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

Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs

Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.

Altered expression of collagen gene family members and its epigenetic background in equine Sarcoids

Alterations in the genes involved in the creation of the extracellular matrix (ECM) were observed in our earlier transcriptome studies of sarcoids and their cell culture model. For a complete characterization of the underlying molecular pathways, it is imperative to comprehend the involvement of ECM modifications in the oncogenic transformation of sarcoid fibroblasts. Thus, the aim of this investigation was to describe the expression patterns of a set of genes that are essential for the rearrangements of the extracellular matrix, namely collagen genes, and elucidate possible mechanisms underlying the observed disruptions. To this end, we applied the RT-qPCR method on BPV-negative skin samples and sarcoid samples (n = 6 and 7; respectively) to perform relative quantification of the expression level of eight genes belonging to the collagen family and carried out an integrative analysis of the obtained data with previously characterized epigenetic signatures. The results showed aberrations in the level of chosen collagen genes in the sarcoids compared to the control, manifesting in their elevated levels in the tumor samples (p-value≤0.05). The upregulation of Col1A2, Col11A1, Col6A3, Col5A2, Col4A1, Col6A6, Col5A1, Col6A2 genes was detected in sarcoid samples. The identified changes were statistically significant (p-value≤0.05) and ranged from 1.43 (Col6A2) to 1.88 (Col6A3). Further investigation into the potential involvement of epigenetic mechanisms in the regulation of collagen gene levels in sarcoids revealed compelling evidence of DNA methylation and microRNAs playing significant roles. The findings suggest a complex interplay between gene expression, epigenetic regulation, and the dysregulation of the ECM in sarcoid pathogenesis.

Reproductive adaptation of Astyanax mexicanus under nutrient limitation

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetra Astyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, lower biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identified insulin-like growth factor 1a receptor (igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies in Astyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.

Pituitary folliculo-stellate cells modulate tumor vasculature and extracellular matrix composition in experimental lactosomatotropinomas

Folliculo-stellate cells (FSCs) constitute 5-10 % of the adenohypophysis and have been proposed as paracrine regulators of pituitary cells. However, their participation in pituitary tumor development remains unclear. We generated a lacto-somatotropic tumor model by subcutaneous injection of GH3 (lacto-somatotrophs) and the FSCs TtT/GF, isolated or combined, in immunodeficient mice, to study the role of the FSCs on tumor formation, hormone secretion, vascularization and extra-cellular matrix involvement. The co-culture of both cell lines let us gain insight into the proliferative and secretory action of FSC in pituitary tumor modulation. Our results showed that initially GH3:TtT/GF tumors had an earlier onset, but lately, TtT/GF cells restrained GH3:TtT/GF tumor growth and their Prl synthesis, although no differences were observed in the proliferative potential of tumor cells in vivo. Instead, TtT/GF cells exerted a direct mitogenic action on GH3 cells in vitro. Moreover, GH3 tumors had fewer irrigating vessels, lower vascular area and a higher VEGF/bFGF ratio that correlated with Hif1a expression, consistent with the tissue hypoxia and hemorrhage. These features were downregulated in their co-injected counterparts, which interestingly showed an increased deposition of collagens, glycoproteins and mucopolysaccharides extra-cellular matrix (EMC) components. Isolated TtT/GF injected cells did not generate tumors, but they developed fibrous masses characterized by collagen and high bFGF production. In conclusion, our results demonstrate that FSCs are dual regulators of pituitary tumor growth, with a mitogenic action on tumor cells but also a restrictive tumor effect on the cancer processes angiogenesis, hypoxia, and ECM remodeling.

An inflammation-associated lncRNA induces neuronal damage via mitochondrial dysfunction

Immune disease-associated non-coding SNPs, which often locate in tissue-specific regulatory elements, are emerging as key factors in gene regulation. Among these elements, long non-coding RNAs (lncRNAs) participate in many cellular processes, and their characteristics make these molecules appealing therapeutic targets. In this study, we have studied lncRNA LOC339803 in the context of neuronal cells, which is located in autoimmunity-associated region 2p15 and recently described to have a proinflammatory role in intestinal disorders. Using human brain samples and a wide variety of in vitro techniques, we have showed a differential function of this lncRNA in neuronal cells. We have further demonstrated the role of LOC339803 in maintaining hexokinase 2 (HK2) levels and thus mitochondrial integrity, partially explaining the implication of the lncRNA in multiple sclerosis (MS) pathogenesis. Our results show the importance of cell-type-specific studies in the case of regulatory lncRNAs. We present LOC339803 as a candidate for further studies as a mitochondrial dysfunction marker or possible therapeutic target in neurodegeneration.

Single-cell RNA sequencing reveals tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in larval zebrafish (Danio rerio)

Perfluorooctanesulfonic acid (PFOS) elicits adverse effects on numerous organs and developmental processes but the mechanisms underlying these effects are not well understood. Here, we use single-cell RNA-sequencing to assess tissue-specific transcriptomic changes in zebrafish (Danio rerio) larvae exposed to 16 µM PFOS or dimethylsulfoxide (0.01 %) from 3-72 h post fertilization (hpf). Data analysis was multi-pronged and included pseudo-bulk, untargeted clustering, informed pathway queries, and a cluster curated for hepatocyte biomarkers (fabp10a, and apoa2). Overall, 8.63 % (2390/27698) genes were significantly differentially expressed. Results from untargeted analysis revealed 22 distinct clusters that were manually annotated to specific tissues using a weight-of-evidence approach. The clusters with the highest number of significant differentially expressed genes (DEGs) were digestive organs, muscle, and otolith. Additionally, we assessed the distribution of pathway-specific genes known to be involved in PFOS toxicity: the PPAR pathway, β-oxidation of fatty acids, the Nfe2l2 pathway, and epigenetic modifications by DNA methylation, across clusters and identified the blood-related tissue to be the most sensitive. The curated hepatocyte cluster showed 220 significant DEGs and was enriched for the Notch signaling pathway. These findings provide insights into both established and novel sensitive target tissues and molecular mechanisms of developmental toxicity of PFOS.

Genome-wide methylation analysis unveils genes and pathways with altered methylation profiles in pterygium

Pterygium is a highly prevalent ocular surface disease, particularly in equatorial regions, with no pharmaceutical intervention available and surgical excision remaining the only treatment option. Ultraviolet (UV) radiation from sunlight is widely recognized as the primary cause of pterygium. While chronic UV exposure induces epigenetic changes in the skin contributing to skin cancer, comprehensive studies on epigenetic alterations in pterygium remain unpublished, and causal relationships have yet to be established. This study aimed to investigate genome-wide methylation changes in pterygium using the Illumina Infinium Epic v2.0 Methylation array. We identified 1052 hypermethylated CpGs (499 genes) and 687 hypomethylated CpGs (340 genes) in pterygium tissue compared to control conjunctival tissue from patients undergoing cataract surgery (Δβ>|0.1|, P < 0.05). Hypomethylated genes were mainly associated with PI3K-Akt and MAPK pathways, while hypermethylated genes were enriched in pathways related to oxidative stress, autophagy, DNA repair, and Wnt signaling inhibition. Comparing these findings with transcriptomic datasets revealed 28 hypermethylated genes with downregulated transcripts and 74 hypomethylated genes with upregulated transcripts. qPCR validation confirmed upregulation of hypomethylated genes (MMP2, FBLN5, ZEB1) and downregulation of hypermethylated genes (SAMSN1, CBX4) at the transcript level. These findings suggest that dysregulated DNA methylation may contribute to pterygium pathogenesis by upregulating genes involved in cell proliferation, survival, angiogenesis, fibrosis, and extracellular matrix remodeling, while silencing genes associated with oxidative stress response, autophagy, and DNA damage repair. These insights into the global methylation landscape of pterygium open avenues for detailed functional analysis, potentially guiding targeted therapeutic strategies.

Eriocheir sinensis CD63 activate mitochondria-mediated apoptosis to resist Spiroplasma eriocheiris infection

CD63, a member of the tetraspanins, is involved in cell movement, adhesion, immune response. Nevertheless, the role of CD63 in combating pathogen infections in invertebrates remains largely unclear. Tremor disease, whose pathogen is Spiroplasma eriocheiris, is one of the most prevalent illnesses affecting Eriocheir sinensis. EsCD63 is 1474 bp, with a 756 bp open reading frame that encodes for 252 amino acids. The qPCR data demonstrated that gills showed significant levels of transcription for EsCD63, followed by hemocytes, hepatopancreas, intestines and nerves, while showing low levels of transcription in the heart and muscles. After infection with S. eriocheiris, an obvious drop in the transcription level of EsCD63 was observed. Both the amount of S. eriocheiris copies in hemocytes and the mortality of E. sinensis significantly increased after the injection of chemically synthesized EsCD63 siRNA and stimulation with S. eriocheiris. After EsCD63 interference, the phagocytosis of hemocytes to S. eriocheiris, the apoptosis of hemocytes, and reactive oxygen species level of hemocytes were all decreased significantly, by laser scanning confocal microscopy and flow cytometry analysis. Meanwhile, the mitochondrial membrane potential of hemocytes was increased after EsCD63 interference. These findings indicated that EsCD63 was crucial for E. sinensis immunity and defense mechanisms against infection of S. eriocheiris.

Matured hiPSC-derived cardiomyocytes possess dematuration plasticity

Human induced Pluripotent Stem Cell-derived cardiomyocytes (hiPSC-CMs) are increasingly used to identify potential factors capable of inducing endogenous cardiomyocyte proliferation to regenerate the injured heart. L-type calcium channel blockers have previously been identified as a class of factors capable of inducing matured hiPSC-CMs to proliferate. However, the mechanism by which L-type calcium channel blockers promote hiPSC-CM proliferation remains unclear. Here we provide evidence that matured hiPSC-CMs possess plasticity to undergo dematuration in response to certain pharmacological compounds. Consistent with primary cardiomyocyte maturation during perinatal development, we found that centrosome disassembly occurs in hiPSC-CMs during plate-based, temporal, maturation. A small molecule screen identified nitrendipine, an L-type calcium channel blocker, and 1-NA-PP1, a Src kinase inhibitor, as factors capable of inducing centrosome reassembly in a subpopulation of hiPSC-CMs. Furthermore, centrosome-positive hiPSC-CMs were more likely to exhibit cell cycle activity than centrosome-negative hiPSC-CMs. In contrast, neither nitrendipine or 1-NA-PP1 induced centrosome reassembly, or cell cycle activity, in neonatal rat ventricular myocytes (NRVMs). Differential bulk transcriptome analysis indicated that matured hiPSC-CMs, but not NRVMs, treated with nitrendipine or 1-NA-PP1 undergo dematuration. ScRNA transcriptome analysis supported that matured hiPSC-CMs treated with either nitrendipine or 1-NA-PP1 undergo dematuration. Collectively, our results indicate that matured hiPSC-CMs, but not primary NRVMs, possess plasticity to undergo dematuration in response to certain pharmacological compounds such as L-type calcium channel blockers and Src-kinase inhibitors. This study shows that once mature, hiPSC-CMs may not maintain their maturity under experimental conditions which may have implications for experimental systems where the state of hiPSC-CM maturation is relevant.

Taiwan Chingguan Yihau may improve post-COVID-19 respiratory complications through PI3K/AKT, HIF-1, and TNF signaling pathways revealed by network pharmacology analysis

The emergence of new SARS-CoV-2 variants with a higher contagious capability and faster transmissible speed has imposed an incessant menace on global health and the economy. The SARS-CoV-2 infection might reoccur and last much longer than expected. Thence, there is a high possibility that COVID-19 can cause long-term health problems. This condition needs to be investigated thoroughly, especially the post-COVID-19 complications. Respiratory tract disorders are common and typical complications after recovery. Until now, there has been a lack of data on specialized therapeutic medicine for post-COVID-19 complications. The clinical efficacy of NRICM101 has been demonstrated in hospitalized COVID-19 patients. This herbal medicine may also be a promising therapy for post-COVID-19 complications, thanks to its phytochemical constituents. The potential pharmacological mechanisms of NRICM101 in treating post-COVID-19 respiratory complications were investigated using network pharmacology combined with molecular docking, and the results revealed that NRICM101 may exert a beneficial effect through the three primary pathways: PI3K/AKT, HIF-1, and TNF signaling pathways. Flavonoids (especially quercetin) have a predominant role and synergize with other active compounds to produce therapeutic effectiveness. Most of the main active compounds exist in three chief herbal ingredients, including Liquorice root (Glycyrrhiza glabra), Scutellaria root (Scutellaria baicalensis), and Mulberry leaf (Morus alba). To our knowledge, this is the first study of the NRICM101 effect on post-COVID-19 respiratory complications. Our findings may provide a better understanding of the potential mechanisms of NRICM101 in treating SARS-CoV-2 infection and regulating the immunoinflammatory response to improve post-COVID-19 respiratory complications.

Beneficial effects of Glc-1,6-P2 modulation on mutant phosphomannomutase-2

The metabolite Glucose-1,6-bisphosphate (Glc-1,6-P2) plays a vital role in human metabolism, and is a crucial activator and stabilizer for phosphomannomutase-2 (PMM2) - mutations within this protein propagate the most common congenital disorder of glycosylation (PMM2-CDG). In vivo, Glc-1,6-P2 is hydrolysed by phosphomannomutase-1 (PMM1), predominantly in the brain, under the influence of inosine monophosphate (IMP). In the present study, we employed knock-out PMM1 in Arg141His/Phe119LeuPMM2 patient-derived fibroblasts and investigated the phenotypic improvement. Increased Glc-1,6-P2 was associated with glycosylation enhancement, confirmed by glycan profiling. Previously identified PMM2-CDG biomarkers, such as LAMP1, PTX3 and lysosomal enzymes showed empirical imrovement- these findings were corroborated by metabolomic and proteomic analysis. Moreover, our results support the potential of Glc-1,6-P2 modulation for PMM2-CDG, potentiating novel perspectives in drug discovery.

Intrinsically Disordered Regions Define Unique Protein Interaction Networks in CHD Family Remodelers

Chromodomain helicase DNA-binding (CHD) enzymes play a pivotal role in genome regulation. They possess highly conserved ATPase domains flanked by poorly characterized and intrinsically disordered N- and C-termini. Using mass spectrometry, we identify dozens of novel protein-protein interactions (PPIs) within the N- and C-termini of human CHD family members. We also define a highly conserved aggregation-prone region (APR) within the C-terminus of CHD4 which is critical for its interaction with the nucleosome remodeling and deacetylase (NuRD), as well as ChAHP (CHD4, activity-dependent neuroprotective protein (ADNP), and HP1γ) complexes. Further analysis reveals a regulatory role for the CHD4 APR in gene transcription during erythrocyte formation. Our results highlight that the N- and C-termini of CHD chromatin remodelers shape protein interaction networks that drive unique transcriptional programs.

Comparative proteomic profiling of glioblastoma and healthy brain cell-derived extracellular vesicles reveals enrichment of cancer-associated proteins

Extracellular vesicles (EVs)-mediated cellular communication plays a role in cancer development and progression. This study focuses on identifying glioblastoma-specific EV protein markers through a comparative mass spectrometry bottom-up proteomic analysis of the LN-229 cell line and human neurons, astrocytes, and endothelial brain cells (HEBCs) using timsTOF Pro 2 instrument. The statistically significant upregulated proteins with fold change greater than 2 in the glioblastoma-derived EVs were clustered based on physical and functional interactions using the STRING database and analyzed using Gene Ontology enrichment. LN229-derived EVs contained an average of 2635 proteins, while human astrocytes, neurons, and HEBC encapsulated 2647, 716, and 2285 proteins, respectively. NanoParticle Tracking Analysis indicated that glioblastoma-derived EVs exhibited greater size variability compared to EVs from healthy cells. Statistical analysis identified 25 statistically significant proteins with increased levels in LN229 EVs relative to at least two healthy cell lines suggesting their potential as glioblastoma markers. Functional clustering using the STRING database and GO analysis indicated involvement in epigenetic regulation, metastasis, angiogenesis, and protein folding. Post-translational modification analysis identified a subset of 17 proteins unique to the cancer-derived EVs involved in chromatin regulation, extracellular matrix remodeling, and basement membrane organization pathways, highlighting their role in tumor progression.

Neuroprotective effects of Centella asiatica against LPS/amyloid beta-induced neurodegeneration through inhibition of neuroinflammation

Protein aggregation and microglia-mediated neuroinflammation are the major contributors to the progression of neurodegeneration. Currently, available drugs for neurodegenerative diseases have limited efficacy and are associated with several side effects; suggesting a need to discover novel therapeutic agents. Therefore, we aim to evaluate the neuroprotective effects of C. asiatica against amyloid beta (Aβ) and lipopolysaccharides (LPS)-induced neurodegeneration using human microglia and neuronal cell-based models. To identify potential molecular targets of C. asiatica, network pharmacology-based approaches were used along with molecular docking, followed by experimental validation via indirect ELISA, Western blotting, and indirect immunofluorescence assays. Our results from network pharmacology, molecular docking, and cell-based models, exhibited that AKT1, TNF-α, STAT3, CASP3, PTGS2, MAPK1, APP, and NF-κB are the potential molecular targets of C. asiatica. Further, we have found that C. asiatica treatment reduces LPS/Aβ-induced cell death, NO production, and LDH release in microglia and neuronal cells. The anti-neuroinflammatory effect of C. asiatica was further observed via the reduction of LPS, Aβ, and LPS+Aβ-induced neuroinflammatory markers; TNF-α, IL6, IL-1β, AKT1, INOS, NF-κB, MAPK3, and PTGS2 in microglia cells. Moreover, neurodegenerative and apoptotic markers; APP, α-syn, P-tau STAT3, and CASP3 were reduced upon C. asiatica treatment in neuronal cells, suggesting its neuroprotective properties. For the first time, we have shown the neuroprotective effects of C. asiatica against LPS, Aβ, and LPS+Aβ -induced neurodegeneration via inhibition of neuroinflammation and neurodegenerative markers. The outcomes of the study suggested that C. asiatica could be a promising candidate for neuroinflammation-mediated neurodegenerative diseases like Parkinson's and Alzheimer's.

Evolutionary Systems Biology Identifies Genetic Trade-offs in Rice Defense against Aboveground and Belowground Attackers

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, and O. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant-defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different aboveground and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at the KSL8 and MG1 loci on chromosome 11. KSL8 encodes the first committed step toward the biosynthesis of either stemarane-type or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking out KSL8-jap and CPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance to S. frugiperda and decreased resistance to M. incognita. Furthermore, MG1 resides in a haplotype that provided resistance to M. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungus Magnaporthe oryzae and other pests and pathogens. Finally, KSL8 and MG1 alleles are located within trans-species polymorphic haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms at KSL8 and MG1 may be maintained through complex and diffuse community interactions.

The NONO protein regulates nonclassical DNA structure: Effects on circadian genes and DNA damage

The DBHS protein family of Nono, PSPC1, and SFPQ regulates diverse aspects of RNA metabolism. Whether these proteins share similar functions is currently unknown. In mouse embryonic fibroblasts (MEFs), we observed around 2000 circadian and non-circadian genes regulated by Nono and PSPC1, with only 35% in common. Considering specifically circadian genes, up- or downregulation by Nono and PSPC1 depends mainly on the gene phase. We postulated a regulatory role of Nono on R-loops, the class of non-B DNA structures that form during transcription. We confirmed this by showing a broad effect of Nono on genome-wide R-loop homeostasis. Interestingly, the R-loop regulation by Nono occurs in a time-of-day dependent manner among the circadian genes. Moreover, we showed a protective role of Nono in a DNA damage cellular model that involves R-loop accumulation. Further studies are required to understand the circadian regulation of R-loops and their implications on gene regulation and disease.

DLK1 Distinguishes Subsets of NF1-Associated Malignant Peripheral Nerve Sheath Tumors with Divergent Molecular Signatures

PURPOSE

Malignant peripheral nerve sheath tumor (MPNST) is the leading cause of premature death among individuals with neurofibromatosis type 1 (NF1), and the transcriptional aberrations that precede malignant transformation and contribute to MPNST tumorigenesis remain poorly defined. Alterations involving CDKN2A and components of PRC2 have been implicated as early drivers of peripheral nerve sheath tumor (PNST) evolution, but these events do not occur in all MPNST. Accordingly, emerging data have begun to highlight the importance of molecular-based stratification to improve outcomes in patients with NF1-PNST.

EXPERIMENTAL DESIGN

In this study, we perform an integrated analysis of multiple, independent datasets obtained from human patients with NF1 to gain critical insights into PNST evolution and MPNST heterogeneity.

RESULTS

We show that delta-like noncanonical Notch ligand 1 (DLK1) is significantly increased in MPNST and provide evidence that DLK1 overexpression may precede histologic changes consistent with malignancy. In complementary analyses, we find that serum levels of DLK1 are significantly higher in both mice and humans harboring MPNST compared with those without malignancy. Importantly, although DLK1 expression is increased in MPNST overall, through the integration of multiple, independent datasets, we demonstrate that divergent levels of DLK1 expression distinguish MPNST subsets characterized by unique molecular programs and potential therapeutic vulnerabilities. Specifically, we show that overexpression of DLK1 is associated with the reactivation of embryonic signatures, an immunosuppressive microenvironment, and a worse overall survival in patients with NF1-MPNST.

CONCLUSIONS

Collectively, our findings provide critical insights into MPNST tumorigenesis and support prospective studies evaluating the utility of DLK1 tissue and serum levels in augmenting diagnosis, risk assessment, and therapeutic stratification in the setting of NF1-PNST.

Exploring the functional, protective, and transcriptomic effects of GIP on cytokine-exposed human pancreatic islets and EndoC-βH5 cells

Immune-mediated beta-cell destruction and lack of alpha-cell responsiveness to hypoglycaemia are hallmarks of type 1 diabetes pathology. The incretin hormone glucose-dependent insulinotropic polypeptide (GIP) may hold therapeutic potential for type 1 diabetes due to its insulinotropic and glucagonotropic effects, as well as its cytoprotective effects shown in rodent beta cells. To further increase our understanding of GIP's effects on human beta cells, we here examined the functional, protective, and transcriptomic effects of GIP in human EndoC-βH5 beta cells and isolated human islets in the presence or absence of proinflammatory cytokines (interferon (IFN)-γ ± interleukin (IL)-1β) as a mimic of type 1 diabetes. GIP dose-dependently augmented glucose-stimulated insulin secretion from EndoC-βH5 cells and increased insulin and glucagon secretion from human islets at high and low glucose concentrations, respectively. The insulinotropic effect of GIP in EndoC-βH5 cells was abrogated by KN-93, an inhibitor of calcium/calmodulin-dependent protein kinase 2 (CaMK2). GIP did not prevent cytokine-induced apoptosis in EndoC-βH5 cells or human islets, and GIP did not protect against cytokine-induced functional impairment in EndoC-βH5 cells. GIP treatment of human islets for 24 h had no effects on the transcriptome and did not modulate cytokine-induced transcriptional changes. However, GIP augmented IL-1β + IFNγ-induced secretion of interleukin (IL)-10 and c-c motif chemokine ligand (CCL)-2 from human islets while decreasing the secretion of c-x-c motif chemokine ligand (CXCL)-8. In EndoC-βH5 cells, GIP reduced IFN-γ-induced secretion of tumor necrosis factor (TNF)-α, IL-2, IL-6, and IL-10 but increased the secretion of CXCL8, CCL2, CCL4, and CCL11. In conclusion, our results suggest that the insulinotropic effect of GIP is CaMK2-dependent. Furthermore, our findings indicate that GIP neither exerts cytoprotective effects against cytokines nor modulate the transcriptome of human islets. GIP may, however, exert selective modulatory effects on secreted inflammatory factors from cytokine-exposed beta cells and islets.

Genome-based reclassification of the family Stappiaceae and assessment of environmental forcing with the report of two novel taxa, Flexibacterium corallicola gen. nov., sp. nov., and Nesiotobacter zosterae sp. nov., isolated from coral and seagrass

Two novel strains, MaLMAid0302T and SPO723T, isolated from coral and eelgrass, respectively, were distinguished from other Stappiaceae species based on phenotypic, biochemical, phylogenetic, and chemotaxonomic traits. Taxonomic challenges within the family Stappiaceae were addressed using a taxogenomic approach with iterative clustering, establishing an optimal average amino acid identity (AAI) threshold (71.92-72.88%) for genus delineation. This analysis led to major taxonomic revisions, including the establishment of new genera-Parapolycladidibacter, Astericibacter, Flexibacterium, Aliiroseibium, Laciiroseibium, Soliroseibium, Novilabrenzia, Litoriroseibium, and Algilabrenzia-as well as the reassignment of several species: Hongsoonwoonella albiluteola comb. nov., Parapolycladidibacter stylochi gen. nov., comb. nov., Astericibacter flavus gen. nov., comb. nov., Nesiotobacter exalbescens comb. nov., Aliiroseibium hamelinense gen. nov., comb. nov., Laciiroseibium aquae gen. nov., comb. nov., Soliroseibium sediminis gen. nov., comb. nov., Novilabrenzia suaedae gen. nov., comb. nov., Novilabrenzia litorale gen. nov., comb. nov., Litoriroseibium aestuarii gen. nov., comb. nov., Litoriroseibium limicola gen. nov., comb. nov., and Algilabrenzia polysiphoniae gen. nov., comb. nov. Given this extensive taxonomic reclassification of the family Stappiaceae, strain SPO723T (=KCCM 42324T = JCM 14066T) was classified as Nesiotobacter zosterae sp. nov., and Flexibacterium corallicola MaLMAid0302T (=KCTC 92348T = JCM 35474T) was designated as the type species of the newly established genus Flexibacterium. Close phylogenetic ties to Pseudovibrio, known for symbiosis, prompted analysis of niche-specific genetic compositions. Canonical Correspondence Analysis attributed 64% of genomic variation to phylogenetic forcing and 36% to environmental forcing. Functional adaptations included pectin and aromatic compound degradation in sediment strains, nitrogen reduction in flatworm strains, and sulfur metabolism in coral strains. The eelgrass strain exhibited dTDP-L-rhamnose synthesis, potentially aiding biofilm formation for adhesion in dynamic environments. These findings emphasize the roles of both environmental and phylogenetic forcing in shaping genomic diversity and highlight the ecological importance of the family Stappiaceae in marine habitat-associated niches.

Ribonuclease activity undermines immune sensing of naked extracellular RNA

Cell membranes are thought of as barriers to extracellular RNA (exRNA) uptake. While naked exRNAs can be spontaneously internalized by certain cells, functional cytosolic delivery has been rarely observed. Here, we show that extracellular ribonucleases (RNases)-primarily from cell culture supplements-have obscured the study of exRNA functionality. When ribonuclease inhibitor (RI) is added to cell cultures, naked exRNAs can trigger pro-inflammatory responses in dendritic cells and macrophages, largely via endosomal Toll-like receptors (TLRs). Moreover, naked exRNAs can escape endosomes, engaging cytosolic RNA sensors. In addition, naked extracellular mRNAs can be spontaneously internalized and translated by various cell types in an RI-dependent manner. In vivo, RI co-injection amplifies naked-RNA-induced activation of splenic lymphocytes and myeloid leukocytes. Furthermore, naked RNA is inherently pro-inflammatory in RNase-poor compartments like the peritoneal cavity. These findings demonstrate that naked RNA is bioactive without requiring vesicular encapsulation, making a case for nonvesicular-exRNA-mediated intercellular communication.

Neuromuscular junction transcriptome analysis of spinal and bulbar muscular atrophy mice implicates sarcomere gene expression and calcium flux dysregulation in disease pathogenesis

X-linked Spinal and Bulbar Muscular Atrophy (SBMA) is a rare, late-onset neuromuscular disease caused by a CAG repeat expansion mutation in the androgen receptor (AR) gene. SBMA is characterized by progressive muscle atrophy of both neurogenic and myopathic etiologies. Previous work has established that mutant AR expression in skeletal muscle could be a significant contributor to neuromuscular decline, yet the mechanisms involved remain ill-defined. As AR is a nuclear hormone receptor transcription factor, we sought to define early changes in gene expression in skeletal muscle of pre-symptomatic SBMA mice, with a focus on transcriptional changes at the neuromuscular junction (NMJ). We describe loss of key NMJ-specific genes in synaptic muscle regions of pre-symptomatic SBMA mice, while extrasynaptic muscle features a coordinated loss of sarcomere genes that coincides with ectopic re-expression of certain NMJ genes. Furthermore, SBMA muscle prominently features dysregulated calcium flux, likely stemming from a compensatory response to early atrophy that greatly exacerbates over time. The SERCA activator CDN1163 conferred a mild rescue in function and muscle size in SBMA mice, while genetic deletion of the gene encoding Myf6/MRF4, a negative regulator of sarcomere gene expression and predicted AR interactor, did not ameliorate muscle atrophy. These studies suggest that modulation of calcium flux could be a promising pharmacological target in SBMA.

Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism

Rice eating and cooking quality (ECQ) is significantly influenced by the physicochemical properties of rice starch. This study integrates whole-genome resequencing, transcriptomic data, and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits. A TWAS (transcriptome-wide association study) identified 285 transcripts linked to 6 ECQ traits. Genome-wide mapping of these transcripts revealed 21 747 local eQTLs (expression quantitative trait loci) and 45 158 distal eQTLs. TWAS and eQTL analysis detected several known and novel genes, including starch synthesis-related genes, heat shock proteins, transcription factors, genes related to ATP accumulation, and UDP-glucosyltransferases, showcasing the complex genetic regulation of rice ECQ. WGCNA (weighted gene co-expression network analysis) uncovered key co-expression networks, including a module that links alpha-globulin1 (GLB1) to starch and sucrose metabolism. Genetic diversity analysis of the GLB1 gene across a Korean rice collection identified 26 haplotypes, with indica and aus forming 7 and 3 haplotypes, respectively, which showed significant phenotypic effects on ECQ traits. CRISPR-Cas9-created knockout lines validated these findings, demonstrating that loss of GLB1 function caused significant changes in seed storage proteins, reduced amylose content, altered starch granules, and modified pasting properties without affecting plant phenotypes. By integrating TWAS, eQTL mapping, haplotype analysis, gene expression networks, and CRISPR validation, this study establishes GLB1 as a regulator of ECQ, linking starch biosynthesis and protein accumulation pathways. This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice, demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.

Let-7 restrains an epigenetic circuit in AT2 cells to prevent fibrogenic intermediates in pulmonary fibrosis

MicroRNA-mediated post-transcriptional regulation of lung alveolar type 2 (AT2) and AT1 cell differentiation remains understudied. Here, we demonstrate that the let-7 miRNA family plays a homeostatic role in AT2 quiescence by preventing the uncontrolled accumulation of AT2 transitional cells and promoting AT1 differentiation. Using mouse and organoid models, we show that genetic ablation of let-7a1/let-7f1/let-7d cluster (let-7afd) in AT2 cells prevents AT1 differentiation and leads to KRT8 transitional cell accumulation in progressive pulmonary fibrosis. Integration of AGO2-eCLIP with RNA-sequencing identified direct let-7 targets within an oncogene feed-forward regulatory network, including BACH1/EZH2/MYC, which drives an aberrant fibrotic cascade. Additional CUT&RUN-sequencing analyses revealed that let-7afd loss disrupts histone acetylation and methylation, driving epigenetic reprogramming and altered gene transcription in profibrotic AT2 cells. This study identifies let-7 as a central hub linking unchecked oncogenic signaling to impaired AT2 cell plasticity and fibrogenesis.

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.

Calorie-restriction treatment mitigates the aging in rat liver model

The aging process promotes progressive impairment of homeostasis and the increase of the risk of disease and death. A major hallmark of the aging process is the systemic chronic inflammation which strongly contributes to the onset of aging-related diseases. In the liver, the aging condition drives the hepatocytes to develop a metabolic dysfunction-associated steatosis. Caloric restriction (CR) is a remarkable strategy to delay biological aging, occurring through several mechanisms. In this study we aimed to explore, employing an in vivo rat model, the impact of CR on aging-mediated liver inflammation markers. The experiments were performed on 14 male Sprague-Dawley rats (24 months old). At 18 months old, rats were allocated into two groups: the normal diet (ND) group was continued ad libitum diet, and the CR regimen group was fed a diet of the same chow restricted to 60% of the intake. All animals were sacrificed at 24 months old. Compared to the ND group, morphological examination of the liver revealed a lower level of fibrosis in the CR group, concomitantly with a reduced expression of key fibrotic markers, such as collagen I, fibronectin, and αSMA. Furthermore, CR improved the liver oxidative balance, as showed by the increased expression of two scavenging enzymes, SOD1/SOD. Moreover, we reported concomitant reduction of NLRP3 inflammasome signalling. Interestingly, CR significantly improved the signalling of key members of the nutrition-sensitizing affected by aging, AMPK/SIRT1/LKB1. Collectively our findings support the evidence on the metabolic benefits of CR about aging-related liver inflammation, by inducing a morphological improvement that mirrors the decrease in the expression of inflammatory molecular markers.

Integrative multi-transcriptomic analysis uncovers core genes and potential defense mechanisms in rice-Magnoporthe oryzae interaction

KEY MESSAGE

Multiple transcriptomic comprehensive analyses highlight key genes and cast new light on multifaceted pathways that may be important arenas in rice innate immunity against Magnoporthe oryzae blast disease. Magnaporthe oryzae (MOR) poses a significant threat to rice production worldwide. However, defense mechanisms in rice against MOR remain inadequately defined. In this study, a multi-transcriptomic integrative analysis on 441 samples from diverse microarrays and RNA-seq sets was conducted to reveal critical factors in rice defense against MOR infection. A robust pattern of 3534 upregulated genes and 2920 repressed genes was commonly identified across all MOR-infected arrays and RNA-seq profiles. Interestingly, enrichment analysis revealed a consistent triggering of endoplasmic reticulum (ER)-related mechanisms and citric acid cycle (TCA) influx in rice response to MOR infection across all the transcriptome profiles, suggesting their critical role in modulating rice immunity against the pathogen. By contrast, chloroplast and photosynthesis pathways were frequently repressed across all the profiles. Among ER-related mechanisms, the phagosome pathway involved in the activation of NADPH oxidase was highly triggered in early response to MOR infection. Moreover, WGCNA analysis highlighted four key co-expressed gene modules and 80 significant hub genes associated with MOR infection. Among the core genes, Sec61 gene involved in the ER-translocation process was identified along with OsMFP (peroxisomal oxidation gene) and OSAHH gene (involved in cyclic-trans-methylation). Furthermore, MPK6, WRKY24, NUP35, and NPR1 genes were observed as core co-expressed genes, suggesting their significance in regulating rice immunity against MOR. Our findings elucidate key genes and multifaceted mechanisms in rice-MOR interaction, proposing new informative clues that can be exploited to improve rice resistance against blast disease.

Identification of targetable vulnerabilities of PLK1-overexpressing cancers by synthetic dosage lethality

Chromosomal instability (CIN) drives tumor heterogeneity, complicating cancer therapy. Although Polo-like kinase 1 (PLK1) overexpression induces CIN, direct inhibition of PLK1 has shown limited clinical benefits. We therefore performed a genome-wide synthetic dosage lethality (SDL) screen to identify effective alternative targets and validated over 100 candidates using in vivo and in vitro secondary CRISPR screens. We employed direct-capture Perturb-seq to assess the transcriptional consequences and viability of each SDL perturbation at a single-cell resolution. This revealed IGF2BP2 as a critical genetic dependency that, when targeted, downregulated PLK1 and significantly restricted tumor growth. Mechanistic analyses showed that IGF2BP2 loss disrupted cellular energy metabolism and mitochondrial ATP production by downregulating PLK1 levels as well as genes associated with oxidative phosphorylation. Consistent with this, pharmacological inhibition of IGF2BP2 severely impacts the viability of PLK1-overexpressing cancer cells addicted to higher metabolic rates. Our work offers a novel therapeutic strategy against PLK1-driven heterogeneous malignancies.

Role of Maternal Obesity in Offspring Cardiovascular Development and Congenital Heart Defects

BACKGROUND

Congenital heart disease is a leading cause of death in newborns, yet many of its molecular mechanisms remain unknown. Both maternal obesity and diabetes increase the risk of congenital heart disease in offspring, with recent studies suggesting these conditions may have distinct teratogenic mechanisms. The global prevalence of obesity is rising, and while maternal obesity is a known risk factor for fetal congenital heart disease, the specific mechanisms are largely unexplored.

METHODS AND RESULTS

We used a murine model of diet-induced maternal obesity, without diabetes, to produce dams that were overweight but had normal blood glucose levels. Embryos were generated and their developing hearts analyzed. Transcriptome analysis was performed using single-nucleus and bulk RNA sequencing. Global and phospho-enriched proteome analysis was performed using tandem mass tag-mass spectroscopy. Immunobloting and histologic evaluation were also performed. Analysis revealed disrupted oxidative phosphorylation and reactive oxygen species formation, with reduced antioxidant capacity, evidenced by downregulation of genes Sod1 and Gp4x, and disrupted Hif1a signaling. Evidence of oxidative stress, cell death signaling, and alteration in Rho GTPase and actin cytoskeleton signaling was also observed. Genes involved in cardiac morphogenesis, including Hand2, were downregulated, and fewer mature cardiomyocytes were present. Histologic analysis confirmed increased cardiac defects in embryos exposed to maternal obesity.

CONCLUSIONS

These findings demonstrate that maternal obesity alone can result in cardiac defects through mechanisms similar to those associated with maternal hyperglycemia. This study provides valuable insight into the role of maternal obesity, a growing and modifiable risk factor, in the development of the most common birth defect, congenital heart disease.

Epidermal loss of PRMT5 leads to the emergence of an atypical basal keratinocyte-like cell population and defective skin stratification

During skin development, ectoderm-derived cells undergo precisely coordinated proliferation, differentiation, and adhesion to yield stratified epidermis. Disruptions in these processes can result in congenital anomalies including ectodermal dysplasia and harlequin ichthyosis. Protein Arginine Methyl Transferase 5 (PRMT5)-an enzyme responsible for methylating arginine residues in histones and other proteins-maintains progenitor status in germ and limb bud cells. Similarly, in vitro evidence suggests that PRMT5 prevents differentiation of basal keratinocytes, leading us to hypothesize that PRMT5 preserves the stem-cell phenotype of keratinocytes in vivo. To test this possibility, we generated conditional knockout (cKO) mice lacking Prmt5 in early ectoderm (E7.5), impacting the entire epidermis. Prmt5 cKOs exhibited gross skin defects, compromised skin barrier function, and reduced postnatal viability. Histological analyses revealed significant defects in epidermal stratification, without alterations in apoptosis or proliferation. Single-cell RNA and ATAC-seq analysis identified an atypical population of basal keratinocyte-like cells in Prmt5 cKOs, that exhibited a senescence-like program, characterized by increased Cdkn1a (p21), elevated senescence-associated secretory phenotype (SASP) molecules (Igfbp2), and decreased developmental transcription factor (Trp63) expression. Our findings suggest that PRMT5 prevents basal keratinocyte senescence by repressing Cdkn1a, shedding light on the epigenetic regulation of basal keratinocyte maintenance and senescence in congenital skin disorders.

Dual pathogenic mechanisms in lysinuric protein intolerance: Interplay between hyperammonemia and cellular metabolic dysregulation in astrocyte injury

BACKGROUND

Lysinuric protein intolerance (LPI) is a rare genetic disorder characterized by an inherited defect in cationic amino acid transport caused by pathogenic variants in the SLC7A7 gene. While LPI causes systemic complications, the underlying cellular mechanisms remain poorly understood. This study investigated the cellular characteristics of LPI, focusing on intracellular metabolite profiles and astrocyte response to hyperammonemia.

OBJECTIVES

To examine intracellular metabolite changes in LPI patients and to evaluate the response of patient-derived astrocytes to ammonia exposure.

METHODS

Peripheral blood mononuclear cells (PBMCs) from three LPI patients and three healthy controls were analyzed for intracellular metabolite profiles using capillary electrophoresis-fourier transform mass spectrometry. Induced pluripotent stem cells were generated from a patient's PBMCs and differentiated into astrocytes. We evaluated LPI-astrocytes and their response to ammonia treatment by RNA sequencing, gene expression profiling, and cell viability assays.

RESULTS

Metabolite analysis revealed significant intracellular metabolite imbalances in LPI patients, with increases of 21 metabolites including 11 amino acids. LPI-astrocytes exhibited distinct cellular characteristics regarding altered gene expression and enhanced cell cycle progression. When exposed to ammonia, the astrocytes demonstrated markedly lower cell viability and increased reactive oxygen species (ROS) production compared to control astrocytes. N-acetylcysteine supplementation significantly ameliorated ammonia-induced cytotoxicity.

CONCLUSIONS

SLC7A7 dysfunction leads to intracellular metabolite disturbances and an increase in vulnerability to ammonia toxicity through ROS production of astrocyte, suggesting hyperammonemia and amino acid deficiencies as potential therapeutic targets in LPI patient care.

Novel thiazolones for the simultaneous modulation of PPARγ, COX-2 and 15-LOX to address metabolic disease-associated portal inflammation

A hybrid pharmacophore model, based on structural motifs previously identified by our team, was employed to generate ligands that simultaneously target COX-2, 15-LOX, and PPARγ in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). Notable COX-2 inhibitory activities (IC50 = 0.065-0.24 μM) were observed relative to celecoxib (IC50 = 0.049 μM). The two most effective 15-LOX inhibitors, 2a and 2b, exhibited 69 % and 57 % of quercetin's action, respectively. Utilizing the rat hemi-diaphragm model to assess in vitro glucose uptake capacity, compounds 2a and 2b demonstrated significant glucose uptake potential in the absence of insulin, surpassing that of pioglitazone. Compound 2a activated PPARγ with an EC50 value of 3.4 μM in a Gal4-hybrid reporter gene assay, indicating partial agonistic action. Interesting binding interactions with targets of interest were identified by molecular docking studies. As well, the expression levels of 20-HETE, Il-1β and TNF-α were decreased in LPS-challenged RAW264.7 macrophages upon treatment with compound 2a. The pharmacokinetic analysis of 2a and assessment of its in vivo efficacy in addressing hepatic impairment in rat models of diabetes and pre-diabetes were carried out. Together, these findings may offer preliminary insights into the potential of these compounds for further refinement in the existing therapeutic arsenals for metabolic diseases.

RBM10 loss promotes metastases by aberrant splicing of cytoskeletal and extracellular matrix mRNAs

RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon inclusion events included vinculin (VCL), tenascin C (TNC), and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse HrasG12V/Rbm1OKO thyrocytes develop metastases that are reversed by RBM10 expression or by combined knockdown of VCL, CD44, and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusion in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFκB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers.

Conserved role of the SERK-BIR module in development and immunity across land plants

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs), which are subfamily II of leucine-rich repeat receptor-like kinases (LRR-RLKs), play diverse roles in development and immunity in the angiosperm Arabidopsis thaliana. AtSERKs act as co-receptors for many LRR-RLKs, including BRASSINOSTEROID INSENSITIVE 1 (BRI1) and FLAGELLIN SENSITIVE 2 (FLS2).1,2,3,4 The conserved tyrosine (Y) residue in AtSERK3 is crucial for signaling specificity in differentiating BRI1- and FLS2-mediated pathways.5 BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASES (BIRs) interact with SERKs under resting conditions, negatively regulating SERK-mediated pathways.6,7 SERK and BIR are highly conserved in land plants, whereas BRI1 and FLS2 homologs are absent or poorly conserved in bryophyte lineages.8,9 The biological functions of SERK homologs in non-flowering plants are largely unknown. The genome of the liverwort Marchantia polymorpha encodes single homologs for SERK and BIR, namely MpSERK and MpBIR.9 We here show that Mpserk disruptants display growth and developmental defects with no observable sexual or vegetative reproduction. Complementation analysis revealed a contribution of the conserved Y residue of MpSERK to growth. Proximity-labeling-based interactomics identified MpBIR as a MpSERK interactor. Mpbir disruptants displayed defects in reproductive organ development. Patterns of development- and immunity-related gene expression in Mpserk and Mpbir were antagonistic, suggesting that MpBIR functions as an MpSERK repressor. The pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 grew poorly on Mpbir, indicating a significant role of the MpSERK-MpBIR module in immunity. Taken together, we propose that the SERK-BIR functional module was already regulating both development and immunity in the last common ancestor of land plants.

Novel dihydrochalcone from Fissistigma latifolium targets STAT3 and survivin to overcome multidrug resistance cancers in vitro and in vivo

BACKGROUND

Multidrug resistance (MDR) remains a significant challenge in cancer chemotherapy, with no FDA-approved drugs currently available for its treatment. Natural chalcones, known for their diverse bioactivities, have emerged as potential therapeutic candidates.

PURPOSE

This study aimed to investigate the potential of 4,6-dimethoxy-2,5-quinodihydrochalcone (DODHC), a compound derived from Fissistigma latifolium, in overcoming MDR in cancer and to elucidate its underlying molecular mechanisms.

METHODS

The reversal effects of DODHC on MDR were evaluated using cytotoxicity assays. The molecular mechanisms were explored through apoptosis- and cell cycle-related assays, STAT3 ELISA, western blotting, docking simulations, and a zebrafish model. The impact of DODHC on P-glycoprotein (P-gp) activity was assessed using the Calcein-AM uptake assay.

RESULTS

DODHC promoted apoptosis in MDR cancer cells by suppressing survivin expression and activating the extrinsic apoptotic pathway. It also induced G2/M phase cell cycle arrest by downregulating cell division control protein 2 (CDC2) and cyclin B1 (CCNB1), thereby inhibiting cell proliferation. Additionally, DODHC reduced both total and phosphorylated STAT3 levels in MDR cancer cells without affecting P-gp activity. In vivo, DODHC significantly inhibited tumor growth in MDR cancer models, both as a monotherapy and in combination with paclitaxel.

CONCLUSION

This study highlights DODHC as a dual inhibitor of STAT3 and survivin, demonstrating its potential as a promising candidate for the treatment of MDR cancers.

Postoperative Stress Accelerates Atherosclerosis through Inflammatory Remodeling of the HDL Proteome and Impaired Reverse Cholesterol Transport

BACKGROUND

Over 10 million patients undergoing non-cardiac surgery annually experience major cardiovascular complications within 30 days, many due to destabilized atherosclerotic plaques. Reverse cholesterol transport (RCT), a key pathway for cholesterol removal by HDL and apoA-I, is critical in preventing plaque progression. While surgery-induced inflammation is known to impair HDL function, its effects on RCT and plaque stability remain unclear.

METHODS

To isolate the impact of surgical inflammation, independent of blood loss, we developed an abdominal laparotomy model in apoE -/- mice on a Western diet, minimizing blood loss and avoiding perioperative blood sampling. We assessed plasma cholesterol efflux capacity, performed proteomic analysis of HDL, and analyzed atherosclerotic plaques for lipid content, perilipin-2 (PLIN2), cleaved-caspase-3 (c-Casp-3), and necrotic core expansion. A novel dual-label, dual-cell-type in vivo RCT model was developed to compare RCT from macrophage-derived (BMDMs) and vascular smooth muscle cells (VSMCs)-derived foam cells. Recombinant apoA-I (rApoA-I) was tested for therapeutic rescue of impaired RCT.

RESULTS

Surgery significantly reduced RCT for at least 48 hours, paralleled by a drop in cholesterol efflux capacity and inflammatory remodeling of HDL, marked by elevated serum amyloid A (SAA1/2) and reduced apoA-I. Plaques showed a 1.6-fold increase in intracellular lipids and PLIN2 expression at 24 hours post-surgery, with elevated c-Casp-3 indicating lipid-driven apoptosis. Foam cell analysis revealed increased PLIN2 in both CD45 + (leukocyte) and CD45 - (non-leukocyte) subtypes, with leukocyte foam cells expressing higher PLIN2. c-Casp-3 + apoptotic cells were predominantly PLIN2 high and of both leukocytic and non-leukocytic origin. By day 15, the necrotic core area increased by 1.5-fold with sustained loss of plaque cellularity. Using our dual-cell-type RCT model, we found that surgery significantly impaired BMDM RCT in vivo , while VSMC RCT remained largely unaffected, highlighting foam cell subtype-specific vulnerability to surgical inflammation. These findings were mirrored in general surgery patients, whose postoperative plasma exhibited markedly reduced cholesterol efflux capacity. In mice, rApoA-I treatment partially restored RCT and reduced plaque lipid accumulation.

CONCLUSIONS

Surgical inflammation acutely impairs HDL function and RCT, triggering lipid accumulation, foam cell apoptosis, and accelerated plaque destabilization independent of blood loss. Immediate restoration of apoA-I at the time of surgery, aiming to counteract the acute phase response, may offer a targeted strategy to reduce postoperative cardiovascular risk.

TEAD-Independent Cell Growth of Hippo-Inactive Mesothelioma Cells: Unveiling Resistance to TEAD Inhibitor K-975 through MYC Signaling Activation

Inactivation of tumor-suppressive Hippo signaling pathway is frequently observed in mesothelioma, which leads to the activation of yes-associated protein (YAP) and TAZ (also known as WW domain-containing transcription regulator 1; YAP/TAZ) transcriptional coactivators. YAP/TAZ form complexes with TEAD family members, DNA-binding proteins, to activate transcription, which promotes cancer cell growth and proliferation. Recently developed TEAD inhibitors exhibit antitumor activity by inhibiting the formation of the transcription complex through binding to TEAD; however, the antitumor activity of TEAD inhibitors against mesothelioma remains to be fully elucidated. Here, we show that the TEAD inhibitor K-975 acts as a pan-TEAD inhibitor and selectively inhibits the binding of TEAD-binding proteins, especially YAP/TAZ, in mesothelioma cells. In studies using a panel of mesothelioma cell lines, K-975 showed a significant growth inhibitory effect on Hippo-inactivated mesothelioma cells, but some of these cell lines exhibited primary resistance to K-975. Differential gene expression analysis revealed that cells resistant to K-975 exhibited activation of MYC signaling in the presence of K-975, and cells overexpressed with MYC showed strong drug resistance, in vitro and in vivo. Our study revealed the features of a subset of mesothelioma cells that proliferate in a TEAD-independent manner and provides important insights for the successful development of therapeutic strategies for mesothelioma with Hippo pathway inactivation.

Transcriptomic and epigenomic consequences of heterozygous loss-of-function mutations in AKAP11, a shared risk gene for bipolar disorder and schizophrenia

The gene A-kinase anchoring protein 11 (AKAP11) recently emerged as a shared risk factor between bipolar disorder and schizophrenia, driven by large-effect loss-of-function (LoF) variants. Recent research has uncovered the neurophysiological characteristics and synapse proteomics profile of Akap11-mutant mouse models. Considering the role of AKAP11 in binding cAMP-dependent protein kinase A (PKA) and mediating phosphorylation of numerous substrates, such as transcription factors and epigenetic regulators, and given that chromatin alterations have been implicated in the brains of patients with bipolar disorder and schizophrenia, it is crucial to uncover the transcriptomic and chromatin dysregulations following the heterozygous knockout of AKAP11, particularly in human neurons. This study uses genome-wide approaches to investigate such aberrations in human induced pluripotent stem cell (iPSC)-derived neurons. We show the impact of heterozygous AKAP11 LoF mutations on the gene expression landscape and profile the DNA methylation and histone acetylation modifications. Altogether we highlight the involvement of aberrant activity of intergenic and intronic enhancers, which are enriched in PBX homeobox 2 (PBX2) and Nuclear Factor-1 (NF1) known binding motifs, respectively, in transcription dysregulations of genes mainly involved in DNA-binding transcription factor activity, actin binding and cytoskeleton regulation, and cytokine receptor binding. We also show significant downregulation of pathways related to ribosome structure and function, a pathway also altered in BD and SCZ post-mortem brain tissues and heterozygous Akap11-KO mice synapse proteomics. A better understanding of the dysregulations resulting from haploinsufficiency in AKAP11 improves our knowledge of the biological roots and pathophysiology of BD and SCZ, paving the way for better therapeutic approaches.

Molecular characterization of doublesex and Mab-3 (DMRT) gene family in Ctenopharyngodon idella (grass carp)

Doublesex and Mab-3 (DMRT) gene family is a diverse group of transcriptional factors crucially involved in sex differentiation and biological processes such as body growth and differentiation in vertebrates. In this study, we analyzed DMRT genes structural characterization and physiochemical properties, and elucidated their functional role as a ligand of different gonadal receptors including androgen (AR), estrogen β (ER-β), estrogen γ (ER-γ), and progesterone (PR). All six genes of the DMRT gene family in grass carp (Ctenopharyngodon Idella Valenciennes, 1844) exhibited an acidic nature. These DMRT genes are primarily localized in the nucleus, where they play a role in DNA binding via doublesex DNA binding motif. All the DMRT gene pairs are under strong purifying selection with two segmental duplications envisaged about 18.30 (DMRT3a/DMRTA2) and 24.90 (DMRT2b/DMRT2a) million years ago (MYA). Recombination analysis revealed six potential recombinant breakpoints posing substantial evolutionary pressure for diverse cellular functioning of DMRT isoforms. Moreover, the DMRTA1 protein had a highest binding affinity of - 270.42 and - 267.16 for androgen receptors (AR) and progesterone receptors (PR), whereas, for estrogen receptors ER-β and ER-γ, the maximum binding affinity was observed with DMRT2a and DMRT2b proteins showing a docking score of - 254.22 and - 261.71, respectively. First time we studied the binding scores and interface residues of the DMRT genes as a ligand of gonadal receptors that play a crucial role in fish growth, sex development and differentiation, and spermatogenesis and oocyte maturation. The present study provides a molecular basis for DMRT genes in grass carp that may serve as a reference for in-depth phylogenomic study in other species.

Fetal Fibroblast Heterogeneity Defines Dermal Architecture during Human Embryonic Skin Development

To investigate the heterogeneity of fibroblasts in human fetal skin, we analyzed published single-cell RNA-sequencing data (7 and 16 weeks after conception) and performed single-molecule FISH to map their spatial distribution and predicted dynamic interactions. Clustering revealed 8 fibroblast populations with changes in developmental stage-specific abundance. Proliferative cells (MKI67+) were present at all stages. The appearance of dermal papilla (PRDM1+) and hair follicle (SLC26A7+) fibroblasts coincided with hair follicle maturation, whereas fibroblasts (apolipoprotein E positive) specifically associated with blood vessels increased in abundance as the vessels developed. HOXC5 was a marker of the most abundant fibroblasts 7-8 weeks after conception; this cluster was diminished 9-13 weeks after conception and undetectable subsequently. A second population (PLAT+) decreased in abundance with the same kinetics. Fibroblasts corresponding to papillary dermis (GRP+) were predominant 9-13 weeks after conception, whereas reticular dermal fibroblasts (ASPN+) were the major cluster 14-16 weeks after conception. Partition-based graph abstraction and pseudotime analysis indicated that the HOXC5+ fibroblasts were closely connected with the papillary and hair follicle fibroblasts, whereas the PLAT+ fibroblasts were connected with reticular and vascular fibroblasts. Dermal papilla fibroblasts were the most highly differentiated. Integration of fetal and adult datasets distinguished the adult and fetal papillary clusters from the reticular clusters.

A critical genetic interaction between Gemin3/Ddx20 and translation initiation factor NAT1/eIF4G2 drives development

Gemin3 (Gem3) or DEAD-box RNA helicase 20 (Ddx20) has been mostly implicated in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) as part of the SMN-Gemins complex. Nonetheless, several studies have hinted at its participation in diverse snRNP-independent activities. Here, we utilised a narrow unbiased genetic screen to discover novel Gem3 interactors in Drosophila with the aim of gaining better insights on its function in vivo. Through this approach, we identified a novel genetic interaction between Gem3 and NAT1, which encodes the Drosophila orthologue of translational regulator eIF4G2. Despite lack of a physical association, loss of NAT1 function was found to downregulate Gem3 mRNA levels. Extensive convergence in transcriptome alterations downstream of Gem3 and NAT1 silencing further supports a functional relationship between these factors in addition to showing a requirement for both in actin cytoskeleton organisation and organism development, particularly neurodevelopment. In confirmation, flies with either Gem3 or NAT1 depletion exhibited brain growth defects and reduced muscle contraction. Severe delays in developmental progression were also observed in a newly generated Gem3 hypomorphic mutant. Our data linking Gemin3 to a key component of the translational machinery support an emerging role for Gemin3 in translation that is also critical during organism development.

Overfeeding in rainbow trout (Oncorhynchus mykiss): Metabolic disruptions, impaired immunity, and increased infection risk

Excess adiposity impairs immune function and host defense in obese individuals, but studies on this concept in fish remain limited. In aquaculture, rapid growth is often encouraged through intensive farming practices, leading to overfeeding and negatively impacting production. This study aimed to induce obesity in rainbow trout through overfeeding, exploring metabolic abnormalities, immune response alterations, and infection susceptibility via transcriptomic and metabolomic analyses. In the overfed group, fish were fed until they refused to eat, while the control group was fed according to recommended feeding rates for four weeks. Sampling was conducted at weeks 1, 2, and 4 for serological, histopathological, metabolomic, and transcriptomic analyses. After four weeks, mortality rates were compared following Aeromonas salmonicida challenge, and immunological changes assessed one day post-infection. Overfed fish exhibited significant increases in weight gain (WG), body mass index (BMI), elevated AST/ALT levels, hepatocyte hypertrophy, lipid droplet formation, and triglyceride accumulation. At 1, 2, and 4 wpf, the overfed group exhibited distinct metabolic changes, with key alterations in glycolysis/gluconeogenesis, lipid metabolism and amino acid metabolism. KEGG analysis of transcriptomic data revealed a significant decrease in complement and coagulation cascades, including C3, FB, FH, an FI, accompanied by heightened TNF and IL-17 signaling pathways, involving the upregulation of genes such as TNF-α, IL-1β, and IL-6, indicating an enhanced inflammatory response. The overfed group experienced higher mortality post-infection. Excess energy from overfeeding led to hepatic fat accumulation, liver damage, and reduced innate immune responses, particularly in complement activation. These physiological disruptions compromised immune function, highlighting the detrimental effects of overfeeding-induced obesity on fish health. This study offers critical insights into the immunological mechanisms linking obesity to increased disease susceptibility.

Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy

Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this study, we identified suppressor of Tom1 (Stm1) as a molecular link between ribosome protection and biogenesis in Saccharomyces cerevisiae. While Stm1 was previously described as a dormancy factor, we show that it activates Ifh1, a transcriptional activator of ribosomal protein genes. Stm1 transiently localizes to the nucleolus, where it interacts with pre-ribosomes and directly binds RNA and Ifh1 through its C-terminal intrinsically disordered region (IDR). Although the IDR is dispensable for ribosome protection, its loss compromises cell growth. The IDR is phosphorylated upon nutrient starvation, which disrupts its interaction with Ifh1. Our findings reveal a molecular pathway sensing and adjusting ribosome abundance in response to nutrient availability, reinforcing the relevance of regulated ribosome homeostasis in physiology and disease.

Quantitative proteomics identifies plasma protein alterations that associate with metabolic and thrombotic profile changes after bariatric surgery

OBJECTIVE

Roux-en-Y gastric bypass (RYGB) surgery has been shown to lead to favourable health outcomes in obese patients. However, the molecular changes that occur and how they relate to clinical measures are poorly understood. Here, we characterise the proteomic alterations that occur in plasma of RYGB patients before and 9 months after surgery using quantitative proteomics.

METHODS

Plasma proteomics was performed by sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) to identify and quantify differentially abundant proteins. Relationships between significantly altered proteins and clinical markers were examined. A gene set enrichment analysis was also conducted to identify altered pathways.

RESULTS

From the proteomic analysis, 27 proteins increased, and 43 proteins decreased in abundance 9 months after surgery, providing insights into the physiological changes that accompany weight loss. Proteins including sex hormone binding globulin (SHBG), inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3) and apolipoprotein D (APOD), which increased in abundance post-surgery, highlight improvements in lipid regulation, insulin sensitivity and inflammation. Proteins involved in coagulation, including α2-macroglobulin, kallikrein-B1, prothrombin, and factor (FX, FXI and FXII), exhibited reduced levels, aligning with a decrease in thrombotic potential.

CONCLUSIONS

These findings provide a mechanistic understanding of how bariatric surgery leads to systemic changes in metabolic and haemostatic pathways, thus favourably modulating the risk of developing cardiovascular disease.

Lymphatic Activation of ACKR3 Signaling Regulates Lymphatic Response After Ischemic Heart Injury

BACKGROUND

Ischemic heart disease is a prevalent cause of death and disability worldwide. Recent studies reported a rapid expansion of the cardiac lymphatic network upon ischemic heart injury and proposed that cardiac lymphatics may attenuate tissue edema and inflammatory mechanisms after ischemic heart injury. Nevertheless, the mechanisms through which hypoxic conditions affect cardiac lymphangiogenesis and function remain unclear. Here, we aimed to characterize the role of the AM (adrenomedullin) decoy receptor ACKR3 (atypical chemokine receptor-3) in the lymphatic response following ischemic heart injury.

METHODS

Spatial assessment of ACKR3 signaling in the heart after ischemic heart injury was conducted using ACKR3-Tango-GFP (green fluorescent protein) reporter mice. Roles of ACKR3 after ischemic heart injury were characterized in Ackr3∆Lyve1 mice and in cultured human lymphatic endothelial cells exposed to hypoxia.

RESULTS

Using the novel ACKR3-Tango-GFP reporter mice, we detected activation of ACKR3 signaling in cardiac lymphatics adjacent to the site of ischemic injury of left anterior descending artery ligation. Ackr3∆Lyve1 mice exhibited better survival after left anterior descending artery ligation, especially within the first couple of days post-injury, and were protected from the formation of acute tissue edema. Ackr3∆Lyve1 mice exhibited a denser cardiac lymphatic network after left anterior descending artery ligation, especially in the injured tissues. Transcriptomic analysis revealed changes in cardiac lymphatic gene expression patterns that have been associated with extracellular matrix remodeling and immune activation. We also found that ACKR3 plays a critical role in regulating continuous cell-cell junction dynamics in lymphatic endothelial cells under hypoxic conditions.

CONCLUSIONS

Lymphatic expression of ACKR3 governs numerous processes following ischemic heart injury, including the lymphangiogenic response, edema protection, and overall survival. These results expand our understanding of how the heart failure biomarker AM, regulated by lymphatic ACKR3, may exert its roles after ischemic cardiac injury.

Network-Based Integrative Analysis to Identify Key Genes and Corresponding Reporter Biomolecules for Triple-Negative Breast Cancer

BACKGROUND

The malignant neoplasm of the TNBC is the leading cause of death among Indian women. Recent studies identified the global burden of TNBC affecting approximately more than 40 percent of all BC cases in women worldwide. The absence of expression of receptors such as ER, PR, and HER2 characterizes TNBC.

OBJECTIVES

Due to the lack of specific targets, standard treatment options for TNBC are limited. This integrative study aims to identify key genes and provide insights into the underlying molecular mechanisms of TNBC, which can potentially lead to the development of more effective therapeutic strategies.

MATERIAL AND METHODOLOGY

This study integrates PPI and WGCNA analysis of TNBC-related datasets (GSE52194 and GSE58135) to identify key genes. Subsequently, downstream analysis is conducted to explore potential therapeutic targets for TNBC.

RESULTS

The present study renders the potential 13 key genes (PLCG2, CXCL10, CDK1, STAT1, IL6, PLK1, CCNB1, AURKA, NDC80, EGFR, 1L1B, FN1, BUB1B), along with their associated 6 TFs and 20 miRNAs, as reporter biomolecules around which the most significant changes occur. There were some miRNAs hsa-mir-449b-5p, hsa-let-7b-5p, hsa-mir-26a-5p, hsa-mir-155-5p, hsa-mir-24-3p, hsa-mir-212-3p, hsa-mir-21-5p, hsa-mir-210-3p and hsa-mir-20a-5p whose association with other cancers and other BC subtypes have been reported but their association with TNBC need to be explored. Further, enrichment and cumulative survival analysis support the disease association of identified key genes with TNBC.

CONCLUSION

This integrative analysis could be regarded for experimental inspection as it provides the platform for future researchers in drug designing and biomarker discovery for TNBC diagnosis and treatment.

Mitochondrial metabolism and hypoxic signaling in differentiated human cardiomyocyte AC16 cell line

Cardiovascular diseases are associated with an altered cardiomyocyte metabolism. Because of a shortage of human heart tissue, experimental studies mostly rely on alternative approaches including animal and cell culture models. Since the use of isolated primary cardiomyocytes is limited, immortalized cardiomyocyte cell lines may represent a useful tool as they closely mimic human cardiomyocytes. This study is focused on the AC16 cell line generated from adult human ventricular cardiomyocytes. Despite an increasing number of studies employing AC16 cells, a comprehensive proteomic, bioenergetic, and oxygen-sensing characterization of proliferating vs. differentiated cells is still lacking. Here, we provide a comparison of these two stages, particularly emphasizing cell metabolism, mitochondrial function, and hypoxic signaling. Label-free quantitative mass spectrometry revealed a decrease in autophagy and cytoplasmic translation in differentiated AC16, confirming their phenotype. Cell differentiation led to global increase in mitochondrial proteins [e.g. oxidative phosphorylation (OXPHOS) proteins, TFAM, VWA8] reflected by elevated mitochondrial respiration. Fatty acid oxidation proteins were increased in differentiated cells, whereas the expression levels of proteins associated with fatty acid synthesis were unchanged and glycolytic proteins were decreased. There was a profound difference between proliferating and differentiated cells in their response to hypoxia and anoxia-reoxygenation. We conclude that AC16 differentiation leads to proteomic and metabolic shifts and altered cell response to oxygen deprivation. This underscores the requirement for proper selection of the particular differentiation state during experimental planning.NEW & NOTEWORTHY Proliferating and differentiated AC16 cell lines exhibit distinct proteomic and metabolic profiles with critical implications for experimental design. Proliferating cells predominantly utilize glycolysis and are highly sensitive to hypoxia, whereas differentiated cells display enhanced mitochondrial biogenesis, oxidative phosphorylation, and resistance to anoxia-reoxygenation. These findings provide novel insights into the metabolic adaptations during differentiation and highlight the necessity of selecting the appropriate cellular stage to ensure accurate experimental outcomes.

Metallothionein as a biomarker of aquatic contamination in fish: An in silico and in vitro approach using zebrafish as experimental model organism

Human activities contaminate aquatic ecosystems with chemicals like metals and pesticides. Fish, sensitive to pollution, are key toxicological models. Metallothionein (Mt) expression, a biomarker for metal contamination, varies depending on the chemical exposure. This study investigated differences in metal affinity for Zn2+ binding sites of proteins and Mt induction by the insecticides dichlorvos (DDPV) and deltamethrin (DTM) in Danio rerio. First, D. rerio Zn-binding protein structures with different cell functions were used to evaluate the difference between the binding scores of five metals with the binding site with highest affinity for Zn2+ through molecular docking and from there to infer the most potent inducers. Cadmium ion was found to have the highest binding score mean for the selected proteins (Cd2+>Cu2+>Pb2+>Mn2+>Cu+>Hg2+), and, thus, cadmium chloride (CdCl2) was used as a positive control for Mt induction in D. rerio larvae. D. rerio embryos were exposed to sublethal concentrations of Cd (100 μg L-1), DDPV (1 mg L-1), and DTM (0.01 μg L-1) up to 96 h post-fertilization (hpf). Larvae exposed to Cd and DDPV showed increased Mt levels, whereas DTM exposure had no effect. Proteomic analyses suggest that Mt induction in D. rerio larvae exposed to Cd follows a distinct mechanism from DDPV exposure. Enrichment analysis supports a possible link between DDPV exposure and oxidative stress-induced Mt expression. In contrast, Cd-induced Mt expression likely involves metal transcription factor activation by Zn2+. These differences in responsiveness highlight the need for careful consideration when using Mt as a biomarker of metal contamination.

Direct mRNA-to-sgRNA conversion generates design-free ultra-dense CRISPRi libraries for systematic phenotypic screening

CRISPR interference (CRISPRi) is a versatile tool for high-throughput phenotypic screening. However, rational design and synthesis of the single-guide RNA (sgRNA) library required for each genome-wide CRISPRi application is time-consuming, expensive, and unfeasible if the target organisms lack comprehensive sequencing and characterization. We developed an ultra-dense random sgRNA library generation method applicable to any organism, including those that are not well-characterized. Our method converts transcriptome-wide mRNA into 20 nt of sgRNA spacer sequences through enzymatic reactions. The generated sgRNA library selectively binds to the non-template strand of the coding sequence, leading to more efficient repression compared to binding the template strand. We then generated a genome-scale library for Escherichia coli by applying this method and identified essential and auxotrophic genes through phenotypic screening. Furthermore, we tuned the production levels of lycopene and violacein and identified new repression targets for violacein production. Our results demonstrated that a genome-scale sgRNA library can be generated without rational design and can be utilized simultaneously in a range of phenotypic screenings.

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.