Biology subjects

Link, S.

Publications and source records attributed to Link, S..

6 recordsLinked to original sources

bioRxiv2026

Systematic De-Risking of TCR-Mimic Therapeutics Through Proteome-Wide Off-Target Landscaping and a Generalizable Design Rule Framework

TCR-mimic (TCRm) antibodies targeting peptide-human leukocyte antigen (pHLA) complexes enable precision immunotherapy against intracellular antigens, including cancer-testis antigens (CTAs). Achieving high specificity, however, remains challenging because of the vast diversity of the human immunopeptidome and the associated risk of off-target recognition. Here, we introduce ValidaTe, a unified framework for the proteome-scale prediction, validation, and mitigation of off-target liabilities in pHLA-directed therapeutics. ValidaTe integrates rational target prioritization, peptide-centric binder selection, proteome-wide off-target prediction, and therapeutic engineering into a hierarchical de-risking workflow. Using the CTA MAGE-A4 as a proof-of-concept, we identify the TCRm antibodies VR-4 and VR-6 with superior specificity and demonstrate how this workflow enables the discovery of safer pHLA-targeted binders. Furthermore, ValidaTe establishes the basis for the WiFi (Widened Fingerprint) engineering principle, which rationally combines TCRms with complementary off-target fingerprints in trivalent T-cell engagers to minimize unintended interactions while preserving potent target-specific activity. Together, these findings establish a generalizable framework for the rational development of safer and more selective pHLA-targeted therapeutics. We further discuss how orthogonal proteomic characterization may complement this workflow as a final layer of translational safety assessment prior to clinical development. TeaserValidaTe accelerates safe pHLA-targeted immunotherapy through proteome-wide off-target mapping and WiFi design

immunology↗

bioRxiv2026

Mitochondrial protein import stress causes progressive neurodegeneration opposed by PERK - eIF2α signalling

Mitochondrial dysfunction and impairments of the mitochondrial protein import system are often linked to neurodegenerative disease, but whether import stress per se causes neurodegeneration has not been tested. Here, we adapted the yeast clogger system to Drosophila motoneurons to block TOM-TIM23-mediated import with temporal control. Sustained import stress converts somatic mitochondria into donut-shaped structures, depletes functional mitochondria from synaptic terminals, and causes progressive neurodegeneration with impaired neurotransmitter release and locomotor dysfunction. This neurodegeneration is mechanistically distinct from mitochondrial absence, as miro mutant neurons that completely lack presynaptic mitochondria do not degenerate. Import-stressed motoneurons activate multiple protective programmes, including chaperone remodelling, metabolic repression, and translational control through the eIF2 kinase PERK. Both pharmacological PERK inhibition and reversal of translational attenuation via ISRIB accelerate neurodegeneration, whereas PERK overexpression alone is sufficient to cause it, defining a protective range of eIF2-dependent translational control. The observation that PERK inhibition is protective in protein misfolding models but detrimental during import stress shows that the nature of mitochondrial dysfunction determines the molecular consequence of translational control in neurodegeneration.

neuroscience↗

bioRxiv2026

Ultrasound-enhanced retinal delivery of engineered viral vectors

The goal of this study was to examine Focused Ultrasound Blood-Retina Barrier Opening (FUS-BRBO) as a method to deliver gene therapy to the eye. We compared AAV.FUS.3, an engineered variant optimized for FUS-enhanced delivery to the central nervous system, and AAV9 for their utility as retinal gene vectors. To achieve this, mouse eyes were insonated by 4.667 MHz FUS in a custom-designed nosecone and vectors administered intravenously. We found 2.1-fold improvement of transduction of AAV.FUS.3 over AAV9 in the insonated area and 19.5-fold improvement over the uninsonated retina. Within that area, the ganglion cell layer showed the highest levels of transduction at 22% for AAV.FUS.3. We observed no gross tissue damage, change in retinal layer thickness, or increase in inflammation markers within the retina. FUS-BRBO has the potential to non-surgically deliver AAV-based vectors to spatially-defined regions of the retina. AAV.FUS.3 showed significantly improved transduction over AAV9 at the same dose. Further research to improve efficiency of delivery to the outer retina could expand the utility of FUS-BRBO.

bioengineering↗

bioRxiv2025

Compartmentalization of mRNA and Translation by Desmosomes

Subcellular compartmentalization enables cells to concentrate and locally regulate functions. Here we find that translational machinery is compartmentalized to the cell cortex in epidermal cells. Furthermore, we observed broad enrichment of transcripts at the cortex, establishing a novel axis of mRNA organization in these cells. Mechanistically, we identified the desmosomal protein, desmoplakin, to be essential for cortical recruitment of both ribosomes and mRNAs, through distinct mechanisms. While mRNA localization is usually proposed to promote local translation, we found that most cortical transcripts were translationally repressed. These findings reveal spatial and transcript-dependent features of the cortical translatome. One mediator of this regulation is the RNA-induced Silencing Complex (RISC) which is also cortically enriched in a desmoplakin-dependent manner. Under homeostatic conditions, cortical RISC associates with transcripts for cell adhesion and the cytoskeleton. Upon wounding RISC is delocalized from the cortex and its associated transcripts become translationally upregulated. Together our data demonstrate a desmosome-dependent cortical compartmentalization of translation that dynamically responds to barrier perturbations, including wounding.

cell biology↗

bioRxiv2020

SPATIAL ORGANIZATION OF TRANSCRIBED EUKARYOTIC GENES

Despite the well-established role of nuclear organization in gene expression regulation, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here, we make use of several long highly expressed genes and demonstrate that they form transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across microns resembling lampbrush loops and polytene puffs. Extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent RNPs. Our data contradict the model of transcription factories and indicate that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation can represent a general aspect of eukaryotic transcription.

cell biology↗

bioRxiv2019

Morphogenesis is transcriptionally coupled to neurogenesis during olfactory placode development

Sense organs acquire their distinctive shapes concomitantly with the differentiation of sensory cells and neurons necessary for their function. While our understanding of the mechanisms controlling morphogenesis and neurogenesis in these structures has grown, how these processes are coordinated remains largely unexplored. Neurogenesis in the zebrafish olfactory epithelium requires the bHLH proneural transcription factor Neurogenin1 (Neurog1). To address whether Neurog1 also controls morphogenesis in this system, we analysed the morphogenetic behaviour of early olfactory neural progenitors in neurog1 mutant embryos. Our results indicate that the oriented movements of these progenitors are disrupted in this context. Morphogenesis is similarly affected by mutations in the chemokine receptor gene, cxcr4b, suggesting it is a potential Neurog1 target gene. We find that Neurog1 directly regulates cxcr4b through an E-boxes cluster located just upstream of the cxcr4b transcription start site. Our results suggest that proneural transcription factors, such as Neurog1, directly couple distinct aspects of nervous system development. One Sentence SummaryNeurog1 controls olfactory organ morphogenesis via cxcr4b

developmental biology↗