Biology subjects

Li, K.

Publications and source records attributed to Li, K..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of analysis designed to meet diverse research needs. PromptGenie is a multi-agent system that enables stepwise, human-in-the-loop workflows using prevalidated domain-standard tools. Within PromptGenie, specialized agents--including DataAgent, OmicsAgent, AnalysisAgent, and QAgent--collaborate to manage tasks such as data ingestion, pipeline execution, statistical analysis, and interactive summarization. DiscoverFlow provides integrated, automated workflows for large-scale multi-omics analysis, offering end-to-end execution and streamlined orchestration. ToolsGenie complements these modes by dynamically generating executable bioinformatics code for custom, user-defined analyses, enabling flexibility beyond standardized workflows. PromptGenie and DiscoverFlow leverage a suite of domain-specific tools, including Omics Tools for standardized omics pipelines, Analysis Tools for downstream statistical interpretation, and MLGenie for machine learning and multi-omics modeling. We present the design, capabilities, and validation of these components, highlight their integration into automated and customizable workflows, and discuss extensibility, monitoring, and compliance. PromptBio aims to democratize high-throughput bioinformatics through a large language model-powered, natural language understanding, workflow generation and agent orchestration.

bioinformatics↗

bioRxiv2025

High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of freely swimming zebrafish larvae

Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural 3D movements and postural dynamics. Here, we present a novel high-throughput 24-camera array microscope with a co-designed "mirrored well plate" that allows for snapshot imaging of up to 48 wells over a 118 mm x 82 mm field of view from two orthogonal directions (i.e., a top-view and side-view). Accurate 3D position estimation and tracking is achieved with an efficient machine learning algorithm that scales well to high-throughput measurements. The proposed approach automates parallelized 3D model organism behavioral analysis, providing 3D skeletal tracking, swim bladder morphological dynamics, and kinematics of up to 48 swimming zebrafish larvae at up to several hundred frames per second. The result is an efficient and scalable solution for high-throughput 3D behavioral studies with broad compatibility with standard workflows across laboratories and procedures working with pharmacology, toxicology, and neuroscience.

animal behavior and cognition↗

bioRxiv2025

A Universal RT-qPCR Method for DNA Aptamer Quantification

Aptamers are widely used in various applications; however, their quantification methods remain underdeveloped. In this study, we established a universal RT-qPCR-based method for DNA aptamer quantification. By incorporating reverse transcription, primers and probes could be added to aptamers, enabling their detection via qPCR (Figure 1). We developed a software tool for primer and probe design and optimized the reverse transcription process. Two aptamers, CD9-aptamer and CD63-aptamer, were selected as model systems representing two distinct aptamer types: the CD9-aptamer contains an intrinsic primer-binding site within its sequence, whereas the CD63-aptamer does not. Using this method, the limit of detection (LOD) for CD9-aptamer reached 10-14 M, while the LOD for CD63-aptamer was 10-12 M. Compared to existing quantification methods, this approach significantly improves accuracy and cost-effectiveness. Additionally, the method supports SYBR Green, TaqMan, and one-step RT-qPCR assays, broadening its applicability and enhancing precision for various aptamer-based applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/662296v1_fig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@44ec4corg.highwire.dtl.DTLVardef@f59184org.highwire.dtl.DTLVardef@2480fdorg.highwire.dtl.DTLVardef@906845_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Schematic illustration of RT-qPCR-Based Aptamer Quantification. C_FIG

molecular biology↗

bioRxiv2025

ADAR1 Restricts Poliovirus Infection through dual disruption of translation initiation and protein coding

Viral RNAs (vRNAs) interact with hundreds of host proteins, but how these interactions shape viral infection remains largely unknown. Here we developed a mass-spectrometry approach to identify cellular RNA-binding proteins (RBPs) that enhance or inhibit infection by modulating vRNA translation. We identified 130 RBPs that associate with polysomes in human cells infected with poliovirus, including known regulators of cap-independent translation from the viral internal ribosome entry site (IRES). We find that adenosine deaminase acting on RNA (ADAR1) is recruited to polysomes during infection and edits 3 sites in the vRNA, reducing viral replication. Two edits occur in the IRES and impair internal translation initiation, while the third edit occurs in the coding region and triggers an amino acid substitution. Incorporation of this threonine-to-alanine mutation into the viral genome attenuated replication. We conclude that ADAR1 restricts poliovirus infection by both reducing vRNA translation and introducing a recurrent coding error.

cell biology↗

bioRxiv2025

NUSAP1 regulates mitotic processes via KIF2C interaction and AURKA phosphorylation in primary microcephaly

Primary microcephaly (PM) is a neurodevelopmental disorder characterized by a significantly smaller head than normal. Despite the identification of several genes associated with PM subtypes, the etiology remains unclear in a significant proportion of patients. Here, we reported two de novo nonsense mutations in the NUSAP1 gene identified in two independent PM families: c.1209 C>G (p.Tyr403*) and c.1213C>T (p.Gln405*). Nusap1-edited mouse models, designed to mimic Human NUSAP1 mutations, replicated the microcephaly phenotype, characterized by a small brain and thinner cerebral cortex. We demonstrated that Nusap1 was specifically expressed in neural stem/progenitor cells (NSPCs), and the number of NSPCs was significantly reduced in Nusap1-edited mice. In vitro experiments revealed that NUSAP1 mutations disrupted mitotic metaphase chromosome alignment, increased polyploidy, induced cell cycle arrest, and promoted apoptosis. Co-IP confirmed direct interactions between NUSAP1 and KIF2C, and showed that truncating mutations impaired their binding. Furthermore, NUSAP1 rescued the cell cycle arrest and increased apoptosis caused by KIF2C overexpression in NUSAP1 KO HEK293T cells, whereas the mutant truncated protein failed to exert such a rescue effect. We also uncovered an interaction between NUSAP1 and Aurora kinase A (AURKA). Intriguingly, subsequent experiments revealed that AURKA-mediated phosphorylation of NUSAP1 modulates its binding affinity to KIF2C. In conclusion, our findings established NUSAP1 as a novel pathogenic gene for PM. We proposed a model in which AURKA-mediated phosphorylation of NUSAP1 regulates its interaction with KIF2C, balancing spindle microtubule stability and depolymerization to ensure proper sister chromatid segregation. Disruptions in this pathway impair NSPCs mitosis, thereby affecting neocortical development.

genetics↗

bioRxiv2025

Application of spatial transcriptomics across organoids: a high-resolution spatial whole-transcriptome benchmarking dataset

Stem cell-derived organoids hold promise to model tissue-specific disease. To enable this, it is crucial to assess how transcriptional signatures, cellular organisation and composition of organoids compare to in vivo counterparts. However, technologies which elucidate regional molecular identity, like spatial transcriptomics, have been challenging to apply to organoids. This study presents the first systematic profiling of multiple stem cell derived organoid models (brain, heart muscle, heart valve, kidney, lung, cartilage, and haematopoietic) with Stereo-seq, a full transcriptome, spatial transcriptomics assay using on-chip in situ RNA capture at subcellular resolution. It describes optimisation of this assay to characterise organoids, use of multiple organoid samples on a single chip, assess differences in RNA capture efficiency compared to reference tissues and its limitations. This study introduces a bespoke analysis method that partitions samples into regions and further characterises them. These findings inform future works to characterise organoids using spatial transcriptomics, providing insights in optimising RNA capture of multiple organoids across a chip and novel methods for regional analysis.

bioinformatics↗

bioRxiv2025

CRIS: A Centralized Resource for High-Quality RNA Structure and Interaction Data in the AI Era

As interest in RNA-based therapeutics expands, there is a growing demand for RNA structure elucidation and RNA-RNA interactions in both academic and clinical settings. Despite rapid advances in methods for RNA structure determination, the field faces persistent challenges in data reproducibility, quality control, and accessibility, largely due to inconsistencies in data processing and analysis workflows. Concurrently, methodological improvements have generated increasingly complex datasets, which necessitate a standardized framework. Here, we present the Crosslinking-based RNA Interactomes and Structuromes (CRIS) database, a comprehensive resource designed to address these limitations. Among existing experimental and computational approaches for RNA structure characterization, crosslinking-based technologies offer superior reliability, high throughput, and high resolution. CRIS provides rigorously curated datasets, standardized workflows, and user-friendly tools, together with built-in quality metrics and detailed visualization guidance to ensure reproducibility and transparency while pairing seamlessly with existing experimental pipelines. By delivering high-complexity RNA datasets alongside accessible computational tools, CRIS serves as a standardized reference for both new and existing data, facilitating investigation through comparative analyses and providing a training resource for deep learning-based computational exploration. This will enable integration into machine learning workflows for large scale, novel RNA structure discovery.

bioinformatics↗

bioRxiv2025

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria

Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detecting these interactions and localizing potential binding sites. However, its original workflow is limited in throughput, sample compatibility and accessible protein targets. Here, we introduce a high-throughput adaptation - HT-PELSA - that increases sample processing efficiency 100-fold while maintaining high sensitivity and reproducibility. HT-PELSA substantially extends the capabilities of the original method by enabling sensitive protein-ligand profiling in crude cell, tissue and bacterial lysates, making it possible to identify membrane protein targets in diverse biological systems. We demonstrate that HT-PELSA can precisely and accurately determine binding affinities of small molecule inhibitors, sensitively detect direct and allosteric ATP binding, and reveal off-target interactions of a marketed kinase inhibitor in heart tissue. By enhancing scalability, reducing costs, and enabling system-wide drug screening across a wide range of sample types, HT-PELSA - when combined with next-generation mass spectrometry - offers a powerful platform poised to accelerate both drug discovery and basic biological research.

cell biology↗

bioRxiv2025

ARAP2 regulates responses to interferon-gamma by restricting SOCS1

Interferon-gamma (IFN{gamma}) is critical for immunity against intra-macrophagic pathogens, signaling through the JAK-STAT pathway to induce a tyrosine-phosphorylation cascade that ensures a potent immune response. Excessive JAK-STAT signaling can drive hyperinflammation and autoimmunity, and thus signaling is tightly and selectively regulated by the IFN{gamma}-inducible protein, Suppressor of Cytokine Signaling 1 (SOCS1). SOCS1 inhibits signaling by directly blocking JAK kinase activity. Here we identified a SOCS1-interacting partner, ARAP2 that fine-tunes SOCS1 function. We report that tyrosine 415 in ARAP2 binds the SOCS1-Src Homology 2 (SH2) domain and limits the ability of SOCS1 to inhibit IFN{gamma} signaling. Our findings show that ARAP2 promotes the IFN{gamma} response through a phosphorylation dependent interaction with the negative regulator SOCS1.

cell biology↗

bioRxiv2025

Angel Wing: a class of alternative splicing regulators in animals

Alternative splicing (AS) regulates the diversity and level of the proteome. The specificity in AS is in turn regulated by RNA binding proteins, but our understanding of how they act is far from complete. Here we identify the Angel wing (Anw) protein as a novel AS regulator. Loss of Anw in Drosophila disrupts splicing in muscle genes and subsequently muscle function. Based on a mini-gene assay in which Anw and its RNA targets are co-expressed in cultured cells, we demonstrated orthologous splicing regulation of the minigene transcripts, interaction between Anw and its RNA targets, and a remarkable functional conservation among Anw homologs. Anw forms nuclear foci, and genetic ablation of Anw domains suggests that maintaining distinctive features of these foci is important for its function. The evolution of Anw is dynamic with gene gains and losses, but preserves a cross-phyla "ultra conserved element" as an alternative exon that potentially regulates its own level by non-sense mediated mRNA decay. As the human anw homolog is a candidate gene for myasthenia gravis, our work suggests a mechanism for cellular dysfunction in this disease.

genetics↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

Lymphatic Malformations with Activating KRAS Mutations Impair Lymphatic Valve Development Through Matrix Metalloproteinases

BACKGROUNDLymphatic malformations (LMs) are lesions due to inherited or somatic mutations that lead to a defective lymphatic vasculature. Activating KRAS mutations have been identified recently in LM patients with lymphedema, chylous ascites, or life-threatening chylothorax. In a LM mouse model, KRAS mutations are associated with a loss of lymphatic valves, which has been proposed to cause chylothorax via retrograde lymph flow into the pleural space. However, the mechanisms underlying the loss of lymphatic valves are unknown. METHODSTo investigate the mechanisms leading to valve loss, we combined the lymphatic-specific and tamoxifen-inducible Flt4CreERT2 with Kras-loxP-stop-loxP-G12D (Kras+/G12D) mice and Prox1GFP reporter mice to induce the restricted expression of KRAS-G12D and enable valve quantification in postnatal pups. Human dermal lymphatic endothelial cells (hdLECs) expressing KRAS-G12D were probed for changes in mRNA and protein expression with qRT-PCR, western blot, and gel zymography, and mechanistic studies were performed using 3D cell culture in collagen matrices. RESULTSOur data showed that lymphatic-specific expression of KRAS-G12D significantly attenuated valve development in the mesentery, diaphragm, and ear skin. qRT-PCR, western blot, and gel zymography using hdLECs expressing KRAS-G12D revealed the upregulation of the plasminogen activator (PA) pathway and matrix metalloproteinases (MMPs). The MMPs were sufficiently activated by plasmin, the product of the PA pathway, in hdLECs grown in a 3D collagen matrix, indicating a role for MMPs in the degradation of valve ECM core. Furthermore, a broad-spectrum MMP inhibitor given to Flt4CreERT2;Kras+/G12D mice rescued lymphatic valve development. CONCLUSIONSWe conclude that hyperactive KRAS signaling upregulates MMPs that become excessively activated by the upregulation of the PA pathway. MMPs then degrade the lymphatic valve ECM core preventing valve formation.

pathology↗

bioRxiv2025

DiCE: Differential Centrality-Ensemble Analysis Based on Gene Expression Profiles and Protein-Protein Interaction Network

Uncovering key genes that drive diseases and cancers is crucial for advancing understanding and developing targeted therapies. Traditional differential expression analysis often relies on arbitrary cutoffs, missing critical genes with subtle expression changes. Some methods incorporate protein-protein interactions (PPIs) but depend on prior disease knowledge. To address these challenges, we developed DiCE (Differential Centrality-Ensemble), a novel approach that combines differential expression with network centrality analysis, independent of prior disease annotations. DiCE identifies candidate genes, refines them with an information gain filter, and reconstructs a condition-specific weighted PPI network. Using centrality measures, DiCE ranks genes based on expression shifts and network influence. Validated on prostate cancer datasets, DiCE identified genes over-represented in key pathways and cancer fitness genes, significantly correlating with disease-free survival (DFS), despite DFS not being used in selection. DiCE offers a comprehensive, unbiased approach to identifying disease-associated genes, advancing biomarker discovery and therapeutic development. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/638654v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1ce9b81org.highwire.dtl.DTLVardef@14352e1org.highwire.dtl.DTLVardef@f63caeorg.highwire.dtl.DTLVardef@a0086_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Structural basis for the RC-LH1 supercomplex of Dinoroseobacter shibae for anaerobic anoxygenic photosynthesis

Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, the architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present the 2.4-[A] cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 {beta}-subunits, each containing two spheroidenones per {beta}-heterodimer--a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, accounting for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown protein-LRC (Light-Respiratory Connector), which structurally bridges the RC and LH1 components and exhibits homology to NADH oxidoreductase subunit E, suggesting a functional coupling between photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.

biochemistry↗

bioRxiv2025

PELSA-Decipher: a software tool for the processing and interpretation of ligand protein interaction dataset acquired by PELSA

Knowledge of protein-ligand interactions is essential for comprehending various aspects of life science, including drug mechanisms of action, regulatory processes in cellular metabolism and signaling, etc. Recently, a robust ligand modification-free method, termed as peptide-centric local stability assay (PELSA), is developed to identify the protein targets and binding regions of diverse ligands at proteomics scale. This method has unprecedented sensitivity and can be broadly applied to ligands including drugs, metabolites, metal ions, antibodies tec. However, the extraction of key information on ligand-protein interaction, including the binding protein, binding site, and binding affinity, is not a trivial task, which hampers the wide utilization of PELSA strategy by the research community. To address this, we developed a software tool, PELSA-Decipher, to facilitate the efficient processing of dataset obtained in PELSA experiment, including raw data processing, result visualization, and the generation of reports and high-quality images, thereby will greatly promote the broader applications of PELSA strategy. The PELSA-Decipher software can be downloaded free of charge from the website https://github.com/DICP-1809.

bioinformatics↗

bioRxiv2025

Evaluating a Standard Benchmark for Gene Prioritization: The InheriNext(R) Algorithm's Integration of Genomic and Phenotypic Information

This study presents a comprehensive benchmark analysis of InheriNext(R), a domain-specific, AI-powered tool designed for phenotype-driven pathogenic variant prioritization. For this study, 7,244 whole exome test cases were generated using phenotype and genotype data from Phenopackets, along with pools of variants from healthy individuals to serve as genomic backgrounds. Performance was evaluated across diverse testing scenarios and compared against four established tools. The results show InheriNext(R) achieving a 98.6% sensitivity in identifying pathogenic variants and consistent performance across diverse tests for variant types, phenotype counts, and disease groups--supporting the robustness and adaptability of its methodology. Sharing these benchmarking results and samples is intended to drive progress by assisting clinicians and researchers in evaluating interpretation tools and identifying areas for improvement.

genomics↗

bioRxiv2025

Sulfinyl Aziridines as Stereoselective Covalent Destabilizing Degraders of the Oncogenic Transcription Factor MYC

While MYC is a significant oncogenic transcription factor driver of cancer, directly targeting MYC has remained challenging due to its intrinsic disorder and poorly defined structure, deeming it "undruggable." Whether transient pockets formed within intrinsically disordered and unstructured regions of proteins can be selectively targeted with small molecules remains an outstanding challenge. Here, we developed a bespoke stereochemically-paired spirocyclic oxindole aziridine covalent library and screened this library for degradation of MYC. Through this screen, we identified a hit covalent ligand KL2-236, bearing a unique sulfinyl aziridine warhead, that engaged MYC in vitro as pure MYC/MAX protein complex and in situ in cancer cells to destabilize MYC, inhibit MYC transcriptional activity and degrade MYC in a proteasome-dependent manner through targeting intrinsically disordered C203 and D205 residues. Notably, this reactivity was most pronounced for specific stereoisomers of KL2-236 with a diastereomer KL4-019 that was largely inactive. Mutagenesis of both C203 and D205 completely attenuated KL2-236-mediated MYC degradation. We have also optimized our initial KL2-236 hit compound to generate a more durable MYC degrader KL4-219A in cancer cells. Our results reveal a novel ligandable site within MYC and indicate that certain intrinsically disordered regions within high-value protein targets, such as MYC, can be interrogated by isomerically unique chiral small molecules, leading to destabilization and degradation.

cancer biology↗

bioRxiv2025

In vivo anti-FAP CAR T therapy reduces fibrosis and restores liver homeostasis in metabolic dysfunction-associated steatohepatitis

In this study, we aimed to determine the efficacy of in vivo chimeric antigen receptor (CAR) T cell therapy, generated by targeted lipid nanoparticles (t-LNPs), as an anti-fibrotic in metabolic dysfunction-associated steatotic liver disease. Hepatic fibrosis is a key predictor of mortality in liver disease, driven by fibrogenic hepatic stellate cells (HSCs). In heart, chimeric antigen receptor (CAR) T cells targeting fibroblast activation protein alpha (FAP) reduce murine cardiac fibrosis. However, the value of this approach in liver is unknown. We explored the anti-fibrotic potential of in vivo-generated anti-FAP CAR T cells in metabolic dysfunction-associated steatohepatitis (MASH), a highly prevalent disease with no approved anti-fibrotic therapies. We first established that FAP expression in both human and murine MASH is specific to HSCs. We then used flow cytometry, Sirius Red morphometry, digital pathology analysis, and single nuclear RNA-sequencing to assess the impact of anti-FAP CAR T cell therapy on murine MASH. Anti-CD5 targeted-LNPs carrying anti-FAPCAR mRNA generate activated, transient anti-FAP CAR T cells, which significantly reduced fibrosis by depleting pro-fibrogenic HSCs, and by modulating immune cells, endothelial cells and hepatocytes in a non-cell autonomous manner to mitigate inflammation and restore hepatic homeostasis. These findings reinforce the potential of in vivo CAR T therapy to attenuate a highly morbid and pervasive liver disease through integrated, multicellular salutary effects. One Sentence SummaryRNA-based treatment transiently reprograms immune cells to target scar-forming cells in fatty liver disease, thus improving liver health overall.

cell biology↗