Life Science Alliance

Intestinal epithelial cells are central players in mucosal barrier integrity and host-microbe interactions. Genetic studies have revealed that epithelial dysfunction is a key contributor to the pathogenesis of inflammatory bowel disease. Non-SMC condensin II complex subunit D3 (NCAPD3) is essential for chromatin organization and stability. NCAPD3 also promotes antimicrobial defense and autophagy responses in vitro. NCAPD3 expression is decreased in intestinal epithelial cells from patients with ulcerative colitis; however, it is not known whether loss of NCAPD3 expression drives intestinal barrier dysfunction or is a result of disease-associated inflammation. To investigate this relationship in vivo, a tissue-specific approach was required, as global constitutive knockout of NCAPD3 is embryonic lethal. Therefore, a transgenic mouse line with doxycycline-inducible expression of a short hairpin RNA targeting NCAPD3 restricted to villin-expressing cells was generated (NCAPD3KD mice) to enable the study of NCAPD3 function in the intestinal epithelium. Treatment of NCAPD3KD mice with 9-tert-butyl doxycycline resulted in [~]75% reduction of NCAPD3 protein in EpCAM intestinal cells. Short-term epithelial NCAPD3 knockdown did not induce spontaneous colitis but was associated with increased serum amyloid A and a trend towards increased intestinal permeability. Upon dextran sodium sulfate or Salmonella enterica serovar Typhimurium {Delta}AroA challenge, NCAPD3KD mice exhibited exacerbated weight loss, higher disease activity, increased histopathological damage, abnormal colonic cytokines and chemokines, and significantly increased intestinal permeability. These results indicate that NCAPD3 expression in the intestinal epithelium is required for optimal barrier maintenance and antimicrobial defense under chemical or microbial stress. These findings support prior in vitro observations and solidify NCAPD3 as a regulator of intestinal epithelial barrier function and mucosal host defense. Author SummaryNCAPD3 is a multifunctional protein with established roles in chromatin organization, genome stability, mitochondrial function, and antimicrobial defense. Dysregulated NCAPD3 is implicated in human diseases, such as inflammatory bowel disease (IBD) and microcephaly; however, due to its essential role in cellular division, determination of whether NCAPD3 loss drives these pathologies in vivo has been lacking. Using a new transgenic mouse model that selectively reduces NCAPD3 expression in intestinal epithelial cells, our study establishes NCAPD3 as an epithelial regulator of the mammalian intestine that enhances epithelial barrier resilience and antimicrobial defense during stress. Although dispensable for short-term basal homeostasis, NCAPD3 function becomes critical during epithelial injury and enteric infection. Reduced NCAPD3 expression may therefore lower the threshold for inflammatory disease by weakening barrier integrity, amplifying inflammatory cascades, and impairing antimicrobial defenses. These findings position NCAPD3 as a potential modulator of IBD susceptibility and highlight chromatin organization as an important, previously underappreciated layer of intestinal epithelial regulation.

Common sex chromosome aneuploidies (SCAs) often present with cognitive and cardiovascular dysfunction in humans. To address SCA effects on gene expression and DNA methylation in relevant cell types, we differentiated neural precursor cells (NPCs) and cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) with different numbers of sex chromosomes, including isogenic and independent lines. As expected, the expression of genes that escape X inactivation (escapees) mostly increases with the number of inactive X chromosomes (Xi). However, allelic analysis shows dampening of escapees specifically on the Xi in XXY compared to XX in both NPCs and CMs, revealing a novel type of dosage compensation in SCA. In contrast, Y-linked gene expression is higher in XXY versus XY NPCs, but the opposite is observed in CMs. This may explain the greater number of differentially expressed autosomal genes in NPCs versus CMs with an added Y chromosome, while effects of added X chromosomes are similar between cell types. Concordantly, changes in autosomal DNA methylation are mainly driven by the presence of a Y chromosome. These findings highlight the cell-type specificity of sex-linked and autosomal gene regulation in SCA conditions. HighlightsO_LISex chromosome aneuploidy induces cell-type specific changes in gene expression C_LIO_LIDampening of the inactive X chromosome in XXY alleviate X overexpression C_LIO_LIHigh Y-linked gene expression in XXY neuronal precursor cells but not cardiomyocytes C_LIO_LISex chromosome aneuploidy disrupts sex biases in autosomal gene expression C_LI

Image-based spatial transcriptomics depends on cell segmentation to assign transcripts to individual cells, but how segmentation algorithms perform across tissues with distinct cellular architectures is poorly understood. This study presents the broadest independent benchmark to date of cell segmentation algorithms for spatial transcriptomics, comparing five approaches across ten mouse tissues using a 5,006-gene Xenium panel. To quantify segmentation errors, Co-expression Rejection in Segmentation Purity (CRISP) was developed, an open-source tool available in R and Python that measures cell purity through tissue-specific mutually exclusive marker co-expression without requiring ground truth annotations. This benchmark revealed that segmentation algorithms face a fundamental tradeoff between maximizing transcript capture and maintaining cell purity, and that the severity of this tradeoff is tissue-dependent. Proseg achieved the highest average performance across tissues, though the magnitude of its advantage varies with tissue architecture. Overall, CRISP provides per-tissue performance profiles as a practical resource for algorithm selection.

BackgroundTau aggregation is the defining feature of tauopathies, however, the mechanisms by which distinct tau strains drive disease-specific responses remain unclear. Existing models largely rely on recombinant tau seeding or tau overexpression, which fail to capture the biochemical diversity of pathological tau. The aim of this study was to develop a robust and reproducible human cell-based model of disease-specific tau pathology and to use this model to determine how tau from unique diseases impact tau accumulation and lysosomal dysfunction. MethodsPatient-derived tau aggregates were enriched from post-mortem brain tissue obtained from sporadic Alzheimers disease (AD), Picks disease (PiD), progressive supranuclear palsy (PSP), and control cases using phosphotungstic acid precipitation. Patient-derived tau preparations were biochemically characterised by immunoblotting and mass spectrometry and normalised for tau content prior to seeding. Patient-derived tau aggregates were seeded into multiple human immortalised cell lines (SH-SY5Y, M03.13, U-87 MG, and U-118 MG cells) and iPSC-derived astrocytes. Tau seeding efficiency, aggregate morphology, and integrity of the autophagy-lysosomal pathway was assessed using quantitative imaging approaches. ResultsPatient-derived tau seeds retained disease-specific phosphorylation patterns and isoform composition and led to reproducible, dose-dependent insoluble tau accumulation in all cell lines tested. Despite equivalent tau input and similar background protein composition, PiD-derived tau had the most aggressive pathological signature, showing the highest number of tau aggregates per cell and inducing system wide disruptions in the autophagy lysosomal system including increased SQSTM1 puncta and lysosomal damage markers. Seeding with AD-derived tau led to a high number of tau aggregates per cell and more specifically depleted the lysosomal protease CTSD and uniquely co-seeded A{beta} pathology. Seeding with PSP-derived tau resulted in only a moderate number of tau aggregates per cell and uniquely caused increased lysosomal biogenesis. ConclusionsTogether, these results demonstrate that intrinsic properties of human tau strains drive disease-specific cellular responses and establish a scalable, physiologically relevant platform for dissecting tau-cell interactions and screening therapeutics across tauopathies.

S-acylation is the addition of fatty acids to cysteine residues to regulate protein function and localization. S-acylation is catalyzed by the ZDHHC (Asp-His-His-Cys) family of protein S-acyltransferases (PATs), which S-acylate protein substrates by first auto-S-acylating the catalytic cysteine of the DHHC active site followed by transfer to the substrate. ZDHHC13 and ZDHHC17 are related ankyrin repeat domain (ANK) PATs that S-acylate multiple neuronal proteins, including huntingtin (HTT), the protein mutated in Huntington disease. However, unlike ZDHHC17 and other human PATs, ZDHHC13 possesses a non-canonical DQHC active site. As the first histidine is essential for auto-S-acylation, it is unclear if ZDHHC13 is catalytically active. Our phylogenetic analysis of eukaryotic ANK-containing PATs shows that ZDHHC13 orthologues are more divergent compared to ZDHHC17. While the ZDHHC17 DHHC is highly conserved, the motif varies among ZDHHC13 orthologues, with some vertebrate lineages containing a serine in place of the catalytic cysteine. Interestingly, we found that the ZDHHC13 S-acylation is lower than that of ZDHHC17, but the ZDHHC13 catalytic cysteine is indeed S-acylated. While expression of wild type (WT) ZDHHC13 in ZDHHC13 deficient HEK293T cells increased S-acylation of a HTT1-588 fragment, surprisingly, expression of catalytically dead DQHS ZDHHC13 was still able to facilitate HTT1-588 S-acylation equally. This suggests the ZDHHC13 catalytic cysteine is not required for S-acylation of target proteins, suggesting ZDHHC13 may coordinate another PAT. Indeed, we identified ZDHHC13 in high-molecular weight complexes. Our results indicate that ZDHHC13 is a likely pseudoenzyme that may function via a non-conventional mechanism reliant on other PATs. This work broadens our understanding of the function of this non-canonical PAT.

Both splicing and kinase signaling are biochemical processes that fundamentally determine and shape cell physiology. Although there has been some indication that there is an interaction between the two - splicing can alter the availability of exons encoding kinase targets and kinases can phosphorylate splicing factors - it has yet to be established the extent to which altering splicing factor expression impacts kinase signaling networks. In this work, we implemented a data-driven analysis using ENCODE RNA-sequencing data and prior work mapping post-translational modifications onto splice events to identify candidate splice factor perturbations that show extensive alterations to phosphorylation-encoding protein products. We then replicated the ENCODE knockdown experiments and performed global phosphoproteomics for two candidates, U2AF1 and SRSF3, complementing the transcription-level data. Both knockdowns showed extensive changes in phosphorylation and kinase activities, both basally and upon receptor tyrosine kinase stimulation. U2AF1 knockdown drove decreased JNK-associated cell death signaling but elevated chromosome regulation through CSNK2A1, PLK, and EIF2AK4 activity. SRSF3 knockdown, on the other hand, led to decreased cell cycle signaling through CDK and HIPK2 but increased cytoskeletal signaling through various PAKs. In addition, we found a striking enrichment of phosphorylated splicing regulators in both knockdowns that were linked to their splicing activity, such as HNRNPC, suggesting potential feedback and crosstalk between splice factors through signaling pathway activation. Importantly, comparison of differential phosphorylation measurements from this study to mRNA expression and splicing measurements from ENCODE revealed significant knockdown-dependent protein regulation, not captured by transcriptomic measurements alone, underscoring the value of phosphoproteomic profiling after splice factor perturbations. Combined, the transcriptomics and phosphoproteomics reveal deep interconnection between the two processes that are relevant to understanding cell signaling in health and disease.

Diabetes mellitus is characterized by chronic hyperglycemia and loss of pancreatic {beta}-cell function and mass. Current therapies focus on {beta}-cell protection and regeneration, led by GLP-1 receptor agonists. The G protein -subunit (Gs) acts as a key signaling node downstream of numerous GPCRs, integrating diverse signals that impact {beta}-cell mass and function. Elucidating the integrative role of pancreatic Gs signaling is thus crucial for understanding {beta}-cell biology. Our map of the pancreatic Gs-coupled GPCR landscape reveals sophisticated, cell-type-specific networks, positioning Gs as a central hub for intra-pancreatic communication. Previous studies in mice with {beta}-cell-specific or whole-pancreatic Gs deletion demonstrated reduced {beta}-cell mass, impaired insulin secretion, and glucose intolerance. The stronger phenotype in the whole-pancreas model--marked by -cell expansion and abnormal distribution--points to a crucial role for Gs in differential control of postnatal - and {beta}-cell proliferation. Here, we analyze the organ-wide consequences of Gs deletion using pancreas-specific Gs knockout mice (PGsKO). Consistent with prior findings, PGsKO mice exhibit reduced weight gain from four weeks and severe diabetes due to decreased {beta}-cell mass and concomitant -cell expansion. Furthermore, Gs loss induces profound architectural and functional defects in the exocrine pancreas, linked to YAP reactivation in acinar cells. Importantly, we observed attempted {beta}-cell regeneration in PGsKO mice. Although insufficient to reverse diabetes, our results delineate the full pancreatic phenotype that may facilitate these regenerative efforts and suggest that strategically biasing GPCR signaling network away from Gs could be a viable strategy to promote {beta}-cell regeneration from other pancreatic cell types. ARTICLE HIGHLIGHTSO_LIGs is a central signaling hub that integrates diverse GPCR inputs across pancreatic cell types, yet its organ-wide role remained poorly defined. C_LIO_LIWe addressed how pancreas-wide Gs deletion disrupts both endocrine and exocrine compartments, and whether regenerative programs are engaged. C_LIO_LIGs loss caused severe diabetes through {beta}-cell loss and -cell expansion, induced profound exocrine defects with YAP reactivation, and triggered attempted {beta}-cell regeneration from ducts and potentially other cell types. C_LIO_LIOur findings suggest that strategically biasing GPCR signaling away from Gs could promote regeneration from non-{beta}-cell sources, offering new therapeutic avenues for diabetes. C_LI

BackgroundHeterozygous c.283+1G>A and c.283G>A variants in the THRB gene, encoding for thyroid hormone receptor (TR){beta}1 and {beta}2, lead to autosomal dominant macular dystrophy (ADMD). We report the detailed clinical characterization of two first-degree relatives with ADMD, heterozygous for THRB c.283+1G>A, and an unrelated ADMD patient with a novel variant, c.283G>C. The genomic and molecular consequences of both variants were studied. MethodsgDNA and mRNA were obtained from leukocytes. Clinical characterization included biochemistry, bone density and body composition, ECG, echocardiography, ultrasound, audiometry and color-vision. In vitro assays investigated TR function and DNA binding. ResultsThe patients manifested no resistance to thyroid hormone beta (RTH{beta}) and had normal FT4 and TSH. Detailed studies in two patients showed no goiter, tachycardia, hypercholesterinemia or hepatic steatosis. Hearing was not impaired. Both had impaired color vision and reduced bone density. RT-PCR from all three patients revealed skipping of exon 4 exclusive to TR{beta}1, producing a deletion of 87 amino acids in the N-terminal domain (TR{beta}1{Delta}NTD). In vitro, DNA-binding affinity of TR{beta}1{Delta}NTD to DR4-TRE with or without RXR was comparable to TR{beta}1WT. Surprisingly, TR{beta}1{Delta}NTD was transcriptionally twice more active than TR{beta}1WT with a similar EC50 for T3, demonstrating gain-of-function of TR{beta}1{Delta}NTD. THRA expression in leukocytes was increased by 3-fold compared to unrelated controls and different from RTH{beta} patients. ConclusionThese THRB splice site variants produce TR{beta}1 exon 4 skipping, resulting in a gain-of-function mutant, TR{beta}1{Delta}NTD. This explains the dominant ADMD phenotype devoid of RTH{beta} and suggests a TR{beta}1 gain-of-function syndrome.

In our society, ageing, longevity, and neurodegenerative diseases are major concerns of public health. Recently, in Drosophila, we have identified a new cluster of three snoRNAs, including jouvence, and showed that each of them affect longevity and neurodegeneration. As these snoRNAs are required in the epithelium of the gut, these results point-out a causal relationship between the epithelium of the gut and the neurodegenerative lesions through the metabolic parameters, indicating a gut-brain axis. Here, we demonstrate that each snoRNA pseudouridylates a specific site on ribosomal-RNA, which consequently affects the amount of ribosomes as well as the translational efficacy. Moreover, using TRAP experiment assay, we also show that these lacks of pseudouridylations modify the translation of specific genes involved in lipid metabolism. Consequently, these lead to a chronic deregulation of trigycerides and sterols levels, whose correlate to an increase of neurogenerative lesions in old flies, as well as to a modification of longevity.

Notothenioids are a well characterised species flock endemic to the Antarctic and an important model group for the study of genome adaptation to extreme cold. We used a new reference assembly and clade-wide comparative genomic analysis to investigate cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation. A new phased assembly of a model notothenioid, Harpagifer antarcticus, demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the afgp locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the afgp locus expansion in H. antarcticus through segmental tandem duplications involving two pairs of afgp genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation. Diversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to analyse cellular heterogeneity, enabling detailed mapping of cellular progression. Trajectory inference tools construct trajectories from scRNA-seq data, facilitating the tracing of cellular progression through developmental pathways. PathPinpointR (PPR) is a lightweight and user-friendly R package developed to predict and compare the positions of scRNA-seq samples along reference biological trajectories, such as those created from large cell atlas projects. PPR utilises sets of switching-gene events from reference trajectories as indicators of cellular progression. By applying these positional indicators to query datasets, each cell can be accurately assigned a pseudo-time value, providing predictive insight into its position along a trajectory. This information can be used to stage cells within an established developmental process, or to evaluate how different patient samples compare when mapped onto reference disease or drug response trajectories. AvailabilityPathPinpointR is available at https://github.com/moi-taiga/PathPinpointR. Contacto.j.l.rackham@soton.ac.uk

The advances of sequencing technologies and the availability of high-quality genome assemblies for many genotypes per species, give the opportunity to improve sequence alignment rate and quality, and the variant calling accuracy by including all genomic variations in a graph reference, called a pangenome graph. Because the process of building and analysing a pangenome graph is still complex, with related software packages under development, there is an important need for releasing user-friendly pipelines for this emerging research area. Pan1C is a pipeline based on a chromosome-by-chromosome graph construction strategy. It integrates two complementary strategies for building pangenomes and produces informative metric plots and graphics using a large set of tools. By benchmarking Pan1C on human, fungal, and wheat assemblies, which span a wide range of genome sizes and complexities, we showed the interest of Pan1C for assembly and graph validation as well as for performing primary analyses.

Large language model (LLM) agents are increasingly used to synthesize heterogeneous bioinformatics evidence, but their reliability for high-volume biological annotation remains poorly characterized. We evaluated three agent configurations on a controlled protein annotation task: Claude App with Claude Opus 4.7, Claude Code CLI with Claude Opus 4.7 and Claude Scientific Skills, and Codex App with GPT-5.4 and Claude Scientific Skills. Each configuration was run three times on the same verbatim prompt, the same 73 selected orthogroup FASTA files (1,705 protein sequences), and the same local evidence: Swiss-Prot BLASTP output, Pfam/HMMER domain hits, DeepTMHMM topology predictions, and SignalP secretion predictions. We audited the nine outputs for coverage, biological correctness, missing evidence, hallucinated or over-specific annotations, and within-method consistency, then merged the best-supported evidence into a final orthogroup annotation table. All nine runs covered all 73 orthogroups, indicating that the agents could retrieve and organize the complete input set. However, normalized calcification-relevance calls were only moderately reproducible: within-method exact tier agreement ranged from 0.397 to 0.685 for Claude App (mean 0.562), 0.342 to 0.740 for Claude Code (mean 0.516), and 0.411 to 0.630 for Codex App (mean 0.539), and the per-run number of high-confidence calls varied from 0 to 12 across the nine runs. The final curated table retained 3 high-confidence, 9 moderate, 18 watchlist, and 43 low-relevance orthogroups. The most robust direct candidates were sulfatase (OG0017138) and sulfotransferase (OG0020703) families and an FG-GAP/integrin-like surface protein family (OG0018986), whereas common error modes included elevating pentapeptide-repeat orthogroups on motif evidence alone, treating weakly secreted housekeeping enzymes as matrix proteins, and taking low-complexity BLAST labels at face value. Skill-enabled agents improved file handling, evidence traceability, and reproducibility of computational checking, but they did not eliminate biological overinterpretation. These results support a best-practice workflow in which LLM agents draft annotations only after deterministic evidence tables are generated, with explicit scoring rules, provenance columns, run-to-run replication, and expert review of high-impact claims.

CRISPR genome editing has shown tremendous potential in genetic improvement of citrus. So far, citrus genome editing has been conducted using juvenile tissues resulting in genome-edited citrus plants that require multiple years before they can produce flowers and fruit. Here we tested whether citrus genome editing via mature tissue transformation can overcome such a hurdle. CsLOB1 is a susceptibility gene for citrus canker caused by Xanthomonas citri subsp. citri (Xcc). The transcription activator-like effector PthA4 of Xcc activates CsLOB1 by binding to the effector-binding element in its promoter (EBEpthA4-CsLOBP). In Valencia sweet orange, two CsLOB1 promoter alleles are present: TI CsLOBP, and TII CsLOBP. We specifically utilized a CRISPR/Cas9 construct (GFP-p1380N-Cas9/sgRNA:CsLOBP2) targeting EBEpthA4 in TI CsLOBP but not TII CsLOBP to test genome editing efficacy and off-target mutations. GFP-p1380N-Cas9/sgRNA:CsLOBP2 function was first validated using Xcc-facilitated agroinfiltration in Valencia leaves. The construct was subsequently introduced into Valencia mature internodal stem segments via Agrobacterium-mediated transformation, generating three independent transgenic lines (#V2, #V3 and #V5). Targeted mutations in EBEpthA4-TI CsLOBP were detected in all three lines with mutation frequencies of 100%, 21.43% and 41.94% in #V2, #V3 and #V5, respectively, while no mutations were detected in TII CsLOBP. Infection with Xcc{Delta}pthA4:dCsLOB1.3, carrying a designer TALE that specifically activates TI CsLOBP, resulted in reduced canker symptoms in #V2. Importantly, all three EBEpthA4-TI CsLOBP edited lines flowered within 15 months. In sum, these results demonstrate that CRISPR/Cas9-mediated genome modification through mature citrus transformation can achieve high genome editing efficacy and overcome the juvenility.

Microglia, the resident macrophages of the central nervous system, are recognized for their heterogeneity and integral role in brain function and diseases. In the context of high fat diet (HFD) feeding and obesity, microglia become overactive, acquiring a prevailing lipid associated microglial phenotype (also known as LAM). Yet, how microgliosis is induced and regulated remains unclear. Here we report a key role for the Complement 3a Receptor (C3aR), on HFD-induced hypothalamic gliosis and weight gain in mice. HFD consumption leads to elevated microglial expression of C3aR, which parallels widespread accumulation of reactive microglia, selectively in the hypothalamus. Conditional microglial C3aR deletion protects mice from HFD-induced hypothalamic reactive microgliosis. C3aR deletion or pharmacological antagonism opposes HFD-induced weight gain in male but not female mice. Mechanistically, we demonstrated that C3aR is essential for lipid-induced lipid droplet formation, and acquisition of a LAM molecular signature. In summary, we uncovered a previously unknown role for C3aR in the acquisition of a LAM signature driving diet-induced gliosis, identifying this receptor as a new viable therapeutic candidate for conditions associated with hypothalamic neuroinflammation.

The ovary contains two major somatic lineages, granulosa cells and interstitial cells, that arise from progenitors within the coelomic epithelium. However, how these two lineages diverge during ovarian development remains unclear. By analyzing joint single-nucleus transcriptomic and chromatin accessibility profiles of murine ovarian cells at the onset of ovary formation, we identified two somatic progenitor populations from the coelomic epithelium distinguished by expression of the nuclear receptors Nr5a1 and Nr2f2. Based on their transcriptomic trajectories, the Nr5a1+ epithelial cells preferentially transitioned toward the granulosa lineage whereas the Nr2f2+ epithelial cells differentiated into mesenchymal populations. This lineage relationship was supported by Nr2f2 lineage tracing experiments that fetal Nr2f2+ progenitors contribute to ovarian interstitial cells postnatally. To define the molecular features underlying this divergence, we performed differential gene expression and chromatin accessibility analyses and found that Nr2f2+ epithelial cells, but not Nr5a1+ cells, were enriched for Notch pathway components and Notch effector motifs. Consistently, lineage tracing of Notch-responsive cells marked Nr2f2+ interstitial cells in postnatal ovaries, whereas ectopic Notch activation in Nr5a1+ cells promoted expansion of the interstitial population accompanied by reduced granulosa cells. By integrating motif analysis with accessible chromatin-gene linkage, we also identified downstream targets regulated by Notch effectors in Nr2f2+ cells, which showed concordant changes upon ectopic Notch activation. These findings demonstrate that somatic cell fate is established early during ovarian development, with active Notch signaling specifying the interstitial lineage and a balanced Notch activity required for proper somatic lineage establishment. Significance StatementProper differentiation of somatic cell types in the fetal ovary lays the foundation for future ovarian function in adulthood. Understanding how each cell type is formed is essential for developing methods to intervene in ovarian diseases caused by cellular dysfunction. Given that common somatic progenitors give rise to both supporting and interstitial lineages, a main unanswered question is how these two lineages diverge apart from each other during ovarian development. By integrating joint single-nucleus transcriptomic and chromatin accessibility assays with lineage tracing, single cell RNA-sequencing, and mouse genetic models, we demonstrate the role of Notch signaling in specifying the interstitial lineage and separating it from the supporting cell fate.

Obesity affects one in three adults and is complicated by adipose inflammation, lipotoxicity and cell death. We previously identified RIPK1 as a genetic determinant of human obesity risk and adipose inflammation. Because RIPK1 is the apical kinase in the necroptosis pathway upstream of RIPK3 and the executioner protein MLKL, and emerging evidence links MLKL to lipid metabolism, MLKL has surfaced as a potential metabolic regulator. However, conflicting findings in Mlkl knockout mice fed a high fat diet have left its therapeutic relevance unresolved. MLKL has not been previously targeted through therapeutic knockdown in vivo in the context of diet-induced obesity. Here, we evaluated two independent MLKL antisense oligonucleotides (ASOs) in high fat diet (HFD)-fed C57BL/6J mice. In a 24-week progression model, MLKL ASO markedly reduced body weight, fat mass and hepatic steatosis compared with controls, while preserving lean mass. MLKL knockdown also lowered the respiratory exchange ratio, indicating a shift toward increased fat oxidation. In the intervention model, once obesity was established after 12 weeks of HFD feeding, both MLKL ASOs, and similarly, two independent RIPK1 ASOs, reversed weight gain and improved systemic glucose control. In vitro, MLKL-CRISPR/Cas9 knockout blocked 3T3-L1 adipogenesis, indicating a requirement for MLKL during adipocyte differentiation. However, in mature adipocytes, MLKL siRNA reduced palmitic acid-induced lipid accumulation, increased isoprenaline-stimulated lipolysis, and prevented TNF-mediated suppression of insulin-mediated AKT signalling and glucose uptake. Collectively, these findings demonstrate that partial MLKL suppression reprograms whole-body energy metabolism, enhances insulin sensitivity and limits diet-induced adiposity. MLKL, therefore, represents a promising and mechanistically novel therapeutic target for obesity and insulin resistance.

Cellular organelle content is fairly constant within a given cell type. This is accomplished in part by ensuring equitable organelle partitioning during division. Much of our understanding of organelle inheritance has come from investigating cells that divide in half producing two daughter cells. However, more elaborate division strategies that give rise to multiple daughters are not uncommon in nature. Here, we present the first characterization of organelle inheritance in a fungus that grows by multi-budding, producing several (2-20) daughter cells in a single cell cycle. We find that some organelles (mitochondria and ER) are evenly delivered to all growing buds, while others (vacuole and peroxisomes) are more variably inherited. We discuss the implications of even and uneven inheritance for this polyextremotolerant fungus capable of growing in dynamic, and diverse, environments.

The central role of microglia in CNS function in health and disease has resulted in large interest in targeting microglial as treatments for neurodegenerative disease; understanding the factors that regulate microglial gene expression will be crucial to this goal. microRNAs (miRNAs) are among the most abundant post transcriptional regulators of gene expression. miRNAs suggests miRNA were likely key to significant evolutionary events as regulators of gene expression. The miRNAome of microglia is critical to their correct functioning but the miRNA that define microglia identity and regulate key functions have not been fully defined. In this study we performed a detailed analysis of the microglial miRNAome to identify miRNA enriched in microglia that are conserved across species (human, mouse, and xenopus). We further characterised the expression of these conserved miRNAs during demyelination and remyelination and identified conserved function of a microglial-enriched miRNA across species. These findings reveal evolutionary conservation of specific miRNAs, suggesting an important role in establishing and maintaining microglial identity. They also highlight miRNAs that may be critical for microglial function in the central nervous system in both health and disease. Overall, this work advances our understanding of the factors that regulate microglial gene expression.

Cerebral malaria is a severe neurological complication of Plasmodium falciparum infection. Damage of the blood-brain barrier (BBB) and endothelial dysfunction are established drivers of the disease pathology, however, whether astrocytes, a major constituent of the BBB, influence the disease outcome remains unclear. Using the murine model of experimental cerebral malaria (ECM), we show that astrocytes decisively regulate the outcome of ECM and the deubiquitinating enzyme OTUD7B in astrocytes fosters the disease. Mice lacking astrocytic OTUD7B showed reduced brain pathology and were protected from ECM compared with wildtype littermate controls. Transcriptomic profiling of ex vivo-isolated astrocytes revealed reduced proinflammatory chemokines and cytokines in the absence of OTUD7B. Plasmodium infection-associated microvesicles triggered a pro-inflammatory response in astrocytes, which was dependent on OTUD7B. Mechanistically, OTUD7B cleaved K48-linked ubiquitin chains from TRAF3 and TRAF6 upon stimulation with microvesicles or activation of TLR3/TLR9 by plasmodial nucleic acids. The OTUD7B-dependent TRAF3 and TRAF6 stabilization led to sustained NF-{kappa}B and p38 MAP kinase signaling and CXCL10 expression. Therapeutic silencing of CNS Otud7b or Cxcl10 expression after disease onset protected mice from ECM, identifying the cerebral OTUD7B-Cxcl10 axis as an attractive therapeutic target.