Biology subjects

Lee, C.

Publications and source records attributed to Lee, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Pfcrt copy number amplification detected in a Plasmodium falciparum outbreak

Antimalarial resistance is one of the greatest threats to malaria elimination. Following an outbreak of Plasmodium falciparum infection in Sabah Malaysia in 2019, 98 samples were sequenced to search for adaptations driving the outbreak. The genomic data revealed evidence of clonal expansion of a strain carrying multiple copies of the chloroquine resistance transporter gene (pfcrt) in 86 cases. A TaqMan qPCR assay was developed to quantify pfcrt copy number, confirming the in silico evidence of duplication. Whilst point mutations in pfcrt have been associated with resistance to chloroquine and other drugs, copy number amplification has not been widely explored as a resistance mechanism. We investigated the genetic architecture of the duplication, revealing a wildtype haplotype (3D7 reference-type with 76K variant) and a novel mutant (with 76T mutation). Application of the TaqMan assay in 43 P. falciparum cases from neighbouring Palawan Island, the Philippines, identified a further two cases with pfcrt duplication. Assessment of the global genomic data in the MalariaGEN Pf8 repository identified a further 86 cases, including 73 (85%) from West Africa with evidence of pfcrt duplication. Amongst 47 monoclonal MalariaGEN cases, majority (95%) comprised wild type and mutant variants at codon 76. Our study reveals a potential previously unconsidered antimalarial resistance mechanism for P. falciparum and provides an assay for surveillance in other populations.

genomics↗

bioRxiv2026

Holotomography reveals biophysical remodeling of mouse oocytes during post-ovulatory aging

Routine assessment of oocyte state in reproductive biology and clinical embryology still relies largely on two-dimensional transmitted-light morphology, leaving the underlying three-dimensional intracellular organization largely unmeasured. Here, we use holotomography to reconstruct volumetric refractive index (RI) distributions in unlabeled live mouse oocytes and combine this imaging with sparse-annotation, AI-assisted compartment segmentation and multidimensional feature extraction across geometry, RI statistics, dry-mass density, and intracellular texture. Applied to an in vitro model of post-ovulatory aging, holotomography-derived biophysical profiles separated fresh and aged oocytes more strongly than two-dimensional brightfield-derived features, and feature-family ablation indicated that non-morphological descriptors contributed substantially to this separation. At the population level, aged oocytes showed coordinated ooplasmic remodeling, including reduced volume, increased RI heterogeneity, and increased dry-mass density while total dry mass was broadly conserved. These findings demonstrate a label-free quantitative framework for detecting post-ovulatory aging-associated biophysical remodeling in intact mammalian oocytes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/733271v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@c7257aorg.highwire.dtl.DTLVardef@6d92f0org.highwire.dtl.DTLVardef@1c9f7eborg.highwire.dtl.DTLVardef@b36637_HPS_FORMAT_FIGEXP M_FIG C_FIG

Developmental Biology↗

bioRxiv2026

Human meningiomas arise from developmental meningeal mosaicism

Meningioma is the most common primary intracranial tumour, yet its genetic origin and the temporal sequence of mutational events remain poorly defined. Here, we analysed 80 triple-matched tumour, histologically normal meninges, and blood samples from 22 patients. NF2 or TRAF7 driver mutations are detectable in phenotypically normal meninges in 81.8% of cases (95% CI: 59.7-94.8%; VAF [~]0.02%), corroborated by high-depth sequencing, single-cell cloning, and phylogenetic analysis. By distinguishing developmental mosaic mutations from postnatal tumour-private mutations, we revealed distinct mutational signatures and resolved the temporal sequence of meningioma evolution. The developmental origin was further underscored in patients with multiple meningiomas, where identical driver mutations were shared across genomically distinct tumours and meninges, and in intraventricular meningiomas (IVM), where driver mutations were detected in distant cranial dura. Reconstruction of mutational timing revealed lineage-specific trajectories, linking mosaicism to diverse disease presentations including solitary meningioma, IVM, meningiomatosis, and NF2-related schwannomatosis. Together, these findings reveal an early origin of human meningioma, in which developmental mosaicism establishes a pre-neoplastic field within the meninges, providing a developmental framework for adult tumourigenesis.

Cancer Biology↗

bioRxiv2026

Mtf2 Safeguards Naïve Pluripotency by Restricting Trophectoderm Competence

The first fate decision in mammalian embryos segregates embryonic and extraembryonic lineages, establishing a largely irreversible transition from totipotency to pluripotency. The mechanisms that enforce this unidirectionality remain incompletely understood. Here, we identify the PRC2.1 subunit Mtf2 as a key epigenetic barrier that safeguards lineage fidelity in naive embryonic stem cells (ESCs). Despite globally elevated H3K27me3 levels in naive ESCs, loss of Mtf2 derepresses trophectoderm (TE) regulators, enhances cellular plasticity, generating both ICM- and TE-like populations. Mtf2-deficient cells readily acquire expanded potential with extraembryonic competence and form blastoids without trophoblast stem cell supplementation, whereas loss of the PRC2.2 subunit Jarid2 has minimal effects. Integrated CUT&Tag and transcriptomic analyses reveal that Mtf2 directly represses TE-associated genes in naive ESCs. Thus, reduced Mtf2 occupancy permits their activation in expanded potential states. Collectively, our findings establish Mtf2 as a central epigenetic barrier that stabilizes naive pluripotency and restricts inappropriate acquisition of extraembryonic fate.

Developmental Biology↗

bioRxiv2026

Water oxidation-driven histidine dioxidation enables probe-free proximity labeling

Photocatalytic proximity labeling (photo-PL) has emerged as a powerful tool for spatial proteomics in subcellular compartments. However, many photo-PL toolboxes rely on singlet oxygen (1O2) to generate highly unstable endoperoxide intermediates that must be trapped immediately by high concentrations of exogenous probes. This constraint can bias spatial proteome coverage, particularly in dynamic and heterogeneous compartments such as endosomes and exosomes, where probe accessibility is intrinsically nonuniform. Here, we develop IDM, an organic photocatalyst that generates hydroxyl (*OH) and superoxide (O *-) radicals via water oxidation instead of 1O , enabling a synergistic dual-radical mechanism for probe-free proximal protein mapping in live cells (PF-Map). The resulting radicals dioxidize proximal histidine residues into a persistent dioxidized state (His-2O) that is thermodynamically stabilized as lactam tautomers, which remain electrophilic and chemically addressable after cell lysis. By decoupling histidine oxidation from live{square}cell probe capture, PF{square}Map can minimize spatial bias arising from heterogeneous probe distribution. Applying PF{square}Map to intracellular vesicle trafficking, we find that both PF{square}Map and a probe{square}dependent workflow (PD{square}Map) robustly identify exosome markers, whereas PF{square}Map additionally reveals a hidden vesicle trafficking-related subproteome that PD-Map underestimated. Together, we establish a minimally biased photocatalytic strategy for spatial protein mapping in complex biological systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/731337v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@13da43dorg.highwire.dtl.DTLVardef@1e9cb7corg.highwire.dtl.DTLVardef@2e7557org.highwire.dtl.DTLVardef@19e16c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

SPOTTER: Automated Tissue-Barcoding Platform for Spatial Proteomics and Phosphoproteomics

Spatial proteomics aims to characterize proteome in situ with regional resolution, linking molecular states to tissue architecture and microenvironments. While recent advances have expanded our access to spatially resolved proteomics, major barriers in scalability and throughput remain. Building on our prior SPOT (Spatial Proteomics through On-site Tissue-protein-labeling) framework1, we introduce SPOTTER, a customizable robotic platform that enables automated, micron-scale spatial barcoding directly on intact tissue sections. SPOTTER barcodes proteins by labeling tissue proteins in situ to encode spatial origin across the whole tissue section. This strategy enables unbiased whole-tissue proteome mapping and, for the first time, spatial phosphoproteome profiling from intact sections. Coupled with high-resolution LC-MS/MS, SPOTTER achieves deep proteome and phosphoproteome coverage while preserving histological integrity. By replacing labor-intensive laser capture microdissection workflows and low-plex antibody arrays, SPOTTER provides a scalable route to high-plex spatial proteomics, resolving spatially distinct regions within a single experiment.

bioengineering↗

bioRxiv2026

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function. Here, we integrate single-nucleus Multiome (RNA+ATAC) sequencing, spatial transcriptomics, and computational analyses to map conserved cell type signatures in the adult mouse brainstem and spinal cord. We identify a shared core of neuronal and non-neuronal cell types, alongside region-specific specializations reflecting distinct functions. Spatial data reveal conserved cellular niches across the brainstem-spinal cord boundary, indicating a continuous organizational logic. Cross-region comparisons uncover recurrent gene expression modules and signaling programs that may support shared circuit features. Chromatin accessibility profiling highlights cell-type-specific regulatory programs and implicates Hox transcription factors in positional identity. Notably, cell-type and positional identities are largely orthogonal, with varying regional influence across neuronal classes: motor neurons show strong positional coupling, whereas glutamatergic and GABAergic interneurons show minimal entrainment. This work provides a reference for the shared molecular architecture of these CNS regions.

neuroscience↗

bioRxiv2026

Spatially Resolved Banff Tubulitis and Glomerulitis Scoring in Kidney Allograft Biopsies via Artificial Intelligent-Based Structure Segmentation and Spatial Transcriptomics

BackgroundTubulitis is a defining histologic feature of T cell-mediated rejection (TCMR), while glomerulitis is often characteristic of antibody mediated rejection (AMR). Histologic quantification of tubulitis and glomerulitis using Banff criteria is subject to interobserver variability. Bulk transcriptomic assays (e.g., MMDx) have introduced molecular correlations of tubulitis with TCMR and glomerulitis with AMR, but lack spatial resolution. MethodsWe applied a web-based platform, FUSION (Functional Unit State Identification in Whole Slide Images), to a cohort of 8 cases (n=2 per condition) with kidney allograft biopsy samples acute TCMR, active AMR, chronic active AMR, and no rejection (control). The machine-learning (ML) platform enabled integrated visualization and analysis of spatial transcriptomics (10x Genomics Visium v2) together with high-resolution whole-slide histology. ResultsTranscriptomics-derived immune cell proportions within AI-segmented tubular and glomerular regions were used to generate spatial Banff t- and g-scores. Derived t-scores showed full concordance with pathologist scores in both acute TCMR cases; g-scores showed concordance in 2 of 4 AMR cases, with discordant cases characterized by low absolute immune signal near the classification boundary. ConclusionsWe demonstrate the feasibility of using AI-based FTU segmentation integrated with spatial transcriptomics-derived immune cell proportions to generate spatially informed t- and g-scores aligned with Banff criteria, with full concordance in severe rejection and partial concordance in mild rejection. This approach lays the foundation for validated, spatial transcriptomics-augmented t-scores and g-scores that enhance diagnostic precision, reduces inter-observer variability among renal pathologists, and support potential clinical adoption.

pathology↗

bioRxiv2026

Fixed human pangenome sequences reveal origins of common human traits

Humans possess human-specific traits1,2 such as spoken language and lineage-specific traits such as ape-specific taillessness3,4. Previous efforts to identify the DNA sequences responsible for such human traits were limited by necessary accommodations for poor genome assembly quality and lack of population genomic sampling5-16. Here, we implement new algorithms that combine the near-complete human reference pangenome alignment with a new near-complete simian cross-species alignment to define human- and lineage-specific DNA sequences fixed across human haplotypes. Previously reported FOXP2/NOVA117,18 amino acid substitutions linked to human spoken language and TBXT transposable element insertion contributing to ape taillessness3,4 were unique to their respective clades and fixed in sampled humans. In contrast, widely used sets of candidate human-mutated loci showed limited enrichment for either human specificity or fixation. Integration with candidate cis-regulatory elements19-22 identified putative regulatory sequences specific to humans and linked to human-specific traits like hair reduction23,24 and brain transcriptome patterning25. Although brain-associated fixed regulatory changes were present in all lineages, enrichment for spoken language was human-specific and enrichment for receptive language was ape-specific. This study provides a new pangenome-aware comparative framework and catalogs of candidate genomic loci to trace the evolutionary origins of common human traits and disease risks.

evolutionary biology↗

bioRxiv2026

Mechanics of Esophageal Retraction During Anterior Cervical Discectomy and Fusion

Dysphagia, difficulty swallowing due to irritation or damage to the esophagus, is one of the most common complications following anterior cervical discectomy and fusion (ACDF), the most frequently performed cervical spine procedure in the United States. Surgical retraction hardware imposes sustained compression on the esophagus during surgery, generating nonuniform stress and strain fields that may contribute to temporary postoperative soft tissue damage. Current intraoperative assessment relies on visual inspection and manual inspection by the surgical team and does not provide quantitative measures of esophageal deformation, strain, or retraction displacement. Here, we present a comprehensive mechanics analysis of esophageal compression during ACDF that integrates experiments on esophageal phantoms, nonlinear finite element modeling, and theoretical thick-wall scaling relationships. Modeling results quantify peak contact pressures and corresponding stress distributions, identifying conditions under which circumferential strain in the compressed esophageal wall increases sharply as localized pressures approach the upper physiological range ([~]6-17 kPa). Parametric investigation of retractor blade width, placement depth, and polymeric biocompatible coating properties demonstrates that targeted, yet mechanically simple, design modifications can help to attenuate strain concentrations. In particular, the introduction of compliant polymeric coatings redistributes contact loads and reduces peak wall stress by up to 20% relative to unbuffered blades (17 kPa to 13.5 kPa). Increasing blade width from 20 mm to 50 mm further decreases peak interface stress from 2.48 kPa to 0.45 kPa, corresponding to an 82% reduction. Reducing these stresses may help limit mechanically induced complications such as postoperative dysphagia. Experiments performed on esophageal phantoms with embedded pressure sensors replicate surgical ACDF retraction protocols under displacement-controlled conditions. This setup establishes physiologically relevant loading and enables quantitative validation of computational predictions by correlating measured voltage output with contact pressure and esophageal deformation. Measured relationships between applied retraction displacement, contact pressure, and tissue deformation govern stress amplification during ACDF retraction. Together, these results establish a predictive mechanics framework that links retractor blade design variables to esophageal stress fields, providing quantitative criteria to mitigate soft tissue damage during ACDF. HIGHLIGHTSO_LI2D and 3D finite element models quantify esophageal wall stress during anterior cervical discectomy and fusion (ACDF) retraction. C_LIO_LIRetractor blade geometry influences stress distribution, with wider blades reducing localized tissue loading by up to 82% likely associated with post-surgical dysphagia. C_LIO_LICompliant polymeric buffer layers attenuate pressure and smoothen stress gradients to reduce peak tissue loading by up to 20% during retraction. C_LI

bioengineering↗

bioRxiv2026

A human specific CCG repeat in the RBFOX1 promoter is implicated in speech and autism

Human speech likely arose from regulatory changes for speech-related brain regions, yet causal variants and mechanisms remain unclear. RBFOX1 is a prime candidate, showing specialized expression in vocal learning circuits of human and zebra finch brains and carrying a promoter deletion linked to autism spectrum disorder (ASD) with language dysfunction. Here, we perform integrative analyses with cross-species brain single-cell multi-omic data and the more complete genomes of the Vertebrate Genomes Project. We identify a human-specific CCG insertion in the RBFOX1 promoter, creating a human-unique CCG-repeated motif. This motif is fixed in both archaic and modern humans but is disrupted by rare clinical variants that exhibit language-related phenotypes and autism. Binding motif models predicted, and reporter assays reveal that this human allele drives stronger EGR1-dependent transcription than its chimpanzee allele. Genome-wide, 107 other genes have core promoters with the identical motif; enriched for postsynapse and implicated in ASD, including PTCHD1. At the PTCHD1 promoter, an ASD-causative CCG-repeated variant enhances EGR1-dependent promoter activity, and its activating effects are predicted in human brain regions using AlphaGenome. Our findings suggest that small variations in the number of CCG repeats in promoters can exert a large regulatory effect on complex traits and their associated disorders.

genomics↗

bioRxiv2026

Epigenomic methylome landscape of promoters in vertebrate genomes

Genomic promoters are crucial gene regulatory elements1,2. Yet, comparative analyses of promoter architecture have been constrained by the limited resolution of GC-rich regions in short-read-based genome resources3-6. The Vertebrate Genomes Project (VGP) provides more complete long-read-based assemblies7, which further detect 5-methylcytosine signals directly from PacBio HiFi circular consensus reads8,9. Here, we developed a scalable computational framework to characterize DNA methylomes from HiFi data on high-quality Phase I VGP assemblies with RefSeq gene annotations for 82 vertebrate species spanning seven major taxonomic classes: mammals, birds, reptiles, amphibians, lobe-finned fishes, ray-finned fishes, and cartilaginous fishes. We observed a conserved, transcription start site-centered hypomethylation signature in promoters across all vertebrates, and an unexpected hypermethylation signature near gene boundaries that is discordant with transcripts. In addition to this conserved pattern, there were lineage-specific differences in promoter methylation profiles, with birds showing the most diverse patterns. These epigenetic landscapes track phylogenetic relationships more closely than tissue-type methylation differences and infer lineage-dependent widths of core promoters and broader promoters across major vertebrate classes. Our findings establish a comparative epigenomic framework for profiling promoter methylomes from long-read sequencing data.

bioinformatics↗

bioRxiv2026

A Denisovan-derived Alu insertion in OCA2 contributes to pigmentation diversity in present-day Melanesians

Modern humans inherited DNA from Neanderthals and Denisovans, but the contribution of introgressed structural variants (SVs) to present-day human phenotypes and adaptation remains poorly understood. Here, we used a graph-genome approach to genotype 96,277 SVs in 3,332 present-day humans and three high-coverage archaic hominin genomes, identifying 153 candidate introgressed SVs. These SVs are enriched for signatures of local adaptation compared to non-introgressed SVs (p-value = 3.04 x 10-7). Among these, we focused on a Denisovan-derived Alu insertion located in intron 18 of OCA2, a gene central to pigmentation. This introgressed Alu insertion is most frequently observed (> 60%) in Indigenous people from Bougainville Island of Melanesia, and is significantly associated with increased skin pigmentation in this region. To assess its functional impact, the Alu insertion was introduced into human induced pluripotent stem cells (iPSCs), which were subsequently differentiated into melanocytes. Melanocytes harboring the Alu insertion demonstrated elevated OCA2 expression, increased pigmentation, and higher levels of enhancer activity compared to controls. Collectively, these findings highlight introgressed SVs as a significant source of adaptive and phenotypic diversity in modern humans and implicate the Denisovan-derived Alu insertion in OCA2 in pigmentation variation among present-day Melanesian populations.

genomics↗

bioRxiv2026

MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies

Single-cell mapping methods convert raw, heterogeneous single-cell datasets into interpretable and comparable representations of biological identity. As reference cell-type taxonomies mature, mapping new datasets to shared references has become a central strategy for enabling cross-study integration, reproducible annotation, and cumulative biological knowledge. Here we present MapMyCells, an open-source framework designed to align diverse single-cell omics datasets to hierarchical reference taxonomies with minimal preprocessing. MapMyCells provides out-of-the-box support for an expanding set of high-quality brain cell-type references generated by the Allen Institute for Brain Science, the BRAIN Initiative, and the Seattle Alzheimers Disease Brain Cell Atlas, including whole-brain mouse and human atlases, aging and Alzheimers disease cohorts, and a cross-species consensus taxonomy initially focused on the basal ganglia. MapMyCells enables efficient mapping of hundreds of thousands of cells on standard workstations without specialized hardware, providing a deterministic, scalable, and modality-agnostic approach that is robust across species and molecular assays. The framework produces interpretable confidence metrics and quantitative summaries of mapping performance, allowing users to evaluate assignment precision and accuracy. We demonstrate the mapping of unlabeled transcriptomic, epigenomic, and spatial datasets to reference taxonomies and describe a general workflow for preparing arbitrary hierarchical taxonomies for reference-based mapping. As the ecosystem of single-cell reference atlases expands, MapMyCells offers a practical and reproducible solution for community-scale cell-type annotation and cross-dataset integration, supporting the development of unified and extensible brain cell atlases.

bioinformatics↗

bioRxiv2026

Bioabsorbable Magnesium Metal ScaffoldsImprove Dermal Wound Healing and Tissue Regeneration

ObjectiveEvaluate the effects of bioabsorbable magnesium wires on dermal wound healing and tissue regeneration in a murine full-thickness wound model. Approach6 mm diameter stented dorsal skin wounds were created in C57BL/6J mice and treated with implanted WE43B magnesium alloy wires or PBS control. Wound healing was evaluated on days 7 and 28 by histology, immunohistochemistry, and micro-CT. Finite element analysis modeled mechanical strain distribution due to wire degradation during healing. ResultsAt day 7, magnesium wire-treated wounds showed 100% improved granulation tissue formation, reduced inflammation (37% fewer CD45+ leukocytes and 37% fewer F4/80+ macrophages), increased neovascularization (91% more CD31+ lumens), and 74% more nerve bundles. Improved wound closure (mean difference -1.48 mm) did not reach statistical significance (d = 1.06). By day 28, magnesium-treated wounds showed improved collagen organization and normalized epidermal thickness. The increase in dermal appendages (247%), and vascular density (41%) did not reach statistical significance. Micro-CT confirmed progressive wire degradation. Modeling revealed that degrading wires dynamically altered strain gradients in healing tissue, thereby modulating the spatial mechanical cues that govern fibroblast migration and extracellular matrix (ECM) remodeling. InnovationMagnesium is an essential trace element involved in cellular processes critical to wound repair, including angiogenesis, nerve growth, inflammation modulation, and ECM remodeling. Previous magnesium delivery systems incorporated polymers or other confounding materials that degrade rapidly. We directly applied bioabsorbable pure magnesium metal to provide sustained ion release and favorable mechanical properties to support regenerative healing. ConclusionBioabsorbable magnesium wires support regenerative wound healing by reducing inflammation, enhancing neovascularization, and promoting favorable ECM remodeling without adverse inflammatory reactions. These findings provide a strong rationale to harness magnesium metal use in wound healing applications.

bioengineering↗

bioRxiv2026

Lessons from the equator: a window on the future of vibriosis in a warming Earth

Vibrios are important aquatic human pathogens, causing gastroenteritis, wound infections, and cholera. Vibriosis (non-cholera infection) has been increasing in temperate climates due to correlation between Vibrio abundance and water temperature. However, how warming oceans differentially influence various Vibrio species, and whether incidence is higher in tropical regions, remains understudied. We assembled the first comprehensive dataset of culture-confirmed vibriosis cases outside a temperate climate from equatorial Singapore. Comparison to cases from the detailed United States (US) CDC COVIS system revealed that vibriosis incidence is over two times higher in Singapore than the United States. Causative species also differ markedly, with Vibrio fluvialis and non-toxigenic Vibrio cholerae dominating in Singapore (>40%) but are much less prominent in the United States (<15%). Singapore cases have remained stable in the last decade, while US incidence is rising rapidly, especially for V. fluvialis and V. cholerae (13% and 17% per year). Differences in causative species in Singapore and the United States suggest ecological factors may shape infection dynamics, with some species benefitting more from warming oceans, raising their equatorial prominence. Incidence is stable in Singapore, likely due to slower warming of waters near the equator. In contrast, vibriosis in the United States will likely continue to increase steadily, with changing species composition, likely becoming tropicalized.

microbiology↗

bioRxiv2026

A Scalable Design for Proximity-Inducing Molecules

Chimeric molecules, which bring together an effector enzyme and a protein-of-interest (POI) to add/remove post-translational modifications (PTMs), are furnishing transformative modalities (e.g., PROTACs). However, these chimeras scalability is limited as they employ rare, non-inhibitory binders of effectors. We report GRoup-transfer chimeras for Inducing Proximity (GRIPs) that employ abundantly available effectors inhibitors to append POI binder on the effector using group-transfer handles. To demonstrate scalability, we develop 6 GRIPs classes for 3 PTMs utilizing diverse inhibitor, spanning 16 effector-POI pairs. Furthermore, we report a toolbox of 42 tunable group-transfer handles for Cys/Lys residues and [~]5000 inhibitor-residue pairs for diverse effectors. Using global proteomics, we confirm the specificity for group transfer and PTM editing. GRIPs endowed new functionalities to POI drugs, including preventing rebound signaling upon drug withdrawal, a more potent/persistent inhibition, and inhibitor-induced pathway activation in 4 fully-endogenous systems. In diverse hemi-endogenous systems (tagged POI), GRIPs induced condensate formation with reduced off-targets, cleared pathogenic PTMs, and initiated PTM crosstalk. Overall, GRIPs provide a scalable and versatile platform for PTM editing. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/706349v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@132f70dorg.highwire.dtl.DTLVardef@f9aa62org.highwire.dtl.DTLVardef@12143edorg.highwire.dtl.DTLVardef@f296d4_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Functional and sensitivity profiling of theKITMutation Landscape in Melanoma

Melanoma in Asia presents a unique epidemiological profile, with a higher prevalence of acral and mucosal subtypes compared to Western populations. While KIT mutations are found in up to 15% of Asian melanoma cases, clinical outcomes with KIT inhibitors have been modest due to heterogeneous mutation profiles and a lack of specific patient selection criteria. This study characterizes the landscape of KIT mutations in melanoma using the GENIE database, identifying 86 recurrent hotspots, many of which are variants of unknown significance (VUS). We validated drug sensitivities for key mutations using in vitro and in vivo models. Our results indicate that while the L576P mutation is highly sensitive to multiple inhibitors, the N822K mutation shows resistance to imatinib but responds to sunitinib, nilotinib, and nintedanib. These findings highlight the necessity of genotype-guided therapeutic strategies and provide a rationale for future clinical trials combining broad-spectrum KIT inhibitors with immune checkpoint inhibitors. Translational SignificanceMelanoma subtypes prevalent in Asia, specifically acral and mucosal melanoma, frequently harbor KIT mutations but show poor response rates (23-26%) to the standard-of-care inhibitor, imatinib. This study challenges the current clinical practice of treating all KIT-mutated melanomas uniformly. We demonstrate that specific recurrent mutations, such as N822K, are intrinsically resistant to imatinib but highly sensitive to broad-spectrum inhibitors like sunitinib and nintedanib. By establishing a comprehensive "lookup table" of drug sensitivities for both common and previously uncharacterized KIT variants, this work provides the evidence base required to transition from a "one-size-fits-all" approach to a genotype-guided precision medicine strategy. Furthermore, validating these targets informs the design of next-generation clinical trials, particularly those combining optimal KIT inhibitors with immune checkpoint blockade to improve survival in currently underserved patient populations.

cancer biology↗