iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Two-dimensionally cultured functional hepatocytes generated from human induced pluripotent stem cell-derived hepatic organoids for pharmaceutical research

Human induced pluripotent stem (iPS) cell-derived hepatocyte-like cells (HLCs) are expected to replace primary human hepatocytes (PHHs) as a new stable source of hepatocytes for pharmaceutical research. However, HLCs have lower hepatic functions than PHHs, require a long time for differentiation and cannot be prepared in large quantities because they do not proliferate after their terminal differentiation. To overcome these problems, we here established hepatic organoids (iHOs) from HLCs. We then showed that the iHOs could proliferate approximately 105-fold by more than 3 passages and expressed most hepatic genes more highly than HLCs. In addition, to enable their widespread use for in vitro drug discovery research, we developed a two-dimensional culture protocol for iHOs. Two-dimensionally cultured iHOs (iHO-Heps) expressed most of the major hepatocyte marker genes at much higher levels than HLCs, iHOs, and even PHHs. The iHO-Heps exhibited glycogen storage capacity, the capacity to uptake and release indocyanine green (ICG), albumin and urea secretion, and the capacity for bile canaliculi formation. Importantly, the iHO-Heps had the activity of major drug-metabolizing enzymes and responded to hepatotoxic drugs, much like PHHs. Thus, iHO-Heps overcome the limitations of the current models and promise to provide robust and reproducible pharmaceutical assays.

Transcriptome Analysis of Genes Responsive to Nutrient Level Changes in the Marine Red Alga Pyropia yezoensis (Nori)

The cultivation of the red alga Pyropia (nori) is among the most significant aquaculture industries in East Asia. Nutrient deficiency-induced "discoloration" poses a serious threat to the industry, substantially impacting both harvest quality and production levels. In this study, we conducted transcriptome analysis (RNA-Seq) of P. yezoensis to gain deeper insights into the molecular mechanisms underlying physiological responses to nutrient limitation that lead to discoloration. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis estimated that under nutrient-rich conditions, pathways involved in photosynthesis (carbon fixation) and respiration (tricarboxylic acid [TCA] cycle and glycolysis) are more activated. In contrast, under nutrient-deficient conditions, upregulation of genes related to the uptake of external substances and stress response was observed. Additionally, seven genes (ant1-2, pup, drg2, ankrd, bckdha, lhcb, and an unknown gene) identified from the RNA-Seq results as potential discoloration markers were successfully validated through RT-qPCR analysis. The fundamental molecular insights into discoloration in P. yezoensis provided by this study will aid in developing future discoloration prediction methods and breeding discoloration-resistant Pyropia varieties.

Functional characterization of eicosanoid signaling in Drosophila development

20-carbon fatty acid-derived eicosanoids are versatile signaling oxylipins in mammals. In particular, a group of eicosanoids termed prostanoids are involved in multiple physiological processes, such as reproduction and immune responses. Although some eicosanoids such as prostaglandin E2 (PGE2) have been detected in some insect species, molecular mechanisms of eicosanoid synthesis and signal transduction in insects have not been thoroughly investigated. Our phylogenetic analysis indicated that, in clear contrast to the presence of numerous receptors for oxylipins and other lipid mediators in humans, the Drosophila genome only possesses a single ortholog of such receptors, which is homologous to human prostanoid receptors. This G protein-coupled receptor, named Prostaglandin Receptor or PGR, is activated by PGE2 and its isomer PGD2 in Drosophila S2 cells. PGR mutant flies die as pharate adults with insufficient tracheal development, which can be rescued by supplying high oxygen. Consistent with this, through a comprehensive mutagenesis approach, we identified a Drosophila PGE synthase whose mutants show similar pharate adult lethality with hypoxia responses. Drosophila thus has a highly simplified eicosanoid signaling pathway as compared to humans, and it may provide an ideal model system for investigating evolutionarily conserved aspects of eicosanoid signaling.

Identifying potential tear biomarkers in premature infants with retinopathy of prematurity based on proteome and transcriptome analysis

AIM

To identify the potential tear fluid biomarkers in premature infants with and without retinopathy of prematurity (ROP) based on proteomic and transcriptomic analysis.

METHODS

Tears were collected from the 46 eyes of the 23 enrolled premature infants, with and without ROP. Data-independent acquisition (DIA) mass spectrometry was utilized for the quantitative proteomic analysis of the two groups. Two published transcriptome datasets involving mouse oxygen-induced retinopathy (OIR) model data were selected from the Gene Expression Omnibus (GEO) database. iDEP (integrated Differential Expression and Pathway analysis) were used for differential expression analysis. Gene Ontology (GO)-based functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed.

RESULTS

In this study, a total of 1742 proteins were quantified from the two groups. 55 differentially expressed proteins closely related to immune and angiogenesis processes were identified, including 33 highly expressed as well as 22 lowly expressed in the ROP group. Combined with RNA-seq data from OIR model, we screened two particularly critical proteins, LYN and filamin A (FLNA), which were both expressed at significantly elevated levels.

CONCLUSIONS

According to the findings of the tear proteomics data, we hypothesized two particularly critical proteins, LYN and FLNA, may serve as pivotal regulators of immune and angiogenesis processes in ROP. These results will assist in the provision of new potential targets for the diagnosis of ROP.

Elucidating the transcriptomic response of adult-derived mHypoA-2/12 mouse hypothalamic neuron cell line to cannabidiol (CBD) exposure

Cannabidiol (CBD) is a compound found in Cannabis sativa that is known for its neuroprotective, anti-inflammatory, analgesic, and anxiolytic properties. These properties make it a promising treatment for various neurological conditions. This study aimed to examine the effects of CBD on hypothalamic neurons at the transcriptome level using the adult-derived mHypoA-2/12 mouse cell line. The cells were exposed to four different CBD concentrations (ranging from 0.325 to 3 µM) for 6 and 24 h. Apart from the transcriptome analysis, apoptosis (caspase 3/7 activity) and viability (MTT) assays were performed. The obtained results showed that CBD enhanced cell viability, especially after 24 h of treatment and at lower or intermediate concentrations, and reduced apoptosis, with significant effects at the highest concentration. CBD caused moderate transcriptome profile changes (13 to 69 genes per treatment), with more genes affected at higher concentrations and shorter exposure times, indicating a stronger initial cellular response. Further analysis revealed that CBD affects several biological processes, including: intrinsic apoptosis suppression via p53 modulation, impacting genes like Bbc3, Mdm2, Cdkn1a, and Smad3. Additionally, CBD influenced genes involved in extracellular matrix organization, including metalloproteinases (Mmp-3, Mmp-13) and their inhibitors (Timp1), as well as collagen components (Col11a1) and mitochondrial respiratory chain complexes (mt-Nd5, mt-Nd4). Genes related to serotonin and dopamine biosynthesis, as well as Aldh2, were also impacted, linking CBD's effects in hypothalamic neurons to potential benefits in managing alcohol use disorders. These findings suggest the hypothalamus is a significant target for CBD, warranting further investigation.

Thousand and one amino acid protein kinase 1 suppression improves doxorubicin-induced cardiomyopathy by preventing cardiomyocyte death and dysfunction

AIMS

Doxorubicin (DOX) is one of the most effective chemotherapeutic agents for various types of cancers. However, DOX often causes cardiotoxicity, which is referred to as DOX-induced cardiomyopathy (DIC). Despite extensive research, only a limited number of effective treatments are currently available. In this study, we aimed to identify a potential therapeutic target for DIC by preventing DOX-induced cell injury in cardiomyocytes.

METHODS AND RESULTS

We performed a kinome-wide CRISPR gene knockout screen in human cardiomyocytes derived from pluripotent stem cells (hPSC-CMs) and identified a member of the STE20 kinase family, thousand and one amino acid protein kinase 1 (TAOK1) as a potential regulator of DOX-induced cardiomyocyte death. Using CRISPR-mediated gene knockout and small interfering RNA-mediated gene knockdown, we demonstrated that TAOK1 suppression improved DOX-induced cardiomyocyte death and dysfunction, including sarcomere disarray, contractile dysfunction, DNA damage, and mitochondrial dysfunction in hPSC-CMs. Transcriptome analysis using RNA-seq also showed that DOX-induced mitochondrial dysfunction was attenuated by TAOK1 suppression. In contrast to the protective role of TAOK1 against DOX toxicity in cardiomyocytes, TAOK1 suppression did not induce DOX resistance in human cancer cell lines. DOX-induced activation of p38 mitogen-activated protein kinase (MAPK) was markedly attenuated in TAOK1-knockout hPSC-CMs. Furthermore, DOX-induced cardiomyocyte death and disruption of mitochondrial membrane potential were augmented by TAOK1 overexpression, which was partially attenuated by an inhibitor or knockdown of p38 MAPK or an apoptosis inhibitor. Finally, we demonstrated that TAOK1 suppression using adeno-associated virus (AAV)-mediated gene silencing attenuated DOX-induced myocardial damage, including myocardial fibrosis, apoptosis, and cardiomyocyte atrophy, resulting in improved cardiac function in a mouse model of DIC.

CONCLUSION

Our results indicate that TAOK1 suppression is a promising therapeutic approach for treating DIC in patients with cancer and highlight the advantages of hPSC-CMs as a platform to study drug-induced cardiotoxicity.

Establishment of a murine chronic proximal thoracic aortic aneurysm model by combining periaortic elastase application with oral BAPN administration

This study aimed to develop a chronic proximal thoracic aortic aneurysm (PTAA) model by combining periaortic elastase application with oral administration of 3-aminopropionitrile fumarate salt (BAPN) after surgery. Sixty 8-week-old C57BL/6J male mice were divided into four groups: Sham, Sham + BAPN, Elastase, and Elastase + BAPN. High-resolution micro-ultrasound was performed on days 7, 14, 21, 28, 56, and 90 post-operation to measure aortic diameter. Histopathological, transcriptomic, and bioinformatics analyses were conducted to assess the model's relevance to human PTAA. The operative mortality rate was 10 % (6/60). During follow-up, 4 animals in the elastase + BAPN group and 1 in the elastase group died from aortic rupture. Significant continuous dilation of the proximal thoracic aorta was observed only in the elastase + BAPN group, with average dilation rates of 116.60 %, 178.99 %, and 231.90 % on days 28, 56, and 90, respectively, compared to 66.46 %, 61.13 %, and 68.73 % in the elastase group. Histopathology revealed greater aortic wall thickening, collagen deposition, MMP2 expression, elastin degradation, smooth muscle cell loss, calcification, and immune cell infiltration in the elastase + BAPN group. Transcriptomic analysis identified 3039 differentially expressed genes, enriched in immune and inflammation-related pathways. Weighted gene co-expression network analysis showed significant overlap in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment results between human and murine PTAA-related gene modules which were most positively correlated with PTAA diameters. This study establishes a chronic PTAA model that mimics key features of human disease, providing a valuable tool for investigating PTAA mechanisms and developing new therapies.

Glucosinolates can act as signals to modulate intercellular trafficking via plasmodesmata

Plasmodesmata (PD) allow direct communication across the cellulosic plant cell wall, facilitating the intercellular movement of metabolites and signaling molecules within the symplast. In Arabidopsis thaliana embryos with reduced levels of the chloroplast RNA helicase ISE2, intercellular trafficking and the number of branched PD were increased. We therefore investigated the relationship between altered ISE2 expression and intercellular trafficking. Gene expression analyses in Arabidopsis tissues where ISE2 expression was increased or decreased identified genes associated with the metabolism of glucosinolates (GLSs) as highly affected. Concomitant with changes in the expression of GLS-related genes, plants with abnormal ISE2 expression contained altered GLS metabolic profiles compared with wild-type (WT) counterparts. Indeed, changes in the expression of GLS-associated genes led to altered intercellular trafficking in Arabidopsis leaves. Exogenous application of GLSs but not their breakdown products also resulted in altered intercellular trafficking. These changes in trafficking may be mediated by callose levels at PD as exogenous GLS treatment was sufficient to modulate plasmodesmal callose in WT plants. Furthermore, auxin metabolism was perturbed in plants with increased indole-type GLS levels. These findings suggest that GLSs, which are themselves transported between cells via PD, can act on PD to regulate plasmodesmal trafficking capacity.

Hydrogel-Based Tumor Tissue Microarchitecture Reshapes Dendritic Cell Metabolic Profile and Functions

The extracellular matrix (ECM) plays a pivotal role in immunomodulation, providing structural and biochemical cues that shape immune cell function. In pathological conditions like cancer and chronic inflammation, dysregulated remodeling often results in altered ECM composition and architecture, with fibrillar alignment being a hallmark linked to disease progression. Here, how ECM alignment influences dendritic cell (DC) behavior using 3D biomimetic collagen matrices with controlled fibril anisotropy is investigated. This results show that immature DCs in aligned matrices exhibited increased expression of CD86 and HLA-DR with elevated secretion of CXCL8 and CCL2 chemokines, which may enhance immune cell recruitment. However, transcriptomic and metabolomic analysis revealed significant downregulation of oxidative phosphorylation and an insufficient compensatory shift toward glycolysis, resulting in reduced ATP production. This metabolic constraint correlated with impaired/reduced DC migratory speed and distance. In contrast, mature DCs displayed minimal sensitivity to ECM alignment, maintaining uniform differentiation and functional profiles across matrix conditions. T-cell coculture experiments revealed that ECM alignment dampens T-cell activation and proliferation, likely through direct modulation of T-cell behavior. These findings highlight the stage-specific effects of ECM alignment on DC function, highlighting its role in DC immunomodulation, with implications for therapeutic development in cancer and other pathological contexts.

Microglial ER stress response via IRE1α regulates diet-induced metabolic imbalance and obesity in mice

BACKGROUND

Chronic high-fat diet (HFD) feeding triggers hypothalamic inflammation and systemic metabolic dysfunction associated with endoplasmic reticulum (ER) stress. Glial cells, specifically microglia and astrocytes, are central mediators of hypothalamic inflammation. However, the role of Inositol-Requiring Enzyme 1α (IRE1α), a primary ER stress sensor, in glial cells and its contributions to metabolic dysfunction remains elusive.

OBJECTIVES

To investigate the role of IRE1α in microglia in mediating HFD-induced metabolic dysfunction.

METHODS

Using novel conditional knockout mouse models (CX3CR1GFPΔIRE1 and TMEM119ERΔIRE1), we deleted IRE1α in immune cells or exclusively in microglia and studied its impact on metabolic health and hypothalamic transcriptional changes in mice fed with HFD for 16 weeks.

RESULTS

Deleting IRE1α in microglia significantly reduced LPS-induced pro-inflammatory cytokine gene expression in vitro. IRE1α deletion in microglia protected male mice from HFD-induced obesity, glucose intolerance, and hypothalamic inflammation, with no metabolic benefits observed in female mice. RNA-sequencing revealed significant transcriptional reprogramming of the hypothalamus, including upregulation of genes related to mitochondrial fatty acid oxidation, metabolic adaptability, and anti-inflammatory responses.

CONCLUSIONS

Our findings reveal that IRE1α-mediated ER stress response in microglia significantly contributes to hypothalamic inflammation and systemic metabolic dysfunction in response to HFD, particularly in males, demonstrating an important role of microglial ER stress response in diet-induced obesity and metabolic diseases.

Bi-allelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a neurodevelopmental disorder

The post-transcriptional modification of tRNAs plays a crucial role in tRNA structure and function. Pathogenic variants in tRNA-modification enzymes have been implicated in a wide range of human neurodevelopmental and neurological disorders. However, the molecular basis for many of these disorders remains unknown. Here, we describe a comprehensive cohort of 43 individuals from 31 unrelated families with bi-allelic variants in tRNA methyltransferase 1 (TRMT1). These individuals present with a neurodevelopmental disorder universally characterized by developmental delay and intellectual disability, accompanied by variable behavioral abnormalities, epilepsy, and facial dysmorphism. The identified variants include ultra-rare TRMT1 variants, comprising missense and predicted loss-of-function variants, which segregate with the observed clinical pathology. Our findings reveal that several variants lead to mis-splicing and a consequent loss of TRMT1 protein accumulation. Moreover, cells derived from individuals harboring TRMT1 variants exhibit a deficiency in tRNA modifications catalyzed by TRMT1. Molecular analysis reveals distinct regions of TRMT1 required for tRNA-modification activity and binding. Notably, depletion of Trmt1 protein in zebrafish is sufficient to induce developmental and behavioral phenotypes along with gene-expression changes associated with disrupted cell cycle, immune response, and neurodegenerative disorders. Altogether, these findings demonstrate that loss of TRMT1-catalyzed tRNA modifications leads to intellectual disability and provides insight into the molecular underpinnings of tRNA-modification deficiency caused by pathogenic TRMT1 variants.

Extracellular vesicles modulate metabolic processes in Prymnesium parvum, the causative species of algal blooms

Prymnesium parvum is one of the main contributors to harmful algal blooms, mainly because of its ability to produce prymnesin, a toxin involved in marine specie deaths occurring in these events. At the same time, scientific works are reporting the existence of microalgae-derived extracellular vesicles in different microalgal strains, which as in other species participate in different cellular processes and intra- and intercellular communication. Now, knowing that each of the toxic Prymnesium parvum strains produce one of the three known types of prymnesin, strains PPSR01, SAG 18.97 and UTEX-2797 (that produce the C-type, B-type and A-type prymnesins, respectively) were selected to investigate the proteome of their extracellular vesicles and to elucidate their cellular functions under normal, nitrogen deficient and phosphorus deficient growth conditions. It was observed that although extracellular vesicle size and morphology did not vary significantly between strains, their proteins showed more differences among strains than among treatments. Nonetheless, it was determined that the extracellular vesicles were involved in metabolic processes, compound synthesis, gene expression and cell growth mechanisms. Additionally, significant changes among strains were found in the vesicular proteomes when these were grown in nitrogen-deficient media, whereas phosphorus deficiency only caused changes in the UTEX-2797 strain. Through metabolomic analysis, the extracellular vesicles derived from this last strain were found to transport prymnesin. Together, these findings highlight the role of microalgae-derived extracellular vesicles in the environmental stress response in P. parvum and their impact in algal blooms.

Epstein-Barr Virus-Induced 3 Attributes to TLR7-Mediated Splenomegaly

Epstein-Barr virus-induced 3 (EBI3) functions as a component of the heterodimer cytokine IL-27, which regulates innate and acquired immune responses. The expression of EBI3 gene is induced by Toll-like receptors (TLRs). Repeated treatment with imiquimod (IMQ), a TLR7 agonist, induces splenomegaly and cytopaenia due to increased splenic function. Although immune cell activation is speculated to play a role in chronic infection-mediated splenomegaly, the detailed mechanisms remain unknown. This study shows that IMQ treatment induces marked splenomegaly and severe bicytopaenia (anaemia and thrombocytopaenia) in wild-type mice. In IMQ-treated mice, myeloid cell populations in the spleen increased, and extramedullary haematopoiesis was observed. RNA-seq analysis revealed the upregulation of type I interferon (IFN)-related genes in the spleens of IMQ-treated mice. IMQ-induced pathological changes were partially mitigated by EBI3 deficiency. To investigate the mechanism of the improved phenotypes in the Ebi3 KO mice, we examined the involvement of IL-27, a heterodimer of EBI3 and IL-27p28. The expression of Il27a, which encodes IL-27p28, was increased in the spleen and peripheral blood by IMQ treatment. Furthermore, IL-27 stimulation upregulated type I IFN-related genes in bone marrow-derived macrophage cultures without type I IFN. These findings suggest that EBI3 deficiency mitigated IMQ-mediated pathological changes, presumably via a lack of IL-27 formation. Our study thus provides insights into the molecular mechanisms underlying chronic infection-mediated splenomegaly.

Micro-region transcriptomics profiling of cerebral organoids using a capillary-based microdissection system

Investigating the transcriptome while preserving cellular spatial information facilitates a comprehensive understanding of cellular fates in multicellular organisms. However, the precise and flexible isolation of micro-regions of interest (mROIs) for profiling spatial transcriptomics (ST) remains a challenge. We established a capillary-based tissue microdissection system (CMS), which enables the high-efficiency acquisition of mROIs from cultured cerebral organoids for mRNA sequencing (CMS-seq). Subsequently, neural progenitor cells (NPCs), intermediate progenitors (IPs), mature neurons, and astrocytes were annotated in the cerebral organoids at the stages of days 20 and 60, respectively. Furthermore, astrocytes in the samples from day 20 were found to exhibit a higher tendency to express the SPARC gene whereas those from day 60 showed a stronger tendency to express the NTRK2 gene. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes indicated a higher degree of neural development at the stage of day 60. Finally, a spatial annotation map of cell types of the mROIs was constructed, enabling rapid identification of the cellular composition in each mROI. Therefore, we established an efficient method for ST analysis in cerebral organoids and further exploration of the spatial developmental trajectory.

Source ability is regulated by THOUSAND-GRAIN WEIGHT 6 in rice

An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates rice grain weight and starch accumulation before heading. A 1-bp deletion in tgw6 results in loss of function and enhances grain size and yield. Thus, TGW6 has been a target for breeding strains with increased rice yield. Although the effect of loss of TGW6 function on sink size has been well understood, its impact on source ability (the ability to produce carbohydrates from leaves and supply to sink organs, referred to as shoot carbohydrate accumulation here) has been unclear. Here, we investigated the starch content of leaves, gene expression and carbohydrate translocation using cv. Koshihikari and a near-isogenic line carrying tgw6 (NIL(TGW6)). We found that NIL(TGW6) accumulated more starch in lower leaf sheaths than cv. Koshihikari. Gene analysis of lower leaf sheaths from both lines indicated that the expression of starch synthesis-related genes was up-regulated, and those involved with starch degradation were down-regulated in the NIL(TGW6) line. Measurements of changes in carbohydrate accumulation indicated that the loss of TGW6 function activated carbohydrate translocation and that starch accumulation in the leaf sheath contributed directly to the increase in starch uploaded to the panicles. These results provide new insights into TGW6 function and how it affects the source ability of rice.

Maternal uniparental disomy of chromosome 7: how chromosome 7-encoded imprinted genes contribute to the Silver-Russell phenotype

BACKGROUND

Silver-Russell syndrome (SRS) is a rare congenital growth disorder which is associated with molecular alterations affecting imprinted regions on chromosome 11p15 and maternal uniparental disomy of chromosome 7 (upd(7)mat). In 11p15, imprinted regions contributing to the SRS phenotype could be identified, whereas on chromosome 7 at least two regions in 7q32 and 7p13 are in discussion as SRS candidate regions. We report on DNA and RNA data from upd(7)mat patients and a monozygotic twin pair with a postnatal SRS phenotype carrying a small intragenic deletion within GRB10 to delineate the contribution of upd(7)mat and imprinted genes on this chromosome to the SRS phenotype.

RESULTS

Genome sequencing in the monozygotic twins revealed a 18 kb deletion within the paternal allele of the GRB10 gene. Expression of GRB10 in blood of the twins as well as in cells from upd(7)mat and upd(7q)mat patients was not altered, whereas RNAseq indicates noticeable changes of the expression of other genes encoded by chromosomes 7 and other genomic regions.

CONCLUSIONS

Our data indicate that intrauterine growth restriction as the prenatal phenotype of upd(7)mat is caused by defective paternal alleles of the 7q32 region, as well as by overexpression of the maternal GRB10 allele whereas a defective GRB10 paternal allele does not cause this feature. The altered expression of MEST in 7q32 by upd(7)mat is associated with the complete SRS phenotype, whereas maternalization or deletion of the paternal GRB10 copy and duplication of the chromosomal region 7p12 are associated with a postnatal SRS-like phenotype.

Differential behavior responses and genetic alteration underpinning exercise effectiveness in stress-susceptible mice

Stress susceptibility varies across individuals, influenced by genetic, molecular, and environmental factors. Hence, approaches for exercise treatment as an antidepressant and anxiolytic intervention must consider individual variability. Examining individual adaptation to exercise provides insights into the biology of such variations. We investigated the efficacy of voluntary wheel running (VWR) exercise as a disease-modifying treatment for stress-susceptible (SS) mice subjected to chronic restraint stress. A multidimensional behavior analysis revealed significant variability in VWR efficacy among individuals; while some mice showed substantial behavior phenotypic improvements (SES), others displayed limited/no benefits (SER). A transcriptomic profiling of the ventral hippocampus, a brain region critical to emotional regulation, revealed molecular signatures that promote adaptive changes by restoring cellular repair, energy availability, and synaptic plasticity in SS mice. SER mice exhibited limited behavior resilience and distinct transcriptomic profiles enriched in structural adaptation without functional resilience and glial cell differentiation marked by astrocyte activation or differentiation. These findings suggest that while VWR can mitigates multiple behavior symptoms in stress-susceptible mice, its effectiveness is modulated by distinct biological mechanisms. We highlight the importance of a multivariate framework for behavior assessment and genetic underpinnings, clarifying the variability in responses to stress and exercise's therapeutic efficacy in stress-related disorders.

High Glucose-induced transcriptomic changes in human trabecular meshwork cells

Glaucoma is a leading cause of irreversible blindness, often associated with elevated intraocular pressure (IOP) due to trabecular meshwork (TM) dysfunction. Diabetes mellitus (DM) is recognized as a significant risk factor for glaucoma; however, the molecular mechanisms through which hyperglycemia affects TM function remain unclear. This study investigated the impact of high glucose on gene expression in human TM (HTM) cells to uncover pathways that contribute to TM dysfunction and glaucoma pathogenesis under diabetic conditions. Primary HTM cells were cultured under normoglycemic (5.5 mM) and hyperglycemic (30 mM) conditions for seven days, followed by mRNA sequencing (mRNA-seq) to identify differentially expressed genes, with quantitative PCR (qPCR) used for confirmatory analysis. STRING network analysis was performed to predict potential interactions among upregulated and downregulated genes. mRNA-seq analysis revealed 25 significantly differentially expressed genes in high glucose conditions, including upregulated genes associated with oxidative stress, apoptosis, autophagy, immune response, and fibrosis. Notably, TXNIP gene was significantly upregulated, indicating increased oxidative stress and apoptosis in TM cells, while downregulation of autophagy-related genes, such as HSPA6 and LAMP3, suggests compromised protein quality control. Immune response genes, including CCL7 and CHI3L1, were upregulated, suggesting an inflammatory response to oxidative stress. Increased expression of fibrosis-related genes, such as SNAI1, FGF7, and KRT19, and an increase in ECM proteins like Collagen 1 and FN accumulation and fibril formation suggest increased fibrosis of TM in diabetic conditions, potentially elevating IOP. Metabolic changes in diabetic patients could therefore lead to TM dysfunction, impair aqueous humor outflow, and elevate IOP, thereby increasing glaucoma risk. Targeting oxidative stress and fibrosis pathways offers therapeutic strategies to mitigate glaucoma progression in diabetic populations.

The splicing factor Acin1 is essential for embryonic development but has limited effects on muscle structure and homeostasis

Apoptotic chromatin condensation inducer 1 (Acin1) is an RNA-binding protein involved in the regulation of alternative splicing, but its physiological function remains unclear. Global deletion of Acin1 causes embryonic lethality around E11.5, with mutants exhibiting developmental delays and increased apoptosis. Using conditional knockout mice, we found that skeletal muscle myofiber-specific Acin1 knockout mice (Acin1 MKO) are viable and fertile and that Acin1 MKO mice show enlarged myofibers and ongoing muscle damage and regeneration, characterized by increased central nuclei and embryonic myosin heavy chain expression. RNA-seq analysis revealed that Acin1 deletion altered the expression and splicing patterns of genes crucial for muscle function. Notable changes included modified splicing of genes associated with muscle disease and mitochondrial function, often resulting in the expression of gene variants typical of immature or diseased muscle. These findings suggest that Acin1 is essential for embryonic development and has limited effects on muscle structure and homeostasis via its regulation of gene expression and alternative splicing.

Nanoplastics-mediated physiologic and genomic responses in pathogenic Escherichia coli O157:H7

The widespread occurrence of microplastics (MP) and nanoplastics (NP) in the environment is commonly thought to negatively impact living organisms; however, there remains a considerable lack of understanding regarding the actual risks associated with exposure. Microorganisms, including pathogenic bacteria, frequently interact with MPs/NPs in various ecosystems, triggering physiological responses that warrant a deeper understanding. The present study experimentally demonstrated the impact of surface-functionalized differentially charged polystyrene (PS) NPs on the physiology of human pathogenic Escherichia coli O157:H7 and their influence on biofilm formation. Our results suggest that charged NPs can influence the growth, viability, virulence, physiological stress response, and biofilm lifestyle of the pathogen. Positively-charged NPs were found to have a bacteriostatic effect on planktonic cell growth and affect cellular viability and biofilm initiation compared to negatively charged and uncharged NPs. The transcriptomic and gene expression data indicated significant changes in the global gene expression profile of cells exposed to NPs, including the differential expression of genes encoding several metabolic pathways associated with stress response and virulence. Significant upregulation of Shiga-like toxin (stx1a), quorum sensing, and biofilm initiation genes was observed in NP-exposed biofilm samples. Overall, exposure to NPs did not significantly affect the survival of pathogens but affected their growth and biofilm development pattern, and most importantly, their virulence traits.

Vacuum Ultraviolet (VUV)-Induced Physicochemical Engineering of Titanium: Enhanced Fibroblast Activity, Redox System, and Glycosaminoglycan Binding for Soft Tissue Integration

Bacterial invasion at the titanium-tissue interface causes peri-implant inflammation, posing challenges for implants in orthopedics, maxillofacial prosthetics, and dentistry. This study hypothesized that titanium surface decarbonization improves soft tissue cell adhesion and growth. One-minute vacuum ultraviolet (VUV) light treatment at 172 nm reduced surface carbon from 60% to 29% without altering surface topography, making surfaces hydrophilic and hydro-attractive. Human fibroblasts attached to VUV-treated surfaces 2-4 times more frequently than untreated surfaces, with an even greater increase on tilted and curved surfaces. Fibroblast proliferation rose 2-6 times, with an expedited G1-to-S phase transition. Cell retention under dislodging forces increased 2-5 times on VUV-treated surfaces. RNA sequencing showed upregulation of extracellular matrix production, growth factors, cell cycle progression, antioxidant defenses, and proteoglycan/glycosaminoglycan (GAG)-binding, alongside downregulation of the inflammatory response on VUV-treated titanium surfaces. An oxidative stress test showed minimal adverse effects from hydrogen peroxide on cells on VUV-treated surfaces, attributed to increased intracellular glutathione reserves. Enhanced adhesion on VUV-treated titanium was negated by treating the cells with GAG-cleaving enzymes. These findings demonstrate that VUV-mediated decarbonization enhances fibroblast attachment, proliferation, and adhesion by fostering homeostatic cellular phenotypes involving proteoglycan/GAG interactions and antioxidant defense, offering a strategy to improve the soft tissue sealing around titanium implants.

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.

Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-driven refractory vascular malformations

Congenital vascular malformations, affecting 0.5% of the population, often occur in the head and neck, complicating treatment due to the critical functions in these regions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these areas, tracing them to the cardiopharyngeal mesoderm (CPM), which contributes to the development of the head, neck, and cardiovascular system in both mouse and human embryos. In this study, we investigated the pathogenesis of these malformations by expressing Pik3caH1047R in the CPM. Mice expressing Pik3caH1047R in the CPM developed vascular abnormalities restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R upregulates Vegf-a expression in endothelial cells through HIF-mediated hypoxia signaling. Human samples supported these findings, showing elevated HIF-1α and VEGF-A in malformed vessels. Notably, inhibition of HIF-1α and VEGF-A in the mouse model significantly reduced abnormal vasculature. These results highlight the role of embryonic origins and hypoxia-driven mechanisms in vascular malformations, providing a foundation for the development of therapies targeting these difficult-to-treat conditions.

Novel Directly Reprogrammed Smooth Muscle Cells Promote Vascular Regeneration as Microvascular Mural Cells

BACKGROUND

Although cell therapy has emerged as a promising approach to promote neovascularization, its effects are mostly limited to capillaries. To generate larger or more stable vessels, layering of mural cells such as smooth muscle cells (SMCs) or pericytes is required. Recently, direct reprogramming approaches have been developed for generating SMCs. However, such reprogrammed SMCs lack genuine features of contractile SMCs, a native SMC phenotype; thus, their therapeutic and vessel-forming potential in vivo was not explored. Therefore, we aimed to directly reprogram human dermal fibroblasts toward contractile SMCs (rSMCs) and investigated their role for generating vascular mural cells in vivo and their therapeutic effects on ischemic disease.

METHODS

We applied myocardin and all-trans retinoic acid with specific culture conditions to directly reprogram human dermal fibroblasts into rSMCs. We characterized their phenotype as contractile SMCs through quantitative reverse-transcriptase polymerase chain reaction, flow cytometry, and immunostaining. We then explored their contractility using a vasoconstrictor, carbachol, and through transmission electron microscope and bulk RNA sequencing. Next, we evaluated whether transplantation of rSMCs improves blood flow and induces vessel formation as mural cells in a mouse model of hindlimb ischemia with laser Doppler perfusion imaging and histological analysis. We also determined their paracrine effects.

RESULTS

Our novel culture conditions using myocardin and all-trans retinoic acid efficiently reprogrammed human dermal fibroblasts into SMCs. These rSMCs displayed characteristics of contractile SMCs at the mRNA, protein, and cellular levels. Transplantation of rSMCs into ischemic mouse hind limbs enhanced blood flow recovery and vascular repair and improved limb salvage. Histological examination showed that vascular density was increased and the engrafted rSMCs were incorporated into the vascular wall as pericytes and vascular SMCs, thereby contributing to formation of more stable and larger microvessels. Quantitative reverse-transcriptase polymerase chain reaction analysis revealed that these transplanted rSMCs exerted pleiotropic effects, including angiogenic, arteriogenic, vessel-stabilizing, and tissue regenerative effects, on ischemic limbs.

CONCLUSIONS

A combination of myocardin and all-trans retinoic acid in defined culture conditions efficiently reprogrammed human fibroblasts into contractile and functional SMCs. The rSMCs were shown to be effective for vascular repair and contributed to neovascularization through mural cells and various paracrine effects. These human rSMCs could represent a novel source for cell-based therapy and research.

Transcriptional Profiling to Assess the Effects of Biological Stimulant Atlanticell Micomix on Tomato Seedlings Under Salt Stress

Recent environmental changes in the Mediterranean region, attributable to anthropogenic climate change, present a substantial challenge to the adaptive evaluation of crops and the development of novel improvement strategies. In this study, we established a hydroponic tomato cultivation protocol under in vitro conditions to analyze the transcriptomic profile of seedlings exposed to salinity stress. The study also examined the impact of Atlanticell Micomix, a biological stimulant derived from a mixture of mycorrhizal microorganisms and rhizobacteria, on plant growth and development under standard conditions and in response to moderate salinity. Our transcriptomic analysis indicated a differential effect of biostimulant inoculation compared to the effect induced by salinity stress, involving genes such as GOX3 or DIR1, which are associated with the plant's defense response to adverse conditions. In addition, the presence of a cross-regulatory module between jasmonic acid and auxin, involving potential orthologs of IAA29 and JAZ, was proposed. The application of the biostimulant demonstrated a potential priming effect on the tomato seedlings, which might be useful in reversing the transcriptomic effects caused by salt stress. A comprehensive analysis of the pathways differentially affected by the treatments facilitates further investigation into the mechanisms underlying these effects.

Long-term expansion of basal cells and the novel differentiation methods identify mechanisms for switching Claudin expression in normal epithelia

Epithelia are tightly connected cellular sheets, that shield our body from the external environment. They are continuously maintained by a pooled population of undifferentiated cells through differentiation. However, the maintenance mechanisms remain incompletely understood due to the difficulty of experimentally observing the differentiation process. To address this issue, we developed a culture method for long-term expansion of primary mammary basal cells with a set of compounds, that includes undifferentiated cells. An effective differentiation method regarding Claudin expression was also developed by simply removing compounds. To verify this differentiation-switching technique, we obtained microarray data comparing each differentiation state. Subsequent cellular analysis confirmed key transcription factors in each state: (1) EGR1 in undifferentiated basal cells is important for suppressing Claudin expression through maintaining the epithelial-mesenchymal transition (EMT) transcription factor TWIST1, (2) ELF3 in differentiated cells is important for actin organization and subsequent Claudin localization at the cell-cell border, that corresponds to the amount of GRHL3, an actin organizer. Their relevance was also observed in tissues and organoids. In summary, we present an effective tool for verifying molecular mechanisms that determine Claudin status in normal basal cell differentiation, that would be beneficial in epithelial cell biology, cancer biology, physiology, and regeneration research.

Soluble CTLA-4 regulates immune homeostasis and promotes resolution of inflammation by suppressing type 1 but allowing type 2 immunity

Cytotoxic T-lymphocyte-associated antigen -4 (CTLA-4) is a co-inhibitory receptor that restricts T cell activation. CTLA-4 exists as membrane (mCTLA-4) and soluble (sCTLA-4) forms, but the key producers, kinetics, and functions of sCTLA-4 are unclear. Here, we investigated the roles of sCTLA-4 in immune regulation under non-inflammatory and inflammatory conditions. Effector regulatory T (Treg) cells were the most active sCTLA-4 producers in basal and inflammatory states, with distinct kinetics upon T cell receptor (TCR) stimulation. We generated mice specifically deficient in sCTLA-4 production, which exhibited spontaneous activation of type 1 immune cells and heightened autoantibody/immunoglobulin E (IgE) production. Conversely, mCTLA-4-deficient mice developed severe type 2-skewed autoimmunity. sCTLA-4 blockade of CD80/86 on antigen-presenting cells inhibited T helper (Th)1, but not Th2, differentiation in vitro. In vivo, Treg-produced sCTLA-4, suppressed Th1-mediated experimental colitis, and enhanced wound healing but hampered tumor immunity. Thus, sCTLA-4 is essential for immune homeostasis and controlling type 1 immunity while allowing type 2 immunity to facilitate resolution in inflammatory conditions.

Temporal proteome profiling of Botrytis cinerea reveals proteins involved in plant invasion and survival

Botrytis cinerea is a necrotrophic fungal pathogen that poses a significant threat to many crops. Understanding the proteome dynamics of phytopathogens during infection can help combat plant diseases. However, most proteomics studies in phytopathogens face interference from abundant host proteins. Here, we optimized a solid media that better mimics in-planta conditions and used it to perform the temporal protein dynamics in Botrytis cinerea. An agar media with 20% tomato fruit extract and 2% deproteinised leaf extract was utilized for label-free quantitative proteomics at 12, 36, 72 and 120 hpi. Out of 3244 quantified proteins, 2045 showed differential regulation. Glycosyl hydrolases, pectin esterases, stress protein DDR48, RhoGEF and essential transcription factors were found to be upregulated during the early phase, highlighting their role in fungal virulence. Meanwhile, pathways such as macromolecule synthesis, purine, and carbohydrate metabolism were upregulated in the late-growth phase. Overall, the study provides a comprehensive understanding of proteome dynamics during Botrytis infection.

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics

Oxidative phosphorylation defects result in now intractable mitochondrial diseases (MD) with cardiac involvement markedly affecting prognosis. The mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear. Here, we used spatially resolved transcriptomics and single-nucleus RNA sequencing (snRNA-seq) on the heart of a patient with mitochondrial cardiomyopathy (MCM), combined with an MCM mouse model with cardiac-specific Ndufs6 knockdown (FS6KD). Cardiomyocytes demonstrated the most heterogeneous expression landscape among cell types caused by metabolic perturbation, and pseudotime trajectory analysis revealed dynamic cellular states transitioning from compensation to severe compromise. This progression coincided with the transient up-regulation of a transcription factor, ATF3. Genetic ablation of Atf3 in FS6KD corroborated its pivotal role, effectively delaying cardiomyopathy progression in a female-specific manner. Our findings highlight a fate-determining role of ATF3 in female MCM progression and that the latest transcriptomic analysis will help decipher the mechanisms underlying MD progression.

Characterisation of HER2-Driven Morphometric Signature in Breast Cancer and Prediction of Risk of Recurrence

INTRODUCTION

Human epidermal growth factor receptor 2-positive (HER2-positive) breast cancer (BC) is a heterogeneous disease. In this study, we hypothesised that the degree of HER2 oncogenic activity, and hence response to anti-HER2 therapy is translated into a morphological signature that can be of prognostic/predictive value.

METHODS

We developed a HER2-driven signature based on a set of morphometric features identified through digital image analysis and visual assessment in a sizable cohort of BC patients. HER2-enriched molecular sub-type (HER2-E) was used for validation, and pathway enrichment analysis was performed to assess HER2 pathway activity in the signature-positive cases. The predictive utility of this signature was evaluated in post-adjuvant HER2-positive BC patients.

RESULTS

A total of 57 morphometric features were evaluated; of them, 22 features were significantly associated with HER2 positivity. HER2 IHC score 3+/oestrogen receptor-negative tumours were significantly associated with HER2-related morphometric features compared to other HER2 classes including HER2 IHC 2+ with gene amplification, and they showed the least intra-tumour morphological heterogeneity. Tumours displaying HER2-driven morphometric signature showed the strongest association with PAM50 HER2-E sub-type and were enriched with ERBB signalling pathway compared to signature-negative cases. BC patients with positive HER2 morphometric signature showed prolonged distant metastasis-free survival post-adjuvant anti-HER2 therapy (p = 0.007). The clinico-morphometric prognostic index demonstrated an 87% accuracy in predicting recurrence risk.

CONCLUSION

Our findings underscore the strong prognostic and predictive correlation between HER2 histo-morphometric features and response to targeted anti-HER2 therapy.

Investigating the association between FOK1 polymorphism in the vitamin D receptor (VDR) gene and type 2 diabetes prevalence: A comprehensive analysis

There is mounting evidence that suggests vitamin D insufficiency may have a role in the emergence of type 2 diabetes. Additionally, as VDR mediates the actions of vitamin D, variants in its sequence could have implications in this disease. One of these polymorphisms, Fok1 (rs2228570), has been demonstrated to generate changes in the receptor's structure, causing a shorter protein. The purpose of this research is to establish a potential association between the Fok1 polymorphism and DM2. To achieve such goal, a comprehensive study of this SNP was conducted using functional in-silico analysis and a systematic review with meta-analysis. Additionally, an examination of VDR gene expression in patients with diabetes compared to controls was performed in order to investigate possible differences in expression levels. Our expression analysis showed that VDR has no differential expression between these two groups. To study its functional consequences and stability, different tools were combined, without consistent results. Finally, our systematic review and meta-analysis showed that theFok1 variant was not significantly associated with the DM2 prevalence. This extensive analysis did not provide support for an association between the presence of Fok1 polymorphism and DM2. This result aligns with some previous studies but contrasts others that have reported both protective and risk factors.

Renal and Peripheral Blood Transcriptome Signatures That Predict Treatment Response in Proliferative Lupus Nephritis-A Prospective Study

Mechanisms contributing to non-response to treatment in lupus nephritis (LN) are unclear. We characterised the transcriptome of paired peripheral blood mononuclear cells (PBMCs) and renal tissues in LN before and after cyclophosphamide (CYC) treatment and identified markers that predicted treatment response. Total RNA isolated from paired PBMCs (n = 32) and renal tissues (n = 25) of 16 proliferative LN before CYC treatment, 6 months post-treatment, and during renal flare, was sequenced on Illumina Novaseq-6000 platform. Post-treatment, eight patients were clinical responders (CR), of whom four flared (FL), and eight were non-responders (NR). Comparative transcriptomic analyses before and after treatment within CR, NR, and FL groups was performed using DESeq2. Weighted gene co-expression network analysis (WGCNA) and ROC analysis was performed to identify and validate hub genes predictive of treatment response. Based on this, we observed that pathways such as degradation of cell cycle proteins, expression of G0 and G1 phase proteins, and apoptosis, were upregulated in CR PBMCs post-treatment, while IFN-γ signalling and ECM organisation were downregulated. In NR PBMCs, ECM molecules, neddylation and BCR signalling were upregulated post-CYC treatment, while in NR renal tissue, TLR, IFN and NF-κB signalling pathways were upregulated. In FL PBMCs, neutrophil degranulation and ROS and RNS production in phagocytes were downregulated following treatment, whereas, in the corresponding renal tissue, cell-ECM interactions and ISG15 antiviral mechanism were downregulated. After WGCNA and subsequent ROC analysis, TENM2, NLGN1 and AP005230.1 from PBMCs each predicted NR (AUC-0.91; p = 0.03), while combined model improved prediction (AUC-0.94; p = 0.02). AP005230.1 from renal tissue also predicted non-response (AUC-0.94; p = 0.01) and AC092436.3 from PBMCs predicted renal flare (AUC-0.81; p = 0.04). Our study identified significant DEGs/pathways specific to different treatment outcomes and hub genes that predicted non-response and renal flare.

A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure

Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

CaMKK2 Regulates Macrophage Polarization Induced by Matrix Stiffness: Implications for Shaping the Immune Response in Stiffened Tissues

Macrophages are essential for immune responses and maintaining tissue homeostasis, exhibiting a wide range of phenotypes depending on their microenvironment. The extracellular matrix (ECM) is a vital component that provides structural support and organization to tissues, with matrix stiffness acting as a key regulator of macrophage behavior. Using physiologically relevant 3D stiffening hydrogel models, it is found that increased matrix stiffness alone promoted macrophage polarization toward a pro-regenerative phenotype, mimicking the effect of interleukin-4(IL-4) in softer matrices. Blocking Calcium/calmodulin-dependent kinase kinase 2 (CaMKK2) selectively inhibited stiffness-induced macrophage polarization without affecting IL-4-driven pro-regenerative pathways. In functional studies, CaMKK2 deletion prevented M2-like/pro-tumoral polarization caused by matrix stiffening, which in turn hindered tumor growth. In a murine wound healing model, loss of CaMKK2 impaired matrix stiffness-mediated macrophage accumulation, ultimately disrupting vascularization. These findings highlight the critical role of CaMKK2 in the macrophage mechanosensitive fate determination and gene expression program, positioning this kinase as a promising therapeutic target to selectively modulate macrophage responses in pathologically stiff tissues.

Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones

Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.

Involvement of MID1-COMPLEMENTING ACTIVITY 1 encoding a mechanosensitive ion channel in prehaustorium development of the stem parasitic plant Cuscuta campestris

Parasitic plants pose a substantial threat to agriculture as they attack economically important crops. The stem parasitic plant Cuscuta campestris invades the host's stem with a specialized organ referred to as the haustorium, which absorbs nutrients and water from the host. Initiation of the parasitic process in C. campestris requires mechanical stimuli to its stem. However, the mechanisms by which C. campestris perceives mechanical stimuli are largely unknown. Previous studies have shown that mechanosensitive ion channels (MSCs) are involved in the perception of mechanical stimuli. To examine if MSCs are involved in prehaustorium development upon tactile stimuli, we treated C. campestris plants with an MSC inhibitor, GsMTx-4, which resulted in a reduced density of prehaustoria. To identify the specific MSC gene involved in prehaustorium development, we analyzed the known functions and expression patterns of Arabidopsis MSC genes and selected MID1-COMPLEMENTING ACTIVITY 1 (MCA1) as a primary candidate. The MSC activity of CcMCA1 was confirmed by its ability to complement the phenotype of a yeast mid1 mutant. To evaluate the effect of CcMCA1 silencing on prehaustorium development, we performed host-induced gene silencing using Nicotiana tabacum plants that express an artificial microRNA-targeting CcMCA1. In the CcMCA1-silenced C. campestris, the number of prehaustoria per millimeter of stem length decreased, and the interval length between prehaustoria increased. Additionally, the expression levels of known genes involved in prehaustorium development, such as CcLBD25, decreased significantly in the CcMCA1-silenced plants. The results suggest that CcMCA1 is involved in prehaustorium development in C. campestris.

Harnessing Apple Cell Suspension Cultures in Bioreactors for Triterpene Production: Transcriptomic Insights into Biomass and Triterpene Biosynthesis

Plant cell suspension cultures offer a sustainable method for producing valuable secondary metabolites, such as bioactive pentacyclic triterpenes. This study established a high-triterpene-yielding cell suspension culture from the apple cultivar "Cox Orange Pippin". Through transcriptomic analysis and triterpene profiling across growth phases, we uncovered complex regulatory networks that govern biomass production and triterpene biosynthesis. Key biological processes, including cell cycle regulation, cell wall biosynthesis, lipid metabolism, and stress response mechanisms, play pivotal roles in culture dynamics. Differential gene expression linked to these processes revealed how the culture adapts to growth conditions and nutrient availability at each growth phase. Methyl jasmonate elicitation enhanced phenylpropanoid and flavonoid biosynthesis, along with specific triterpene production pathways, highlighting its potential for optimizing secondary metabolite production. Key enzymes, such as oxidosqualene cyclase 4 and a putative C-2α hydroxylase, were identified as promising targets for future metabolic engineering efforts. This study represents the first in-depth report on the molecular mechanisms underlying plant cell growth in bioreactors, specially focusing on a cell suspension culture derived from a semi-russeted apple cultivar. The findings reveal key regulatory pathways in biomass accumulation and triterpene production, offering valuable insights for optimizing bioreactor cultures for industrial applications.

BLADE-R: streamlined RNA extraction for molecular diagnostics and high-throughput applications

Efficient nucleic acid extraction and purification are crucial for cellular and molecular biology research, yet they pose challenges for large-scale clinical RNA sequencing and PCR assays. Here, we present BLADE-R, a magnetic bead-based protocol that simplifies the process by combining cellular lysis and nucleic acid binding into a single step, followed by a unique on-bead rinse for nuclease-free separation of genomic DNA and RNA. The Agilent TapeStation and RT-qPCR analyses show that RNA extracted from HEK293T cell line using BLADE-R outperforms the TRIzol protocol in terms of time and cost. RNA sequencing reveals no differences in sequence quality or gene count variance between samples processed with BLADE-R and those processed with TRIzol followed by RNA kit clean-up. Additionally, BLADE-R outperformed TRIzol in RNA extraction from frozen tissue and whole blood samples, as confirmed by RT-qPCR. Our protocol can be adapted to a 96-well plate format, enabling RNA purification of up to 96 human blood samples in less time than a single-sample traditional extraction. Using BLADE-R in this format, we confirmed minimal well-to-well contamination in RNA purification, cDNA synthesis, and PCR. Therefore, our novel BLADE-R protocol, suitable for both low and high-throughput formats, is effective even in limited-resource settings for preparing clinical samples for PCR and sequencing assays. Thus, our new BLADE-R technique works well even in low-resource environments to prepare clinical samples for PCR and sequencing experiments. It can be adapted for both low- and high-throughput formats.

Integrative multi-omics analysis of metabolic dysregulation induced by occupational benzene exposure in mice

Type 2 Diabetes Mellitus (T2DM) is a significant public health burden. Emerging evidence links volatile organic compounds (VOCs), such as benzene to endocrine disruption and metabolic dysfunction. However, the effects of chronic environmentally relevant VOC exposures on metabolic health are still emerging. Building on our previous findings that benzene exposure at smoking levels (50 ppm) induces metabolic impairments in male mice, we investigated the effects of benzene exposure below OSHA's Occupational Exposure Limit (OEL) on metabolic health. Adult male C57BL/6 mice were exposed to 0.9 ppm benzene 8 h a day for 9 weeks. We assessed measures of metabolic homeostasis and conducted RNA and proteome sequencing on insulin-sensitive organs (liver, skeletal muscle, adipose tissue). At this dose, exposure caused significant metabolic disruptions, including hyperglycemia, hyperinsulinemia, and insulin resistance. Transcriptomic analysis of liver, muscle, and adipose tissue identified key changes in metabolic and immune pathways especially in liver. Proteomic analysis of the liver revealed mitochondrial dysfunction as a shared feature, with disruptions in oxidative phosphorylation, mitophagy, and immune activation. Comparative analysis with high-dose (50 ppm) exposure showed conserved and dose-specific transcriptomic changes in liver, particularly in metabolic and immune responses. Our study is the first to comprehensively assess the impacts of occupational benzene exposure on metabolic health, highlighting mitochondrial dysfunction as a central mechanism and the dose-dependent molecular pathways in insulin-sensitive organs driving benzene-induced metabolic imbalance. Our data indicate that the current OSHA OEL for benzene is insufficient and needs to be lowered, as they could result in adverse metabolic health in exposed workers, particularly men, following chronic exposure.

Complement is primarily activated in the lung in a mouse model of severe COVID-19

In vitro studies and observational human disease data suggest the complement system contributes to SARS-CoV-2 pathogenesis, although how complement dysregulation develops in severe COVID-19 is unknown. Here, using a mouse-adapted SARS-CoV-2 virus (SARS2-N501YMA30) and a mouse model of COVID-19, we identify significant serologic and pulmonary complement activation post-infection. We observed C3 activation in airway and alveolar epithelia, and pulmonary vascular endothelia. Our evidence suggests the alternative pathway is the primary route of complement activation, however, components of both the alternative and classical pathways are produced locally by respiratory epithelial cells following infection, and increased in primary cultures of human airway epithelia following cytokine and SARS-CoV-2 exposure. This tissue-specific complement response appears to precede lung injury and inflammation. Our results suggest that complement activation is a defining feature of severe COVID-19 in mice, agreeing with previous publications, and provide the basis for further investigation into the role of complement in COVID-19.

Functional characterization of eicosanoid signaling in Drosophila development

20-carbon fatty acid-derived eicosanoids are versatile signaling oxylipins in mammals. In particular, a group of eicosanoids termed prostanoids are involved in multiple physiological processes, such as reproduction and immune responses. Although some eicosanoids such as prostaglandin E2 (PGE2) have been detected in some insect species, molecular mechanisms of eicosanoid synthesis and signal transduction in insects have not been thoroughly investigated. Our phylogenetic analysis indicated that, in clear contrast to the presence of numerous receptors for oxylipins and other lipid mediators in humans, the Drosophila genome only possesses a single ortholog of such receptors, which is homologous to human prostanoid receptors. This G protein-coupled receptor, named Prostaglandin Receptor or PGR, is activated by PGE2 and its isomer PGD2 in Drosophila S2 cells. PGR mutant flies die as pharate adults with insufficient tracheal development, which can be rescued by supplying high oxygen. Consistent with this, through a comprehensive mutagenesis approach, we identified a Drosophila PGE synthase whose mutants show similar pharate adult lethality with hypoxia responses. Drosophila thus has a highly simplified eicosanoid signaling pathway as compared to humans, and it may provide an ideal model system for investigating evolutionarily conserved aspects of eicosanoid signaling.

Outer radial glia promotes white matter regeneration after neonatal brain injury

The developing gyrencephalic brain contains a large population of neural stem cells in the ventricular zone and outer subventricular zone (OSVZ), the latter populated by outer radial glia (oRG). The role of oRG during postnatal development is not well understood. We show that oRG cells increase proliferative capacity and contribute to oligodendrocyte precursor cell (OPC) production following brain injury in human infants and neonatal piglets, whose brains resemble the human brain in structure and development. RNA sequencing revealed oRG-specific transcriptional responses to injury in piglets and showed that the activating transcription factor 5 (ATF5) pathway positively regulates oRG proliferation. Intranasal activation of ATF5 using salubrinal enhanced OSVZ-derived oligodendrogenesis in the injured periventricular white matter and improved functional recovery. These results reveal a key role for postnatal oRG in brain injury recovery and identify ATF5 as a potential therapeutic target for treating white matter injury in infants.

Potential multiple disease progression pathways in female patients with Alzheimer's disease inferred from transcriptome and epigenome data of the dorsolateral prefrontal cortex

Late-onset Alzheimer's disease (AD) is a typical type of dementia for which therapeutic strategies have not yet been established. The database of the Rush Alzheimer's Disease study by the ENCODE consortium contains transcriptome and various epigenome data. Although the Rush AD database may contain a satisfactory amount of data for women, the amount of data for men remains insufficient. Here, based on an analysis of publicly available data from female patients, this study found that AD pathology appears to be nonuniform; AD patients were divided into several groups with differential gene expression patterns, including those related to cognitive function. First, cluster analysis was performed on individuals diagnosed with "No Cognitive Impairment (NCI)," "Mild Cognitive Impairment (MCI)," and "Alzheimer's Disease (AD)" stages in clinical trials using gene expression, and multiple substages were identified across AD progression. The epigenome data, in particular genome-wide H3k4me3 distribution data, also supported the existence of multiple AD substages. However, APOE gene polymorphisms of individuals seemed to not correlate with disease stage. An inference of adjacency networks among substages, evaluated via partition-based graph abstraction using the gene expression profiles of individuals, suggested the possibility of multiple typical disease progression pathways from NCI to different AD substages through various MCI substages. These findings could refine biomarker discovery or inform personalized therapeutic approaches.

LINC02363: a potential biomarker for early diagnosis and treatment of sepsis

BACKGROUND

Sepsis remains a leading cause of global morbidity and mortality, yet early diagnosis is hindered by the limited specificity and sensitivity of current biomarkers.

AIM

The aim of this study was to identify lncRNAs that play a key role in sepsis and provide potential biomarkers for the diagnosis and treatment of sepsis.

METHODS

Transcriptomic data from sepsis patients were retrieved from the Chinese National Genebank (CNGBdb). Differential expression analysis identified 2,348 LncRNAs and 5,125 mRNAs (|FC|≥2, FDR < 0.05). Weighted gene co-expression network analysis (WGCNA) and meta-analysis were applied to screen core genes. Gene set enrichment analysis (GSEA) explored functional pathways, while single-cell sequencing and qPCR validated cellular localization and expression patterns.

RESULTS

WGCNA identified three key genes: LINC02363 (LncRNA), DYNLT1, and FCGR1B. Survival and meta-analyses revealed strong correlations between these genes and sepsis outcomes. GSEA highlighted LINC02363's involvement in "herpes simplex virus type 1 infection," "tuberculosis," and ribosome pathways. Single-cell sequencing showed FCGR1B's broad distribution across immune cells, while DYNLT1 localized predominantly in macrophages. qPCR confirmed significant upregulation of LINC02363 (p < 0.01), FCGR1B (p < 0.05), and DYNLT1 (p < 0.05) in sepsis patients compared to controls.

CONCLUSION

LINC02363 may serve as a new biomarker for the diagnosis and treatment of sepsis.

Integration of Dynamical Network Biomarkers, Control Theory and Drosophila Model Identifies Vasa/DDX4 as the Potential Therapeutic Targets for Metabolic Syndrome

Metabolic syndrome (MetS) is a subclinical disease, resulting in increased risk of type 2 diabetes (T2D), cardiovascular diseases, cancer, and mortality. Dynamical network biomarkers (DNB) theory has been developed to provide early-warning signals of the disease state during a preclinical stage. To improve the efficiency of DNB analysis for the target genes discovery, the DNB intervention analysis based on the control theory has been proposed. However, its biological validation in a specific disease such as MetS remains unexplored. Herein, we identified eight candidate genes from adipose tissue of MetS model mice at the preclinical stage by the DNB intervention analysis. Using Drosophila, we conducted RNAi-mediated knockdown screening of these candidate genes and identified vasa (also known as DDX4), encoding a DEAD-box RNA helicase, as a fat metabolism-associated gene. Fat body-specific knockdown of vasa abrogated high-fat diet (HFD)-induced enhancement of starvation resistance through up-regulation of triglyceride lipase. We also confirmed that DDX4 expressing adipocytes are increased in HFD-fed mice and high BMI patients using the public datasets. These results prove the potential of the DNB intervention analysis to search the therapeutic targets for diseases at the preclinical stage.

Effect of Porphyromonas Gingivalis Infection on Epithelial Rests of Malassez

The epithelial cell rests of Malassez (ERM) are located within the periodontal ligament. They are reportedly involved in maintaining homeostasis, particularly with regards to the thickness of the periodontal ligament. Their role in apical periodontitis lesions remains unclear, however. This study investigated the response of ERM to infection with Porphyromonas gingivalis. After being infected, the morphology of the P. gingivalis-infected cells was observed using confocal laser-scanning microscopy. The gene expression of P. gingivalis-infected and uninfected cells was investigated by RNA-sequencing analysis. Morphological observation showed the invasion and adhesion of P. gingivalis to the surface of ERM. The RNA analysis showed that the gene expression profile significantly differed between the infected and uninfected cells. At an expression level of ≥2 and false discovery rate of <0.1, the infected cells showed a decrease in 99 genes and an increase in 6 compared with in the non-infected cells. Most of the upregulated genes were unique to epithelial cells, such as endothelial cell-specific molecules and cytokeratin 5; the upregulated genes were associated with the immune response, however. These results indicate that ERM upregulate genes associated with epithelial cells and suppress those associated with the immune response following P. gingivalis infection.

Changes in gene expression in healthcare workers during night shifts: implications for immune response and health risks

BACKGROUND

Shift work is common in healthcare, especially in emergency and intensive care, to maintain the quality of patient care. Night shifts are linked to health risks such as cardiovascular disease, metabolic disorders, and poor mental health. It has been suggested that inflammatory responses due to the disruption of circadian rhythm may contribute to health risks, but the detailed mechanisms remain unclear. This study aimed to analyze changes in gene expression in whole blood of healthcare workers before and after a night shift and investigate the molecular pathogenesis of these changes and their impact on health.

METHODS

This was a single-center, prospective, observational study of four medical doctors working night shifts in the emergency department. Blood samples from the subjects were collected before and after the night shift, and RNA sequencing was performed to analyze changes in gene expression in whole blood. The data obtained were analyzed via Ingenuity Pathway Analysis (IPA) core analysis that included canonical pathway analysis, upstream regulator analysis, and functional network analysis. RNA bulk deconvolution was performed to estimate the relative abundance of immune cells. The IPA analysis match feature was also used to assess similarities of gene expression patterns with other diseases.

RESULTS

We identified 302 upregulated and 78 downregulated genes (p < 0.05, |log2-fold change|> 0.5) as genes whose expression changed after the night shift. Canonical pathway analysis revealed that Toll-like receptors and other innate immune response pathways were activated. Upstream regulator analysis and functional network analysis also consistently indicated a predicted activation of innate immune and inflammatory responses. RNA bulk deconvolution showed changes in the proportions of several immune cells. IPA analysis match indicated that gene expression patterns after night shifts were highly correlated with several diseases, including major depressive disorder, in terms of immune and inflammatory responses.

CONCLUSION

The results revealed that innate immune and inflammatory responses are elicited after night shifts in healthcare workers and that gene expression patterns correlate with several diseases in terms of immune and inflammatory responses. These findings suggest that shift work may affect health risks through innate immune and inflammatory responses.

NAD+ prevents chronic kidney disease by activating renal tubular metabolism

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

Arabidopsis root-type ferredoxin:NADP(H) oxidoreductases are crucial for root growth and ferredoxin-dependent processes

Root-type ferredoxin:NADP(H) oxidoreductase (RFNR) is believed to reduce ferredoxin using NADPH in nonphotosynthetic tissues, facilitating ferredoxin-dependent biological processes. However, the physiological functions of RFNR remain unclear due to the difficulty in obtaining mutants lacking redundant RFNR isoproteins. The present study successfully generated Arabidopsis homozygous rnfr1;2 double mutants by traditional crossing and selection. However, they displayed severely stunted roots, challenging subsequent growth and abundant seed recovery. Notably, grafted plants combining mutant scions with wild-type rootstocks exhibited normal growth and produced abundant mutant seeds. Growth analysis employing reciprocal grafts with the wild-type and mutant plants showed that primary root growth was inhibited only when the rootstock was derived from the mutants. Meanwhile, the absence of RFNR1 and 2 in the scion had no apparent impact on shoot and root growth. Root transcriptome analysis revealed that RFNR1 and 2 deficiency upregulated genes encoding ferredoxin-dependent enzymes and root-type ferredoxin, leading to genome-wide reprogramming associated with cell walls, lipids, photosynthesis, secondary metabolism, and biotic/abiotic stress responses. Thus, Arabidopsis RFNR1 and 2 are crucial for root growth and various ferredoxin-dependent biological processes.