality. Plants face these challenges by adjusting biological processes and molecular functions according to the intensity and duration of the stress. The cultivated potato (Solanum tuberosum) is considered sensitive to water deficit, thus breeding efforts are needed to enhance its resilience. To capture novel functional information and gene regulatory networks, we carried out mass spectrometry-based proteomics in potato cell suspensions exposed to abrupt or stepwise osmotic stresses. Both forms of stress triggered significant alterations in protein expression, though with divergent response mechanisms. Stress response pathways orchestrated by key proteins enrolled in primary and secondary metabolism, antioxidant processes, transcriptional and translational machinery and chromatin organization were found in adapted cells. Target metabolites and reactive oxygen species levels were quantified to associate functional outcomes with the proteome study. Remarkably, we also showed that adapted cells tolerate an array of diverse conditions, including anoxia, salt and heat stress. Finally, the expression patterns of genes encoding selected differentially expressed proteins were investigated in potato plants subjected to either drought or salt stress. Collectively, our findings reveal the complex cellular strategies of osmotic stress adaptation, identifying new fundamental genes that could enhance potato resilience.

Large Inversions Shape Diversification and Genome Evolution in Common Quails

Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.

Proteomics analysis of extracellular vesicles during Vibrio anguillarum infection in lumpfish (Cyclopterus lumpus)

Lumpfish (Cyclopterus lumpus) is a native fish of the North Atlantic Ocean used as sea lice biocontrol in Atlantic salmon farms. Lumpfish also has been used as model for marine infectious diseases and immunity. Lumpfish is susceptible to Vibrio anguillarum infection, and upon infection, lumpfish immunity is activated to preclude the disease progression. Extracellular vesicles (EVs) play an important role in early immune cellular communication. Lumpfish EVs and their potential role in immunity have not been explored. Herein, EVs where isolated from serum of naïve lumpfish and from lumpfish infected with V. anguillarum at 5 and 10 days post infection (dpi). EVs characteristics were studied by electron microscopy and nanoparticle tracking, and protein cargo was analysed by Western blot and proteomic analysis. The isolated EVs showed a spherical shape ranging from ∼30 nm to 300 nm in diameter, but at 5 dpi the size variation was higher. A total of 395 proteins were identified. Upregulated proteins were linked to complement pathway/innate immunity, heme/iron binding, defense response to bacterium, apoptotic signaling pathway, and actin binding. Downregulated proteins were associated with ribonucleoprotein/ribosomal protein, transport and translation elongation factor activity, acute phase, protein phosphorylation and apoptotic process. Upon infection V. anguillarum infection, lumpfish EVs cargo was modified, from transporting metabolic proteins to proteins related to immunity. Characterization of peripheral lumpfish EVs protein profile during V. anguillarum infection provided with potential biomarkers repertoire that could be utilised in the development of novel tools to diagnose and control of V. anguillarum infection in finfish aquaculture.

Conservation of the Polyamines Pathway in Ustilaginomycetes A Genomic and Experimental Approach

Polyamines are organic and aliphatic molecules essential for the growth, development, and survival of both eukaryotes and prokaryotes. In fungi, polyamines play a crucial role in cellular differentiation and pathogenesis. Since fungi and animals are closely related evolutionarily, and fungi can be easily genetically manipulated in the lab, they serve as excellent models for studying polyamine metabolism and the molecular mechanisms controlled by these biomolecules. Although the metabolism of polyamines has been extensively studied in model fungi such as Saccharomyces cerevisiae and Ustilago maydis, the conservation of the polyamine biosynthesis pathway in other Ustilaginomycetes, a class of fungi that includes phytopathogens, saprophytes, mutualists, and mycorrhizae, has not been thoroughly investigated. In this study, using a genomic and bioinformatics approach, we analyzed the conservation of the polyamine biosynthesis pathway in Ustilaginomycetes. Additionally, we confirmed the functional conservation of ornithine decarboxylase (Odc), which is involved in the synthesis of putrescine, one of the most important polyamines in fungi and complex multicellular eukaryotic organisms, using genetics and molecular biology tools. Moreover, we identified the differentially regulated genes by this polyamine in U. maydis. This research provides insights into the similarities and differences in the conservation of the polyamine biosynthesis pathway in fungi, and it expands our understanding of the role of polyamines and the mechanisms regulated by these molecules in eukaryotes.

Human skeletal muscle possesses both reversible proteomic signatures and a retained proteomic memory after repeated resistance training

Investigating repeated resistance training (RT) separated by a training break enables exploration of the potential for a proteomic memory of RT-induced skeletal muscle growth, i.e. retained protein adaptations from the previous RT. Our aim was to examine skeletal muscle proteome response to 10-week RT (RT1) followed by 10-week training cessation (i.e. detraining, DT), and finally, 10-week retraining (RT2). Thirty healthy, untrained participants conducted either periodic RT (RT1-DT-RT2, n = 17) or a 10-week no-training control period (n = 13) followed by 20 weeks of RT (n = 11). RT included twice-weekly supervised whole-body RT sessions, and resting vastus lateralis biopsies were obtained every 10 weeks for proteomics analysis using high-end dia-PASEF's mass spectrometry. The first RT period altered 150 proteins (93% increased) involved in, for example, energy metabolism and protein processing compared to minor changes during the control period. The proteome adaptations were similar after the second RT compared to baseline demonstrating reproducibility in proteome adaptations to RT. Many of the proteins induced by RT1 were reversed towards baseline after detraining and increased again after retraining. These reversible proteins were especially involved in aerobic energy metabolism. Interestingly, several proteins which increased after RT1 remain elevated (i.e. retained) after detraining, including carbonyl reductase 1 (CBR1) and proteins involved in muscle contraction, cytoskeleton and calcium binding. Among the latter, calcium-activated protease calpain-2 (CAPN2) has been recently identified as an epigenetic muscle memory gene. We show that resistance training evokes retained protein levels even after 2.5 months of no training, which demonstrates a potential proteomic memory of resistance training-induced muscle growth in human skeletal muscle. KEY POINTS: Repeated resistance training in humans separated by a training break (i.e. detraining) enables the identification of temporal protein signatures over the training, detraining and retraining periods, as well as studying reproducibility of protein changes to resistance training. Muscle proteome adaptations were similar after a second period of resistance training, demonstrating reproducibility in proteome adaptations to earlier resistance training. Many of the proteins induced by resistance training were reversed towards baseline after detraining and increased again after retraining. These reversible proteins were especially involved in aerobic energy metabolism. Several proteins increased after resistance training remain elevated (i.e. retained) after detraining, including carbonyl reductase 1 (CBR1) and calcium-binding proteins such as calpain-2 (CAPN2), a recently identified epigenetic muscle memory gene. Human skeletal muscle experiences retained protein changes following resistance training persisting over 2 months, demonstrating a potential proteomic memory of resistance training-induced muscle growth.

Food Restriction Induces Changes in Ovarian Folliculogenesis, Cell Proliferation, Apoptosis, and Production of Regulatory Peptides in Rabbits

The aim of this study is to examine the influence of food restriction on rabbit ovarian functions. A total of eight females were fed ad libitum (NF), while eight females were subjected to 50% food restriction (RF). One month later, all females were euthanized. Weights and lengths of ovaries and uterine horns were measured. Representative parts of the ovaries were subjected to histomorphometry analysis of folliculogenesis. Granulosa cells were isolated and cell viability, proliferation (accumulation of PCNA, cyclin B1, and BrdU-positive cells), apoptosis (accumulation of bax, caspase 3, and DNA fragmentation) were evaluated. Granulosa cells were subjected to proteomic analysis by using the nano HPLC-Chip-MS/MS method. Estradiol and progesterone release by ovarian and granulosa cells was assessed by ELISA. Ovarian and uterine horn weights were lower in RF than NF. The diameter of follicles and oocytes and the thickness of the theca and granulosa cells were higher in RF than NF. RF showed a lower percentage of cells containing bax and caspase 3, occurrence of DNA fragmented cells, and estradiol and progesterone. RF had higher incorporation of BrdU, a higher proportion of cells containing PCNA and cyclin B1, and a lower percentage of viable cells. RF produced more specific proteins than NF, including peptides involved in cell differentiation, proliferation/division, mitotic cell cycle, and GTP-ase activity. In conclusion, food restriction can activate reproduction by (1) selection of the growing primordial follicles, (2) better transformation of secondary to preovulatory follicles, (3) increasing growth of oocytes, (4) increasing proliferation and decreasing apoptosis in granulosa cells, (5) changes in ovarian secretory activity, and (6) changes in the number of peptides.

Mapping the Interactome of OSCC Prognostic-Associated Proteins NDRG1 and PGK1 Through Proximity Labeling Using TurboID

Oral squamous cell carcinoma (OSCC) is a prevalent type of head and neck cancer, comprising over 90% of all oral malignancies worldwide. The identification of diagnostic and prognostic markers for OSCC is crucial for improving patient outcomes, as early detection and treatment are critical for the successful management of this disease. Previously, we demonstrated that N-myc downstream-regulated gene 1 (NDRG1) and phosphoglycerate kinase 1 (PGK1) are prognostic markers for OSCC; however, their role in OSCC development remains unclear. To investigate this, we used TurboID-based proximity labeling to identify the interactomes of NDRG1 and PGK1 in HEK293 cells. Herein, protein abundance patterns from three time points were used for clustering 364 proteins with a "fast" or "slow" response to biotin. Of these, 65 proteins were also identified in neoplastic islands of OSCC patients from our previous study, and 28 of these proteins have their gene expression associated with prognostic features, including death, metastasis, and relapse. PRM-MS enabled the quantification of 17 of these proteins, providing further evidence of their presence in the OSCC prognostic interactome. Finally, we characterized a prognostic-associated interactome composed of 28 proteins, which enabled the prioritization of candidates that can be further explored in OSCC progression. The mass spectrometry data generated in this study have been deposited in ProteomeXchange with the data set identifier PXD048046.

Hypoglycemia promotes inner blood-retinal barrier breakdown and retinal vascular leakage in diabetic mice

The blood-retinal barrier (BRB) serves as a physiological boundary regulating the passage of nutrients, waste, ions, proteins, and water to and from the retina. In patients with diabetic retinopathy, breakdown of the inner BRB (iBRB) results in damage to the neurovascular unit and is a principal cause of vision loss in the diabetic population. Here, we demonstrate that hypoglycemia, a common consequence of tight glycemic control and high glycemic variability, results in accumulation of the transcription factors hypoxia-inducible factor-1α (HIF-1α) and HIF-2α and the expression of dozens of HIF-dependent vasoactive mediators in the mouse retina. In diabetic mice, this modest increase in HIF-dependent hyperpermeability factors was sufficient to promote vesicular transcytosis, breakdown of the iBRB, and retinal vascular permeability. Genetic inhibition of either HIF-1α or HIF-2α resulted in an incomplete inhibition of the broad increase in HIF-regulated vasoactive gene expression in response to hypoglycemia. We therefore evaluated a pharmacologic dual HIF-1 and HIF-2 inhibitor, 32-134D, as a therapeutic approach to prevent hypoglycemia-induced HIF-dependent vasoactive gene expression. 32-134D effectively inhibited HIF-1α accumulation and HIF-regulated gene expression in human retinal tissue. In diabetic mice, intravitreal administration of 32-134D prevented the increase in expression of HIF-regulated vasoactive genes after transient episodes of hypoglycemia, blocking both breakdown of the iBRB and the promotion of retinal vascular hyperpermeability. Collectively, these observations help explain why patients with diabetes initiating tight glycemic control have worsening of their diabetic retinopathy and provide the foundation for clinical studies assessing HIF inhibition with 32-134D for its prevention.

A response to iron involving carbon metabolism in the opportunistic fungal pathogen Candida albicans

Iron (Fe) is an essential micronutrient, and during infection, the host attempts to starve pathogens of this vital element through a process known as nutritional immunity. Successful pathogens have evolved means to evade this attack, an example being Candida albicans, the most prevalent human fungal pathogen. When Fe-starved, C. albicans induces multiple pathways for Fe uptake using the SEF1 trans-regulator, and we now describe a previously unrecognized effect of Fe on C. albicans metabolism that occurs independent of SEF1. Specifically, Fe limitation leads to inhibition of pyruvate dehydrogenase (PDH) connecting glycolysis to mitochondrial respiration. PDH inactivation involves loss of the LAT1 catalytic subunit harboring a lipoic acid co-factor. Protein lipoylation is a Fe-S dependent process, and lipoylated alpha-ketoglutarate dehydrogenase is also inhibited in Fe-starved C. albicans. SEF1 does not protect against PDH inactivation, and despite SEF1 induction of Fe import genes, cellular Fe levels drop dramatically during chronic Fe starvation. Such loss of LAT1 and lipoylation is also seen in Fe-starved bakers' yeast Saccharomyces cerevisiae. In both yeast species, glucose is diverted toward the pentose phosphate pathway (PPP) and PPP production of NADPH is increased in response to low Fe and PDH loss. Additionally, glucose consumption is lowered in Fe-starved C. albicans, and non-PDH alternatives to producing Ac-CoA are induced, including pyruvate bypass and fatty acid oxidation pathways. C. albicans can adapt well to the effects of micronutrient loss on cell metabolism.

IMPORTANCE

We describe a new response to Fe-starvation in a fungal pathogen involving carbon metabolism. Pyruvate dehydrogenase (PDH) that is central to glucose metabolism is inactivated at the post-translational level in Fe-starved cells. Nevertheless, the fungal pathogen can thrive by activating backup systems for metabolizing glucose. Methods that inhibit these compensatory pathways for carbon metabolism may prove beneficial in future anti-fungal strategies.

Trichoderma afroharzianum T22 Induces Rhizobia and Flavonoid-Driven Symbiosis to Promote Tolerance to Alkaline Stress in Garden Pea

Soil alkalinity is a limiting factor for crops, yet the role of beneficial fungi in mitigating this abiotic stress in garden pea is understudied. In this study, Trichoderma afroharzianum T22 colonised the roots of garden pea cultivars exposed to soil alkalinity in a host-specific manner. In alkaline-exposed Sugar Snap, T22 improved growth parameters, consistent with increased tissue mineral content, particularly Fe and Mn, as well as enhanced rhizosphere siderophore levels. The split-root assay demonstrated that the beneficial effects of T22 on alkaline stress mitigation are the result of a whole-plant association rather than localised root-specific effects. RNA-seq analysis showed 575 and 818 differentially expressed genes upregulated and downregulated in the roots inoculated with T22 under alkaline conditions. The upregulated genes were mostly involved in the flavonoid biosynthetic pathway (monooxygenase activity, ammonia-lyase activity, 4-coumarate-CoA ligase), along with genes related to mineral transport and redox homoeostasis. Further, a flavonoid precursor restored plant health even in the absence of T22, confirming the role of microbial symbiosis in mitigating alkaline stress. Interestingly, T22 restored the abundance of rhizobia, particularly Rhizobium leguminosarum and Rhizobium indicum, along with the induction of NifA, NifD, and NifH in nodules, suggesting a connection between T22 and rhizobia under soil alkalinity. Further, the elevated rhizosphere siderophore, root flavonoid, expression of PsCoA (4-coumarate-CoA ligase) as well as the relative abundance of TaAOX1 and R. leguminosarum diminished when T22 was substituted with exogenous Fe. This suggests that exogenous Fe eliminates the need for microbiome-driven mineral mobilisation, while T22-mediated alkaline stress mitigation depends on flavonoid-driven symbiosis and R. leguminosarum abundance. It was further supported by the positive interaction of T22 on R. leguminosarum growth in alkaline media. Thus, the beneficial effect of T22 on rhizobia likely stems from their interactions, not solely from the improved mineral status, particularly Fe, in plants. This study provides the first mechanistic insights into T22 interactions with host and rhizobia, advancing microbiome strategies to alleviate soil alkalinity in peas and other legumes.

Portrayal of the complex molecular landscape of multidrug resistance in gastric cancer: Unveiling the potential targets

Gastric cancer (GC) is an aggressive malignancy among all Gastrointestinal cancer (GIC) types. Worldwide, among all cancer types, gastric cancer incidence and related mortality remain in fifth position. Multidrug resistance (MDR) in GC presents a major challenge to chemotherapy, and it significantly affects patient survival. A better understanding of the dynamic interaction of cellular factors contributing to MDR phenotype, e.g., the presence and expression of variants of MDR-related genes, including various drug-detoxifying and drug-efflux transporters, and expression of regulatory ncRNAs affecting the expression of MDR-related genes, is required to comprehend the molecular mechanisms for MDR development in GCs. This review article provides a holistic discussion of the cellular factors involved in the MDR development in GC cells, i.e., their roles and cross-talk between specific molecules that give rise to drug-sensitive and drug-resistant phenotypes. Moreover, the pharmacological perspective of drug resistance and the underlying biological processes that allow the escape of GC cells from the cytotoxic effects of drugs have also been discussed. Additionally, this review article provides an in-depth discussion on most potential candidates that can serve as MDR biomarkers in GIC cancer and the growing research interest in non-coding RNAs (ncRNAs) in GC. Notably, the miRNAs, circRNAs, and lncRNAs are not only emerging as crucial prognostic biomarkers of MDR in gastric cancers but also as potential targets for personalized medicine to combat the MDR challenge in GC patients.

Genetic Foundations of Inter-individual Neurophysiological Variability

Neurophysiological brain activity shapes cognitive functions and individual traits. Here, we investigated the extent to which individual neurophysiological properties are genetically determined and how these adult traits align with cortical gene expression patterns across development. Using task-free magnetoencephalography in monozygotic and dizygotic twins, as well as unrelated individuals, we found that neurophysiological traits were significantly more similar between monozygotic twins, indicating a genetic influence, although individual-specific variability remained predominant. These heritable brain dynamics were predominantly associated with genes involved in neurotransmission, expressed along a topographical gradient that mirrors psychological functions, including attention, planning, and emotional processes. Furthermore, the cortical expression patterns of genes associated with individual differentiation aligned most strongly with gene expression profiles observed during adulthood in previously published longitudinal datasets. These findings underscore a persistent genetic influence on neurophysiological activity, supporting individual cognitive and behavioral variability.

A novel three-dimensional model of infantile haemangioma

BACKGROUND

Infantile haemangioma (IH) is vascular tumour in infants that exhibits rapid proliferation and angiogenesis followed by gradual involution. Ten per cent of cases are associated with disfiguring complications that require medical intervention with beta blockers, surgery or laser therapy.

OBJECTIVES

To improve our understanding of the disease mechanisms of IH with an in vitro three-dimensional model.

METHODS

We isolated and expanded CD31+ endothelial cells (HemECs) from patient-derived IH cell lines and grew them as spheroids in STEMdiffTM Endothelial Expansion Medium. The cells were then embedded in an extracellular matrix hydrogel with reduced growth factors to initiate angiogenic sprouting.

RESULTS

HemEC spheroids expressed CD31, glucose transporter 1, vascular endothelial growth factor receptor 2, CD44, vimentin and CD133 but not smooth muscle actin, indicating their similarity to immature IH blood vessels and their angiogenic potential. Proteomic analysis revealed similar homology in terms of protein expression in spheroids and IH tissue. The high-throughput application of the three-dimensional angiogenesis model was tested using propranolol to inhibit sprouting of spheroids with increased toxicity response.

CONCLUSIONS

This study reports the development of a three-dimensional model of IH that closely resembles the angiogenic features of IH for molecular analysis and drug screening.

Genome-wide association analyses identify single-nucleotide polymorphisms associated with in vitro embryo cleavage and blastocyst rates in Holstein bulls

Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.

14-3-3ζ allows for adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation

OBJECTIVE

We previously established the scaffold protein 14-3-3ζ as a critical regulator of adipogenesis and adiposity, but whether 14-3-3ζ exerted its regulatory functions in mature adipocytes or in adipose progenitor cells (APCs) remained unclear.

METHODS

To decipher which cell type accounted for 14-3-3ζ-regulated adiposity, adipocyte- (Adipoq14-3-3ζKO) and APC-specific (Pdgfra14-3-3ζKO) 14-3-3ζ knockout mice were generated. To further understand how 14-3-3ζ regulates adipogenesis, Tandem Affinity Purification (TAP)-tagged 14-3-3ζ-expressing 3T3-L1 preadipocytes (TAP-3T3-L1) were generated with CRISPR-Cas9, and affinity proteomics was used to examine how the nuclear 14-3-3ζ interactome changes during the initial stages of adipogenesis. ATAC-seq was used to determine how 14-3-3ζ depletion modulates chromatin accessibility during differentiation.

RESULTS

We show a pivotal role for 14-3-3ζ in APC differentiation, whereby male and female Pdgfra14-3-3ζKO mice displayed impaired or potentiated weight gain, respectively, as well as fat mass. Proteomics revealed that regulators of chromatin remodeling, like DNA methyltransferase 1 (DNMT1) and histone deacetylase 1 (HDAC1), were significantly enriched in the nuclear 14-3-3ζ interactome and their activities were impacted upon 14-3-3ζ depletion. Enhancing DNMT activity with S-Adenosyl methionine rescued the differentiation of 14-3-3ζ-depleted 3T3-L1 cells. ATAC-seq revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Finally, 14-3-3ζ-regulated chromatin accessibility correlated with the expression of key adipogenic genes.

CONCLUSION

Our study establishes 14-3-3ζ as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3ζ interactome to identify novel pro-adipogenic factors and pathways.

How it all begins: molecular players of the early graviresponse in the non-elongating part of flax stem

Plants have developed two major strategies to adjust their position in response to gravity: differential cell growth on opposing sides of elongating regions and complex processes in non-elongating stem parts, such as the development of reaction wood. Gravistimulation of flax plants induces gravitropic curvature in non-elongating stem parts, largely associated with modifications in phloem and xylem fibers. To gain insight into the key "triggers" and "forward players" that induce negative gravitropic reactions, transcriptome profiling of phloem fibers and xylem tissues from the pulling and opposite stem sides was conducted 1 and 8 h after gravistimulation. The first observed reaction was the activation of processes associated with RNA synthesis and protein folding in both tissues and stem sides, followed by the activation of kinases and transferases. Transcriptomic data revealed rapid and substantial shifts in chloroplast metabolism across all analyzed tissues, including the temporal activation of the branched-chain amino acid pathway, adjustments to light-harvesting complexes, and jasmonic acid biosynthesis. Notably, auxin transporter genes were activated only in the xylem, while other auxin-related genes showed minimal upregulation 1 h after stem inclination in any analyzed sample. Asymmetric changes between stem sides included the sharp activation of ethylene-related genes in the phloem fibers of the opposite stem side, as well as tertiary cell wall deposition in both the phloem and xylem fibers of the pulling stem side during the later stages of the graviresponse. These results provide valuable insights into the mechanisms underlying plant response to gravity.

Characterization of Bunch Compactness in a Diverse Collection of Vitis vinifera L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number

Bunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a genetically diverse collection of 116 Vitis vinifera L. cultivars and lines enriched for table grapes over two seasons. For this, 3D scanning-based morphological data were combined with ground measurements of 14 BC-related traits, observing high correlations among both approaches (R2 > 0.90-0.97). The multivariate analysis suggests that the attributes 'berries per bunch', 'berry weight and width', and 'bunch weight and length' could be considered as the main descriptors for BC, optimizing evaluation times. Then, GWASs based on a set of 70,335 SNPs revealed that GBS analysis in this same population enabled the detection of several SNPs associated with different sub-traits, with a locus for 'berries per bunch' in chromosome (chr) 18 being the most prominent. Enrichment analysis of significant and frequent SNPs found simultaneously in several traits and seasons revealed the over-representation of discrete functions such as alpha-linolenic acid metabolism and glycan degradation. In summary, the utility of 3D automated phenotyping was validated for table grape backgrounds, and new SNPs and candidate genes associated with the BC trait were detected. The latter could eventually become a selection tool for grapevine breeding programs.

Comparison of Spinal Cord Regeneration Capacity in Zebrafish and Medaka

In mammals, spinal cord injury often results in permanent impairment of motor function owing to ineffective tissue regeneration. Unlike mammals, zebrafish have the remarkable ability to regenerate many tissues, including the spinal cord. Cross-species comparison is an attractive approach for revealing regeneration-specific mechanisms, but the large evolutionary distance between species sometimes hinders direct comparison. Recent studies have revealed that another model fish species, medaka, has a low regenerative ability in some tissues, making comparisons with them advantageous to revealing regeneration-specific mechanisms. However, their spinal cord regenerative ability has not been compared to other models. In this study, we functionally and histologically compared the spinal cord regeneration abilities of zebrafish and medaka. Swimming speed recovery was significantly lower in medaka than in zebrafish. Bridging of glia and neural tissue were thinner in medaka than in zebrafish. Axonal extension across the injured site was observed in zebrafish but not in medaka. Comparison of their gene expression profiles revealed genes involved in "Regeneration" were upregulated in zebrafish, whereas genes related to "Synaptic signaling" were downregulated in medaka. These results suggest that the ability to regenerate the spinal cord is lower in medaka than in zebrafish, making medaka an attractive model for revealing the mechanisms of spinal cord regeneration.

Identification of MEF2A, MEF2C, and MEF2D interactomes in basal and Fsk-stimulated mouse MA-10 Leydig cells

BACKGROUND

Myocyte enhancer factor 2 transcription factors regulate essential transcriptional programs in various cell types. The activity of myocyte enhancer factor 2 factors is modulated through interactions with cofactors, chromatin remodelers, and other regulatory proteins, which are dependent on cell context and physiological state. In steroidogenic Leydig cells, MEF2A, MEF2C, and MEF2D are key regulators of genes involved in steroid hormone synthesis, reproductive function, and oxidative stress defense. However, the specific network of myocyte enhancer factor 2-interacting proteins in Leydig cells remains unknown.

OBJECTIVE

To identify the interactome of each MEF2 factor present in Leydig cells.

MATERIALS AND METHODS

TurboID proximity-mediated biotinylation combined with mass spectrometry and bioinformatic analyses were used to identify the protein‒protein interaction networks of MEF2A, MEF2C, and MEF2D in MA-10 Leydig cells under basal and stimulated conditions.

RESULTS

We identified 109 potential myocyte enhancer factor 2-interacting proteins, including some previously known myocyte enhancer factor 2 partners. The interactome for each myocyte enhancer factor 2 factor is dynamic and exhibits unique and shared interaction networks between basal and stimulated conditions. Further analysis through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment categorized these interactions, revealing involvement in pathways related to cellular metabolism, transcriptional regulation, and steroidogenesis.

DISCUSSION AND CONCLUSION

These findings suggest that myocyte enhancer factor 2 factors can participate in diverse transcriptional activities, capable of gene activation or repression, depending on different protein‒protein interactions. In addition, the differential interactome for each myocyte enhancer factor 2 factor suggests unique regulatory roles for each factor in modulating Leydig cell function. Overall, this study provides new mechanistic insights into myocyte enhancer factor 2 action in Leydig cells by identifying interacting partners that likely influence their functions.

Identification of PECAM1 as a Prognostic Biomarker for Lung Adenocarcinoma

Background: Lung cancer continues to be one of the most fatal malignancies globally. Uncovering differentially expressed genes (DEGs) is crucial for advancing our understanding of tumor mechanisms and discovering new therapeutic targets. This study sought to identify key genes linked to prognosis and immune infiltration in lung cancer through the analysis of public gene expression datasets. Methods: We examined three microarray datasets from the Gene Expression Omnibus (GSE10072, GSE33356, and GSE18842) to detect DEGs between tumor and normal lung tissues. Functional enrichment was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to interpret the biological relevance of these genes. Protein-protein interaction (PPI) networks were constructed via STRING and visualized using Cytoscape to screen for central hub genes. The prognostic implications of the hub genes were investigated using Kaplan-Meier Plotter and TIMER2.0 based on data from The Cancer Genome Atlas (TCGA). PECAM1 expression levels and its relationship with immune cell infiltration were further explored using UCSC Xena. Results: A total of 477 DEGs were consistently identified across all three datasets. Among the top 10 down-regulated hub genes, PECAM1 was significantly reduced in tumor tissues. Lower PECAM1 expression was positively associated with better first-progression survival (FPS) in lung cancer patients. This gene was particularly suppressed in lung adenocarcinoma (LUAD) and showed strong correlations with immune cell infiltration. Co-expression analysis revealed that genes linked to PECAM1 are involved in immune-related pathways. Conclusions: Our findings highlight PECAM1 as a potential prognostic biomarker in lung cancer, especially in LUAD. Its association with immune infiltration and patient survival supports its possible utility in early detection and as a candidate for immunotherapy development.

In-frame insertions of SOX10 are highly enriched and characterize a distinct transcriptomic profile in gastrointestinal schwannomas

Gastrointestinal schwannomas are molecularly and histologically distinct from their non-gastrointestinal counterparts, lacking NF2 alterations, although the primary drivers of these tumors are barely understood. A recent study has identified SOX10 in-frame insertions in schwannomas, particularly in intracranial non-vestibular lesions, whereas their role in gastrointestinal schwannomas remains unexplored. Whole exome sequencing of 15 gastrointestinal and two non-gastrointestinal schwannomas revealed recurrent SOX10 in-frame insertions in 14 gastrointestinal cases (93%) without other nerve sheath tumor-related alterations, such as NF2 mutations or SH3PXD2A::HTRA1 fusions (~14% in non-gastrointestinal cases). The prevalence, mutation spectrum, and specificity of SOX10 insertions were validated using Sanger sequencing in a large cohort comprising 61 gastrointestinal and 98 non-gastrointestinal schwannomas, as well as 110 non-schwannomatous mesenchymal and melanocytic neoplasms. SOX10 insertions, occurring within or near the high mobility group box domain, were significantly enriched in gastrointestinal schwannomas (91.8%) compared with non-gastrointestinal cases (5.1%). The most common insertion, p.Y173_Q174insKY, was present in 86.9% of gastrointestinal schwannomas but absent in non-gastrointestinal cases. Another recurrent insertion, p.P175_R176insKYQP, was rare and exclusively found in non-gastrointestinal schwannomas (3/98), while all non-schwannomatous controls were SOX10-normal. SOX10-inserted schwannomas exhibited histologic features characteristic of gastrointestinal schwannomas, including a microtrabecular arrangement of Schwann cells, peripheral lymphoid cuffs, and a lack of encapsulation. Both SOX10-inserted and SOX10-normal schwannomas demonstrated diffuse SOX10 immunoreactivity. The SOX10-inserted group was significantly associated with gastrointestinal locations (p < 0.001), older patients (p < 0.001), fusion negativity (p < 0.001), and larger tumor size (p = 0.013). Gene expression profiling of 44 cases revealed distinct transcriptomic profiles between primarily SOX10-inserted and SOX10-normal groups, with the latter group being classifiable into fusion-poor and fusion-enriched sub-clusters. This study highlights the genetic heterogeneity of schwannomas and suggests that SOX10 insertions play a pivotal role in the tumorigenesis of gastrointestinal schwannomas, distinctly separating them from non-gastrointestinal counterparts and contributing to their unique molecular profile. © 2025 The Pathological Society of Great Britain and Ireland.

Transcriptomic analysis of the TRP gene family in human brain physiopathology

The transient receptor potential (TRP) gene family is vital to cellular physiology, mediating ion flow across membranes and facilitating sensory signal transduction. This article examines the transcriptomic landscape of TRP genes, emphasizing their varying expression across organs, tissues, and cells, with a particular focus on the brain. Analysis reveals a distinct spatial distribution of TRP gene expression, notably enriched in the hippocampus during brain development, highlighting their essential role in neuronal function. Utilizing datasets from the Human Protein Atlas, Allen Human Brain Atlas, and studies on aging and dementia, associations are identified between TRP gene expression and the development or pathophysiology of neural tissue, highlighting the therapeutic potential of TRP channels in addressing, e.g., sensory impairments and cognitive decline. These insights into the regulatory dynamics of TRP channels lay a foundation for developing targeted interventions for neurodegenerative disorders.

Multiomics from Alzheimer's Brains and Mesenchymal Stem Cell-Derived Extracellular Vesicles Identifies Therapeutic Potential of Specific Subpopulations to Target Mitochondrial Proteostasis

Background

Alzheimer's disease (AD) is characterized by complex molecular alterations that complicate its pathogenesis and contribute to the lack of effective treatments. Mesenchymal stem cell-derived extracellular vesicles (EVs) have shown promise in AD models, but results across different EV subpopulations remain inconsistent.

Objectives

This study investigates proteomic and transcriptomic data from publicly available postmortem AD brain datasets to identify molecular changes at both the gene and protein levels. These findings are then compared with the proteomes of various EV subpopulations, differing in size and distribution, to determine the most promising subtype for compensating molecular degeneration in AD.

Design

We conducted a comprehensive analysis of 788 brain samples, including 481 AD cases and 307 healthy controls, examining protein and mRNA levels to uncover AD-associated molecular changes. These findings were then compared with the proteomes of different EV subpopulations to identify potential therapeutic candidates.

Methods

A multi-omics approach was employed, integrating proteomic and transcriptomic data analysis, miRNA and transcription factor profiling, protein-protein network construction, hub gene identification, and enrichment analyses. This approach aimed to explore molecular changes in AD brains and pinpoint the most relevant EV subpopulations for therapeutic intervention.

Results

We identified common alterations in the cAMP signaling pathway and coagulation cascade at both the protein and mRNA levels. Distinct changes in energy metabolism were observed at the protein level but not at the mRNA level. A specific EV subtype, characterized by a broader size distribution obtained through high-speed centrifugation, was identified as capable of compensating for dysregulated mitochondrial proteostasis in AD brains. Network biology analyses further highlighted potential regulators of key therapeutic proteins within this EV subtype.

Conclusion

This study underscores the critical role of proteomic alterations in AD and identifies a promising EV subpopulation, enriched with proteins targeting mitochondrial proteostasis, as a potential therapeutic strategy for AD.

Reshaping the chromatin landscape in HUVECs from small-for-gestational-age newborns

Small for gestational age (SGA), with increased risk of adult-onset cardiovascular diseases and metabolic syndromes, is known to associate with endothelial dysfunction, but the pathogenic mechanisms remain unclear. In this study, the pathological state of human umbilical vein endothelial cells (HUVECs) from SGA individuals was characterized by presenting increased angiogenesis, migration, proliferation, and wound healing ability relative to their normal counterparts. Genome-wide mapping of transcriptomes and open chromatins unveiled global gene expression alterations and chromatin remodeling in SGA-HUVECs. Specifically, we revealed increased chromatin accessibility at active enhancers, along with dysregulation of genes associated with angiogenesis, and further identified CD44 as the key gene driving HUVECs' dysfunction by regulating pro-angiogenic genes' expression and activating phosphorylated ERK1/2 and phosphorylated endothelial NOS expression in SGA. In SGA-HUVECs, CD44 was abnormally upregulated by 3 active enhancers that displayed increased chromatin accessibility and interacted with CD44 promoter. Subsequent motif analysis uncovered activating protein-1 (AP-1) as a crucial transcription factor regulating CD44 expression by binding to CD44 promoter and associated enhancers. Enhancers CRISPR interference and AP-1 inhibition restored CD44 expression and alleviated the hyperangiogenesis of SGA-HUVECs. Together, our study provides a foundational understanding of the epigenetic alterations driving pathological angiogenesis and offers potential therapeutic insights into addressing endothelial dysfunction in SGA.

Exploring Integrin α5β1 as a Potential Therapeutic Target for Pulmonary Arterial Hypertension: Insights From Comprehensive Multicenter Preclinical Studies

BACKGROUND

Pulmonary arterial hypertension (PAH) is characterized by obliterative vascular remodeling of the small pulmonary arteries (PAs) and progressive increase in pulmonary vascular resistance leading to right ventricular failure. Although several drugs are approved for the treatment of PAH, mortality rates remain high. Accumulating evidence supports a pathological function of integrins in vessel remodeling, which are gaining renewed interest as drug targets. However, their role in PAH remains largely unexplored.

METHODS

The expression of the RGD (arginylglycylaspartic acid)-binding integrin α5β1 was assessed in PAs, PA smooth muscle cells, and PA endothelial cells from patients with PAH and controls using NanoString, immunoblotting, and Mesoscale Discovery assays. RNA sequencing was conducted to identify gene networks regulated by α5β1 inhibition in PAH PA smooth muscle cells. The therapeutic efficacy of α5β1 inhibition was evaluated using a novel small molecule inhibitor and selective neutralizing antibodies in Sugen/hypoxia and monocrotaline rat models, with validation by an external contract research organization. Comparisons were made against standard-of-care therapies (ie, macitentan, tadalafil) and sotatercept and efficacy was assessed using echocardiographic, hemodynamic, and histological assessments. Ex vivo studies using human precision-cut lung slices were performed to further assess the effects of α5β1 inhibition on pulmonary vascular remodeling.

RESULTS

We found that the arginine-glycine-aspartate RGD-binding integrin α5β1 is upregulated in PA endothelial cells and PA smooth muscle cells from patients with PAH and remodeled PAs from animal models. Blockade of the integrin α5β1 or depletion of the α5 subunit downregulated FOXM1 (forkhead box protein M1)-regulated gene networks, resulting in mitotic defects and inhibition of the pro-proliferative and apoptosis-resistant phenotype of PAH cells. We demonstrated that α5β1 integrin blockade safely attenuates pulmonary vascular remodeling and improves hemodynamics and right ventricular function and matched or exceeded the efficacy of standard of care and sotatercept in multiple preclinical models. Ex vivo studies further validated its potential in reversing advanced remodeling in human precision-cut lung slices.

CONCLUSIONS

These findings establish α5β1 integrin as a pivotal driver of PAH pathology and we propose its inhibition as a novel, safe, and effective therapeutic strategy for PAH.

Proteomic signatures of retinal pigment epithelium-derived exosomes in myopic and non-myopic tree shrew eyes

Purpose

The retinal pigment epithelium (RPE) transmits growth signals from the neural retina to the choroid in the emmetropization pathway, but the underlying molecular mechanisms remain poorly understood. Here, we compared the proteomic profiles of RPE-derived exosomes between myopic and non-myopic eyes of tree shrews, dichromatic mammals closely related to primates.

Methods

Four myopic (159-210 days of visual experience, DVE) and seven non-myopic eyes (156-210 DVE) of tree shrews were included. Non-cycloplegic refractive error was measured with Nidek autorefractor, and axial ocular component dimensions were recorded with LenStar. Tissue was collected, yielding RPE-lined eyecups, which were subsequently incubated in L-15 culture media for 2 h. The RPE-derived exosomes were then enriched and purified from the incubation media by double ultracentrifugation and characterized by imaging and molecular methods. Exosomal proteins were identified and quantified with mass spectrometry, examined using GO and KEGG analyses, and compared between myopic and non-myopic samples.

Results

Out of 506 RPE exosomal proteins identified, 48 and 41 were unique to the myopic and non-myopic samples, respectively. There were 286 differentially expressed proteins in the myopic samples, including 79 upregulated and 70 downregulated. The top three upregulated proteins were Histone H4 (Fold Change, FC = 3.04, p = 0.09), PTB 1 (FC = 2.59, p = 0.08) and Histone H3.1 (FC = 2.59, p = 0.13), while the top three downregulated proteins were RPS5 (FC = -2.41, p=0.004), ACOT7 (FC=-2.15, p = 0.04) and CRYBB2 (FC = -2.14, p = 0.05). Other differentially expressed proteins included LUM, VCL, SEPTIN11, GPX3, SPTBN1, SEPTIN7, RPL10A, KCTD12, FGG, and FMOD. Proteomic analysis revealed a low abundance of ATP6V1B2 and crystallin beta B2, and a significant depletion of the crystallin protein family (crystallin A2, A3, and B3 subunits) in the myopic samples. The enrichment analyses showed extracellular matrix, cytoskeletal dynamic, and cell-matrix adhesion as the primary components associated with the RPE exosomal proteins in myopic eyes.

Conclusion

Using standard molecular and imaging techniques, this study provides the first demonstration of the ex-vivo RPE exosome biogenesis from tree shrew eyes. The results showed distinct differential expressions of the RPE exosomal proteins between the myopic and non-myopic eyes, with several proteins unique to each group. Future targeted proteomic studies of identified candidate exosomal protein signatures could elucidate the molecular mechanism of RPE exosome-mediated growth signal transmission in the emmetropization pathway.

Localizatome: a database for stress-dependent subcellular localization changes in proteins

Understanding protein subcellular localization and its dynamic changes is crucial for elucidating cellular function and disease mechanisms, particularly under stress conditions, where protein localization changes can modulate cellular responses. Currently available databases provide insights into protein localization under steady-state conditions; however, stress-related dynamic localization changes remain poorly understood. Here, we present the Localizatome, a comprehensive database that captures stress-induced protein localization dynamics in living cells. Using an original high-throughput microscopy system and machine learning algorithms, we analysed the localization patterns of 10 287 fluorescent protein-fused human proteins in HeLa cells before and after exposure to oxidative stress. Our analysis revealed that 1910 proteins exhibited oxidative stress-dependent localization changes, particularly forming distinct foci. Among them, there were stress granule assembly factors and autophagy-related proteins, as well as components of various signalling pathways. Subsequent characterization identified some specific amino acid motifs and intrinsically disordered regions associated with stress-induced protein redistribution. The Localizatome provides open access to these data through a web-based interface, supporting a wide range of studies on cellular stress response and disease mechanisms. Database URL https://localizatome.embrys.jp/.

Integrating network pharmacology and in vivo pharmacological validation to explore the gastroprotective mechanism of Sotetsuflavone against indomethacin-induced gastric ulcer in rats: Involvement of JAK2/STAT3 pathway

Sotetsuflavone (SF) is an antioxidant flavonoid derived from the Cycas thouarsii R.Br. plant. Although SF regulates numerous cellular pathways influencing inflammation, its antiinflammatory benefits against gastric ulcers are less well-studied. Hence, it is imperative to thoroughly understand the potential gastroprotective mechanisms of SF. This study aimed to explore the effectiveness of SF against indomethacin (IND)-induced gastric ulcers. Network analysis and molecular docking were used to identify the specific targets and pathways related to SF and stomach ulcers. To validate the in vivo pharmacological action of SF, 36 rats were divided into six groups. Ulcer index (UI), protective percentage (PP), gastric mucosal mediators, oxidant/antioxidant status, and inflammatory markers (MIF, M-CSF, and AIF-1) were assessed. Additionally, the expression of PI3K, Akt, Siah2, SOCS3, JAK2, and STAT3 was determined. Stomach histopathology and immunohistochemistry were done. Network pharmacology detected 46 overlapping targets between SF and stomach ulcers, with HIF1A as the primary target among the top hubs. The network also revealed that JAK/STAT, PI3K/Akt, and HIF-1A signaling are among the top 50 markedly enriched KEGG pathways. Furthermore, docking results confirmed that SF has a strong binding affinity towards SOCS3, JAK2, STAT3, M-CSF (CSF-1), and AIF-1. Therefore, we hypothesized that the JAK2/STAT3 pathway may be primarily responsible for SF antiinflammatory action. Through up-regulating SOCS3, SF altered the PI3K/Akt pathway, mitigating oxidative stress, blocking the outflow of inflammatory mediators, and impeding gastric ulcer development. Overall, SF, by the SOCS3-mediated JAK2/STAT3 suppression, might considerably reduce oxidative stress, inflammation, and ulceration caused by indomethacin in the stomach.

Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation

Coronavirus disease 2019 (COVID-19) is a multi-systemic illness that became a pandemic in March 2020. Although environmental factors and comorbidities can influence disease progression, there is a lack of prognostic markers to predict the severity of COVID-19 illness. Identifying these markers is crucial for improving patient outcomes and appropriately allocating scarce resources. Here, an RNA-sequencing study was conducted on blood samples from unvaccinated, hospitalized patients divided by disease severity; 367 moderate, 173 severe, and 199 critical. Using a bioinformatics approach, we identified differentially expressed genes (DEGs), alternative splicing (AS) and alternative polyadenylation (APA) events that were severity-dependent. In the severe group, we observed a higher expression of kappa immunoglobulins compared to the moderate group. In the critical cohort, a majority of AS events were mutually exclusive exons and APA genes mostly had longer 3'UTRs. Interestingly, multiple genes associated with cytoskeleton, TUBA4A, NRGN, BSG, and CD300A, were differentially expressed, alternatively spliced and polyadenylated in the critical group. Furthermore, several inflammation-related pathways were observed predominantly in critical vs. moderate. We demonstrate that integrating multiple downstream analyses of transcriptomics, from moderate, severe, and critical patients confers a significant advantage in identifying relevant dysregulated genes and pathways.

Phytochemical analysis of leaf extract of Piper nigrum and investigation of its biological activities

BACKGROUND

This study investigates the phytoconstituents of the less explored leaf of Piper nigrum, a common ethnomedicinal plant as an alternate source for multiple bioactivities.

METHODS

Hydro-ethanolic (1:4) extract of Piper nigrum leaves (PNLE) prepared and profiled using liquid chromatography and mass spectrometry for identification of phytomolecules. Anti-oxidant activity, intracellular reactive oxygen species (ROS) expression, phagocytosis activity, and cytokine expression were estimated using cell-free and cell-based assays. Anti-cancer activity was determined with cancer cell viability, migration inhibition and colony-formation assay. Apoptosis and membrane depolarization assay were done using fluorescent microscopic staining methods while network pharmacology, and molecular docking analysis were done using open source and online tools.

RESULTS

Major phytomolecules identified in PNLE were pentanamide N,N-didecyl, piperettine, curcumin, myristicin, pipernonaline, sesamin, and lupenone. PNLE exhibited anti-bacterial activity with higher activity against Gram-positive bacteria, Staphylococcus aureus. PNLE also showed anti-oxidant and anti-inflammatory activity through neutralization of free radicals; inhibition of intracellular ROS generation; inhibition of phagocytosis and reduction of cytokine (IL-6 and TNF-α) levels. PNLE showed anti-proliferative activity against human breast cancer cells (MDA-MB-231), rat mammary tumor cells (LA7), and mouse melanoma cells (B16-F10) with highest activity against MDA-MB-231 cells. The extract did not inhibit human kidney cells (HEK-293). Further, PNLE treatment significantly inhibited cell migration and colony formation of MDA-MB-231 cells. Fluorescent staining techniques confirmed induction of apoptosis in cancer cells by PNLE. Further, network pharmacology and molecular docking studies revealed that the identified PNLE phytomolecules share 97 targets of out of potential breast cancer and inflammation-related target genes with four best common target proteins among the top hub genes and sesamin showed the highest binding affinity with these important cellular targets.

CONCLUSIONS

Overall, the phytochemical profile of PNLE showed clear presence of important phytomolecules and their association with critical human cellular mechanistic pathways responsible for exhibited bioactivities. This study further establishes the leaf of P. nigrum as an additional anatomical plant part with potent medicinal properties and  as a potential renewable source for bioactive phyomolecules.

Gut microbial metabolites targeting JUN in renal cell carcinoma via IL-17 signaling pathway: network pharmacology approach

The gut microbiome plays a crucial role in renal diseases, influencing conditions such as renal cell carcinoma (RCC), acute kidney injuries, and diabetic nephropathy. Recent studies highlight the association between gut microbial metabolites (GMM) and RCC progression. This study employs a computational network pharmacology framework to explore the mechanistic action of gut microbiota-derived metabolites against RCC. GMM were selected from the gutMgene database and analyzed for common targets using DisGeNET, Gene Card, and OMIM. Downstream analysis included gene ontology, KEGG pathway enrichment, metabolite-target-pathway-disease network construction, and protein-protein interaction analysis. Further, key metabolites were evaluated for drug-likeness, ADMET properties, and molecular docking, followed by molecular dynamics simulations (MDS) to assess complex stability. The JUN/AP-1 gene emerged as the prime target, exhibiting the highest binding affinity with Icaritin (- 5.9 kcal/mol), followed by Quercetin and Luteolin. MDS confirmed the stable binding of Icaritin to the active site throughout the simulation. These GMM may influence anticancer activity through distinct regulatory pathways involving the JUN/AP-1 gene, either by inhibiting or modulating its function. These insights establish a basis for further in vitro and in vivo investigations, supporting the development of microbiome-based therapeutic approaches.

Modeling heart failure by induced pluripotent stem cell-derived organoids

Cardiac organoids offer significant advantages for in vitro studies, as their 3D structure and cellular composition more closely replicate tissue complexity compared to 2D models. This is particularly relevant for studying complex diseases like heart failure (HF), which involve multiple cell types and cardiac structures. Thus, the primary aim of this study was to produce self-assembled, scaffold-free cardiac organoids from induced pluripotent stem cells (iPSCs), capable of simulating key aspects of HF in vitro. Gene expression analysis confirmed a transition from stemness markers (OCT4, NANOG) to cardiac markers (TNNT2, DES), validating their cardiac phenotype. To induce hallmark HF features, endothelin-1 (ET-1) treatment was applied. Key findings indicate that this experimental model successfully reproduced HF pathological markers, including the upregulation of genes encoding atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and the cytoskeletal protein α-skeletal actin (ACTA1), along with changes in microRNA (miR) expression profiles. Functionally, ET-1 treatment reduced organoid contractility, indicating a decline in contractile function-a hallmark of HF. Furthermore, histological analyses by Thioflavin T (ThT) staining, ThT fluorescence assay and filter trap assay on protein extracts demonstrated protein aggregation following ET-1 treatment. Co-administration of various nutraceuticals was shown to mitigate these effects. These findings underscore the value of this ET-1-stimulated cardiac organoid model as a powerful platform for studying HF mechanisms and evaluating novel therapeutic approaches.

Critical roles of chronic BCR signaling in the differentiation of anergic B cells into age-associated B cells in aging and autoimmunity

Age-associated B cells (ABCs) with autoreactive properties accumulate with age and expand prematurely in autoimmune diseases. However, the mechanisms behind ABC generation and maintenance remain poorly understood. We show that continuous B cell receptor (BCR) signaling is essential for ABC development from anergic B cells in aged and autoimmune mice. ABCs exhibit constitutive BCR activation, with surface BCRs being internalized. Notably, anergic B cells, but not nonautoreactive B cells, contributed to ABC formation in these models. Anergic B cells also showed a greater propensity for in vitro differentiation into ABCs, which was inhibited by the expression of the transcription factor Nr4a1. Bruton's tyrosine kinase (Btk), a key BCR signaling component, was constitutively activated in ABCs from aged and autoimmune mice as well as patients with lupus. Inhibiting Btk reduced ABC numbers and ameliorated the pathogenicity of lupus mice. Our findings reveal critical mechanisms underlying ABC development and offer previously unrecognized therapeutic insights for autoimmune diseases.

A systematic review to identify target genes that modulate root system architecture in response to abiotic stress

The exposure of plant roots to soil-related stresses, including drought, high temperatures, salinization, and nutrient deficiency, is on the rise due to climate change caused by human activities. A systematic literature review was conducted, which revealed evidence for conserved genes that modulate root system architecture under specific stress conditions. A collection of Arabidopsis thaliana mutants displaying a root phenotype distinct from the wild type is available in The Arabidopsis Information Resource database. Gene expression data was gathered for specific genes in response to selected abiotic stress treatments. K-means clustering, and fold change analyses identified 118 genes that were upregulated and 185 genes that were downregulated. A dedicated phenotyping approach was used to ascertain that lack of nutrients induced the transition from a 'steep, cheap, and deep' root morphotype to a 'topsoil foraging' root morphotype in the Columbia- 0 reference genotype. The anticipated role of ISOPENTENYLTRANSFERASE 3, LIPOXYGENASE 1, and WEE1 KINASE HOMOLOG as negative regulators of root growth in response to multiple stress signals was assayed. Further research with the candidate genes identified in this study may reveal promising targets for crop improvement.

Transcriptome Profiling and Viral-Human Interactome Insights Into HBV-Driven Oncogenic Alterations in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the primary form of liver cancer that poses a significant global health concern due to its increasing incidence rates and diverse etiology. Chronic infection induced by hepatitis B virus (HBV) is a prominent etiological factor influencing the development of HCC. Although recent advances in multi-omics approaches have facilitated extensive exploration of HCC molecular characteristics, translating the characteristics of subtypes into clinical applications has been challenging due to parameters like limited sample size and complex classifiers for early detection. In the present study, we performed transcriptomics profiling of HBV-infected HCC patient tissue data to gather comprehensive insights into the intricate molecular mechanisms underlying HBV-associated HCC, specifically, viral protein interactions that influence the expression of oncogenes. The 1059 differentially expressed genes (DEGs) identified across two GEO data sets revealed upregulation of cell cycle and mitosis-related genes, alongside downregulation of genes involved in fatty acid degradation and cytochrome P450 activity. CDK1 and CDC20 which are part of the top cluster and hub gene from interactome analysis were identified as potential markers for HBV-positive HCC through gene expression pattern and overall survival analysis. Additionally, 19 DEGs showing significance in HCC development were identified as interacting partners with HBV proteins. Among them, the interaction of HBsAg with ALB and SHBG and their downregulation correlates to the lower testosterone levels identified in HBV and HCC patients. Together, the study enhances the understanding of the heterogeneity and molecular pathogenesis of HBV-positive HCC.

SIAE-Mediated Loss of Sialic Acid Acetylation Contributes to Ulcerative Colitis

Background

Ulcerative colitis (UC) disrupts the colon's protective mucus layer, exposing the epithelium to bacteria and triggering inflammation. This barrier, crucial for intestinal health, depends on complex glycosylation, notably sialic acid modifications. However, the precise role of sialic acid acetylation and the enzyme SIAE (sialic acid acetylesterase) in UC pathogenesis remains unclear. This study investigates the role of glycosylation changes, specifically sialic acid de-acetylation, in UC progression.

Methods

Tissue samples were obtained from patients with ulcerative colitis (UC) and colorectal cancer at the Second Affiliated Hospital of Soochow University. HT-29 cells were utilized to investigate the molecular mechanisms of SIAE in UC pathogenesis. Mass spectrometry was performed to analyze differences in protein and glycoprotein expression. Western blot (WB) and immunohistochemistry (IHC) were used to examine SIAE protein expression changes during inflammation. Furthermore, polymerase chain reaction (PCR) and immunofluorescence were employed to determine the effects of SIAE on sialic acid levels and mucosal immunity.

Results

In this study, we characterized proteins and glycoproteins from patient tissues with UC, finding that sialic acid acetylesterase (SIAE) is upregulated in UC. HT-29 cells exposed to TNF-α induced an inflammatory response with a 5-fold increased expression of SIAE and NEU1 when TNF-α was at a concentration of 100 ng/mL. Mass spectrometry analysis revealed a reduction in acetylation on glycans and glycoproteins, while confocal microscopy confirmed a decrease in sialic acid on the cell surface. Gene expression analysis showed that CDH1, CTNND1, and ITGA8 were significantly downregulated in HT-29 cells stimulated by TNF-α, suggesting a reduction in cell-cell adhesion. SNA lectin-confocal microscopy revealed a reduction of sialic acid on HT-29 cells in TNF-α-induced UC cell models.

Conclusion

This study demonstrates that SIAE is significantly upregulated in ulcerative colitis (UC) tissues and TNF-α-stimulated HT-29 cells, leading to a marked reduction in sialic acid acetylation and cell surface sialic acid levels. These changes correlate with decreased expression of cell adhesion molecules, suggesting a disruption of the mucosal barrier integrity. Consequently, SIAE-mediated sialic acid de-acetylation emerges as a critical factor in UC pathogenesis, potentially serving as both a valuable biomarker and a promising therapeutic target.

DNA repair is essential for Vibrio cholerae growth on thiosulfate-citrate-bile salts-sucrose (TCBS) medium

Thiosulfate-citrate-bile salts-sucrose (TCBS) agar is a selective and differential media for the enrichment of pathogenic Vibrios. We observed that an exonuclease VII (exoVII) mutant of Vibrio cholerae failed to grow on TCBS agar, suggesting that DNA repair mutant strains may be hampered for growth in this selective media. Examination of the selective components of TCBS revealed that bile acids were primarily responsible for the toxicity of the exoVII mutant. Suppressor mutations in DNA gyrase restored growth of the exoVII mutants on TCBS, suggesting that TCBS inhibits DNA gyrase similar to the antibiotic ciprofloxacin. To better understand what factors are important for V. cholerae to grow on TCBS, we generated a randomly barcoded TnSeq (RB-TnSeq) library in V. cholerae and have used it to uncover a range of DNA repair mutants that also fail to grow on TCBS agar. The results of this study suggest that TCBS agar causes DNA damage to V. cholerae similarly to the mechanism of action of fluoroquinolones, and overcoming this DNA damage is critical for Vibrio growth on this selective medium.IMPORTANCETCBS is often used to diagnose cholera infection. We found that many mutant V. cholerae strains are attenuated for growth on TCBS agar, meaning they could remain undetected using this culture-dependent method. Hypermutator strains with defects in DNA repair pathways might be especially inhibited by TCBS. In addition, V. cholerae grown successively on TCBS agar develops resistance to ciprofloxacin.

Effects of life-long hyperlipidaemia on age-dependent development of endothelial dysfunction in humanised dyslipidaemic mice

Little is known, how life-long hyperlipidaemia affects vascular ageing, before atherosclerosis. Here, we characterise effects of mild, life-long hyperlipidaemia on age-dependent endothelial dysfunction (ED) in humanised dyslipidaemia model of E3L.CETP mice. Vascular function was characterised using magnetic resonance imaging in vivo and wire myograph ex vivo. Plasma endothelial biomarkers and non-targeted proteomics in plasma and aorta were analysed. Early atherosclerosis lesions were occasionally present only in 40-week-old or older E3L.CETP mice. However, age-dependent ED developed earlier, in 14-week-old male and 22-week-old female E3L.CETP mice as compared with 40-week-old female and male C57BL/6J mice. Acetylcholine-induced vasodilation in 8-week-old E3L.CETP, especially female mice, was blocked by catalase and attributed to H2O2. In 8-week-old female E3L.CETP mice, changes in plasma proteome in response to hyperlipidaemia were modest, while in male mice a number of differentially expressed proteins were identified that were involved in oxidative stress response, inflammation and regulation of metabolic pathways. In contrast, in older E3L.CETP and C57BL/6J mice, either plasma or aortic proteome displayed similar pattern of vascular ageing, dominating over hyperlipidaemia-induced changes. Interestingly, in 48-week-old male but not female E3L.CETP mice, vascular mitochondrial functional response was impaired. Early resilience of hyperlipidaemia-induced detrimental effects in young female E3L.CETP mice on a functional level was associated with a switch in vasodilation mechanism, blunted systemic proteomic response in plasma and slower ED development as compared to male E3L.CETP mice. The results indicate that profile of early vascular response to risk factors in young age may determine level of ED in older age before atherosclerosis development.

Perfluorooctane sulfonic acid: a possible risk factor of endothelial dysfunction based on in silico and in vitro studies

Perfluorooctane sulfonic acid (PFOS) is a fluorinated chemical utilized in a variety of industrial and household products. PFOS has been detected in human serum and is associated with multiple human adverse health effects. Epidemiological evidence has linked PFOS exposure to endothelial dysfunction, which is a key contributor to atherosclerosis. However, the underlying mechanisms of PFOS-induced endothelial dysfunction associated atherosclerosis has not been investigated. In the present study, human microvascular endothelial cells (HMEC-1) exposed to PFOS (15 μM) for 72 h, mimicking long-term exposure. We further employed integrated RNA-sequencing (RNA-seq) and transcriptomic analysis to identify differentially expressed genes (DEGs) for biological alterations: gene ontology (GO), pathway enrichment analysis (KEGG), protein-protein interaction network and modular clustering analysis. Furthermore, the Metascape database was used for disease association, tissue specificity, and transcription factor analysis. Hub genes were verified using atherosclerosis patient data sets from the GEO dataset. Alteration of hub genes in patients was then validated using immunoblotting and ELISA. Our results revealed that PFOS altered amino acid biosynthesis, lipid metabolism and induced the ER-stress response through the HRI/eIF2α/ATF4 pathway, leading to endothelial dysfunction. Interestingly, we found that PFOS induced inflammation by increasing COX-2, ICAM-1 and IL-6 expression through NF-κB and JAK2/STAT3 pathway in endothelial cells. Moreover, up-regulated C/EBPβ and ATF4 were observed in both patients and PFOS-exposed endothelium, which may use as an early biomarker and may have a potential role in PFOS-induced endothelial dysfunction. These findings provide novel insight into the underlying molecular mechanisms of PFOS-induced endothelial dysfunction associated with atherosclerosis.

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the fetal human brain and human induced pluripotent stem cell (hiPSC)-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders-Cullin 3 (CUL3), DEAD-box helicase 3 X-linked (DDX3X), and Y-box binding protein-1 (YBX1)-by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to more comprehensively resolve the synaptic architecture.

Emulsion adjuvant-induced uric acid release modulates optimal immunogenicity by targeting dendritic cells and B cells

Squalene-based emulsion (SE) adjuvants like MF59 and AS03 are used in protein subunit vaccines against influenza virus (e.g., Fluad, Pandemrix, Arepanrix) and SARS-CoV-2 (e.g., Covifenz, SKYCovione). We demonstrate the critical role of uric acid (UA), a damage-associated molecular pattern (DAMP), in triggering immunogenicity by SE adjuvants. In mice, SE adjuvants elevated DAMP levels in draining lymph nodes. Strikingly, inhibition of UA synthesis reduced vaccine-induced innate immunity, subsequently impairing optimal antibody and T cell responses. In vivo treatment with UA crystals elicited partial adjuvant effects. In vitro stimulation with UA crystals augmented the activation of dendritic cells (DCs) and B cells and altered multiple pathways in these cells, including inflammation and antigen presentation in DCs and cell proliferation in B cells. In an influenza vaccine model, UA contributed to protection against influenza viral infection. These results demonstrate the importance of DAMPs, specifically the versatile role of UA in the immunogenicity of SE adjuvants, by regulating DCs and B cells.

Cholesterol-targeting Wnt-β-catenin signaling inhibitors for colorectal cancer

Most persons with colorectal cancer (CRC) carry adenomatous polyposis coli (APC) truncation leading to aberrant Wnt-β-catenin signaling; however, effective targeted therapy for them is lacking as the mechanism by which APC truncation drives CRC remains elusive. Here, we report that the cholesterol level in the inner leaflet of the plasma membrane (IPM) is elevated in all tested APC-truncated CRC cells, driving Wnt-independent formation of Wnt signalosomes through Dishevelled (Dvl)-cholesterol interaction. Cholesterol-Dvl interaction inhibitors potently blocked β-catenin signaling in APC-truncated CRC cells and suppressed their viability. Because of low IPM cholesterol level and low Dvl expression and dependence, normal cells including primary colon epithelial cells were not sensitive to these inhibitors. In vivo testing with a xenograft mouse model showed that our inhibitors effectively suppressed truncated APC-driven tumors without causing intestinal toxicity. Collectively, these results suggest that the most common type of CRC could be effectively and safely treated by blocking the cholesterol-Dvl-β-catenin signaling axis.

A global overview of shared genetic architecture between smoking behaviors and major depressive disorder in European and East Asian ancestry

BACKGROUND

The co-occurrence of smoking behaviors and major depressive disorder (MDD) has been widely documented in populations. However, the underlying mechanism of this association remains unclear.

METHODS

Genome-wide association studies of smoking behaviors and MDD, combined with multi-omics datasets, were used to characterise genetic correlations, identify shared loci and genes, and explore underlying biological mechanisms. Mendelian randomization (MR) analyses were conducted to infer causal relationships between smoking behaviors and MDD. Druggability analyses were performed to identify potential drugs with both antidepressant and smoking cessation effects.

RESULTS

Extensive overall genetic correlations were found between smoking behaviors and MDD. Furthermore, eighteen local regions showed significant genetic correlations, which could be partly explained by gene co-expression patterns. We identified 24 shared loci and 120 genes, which were enriched in limbic system, GABAergic and dopaminergic neurons, as well as in synaptic pathways. Through integrating with tissue specific information, seven key genes (ANKK1, NEGR1, USP4, TCTA, SORCS5, SPPL3, and USP28) were pinpointed. Notably, druggability analyses supported ANKK1 as a potential drug target for the treatment of MDD and tobacco dependence. MR analyses suggested a bidirectional causal relationship between smoking initiation and MDD. Although findings in East Asian ancestry were limited, the shared locus (chr15:47613403-47,685,504) identified in European ancestry remained significant in East Asian ancestry.

CONCLUSIONS

Our findings suggest the extensive genetic overlap between smoking behaviors and MDD, support the role of limbic system and synapse involved in shared mechanisms, and implicate for prevention, intervention and treatment.

Investigating the Effects of Arabidopsis thaliana Cruciferin Double Knockouts on Amino Acid Profiles, Dry Seed Proteome, and Oxidative Stress Levels

As plant seeds mature, they accumulate large quantities of seed storage proteins, which are a vital source of carbon, nitrogen, and sulfur necessary for establishing the seedling, especially during the transition from the heterotrophic to the photoautotrophic stage. However, seed storage proteins in many crop seeds are deficient in essential amino acids, which cannot be synthesized by humans and monogastric animals and must be obtained from the diet. Lysine and tryptophan are the most deficient amino acids in cereal seeds, while methionine is the most deficient amino acid in legumes. In the last few decades, extensive research has been done to improve the nutritional quality of seed crops. However, much of this effort was hindered due to the conserved natural phenomenon of proteomic rebalancing that 'resets' the seed's protein-bound amino acid composition despite major alterations to the proteomic sink. Neither the underlying regulatory mechanism nor the natural function of proteomic rebalancing is well understood. To address this gap, we used the model organism Arabidopsis thaliana to investigate the impact of cruciferin (CRU) seed storage protein double knockouts on key biological processes. Amino acid analysis showed that the protein-bound amino acid composition and levels did not change in the mutants despite major alterations in the proteome, especially in the double mutant lacking both CRUA and CRUC ( cruac ). This mutant also has the highest free amino acid changes and experienced the most oxidative stress damage compared to other mutants based on analysis of protein carbonylation and glutathione levels. The mutant that lacks CRUA and CRUB ( cruab ), on the other hand, was the least affected in all the traits examined. These results suggest that CRUs are not functionally redundant, and that each CRU is not replaceable by another in Arabidopsis . The results also show that Arabidopsis seed protein-bound amino acid composition is fully rebalanced in the double CRU mutants despite major proteome alteration.

Identification of post-translationally modified MHC class I-associated peptides as potential cancer immunotherapeutic targets

Over the past three decades, the Hunt laboratory has developed advancements in mass spectrometry-based technologies to enable the identification of peptides bound to major histocompatibility complex (MHC) molecules. The MHC class I processing pathway is responsible for presenting these peptides to circulating cytotoxic T cells, allowing them to recognize and eliminate malignant cells, many of which have aberrant signaling. Professor Hunt hypothesized that due to the dysregulation in phosphorylation in cancer, that abnormal phosphopeptides are likely presented by this pathway, and went on to discover the first phosphopeptide presented by the MHC processing pathway. Thereafter, the laboratory continued to sequence MHC-associated phosphopeptides and contributed several improved methods for their enrichment, detection, and sequencing. This manuscript summarizes the most recent advancements in identification of modified MHC-associated peptides and includes the cumulative list of phosphopeptides sequenced by the Hunt lab. Further, many other post-translational modifications (PTMs) were found to modify MHC peptides, including O-GlcNAcylation, methylation, and kynurenine; in total, we present here a list of 2,450 MHC-associated PTM peptides. Many of these were disease specific and found across several patients, thus highlighting their potential as cancer immunotherapy targets. We are sharing this list with the field in hopes that it might be used in investigating this potential. Overall, the Hunt lab's contributions have significantly advanced our understanding of antigen presentation and dysregulation of PTMs, supporting modern immunotherapy and vaccine development efforts.

Integration of multi-omics and single-cell transcriptome reveals mitochondrial outer membrane protein-2 (MTX-2) as a prognostic biomarker and characterizes ubiquinone metabolism in lung adenocarcinoma

Lung adenocarcinoma (LUAD) remains to be one of the most prevalent and highly invasive forms of cancer. Mitochondrial outer membrane protein-2 or Metaxin-2 (MTX2), a key regulator of mitochondrial function, has been linked to cellular bioenergetics and stress response mechanisms. However, its roles in the progression and prognosis of LUAD remain largely unexplored. This study, employed a multi-omics approach, integrating transcriptomic and clinical patient data from public databases, to evaluate the expression and prognostic relevance of MTX2 in LUAD. Single-cell RNA sequencing was utilized to further explore MTX2's role in immune infiltration and interactions within the tumor microenvironment. Additionally, we validated these findings through a series of molecular biology and functional assays. Our results demonstrated that MTX2 expression was higher in LUAD tissues compared to normal lung tissues. Elevated MTX2 levels were significantly associated with poorer overall survival in LUAD patients. Functional analyses revealed that MTX2 regulates mitochondrial bioenergetics and facilitates tumor cell proliferation. Additionally, MTX2 expression was associated with increased immune cell infiltration. A pathway analysis identified cell metabolic and tumor growth pathways regulated by MTX2, supporting its role in tumor progression. Our research identifies MTX2 as a promising prognostic biomarker and therapeutic target for LUAD. Increased expression of MTX2 promotes tumor growth by altering metabolic pathways and modulating the immune response, underscoring its potential as a new target for LUAD treatment.

Identifying Genes Associated with the Anticancer Activity of a Fluorinated Chalcone in Triple-Negative Breast Cancer Cells Using Bioinformatics Tools

Fluorinated chalcones are molecules reported to possess potent anticancer properties against triple-negative breast cancer (TNBC) cells. However, their molecular mechanisms have not yet been fully explored. Using bioinformatics tools, we analyzed the transcriptomes of MDA-MB-231 cells treated with either a novel fluorinated chalcone (compound 3) or a control in order to identify differentially expressed (DE) genes associated with its anticancer activity and determine the biological processes in which these genes are involved. A fluorinated chalcone was synthesized using the Claisen-Schmidt method. The transcriptome of MDA-MB-231 cells was then analyzed on an Illumina NextSeq500, and DE genes with significant changes in expression were identified using the DESeq2 v1.38.0 bioinformatics tool under the strict detection criteria of |log2FC| ≥  2 and adjusted p < 0.05. We identified 504 DE genes, which were enriched in terms related to "regulation of cell death", "cation transport", "response to topologically incorrect proteins", and "response to unfolded proteins". Surprisingly, these genes were involved in "the HSF1-dependent transactivation pathway" and "the attenuation phase pathway". This bioinformatics-based study suggests that the tested fluorinated chalcone could influence HSF-1 silencing in addition to promoting the up-regulation of several genes involved in stress-induced apoptosis. Therefore, the tested compound could have enormous potential as a novel approach for TNBC treatment.