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Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging hallmarks, and we verified key findings in aged human and mouse brain tissue. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins—like the dementia- and ALS-associated protein TDP-43—mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components are typically recruited to stress granules, but aged neurons suffer from chronic cellular stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity and the fai

Paranoia is a distressing and prevalent symptom in schizophrenia spectrum disorders. Virtual reality-based cognitive behavioral therapy for paranoia (VR-CBTp) has been proposed to augment behavioral interventions by providing controlled and safe virtual environments in which social situations inducing paranoid anxiety can be manipulated, allowing for new therapeutical possibilities such as gradual exposure and repetition. This assessor-masked, randomized parallel group superiority trial investigated the efficacy of VR-CBTp compared to standard CBTp. Participants were randomized to receive ten sessions of VR-CBTp or CBTp, both on top of treatment as usual. Intention-to-treat analyses included 254 participants (VR-CBTp: n = 126, CBTp: n = 128). Outcomes were assessed at baseline, treatment cessation and follow-up (6 months after treatment cessation). The primary outcome was Ideas of Persecution subscale from the Green Paranoid Thoughts Scale, measured at treatment cessation. There was no

Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop–wild introgressions. Decades of research into barley’s closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral p

The functional characterization of host-gut microbiome interactions remains limited by the sensitivity of current metaproteomic approaches. Here, we present uMetaP, an ultra-sensitive workflow combining advanced LC-MS technologies with an FDR-validated de novo sequencing strategy, novoMP. uMetaP markedly expands functional coverage and improves the taxonomic detection limit of the gut dark metaproteome by 5000-fold, enabling precise detection and quantification of low-abundance microbial and host proteins. Applied to a mouse model of intestinal injury, uMetaP revealed host-microbiome functional networks underlying tissue damage, beyond genomic findings. Orthogonal validation using transcriptomic data from Crohn’s disease patients confirmed key host protein alterations. Furthermore, we introduce the concept of a druggable metaproteome, mapping functional targets within the host and microbiota. By redefining the sensitivity limits of metaproteomics, uMetaP provides a highly valuable fram

Simian or Human immunodeficiency virus (SIV or HIV) vaccines based on V1-deleted envelope virus-like particles, delivered by the DNA/ALVAC platforms, followed by the ΔV1gp120 boost formulated in Alum, protect 50% and 80% of macaques from mucosal infection with SIVmac251 or Simian-Human immunodeficiency virus, respectively. Adding the Army Liposome Formulation + QS21 (ALFQ) adjuvant to the ΔV1gp120+Alum boost (ALFQA) may enhance protective immune responses. Here, we show that ALFQA protects 58% of female macaques from infection following eleven exposures to SIVmac251, achieving 79% vaccine efficacy. The ALFQA vaccine regimen augments mucosal CD73+CD163+ M2-like macrophages and NKp44+ innate lymphoid cells (ILCs), while reducing NKG2A-NKP44- cells producing interferon-γ. Antibody-Dependent Cellular Cytotoxicity (ADCC) targeting helical V2, and mucosal tolerogenic dendritic cells-10 (DC-10) and envelope-specific interleukin-17+ NKp44+ ILCs, correlate with decreased risk of infection. Plas

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Transcription factors (TFs) regulate gene expression by interacting with DNA in a sequence-specific manner. High-throughput in vitro technologies, such as protein-binding microarrays1–6 and HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment)7,8, have revealed the DNA-binding specificities of hundreds of TFs. However, they have limited ability to reliably identify lower-affinity DNA binding sites, which are increasingly recognized as important for precise spatiotemporal control of gene expression9–19. Here, to address this limitation, we developed protein affinity to DNA by in vitro transcription and RNA sequencing (PADIT-seq), with which we comprehensively assayed the binding preferences of six TFs to all possible ten-base-pair DNA sequences, detecting hundreds of novel, lower-affinity binding sites. The expanded repertoire of lower-affinity binding sites revealed that nucleotides flanking high-affinity DNA binding sites create overlapping lower-affinit

Chromosomal linkages formed through crossover recombination are essential for the accurate segregation of homologous chromosomes during meiosis1. The DNA events of recombination are linked to structural components of meiotic chromosomes2. Imperatively, the biased resolution of double Holliday junction (dHJ) intermediates into crossovers3,4 occurs within the synaptonemal complex (SC), the meiosis-specific structure that mediates end-to-end synapsis of homologues during the pachytene stage5,6. However, the role of the SC in crossover-specific dHJ resolution remains unclear. Here we show that key SC components function through dependent and interdependent relationships to protect dHJs from aberrant dissolution into non-crossover products. Conditional ablation experiments reveal that cohesin, the core of SC lateral elements, is required to maintain both synapsis and dHJ-associated crossover recombination complexes (CRCs) during pachytene. The SC central region transverse-filament protein i

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Although the role of cellular immunity in checkpoint immunotherapy (CPI) for cancer is well established1,2, the effect of antibody-mediated humoral immunity is comparably underexplored. Here we used rapid extracellular antigen profiling3 to map the autoantibody reactome within a cohort of 374 patients with cancer treated with CPIs and 131 healthy control participants for autoantibodies to 6,172 extracellular and secreted proteins (the ‘exoproteome’). Globally, patients with cancer treated with CPIs had diverse autoreactivities that were elevated relative to control individuals but changed minimally with treatment. Autoantibody signatures in patients treated with CPI strikingly distinguished them from healthy individuals. Although associations of specific autoantibodies with immune-related adverse events were sparse, we detected numerous individual autoantibodies that were associated with greatly altered odds ratios for response to therapy. These included autoantibodies to immunomodulat

Cortical function, including sensory processing, is surprisingly resilient to neuron loss during aging and neurodegeneration. In this Article, we used the mouse auditory cortex to investigate how homeostatic mechanisms protect the representational map of sounds after neuron loss. We combined two-photon calcium imaging with targeted microablation of 30–40 sound-responsive neurons in layer 2/3. Microablation led to a temporary disturbance of the representational map, but it recovered in the following days. Recovery was primarily driven by neurons that were initially unresponsive to sounds but gained responsiveness and strengthened the network’s correlation structure. By contrast, selective microablation of inhibitory neurons caused prolonged disturbance, characterized by destabilized sound responses. Our results link individual neuron tuning and plasticity to the stability of the population-level representational map, highlighting homeostatic mechanisms that safeguard sensory processing

The lectin-like oxidized low-density lipoprotein (LDL) receptor-1 (LOX-1) is a key scavenger receptor for oxidized low-density lipoprotein cholesterol (oxLDL), which promotes inflammation and atherosclerosis. Here we evaluated MEDI6570, an antibody that acts as a LOX-1 antagonist, in a randomized, double-blind, dose-finding study in patients with myocardial infarction (MI) and residual inflammation (high-sensitivity C-reactive protein ≥ 1 mg l−1). At 30–365 days after MI, 423 patients (75 women, 348 men) were randomly allocated to 50 mg, 150 mg or 400 mg MEDI6570 or placebo treatment subcutaneously every 4 weeks for 32 weeks. The primary endpoint, the change in the noncalcified plaque volume in the most diseased coronary segment (NCPVMD) by computed tomography angiography, was not significantly different between placebo and MEDI6570 at any dose. The secondary endpoints, global NCPV and low-attenuation plaque volume, were also not different between placebo and MEDI6570 at any dose (all

Centrioles are evolutionarily conserved barrel-shaped organelles playing crucial roles in cell division and ciliogenesis. These functions are underpinned by specific structural sub-elements whose functions have been under investigation since many years. The A-C linker structure, connecting adjacent microtubule triplets in the proximal region, has remained unexplored due to its unknown composition. Here, using ultrastructure expansion microscopy, we characterized two recently identified A-C linker proteins, CCDC77 and WDR67, and discovered MIIP as an additional A-C linker protein. Our findings reveal that these proteins localize between microtubule triplets at the A-C linker, forming a complex. Depletion of A-C linker components disrupt microtubule triplet cohesion, leading to breakage at the proximal end. Co-removal of the A-C linker and the inner scaffold demonstrates their joint role in maintaining centriole architecture. Moreover, we uncover an unexpected function of the A-C li

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Congenital vascular malformations result from abnormal development of the vascular tree, with the aneurysmal malformation of the vein of Galen (VGAM) being the most prevalent neurovascular malformation in neonates, associated with poor outcomes. This condition is linked to germline mutations in the RASA1 and EPHB4 genes, although the underlying developmental mechanisms remain unclear. Here we generate zebrafish models lacking rasa1a and ephb4a that replicate the genetic and structural features of VGAMs. Our findings connect the development of malformations to insufficient fusion of precursor blood vessels, a process regulated by blood flow and the responses of endothelial cells. RASA1 deficiency destabilizes the homeostatic response to blood flow and contributes to impaired flow-mediated activation of MAPK and phosphatidylinositol-3-kinase signaling. By pharmacologically targeting these signaling pathways in mutant models, we restore normal fusion in existing malformations, offering po

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d-2-Hydroxyglutarate (d-2-HG) is a functional endogenous metabolite in various domains of life. Its abnormal accumulation promotes human tumorigenesis. Convenient d-2-HG testing for diagnosis and prognosis of d-2-HG-related diseases remains technically challenging, and there is no analytical method to directly detect d-2-HG in living cells. Here, we identify a d-2-HG-specific transcriptional activator, HgcR, and develop a d-2-HG sensor (DHOR) using HgcR as a sensing moiety. Then, we build a portable device adaptive with DHOR for rapid and low-cost point-of-care d-2-HG testing in serum, urine, and glioma tissue samples. DHOR also allow spatiotemporal resolution of d-2-HG in living bacteria and human cells. We use DHOR to identify d-2-HG transporters from Escherichia coli and human solute carrier 22 family. Overall, DHOR provides a powerful and versatile tool for in vitro and live-cell detection of d-2-HG, offering the opportunity to deepen our understanding about physiological and patho

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RIF1 is a multifunctional protein that regulates DNA replication and repair. RIF1-deficient cells are hypersensitive to DNA replication stress. Of the two alternatively spliced RIF1 isoforms, called RIF1-Short and RIF1-Long, the RIF1-Long isoform is more capable than RIF1-Short in supporting cell recovery from replication stress. Examining replication stress resistance mechanisms specific to RIF1-Long, we find that prolonged replication stress unexpectedly induces interaction of RIF1-Long with BRCA1. Mechanistically, a phosphorylated SPKF motif unique to the RIF1-Long isoform binds the tandem BRCT domain of BRCA1. BRCA1–RIF1-Long interaction is strongly down-regulated through dephosphorylation by RIF1-associated Protein Phosphatase 1. BRCA1–RIF1-Long interaction requires ATR signaling, and occurs predominantly during S phase. Loss of RIF1-Long impairs the formation of RAD51 foci, and reduces the efficiency of homology-mediated repair at broken replication forks. In summary, our investi

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