Biology subjects

Weir, J.

Publications and source records attributed to Weir, J..

9 recordsLinked to original sources

bioRxiv2026

Discovery and Targeting of a Cryptic Human Proteome

First-in-class therapeutics require first-in-class biology. Yet despite decades of genomic and proteomic cataloging, vast regions of the human transcriptome remain dark and their encoded proteins invisible. Here we present RyboCypher, an integrated RNA-sequencing and AI-assisted proteogenomics platform that systematically maps the RyboCypher-derived "dark" transcriptome to unannotated peptides, predicting and empirically identifying cryptic proteins across the uncharted genome. Applied to cancer cell lines, patient tumors, and matched healthy tissues, RyboCypher resolved [~]8.3 million dark RNA isoforms and [~]16 million candidate ORFs. Interrogating these against [~]0.5 billion MS/MS spectra from cellular proteomics, membrane proteomics, and immunopeptidomics datasets (comprising a total of >8,000 raw MS data files ([~]7TB of MS data), derived from 2,229 patient samples), we empirically identified [~]80,000 cryptic peptides ([~]10,000 cancer-associated or cancer-upregulated) at <1% FDR. Altogether, these datasets establish the CypherAtlas, a comprehensive proteogenomic atlas of an unreported proteome comprising thousands of novel proteins, including membrane proteins with targetable extracellular domains, and intracellular proteins accessible through antigen presentation. By linking dark-RNA transcripts, predicted proteins, and patient-level metadata across RyboDyns proprietary experimental data, CypherAtlas further provides the training substrate for multi-modal models such as DarkCypher, which is being developed to prioritize cryptic targets and to forecast their expression in new patient samples. As proof of therapeutic potential, we disclose evidence for a cancer-associated, cryptic protein expressed from the YBX1 locus, (cryptic YBX1; cYBX1) and demonstrate selective in vitro tumor cell killing through a cryptic peptide-MHC (pMHC) complex derived from this protein with a TCR-mimic (TCRm) antibody when formatted as antibody drug conjugates (ADCs). Together, RyboCypher and CypherAtlas establish the dark proteome as a vast and previously inaccessible reservoir of novel targetable biology, laying the foundation for the next generation of first-in-class therapeutics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/743124v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@104c385org.highwire.dtl.DTLVardef@1c065ccorg.highwire.dtl.DTLVardef@5b717forg.highwire.dtl.DTLVardef@1788694_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

A rapid, sensitive, and quantitative high plex biomarker digital detection platform enabled by Hypercoding

Low-cost, multiplexed, and automated assays are needed to make omic technologies more broadly accessible in clinical, research, and commercial settings. We present Hypercoding, a scalable technology for detection and quantitation of multi-omic targets. Drawing from data reliability methods in the telecommunications field, Hypercoding uses fluorescent signals from hybridization with an error-correcting code to enable detection of high-plexity targets from biological samples, such as human DNA. In the presence of the target, a linear DNA construct is circularized, immobilized, and amplified to enable single-molecule detection of a target via rapid readout cycles within a 96-well plate. We demonstrate capability for >10,000 code plexity and accurate (98.7%) genotyping of 209 pharmacogenomic variants. Furthermore, we show computation of copy number variation with whole chromosome and sub-gene resolution, as well as quantitation of target abundance down to 10 fM sensitivity with a dynamic range of up to 10 logs.

genomics↗

bioRxiv2026

Preclinical efficacy of a systemically-administered, second-generation STING agonist that promotes antitumour immunity in combination with radiotherapy

As potent triggers of innate immunity, STING agonists hold promise as active immunotherapeutic agents for cancer treatment. Second-generation STING agonists, suitable for systemic delivery, are being investigated in preclinical research and have entered clinical trials. Here, the novel synthetic STING agonist, BI-1703880 (STINGa), which was designed for intravenous delivery, was investigated for anti-tumour and immunological effects. We show that STINGa activates the STING pathway and results in a transient and dose-dependent upregulation and secretion of interferons and proinflammatory cytokines in vitro and in vivo. We show that intravenous administration of repeated dosing with low-dose STINGa is well tolerated. We report that radiotherapy (RT) and STING agonism synergizes to generate innate immune cell and CD8+ T cell responses that control tumour growth. Anti-tumour activity induced by combined RT / STINGa was reduced in mice lacking a functional immune system. RT / STINGa combination treatment also initiated development of protective immune memory. RT / STINGa upregulated PD-L1, PD-1 and CTLA-4 in the tumour microenvironment. Our findings show that combining RT / STINGa with immune checkpoint inhibitors further increases therapeutic benefit. Our data confirm STING as a therapeutic target in cancer and support the clinical development of BI-1703880 STING agonist, thereby suggesting radiotherapy as a potential combination for enhancing anti-tumour efficacy.

cancer biology↗

bioRxiv2026

In vivo interrogation of transcriptional and epigenetic regulators of lung epithelial regeneration

Effective alveolar repair after viral lung injury requires precise coordination of alveolar type 2 cell (AT2) proliferation and differentiation to restore lung function. To uncover causal regulators of this process in the native tissue environment, we developed SAGE (Stable Adeno-Associated Virus Genomic IntEgration), an engineered AAV system that enables high-throughput in vivo genetic interrogation. SAGE supports both bulk phenotypic screening (SAGE-Perturb) and single-cell transcriptomic profiling (SAGE-Perturb-seq). Using this approach, we identified lysine acetyltransferase 8 (Kat8) as essential for epithelial repair following viral infection through the Non-Specific-Lethal (NSL) complex, and generated a time-resolved, high-resolution functional map of transcription factor knockouts during alveolar repair, revealing transcription factor dependences for distinct alveolar epithelial repair trajectories. This map further defined two independent AT2-derived transitional states: a reparative state, and a pathological state that is transcriptionally similar to the basaloid population observed in human pulmonary fibrosis. Disruption of transcription factors in the NF-{kappa}B pathway prevented the emergence of the pathological transitional state, linking inflammation and maladaptive epithelial remodeling. SAGE represents a versatile platform for functional genomics in vivo, with applications extending across respiratory biology and disease.

genomics↗

bioRxiv2025

In depth characterisation of the tumour microenvironment reveals HHV-8 dependent immune regulation in HIV-associated and classic Kaposi Sarcoma.

BackgroundKaposis sarcoma (KS) is the most common malignancy occurring in people living with HIV (PLWH). The clinical course of KS in PLWH established on combined anti-retroviral therapy (cART) resembles that of classic KS. However, no studies have so far been conducted to compare clinical and immunologic characteristics of these subtypes. ObjectivesTo compare the clinical and biological characteristics of HIV-associated KS in patients with well-controlled viral infection (N=21) and non-HIV associated KS (N=19). MethodsClinical data were prospectively collected from patients treated at the National Centre for HIV malignancies at Chelsea & Westminster Hospital. Archival tumour samples were retrieved to perform targeted transcriptomic analysis using the Nanostring nCounter platform. The results were validated by multiplex immune-fluorescence. ResultsMedian progression free survival (mPFS) was comparable between groups. The tumour microenvironment (TME) of non-HIV associated KS was characterized by upregulation of pathways associated with adaptive and innate immunity and angiogenesis. Transcripts relating to glycolysis and endothelial to mesenchymal transition were upregulated in the TME of HIV-associated cases. Furthermore, the TME of HIV-associated cases was associated with lower infiltration of CD4 activated cell. In both cohorts, we found the expression of HHV-8 genes to positively correlate with activated CD4, CD8, NK and immune checkpoints gene expression. ConclusionsIn conclusion, we showed that the TME of KS in the presence of well-controlled HIV infection is characterized by a lower degree of inflammation and more pronounced epithelial to mesenchymal transition. We also identified intra-tumoral HHV-8 gene expression as a driver of TME composition.

immunology↗

bioRxiv2025

Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors

A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of the tumor mass, the remainder being infiltrating immune cells that presumably are required for the survival of the HRS cells. Until now, there has been no way to characterize the complex Hodgkin lymphoma tumor microenvironment at genome scale. Here, we performed genome-wide transcriptional profiling with spatial and single-cell resolution. We show that the neighborhood surrounding HRS cells forms a distinct niche involving 31 immune and stromal cell types and is enriched in CD4+ T cells, myeloid and follicular dendritic cells, while being depleted of plasma cells. Moreover, we used machine learning to nominate ligand-receptor pairs enriched in the HRS cell niche. Specifically, we identified IL13 as a candidate survival factor. In support of this hypothesis, recombinant IL13 augmented the proliferation of HRS cells in vitro. In addition, genome-wide CRISPR/Cas9 loss-of-function studies across more than 1,000 human cancer cell lines showed that IL4R and IL13RA1, the heterodimeric partners that constitute the IL13 receptor, were uniquely required for the survival of HRS cells. Moreover, monoclonal antibodies targeting either IL4R or IL13R phenocopied the genetic loss of function studies. IL13-targeting antibodies are already FDA-approved for atopic dermatitis, suggesting that clinical trials testing such agents should be explored in patients with Hodgkin lymphoma.

cancer biology↗

bioRxiv2024

15-Lipoxygenase-Mediated Lipid Peroxidation Regulates LRRK2 Kinase Activity

Mutations in leucine-rich repeat kinase 2 (LRRK2) that increase its kinase activity are strongly linked to genetic forms of Parkinsons disease (PD). However, the regulation of endogenous wild-type (WT) LRRK2 kinase activity remains poorly understood, despite its frequent elevation in idiopathic PD (iPD) patients. Various stressors such as mitochondrial dysfunction, lysosomal dyshomeostasis, or vesicle trafficking deficits can activate WT LRRK2 kinase, but the specific molecular mechanisms are not fully understood. We found that the production of 4-hydroxynonenal (4-HNE), a lipid hydroperoxidation end-product, is a common biochemical response to these diverse stimuli. 4-HNE forms post-translational adducts with Cys2024 and Cys2025 in the kinase activation loop of WT LRRK2, significantly increasing its kinase activity. Additionally, we discovered that the 4-HNE responsible for regulating LRRK2 is generated by the action of 15-lipoxygenase (15-LO), making 15-LO an upstream regulator of the pathogenic hyperactivation of LRRK2 kinase activity. Pharmacological inhibition or genetic ablation of 15-LO prevents 4-HNE post-translational modification of LRRK2 kinase and its subsequent pathogenic hyperactivation. Therefore, 15-LO inhibitors, or methods to lower 4-HNE levels, or the targeting of Cys2024/2025 could provide new therapeutic strategies to modulate LRRK2 kinase activity and treat PD.

neuroscience↗

bioRxiv2023

Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes

Programmed DNA double-strand break (DSB) formation is a unique meiotic feature that initiates recombination-mediated linking of homologous chromosomes, thereby enabling chromosome number halving in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We discovered in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms, which are based on a DBF4-dependent kinase (DDK)-modulated interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.

cell biology↗

bioRxiv2022

Cis-regulatory evolution of the potassium channel gene kcnj13 during pigment pattern diversification in Danio fish

Teleost fish of the genus Danio are excellent models to study the genetic and cellular bases of pigment pattern variation in vertebrates. The two sister species Danio rerio and Danio aesculapii show divergent patterns of horizontal stripes and vertical bars that are partly caused by the evolution of the potassium channel gene kcnj13. In D. rerio, kcnj13 is required in melanophores for interactions with xanthophores and iridophores, which cause location-specific pigment cell shapes and thereby influence colour pattern and contrast. Here, we show that cis-regulatory rather than protein coding changes underlie kcnj13 evolution between the two species. D. aesculapii express lower kcnj13 levels and exhibit low-contrast patterns similar to D. rerio mutants. Our results suggest that homotypic and heterotypic interactions between the pigment cells and their shapes diverged between species by quantitative changes in kcnj13 expression during pigment pattern diversification.

evolutionary biology↗