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Parkinson's disease (PD) targets some dopamine (DA) neurons more than others. Sex differences offer insights, with females more protected from DA neurodegeneration. The mammalian vesicular glutamate transporter VGLUT2 and Drosophila ortholog dVGLUT have been implicated as modulators of DA neuron resilience. However, the mechanisms by which VGLUT2/dVGLUT protects DA neurons remain unknown. We discovered DA neuron dVGLUT knockdown increased mitochondrial reactive oxygen species in a sexually dimorphic manner in response to depolarization or paraquat-induced stress, males being especially affected. DA neuron dVGLUT also reduced ATP biosynthetic burden during depolarization. RNA sequencing of VGLUT⁺ DA neurons in mice and flies identified candidate genes that we functionally screened to further dissect VGLUT-mediated DA neuron resilience across PD models. We discovered transcription factors modulating dVGLUT-dependent DA neuroprotection and identified dj-1β as a regulator of sex-specific DA neuron dVGLUT expression. Overall, VGLUT protects DA neurons from PD-associated degeneration by maintaining mitochondrial health.

The extracellular matrix (ECM) supports blood vessel architecture and functionality and undergoes active remodelling during vascular repair and atherogenesis. Vascular smooth muscle cells (VSMCs) are essential for vessel repair and, via their secretome, can invade from the vessel media into the intima to mediate ECM remodelling. Accumulation of fibronectin (FN) is a hallmark of early vascular repair and atherosclerosis. Here we show that FN stimulates VSMCs to secrete small extracellular vesicles (sEVs) by activating the β1 integrin/FAK/Src pathway as well as Arp2/3-dependent branching of the actin cytoskeleton. We found that sEVs are trapped by the ECM in vitro and colocalise with FN in symptomatic atherosclerotic plaques in vivo. Functionally, ECM-trapped sEVs induced the formation of focal adhesions (FA) with enhanced pulling forces at the cellular periphery preventing cellular spreading and adhesion. Proteomic and GO pathway analysis revealed that VSMC-derived sEVs display a cell adhesion signature and are specifically enriched with collagen VI on the sEV surface. In vitro assays identified collagen VI as playing a key role in cell adhesion and invasion directionality. Taken together our data suggests that the accumulation of FN is a key early event in vessel repair acting to promote secretion of collage VI enriched sEVs by VSMCs. These sEVs stimulate directional invasion, most likely by triggering peripheral focal adhesion formation and actomyosin contraction to exert sufficient traction force to enable VSMC movement within the complex vascular ECM network.

Despite advances in artificial intelligence (AI) within cancer research, its application toward realizing differentiation therapy in solid tumors remains limited. Using colorectal cancer (CRC) as a model, we developed a machine learning (ML) framework, CANDiT ( Cancer Associated Nodes for Differentiation Targeting ), to selectively induce differentiation and death of cancer stem cells (CSCs)-a key obstacle to durable response. Centering on one node, CDX2 , a master differentiation factor lost in high-risk, poorly differentiated CRCs, we built a transcriptomic network to identify therapeutic strategies for CDX2 restoration. Network-based prioritization identified PRKAB1 , a stress polarity sensor, as a top target. A clinical-grade PRKAB1 agonist reprogrammed transcriptional networks, induced crypt differentiation, and selectively eliminated CDX2-low CSCs in CRC cell lines, xenografts and patient-derived organoids (PDOs). Multivariate analyses in PDOs revealed a strong therapeutic index, linking efficacy (IC₅₀) to the biomarker-defined CDX2-low state. A 50-gene response signature-derived from an integrated analyses of all three models and trained across multiple datasets-revealed that CDX2 restoration therapy may translate into a ∼50% reduction in recurrence and mortality risk. Mechanistically, treatment activated a differentiation-associated stress polarity signaling axis while dismantling Wnt and YAP-driven stemness programs essential to CSC survival. Thus, CANDiT offers a scalable path to CSC-directed therapy in solid tumors by translating transcriptomic vulnerabilities into precision treatments.

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One sentence summary: In this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk.

Highlights: An ML framework ( CANDiT ) identifies target for differentiation therapy for CRCs Therapy induces crypt differentiation and CSC-specific cytotoxicityCDX2-low state predicts therapeutic response; restoration improves prognosisTherapy dismantles stemness via reactivation of stress polarity signaling.

Recent advances in high-throughput sequencing technologies have made it possible to collect and share a massive amount of omics data, along with its associated metadata. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability by reducing sample interpretability and limiting secondary analyses. In this study, we performed a comprehensive assessment of metadata completeness shared in both scientific publications and/or public repositories by analyzing over 253 studies encompassing over 164 thousands samples, including both human and non-human mammalian studies. We observed that studies often omit over a quarter of important phenotypes, with an average of only 74.8% of them shared either in the text of publication or the corresponding repository. Notably, public repositories alone contained 62% of the metadata, surpassing the textual content of publications by 3.5%. Only 11.5% of studies completely shared all phenotypes, while 37.9% shared less than 40% of the phenotypes. Studies involving non-human samples were more likely to share metadata than studies involving human samples. We observed similar results on the extended dataset spanning 2.1 million samples across over 61,000 studies from the Gene Expression Omnibus repository. The limited availability of metadata reported in our study emphasizes the necessity for improved metadata sharing practices and standardized reporting. Finally, we discuss the numerous benefits of improving the availability and quality of metadata to the scientific community and beyond, supporting data-driven decision-making and policy development in the field of biomedical research. This work provides a scalable framework for evaluating metadata availability and may help guide future policy and infrastructure development.

Comparisons of visual cortex function across blind and sighted adults reveals effects of experience on human brain function. Since almost all research has been done with adults, little is known about the developmental origins of plasticity. We compared resting state functional connectivity of visual cortices of blind adults ( n = 30), blindfolded sighted adults ( n = 50) to a large cohort of sighted infants (Developing Human Connectome Project, n = 475). Visual cortices of sighted adults show stronger coupling with non-visual sensory-motor networks (auditory, somatosensory/motor), than with higher-cognitive prefrontal cortices (PFC). In contrast, visual cortices of blind adults show stronger coupling with higher-cognitive PFC than with nonvisual sensory-motor networks. Are infant visual cortices functionally like those of sighted adults? Alternatively, do infants start like blind adults, with vision required to set up the sighted adult pattern? Remarkably, we find that, in infants, secondary visual cortices are more like those of blind adults: stronger coupling with PFC than with nonvisual sensory-motor networks, suggesting that visual experience establishes elements of the sighted-adult long-range connectivity. Infant primary visual cortices are in-between blind and sighted adults i.e., equal PFC and sensory-motor connectivity. The lateralization of occipital-to-frontal connectivity in infants resembles the sighted adults, consistent with reorganization by blindness. These results reveal instructive effects of vision and reorganizing effects of blindness on functional connectivity.

Neural stem cell (NSC) differentiation is controlled by cell-intrinsic and external signals from the stem cell niche including niche surface glia (SG). However, the mechanisms by which transcription factors drive NSC differentiation within the niche remain largely unknown. Here, we show that the Drosophila melanogaster transcription factor, Chromatin-linked adaptor for MSL proteins (CLAMP) is required for regulation of stemness and proliferation of NSCs, especially of the optic lobe (OL). CLAMP promotes transcription of genes involved in stemness, proliferation, and glial development and represses transcription of genes involved in neurogenesis and niche survival. Consistent with transcriptional changes, CLAMP promotes NSC proliferation and niche SG production, while lack of CLAMP severely and specifically impacts OL development. To identify potential mechanisms by which CLAMP may regulate brain development, we examined CLAMP motifs and available CLAMP ChIP-seq data to determine which genes may be direct versus indirect targets. CLAMP motifs are present at many target genes including the glial-determining gene, glial cells missing, while Tailless, the master regulator of OL-development is directly bound by CLAMP. In accordance to these results, in larval OL NSCs lacking CLAMP, Tailless levels are decreased dramatically, suggesting that CLAMP controls OL neurogenesis via Tailless. Overall, our results suggest that CLAMP regulates a transcriptional program which drives NSC proliferation and differentiation via cell-intrinsic and niche-dependent mechanisms that involve transcriptional regulation of Tailless and niche glia.

Bipolar disorder (BD) is a prevalent psychiatric condition characterized by mood dysregulation, psychosocial impairment, and an increased risk of suicide. The gene ANK3 has been identified as a risk locus for BD through multiple genome-wide association studies (GWAS). However, the mechanisms by which ANK3 variants influence BD pathophysiology and treatment response remain unclear. ANK3 encodes ankyrin-G, a protein that organizes the axon initial segment (AIS) and nodes of Ranvier by scaffolding ion channels and cell adhesion molecules to the cytoskeleton. Recent studies show that ankyrin-G interacts with the GABA_A receptor-associated protein (GABARAP) to stabilize inhibitory synapses, potentially linking ANK3 variants to inhibitory (GABAergic) signaling deficits associated with BD. We previously demonstrated that the BD-associated variant, ANK3 p.W1989R, disrupts the ankyrin-G/GABARAP interaction, resulting in inhibitory deficits and cortical pyramidal neuron hyperexcitability in mice. In this study, we investigate how lithium, a common BD therapeutic, modulates neuronal excitability in this model. Our findings show that chronic lithium treatment selectively enhances presynaptic GABAergic neurotransmission, reduces neuronal hyperexcitability, and partially rescues AIS length, without altering the density of GABAergic synapses. We also show that the selective glycogen synthase kinase-3 beta (GSK-3β) inhibitor Tideglusib recapitulates the enhancement of presynaptic GABAergic signaling. These findings shed new light on how ANK3 variants may contribute to inhibitory deficits in BD and demonstrate that lithium treatment is able to restore these deficits, likely through GSK-3β inhibition. Furthermore, these findings highlight GSK-3β inhibition as a promising therapeutic strategy for treating BD and other neurological disorders affected by GABAergic dysfunction.

Transcription factors (TFs) play a key role in regulating gene expression. We conducted an integrated analysis of chromatin accessibility, DNA methylation, mRNA expression, protein abundance and phosphorylation across eight tissues in fifty rats of equally represented sexes following endurance exercise training (EET) to identify coordinated epigenomic and transcriptional changes and determine key TFs involved. We uncovered tissue-specific EET associated changes and TF motif enrichment across differentially expressed genes (DEGs), accessible regions (DARs), and methylated regions (DMRs). We discovered distinct routes of EET-induced regulation through either epigenomic alterations providing better access for TFs to affect target genes, or via changes in TF expression or activity enabling target gene responses. We identified TF motifs enriched among correlated epigenomic and transcriptomic alterations, DEGs correlated with exercise-related phenotypic and cell type composition changes, and EET-induced activity changes of TFs whose target genes are enriched for DEGs. This analysis elucidates the unique gene regulatory mechanisms mediating diverse transcriptional responses to EET across tissues.

Embryo shape is determined by individual cell mechanics, intercellular interaction strength, and geometrical constraints. Models based on surface tensions at cell interfaces can predict 3D static cellular arrangements within aggregates. However, predicting the dynamics of such arrangements is challenging due to difficulties in measuring temporal changes in tensions. Here, we characterise the spatiotemporal changes in cellular tensions shaping the early nematode embryo using AFM, live microscopy, and tension inference. Using excoriated embryos, we validate a hybrid inference pipeline that calibrates relative inferred tensions temporally using cortical myosin enrichment and absolute tensions using AFM measurements. Applied to embryos within their native shell, we infer a spatiotemporal map of absolute tensions, revealing that ABa, ABp, and EMS compaction is driven by increased tension at free surfaces, while P₂'s initial exclusion is due to high tension at intercellular contacts. We uncover a direct and non-affine contribution of cadherins to cell-cell contact tension, comparable to cadherins' indirect contribution via actomyosin regulation.

The ability to regulate genetic circuits and metabolic pathways is central to cellular control. The existing toolkit is predominantly comprised of local transcription regulators that are unsuitable for exerting control at a global genome-wide scale. Bacterial sigma factors are ideal global regulators as together they direct the RNA polymerase to thousands of transcription sites. Here, we redesigned the promoter specificity of the E. coli housekeeping sigma factor, sigma-70, toward five orthogonal promoter targets not recognized by the native sigma-70. These orthogonal sigma-70 factors were developed by screening a pooled library of computationally designed variants of the -35 DNA recognition helix, each tailored to a specific target promoter. In the redesigned sigma factors new target-specific interactions facilitate new promoter recognition. Activity of the top performing redesigned sigma-70s varied across the promoter targets and ranged from 17% to 77% of native sigma-70 on its canonical active promoter. These orthogonal sigma factors represent a new suite of regulators for global transcriptional control.