Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

We present Korea10K, the largest genomic dataset of the Korean population, comprising 10,239 high-coverage whole genomes (mean depth 30x) with matched multiomic profiles and phenotype data. Korea10K achieves complete and near-complete discovery of very rare and ultra-rare alleles, respectively, at 9,000 Korean genomes. This dataset provides the high-quality population-specific imputation panel, enabling accurate inference of low-frequency variants. Admixture analyses confirm the genetic homogeneity of the Korean population, despite its diverse Y-chromosomal, mitochondrial, and HLA repertoires. This pattern reflects a long and continuous lineage history characterized by persistent internal admixture and genomic homogenization over thousands of years on the Korean peninsula. We also identified 16.8 million genomic variants that directly modify CG sites by creating or abolishing CG dinucleotides, providing the population-scale evidence of coordinated genomic-epigenomic regulatory mechanism in Koreans.

genomics↗

bioRxiv2025

Characterizing spatial functional microniches with SpaceTravLR

The advent of spatial omics has revolutionized our understanding of tissue biology; however, these technologies remain largely descriptive and do not capture how changes in gene regulation propagate across spatial neighborhoods. While in-silico perturbation methods and foundation models aim to model the impact of genetic perturbations, these methods are limited to single-cell approaches that lack spatial resolution. Other studies can delineate morphological domains based on transcriptional similarity, but not spatial functional microniches. We address this major unmet need by developing SpaceTravLR (Spatially perturbing Transcription factors, Ligands and Receptors), a novel interpretable machine learning approach that generalizes across tissues and species, uncovering spatial features linked to functional outcomes, thereby capturing functional microniches with spatial resolution. SpaceTravLR infers how single or combinatorial genetic perturbations rewire signals across the tissue neighborhood, by propagating effects through underlying spatially resolved molecular networks, thereby modeling how perturbations can reshape both the targeted cell and its surrounding neighborhood. SpaceTravLR defines novel spatial microniches across a range of tissues at different scales of organization (niches, neighborhoods and tissues), disease and developmental contexts. SpaceTravLRs perturbation predictions are made solely from spatial omics data and closely align with experimental validation or known outcomes based on mechanistic studies. Critically, our approach enables the generation of mechanistic hypotheses underlying identified niches. We show SpaceTravLR discovered a novel mechanism for Ccr4 that drives the spatial location of a pathogenic population of allergen-specific T helper 2 (Th2) cells as they develop in the lymph node, which was experimentally validated in a murine model. Overall, SpaceTravLR provides a novel interpretable and experimentally validated framework for uncovering how genes act individually and combinatorially through cell-intrinsic and cell-extrinsic circuits to shape spatial tissue organization and function.

systems biology↗

bioRxiv2025

Development of Recombinant Anti-TLR2 Antibodies and PLGA Nanoparticle-based Gene Therapy for the Treatment of Neuropathic Pain

Neuroinflammation is a key contributor to neuropathic pain, with microglial Toll-like receptor 2 (TLR2) playing a central role in initiating and sustaining proinflammatory responses. However, existing TLR2-targeting antibody therapies are limited by poor delivery to the central nervous system and short-lived efficacy. We developed a non-viral gene therapy strategy using biodegradable poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) to deliver recombinant anti-TLR2 antibody genes. High-affinity nanobody and single-chain variable fragment candidates were selected through phage display screening and shown to suppress TLR2-dependent signaling both in vitro and in vivo. In mouse models of neuropathic pain, a single intrathecal administration of PLGA NP-encapsulated antibody genes produced robust and sustained analgesia, accompanied by reduced glial activation and proinflammatory cytokine expression. These findings demonstrate a modular NP-based platform for sustained antibody expression in the central nervous system and establish its potential for the treatment of chronic pain driven by innate immune activation.

neuroscience↗

bioRxiv2025

Primary Cilia Dysfunction in Brown Fat Results in Fatal Thermogenesis Failure in Neonatal Mice

Primary cilium, microtubule-based sensory organelle that has emerged as a central player in coordinating numerous signaling pathways. Although primary cilia are known to regulate cellular signaling and energy metabolism, the relationship between these roles in the context of ciliopathies and brown adipose tissue (BAT) dysfunction remains poorly understood. To elucidate the role of primary cilia in BAT, we generated Ucp1-Cre;Ift88flox/flox mice with BAT-specific ciliary loss. There were no significant differences in body size, weight, or BAT weight relative to body weight between P0 Ucp1-Cre;Ift88flox/flox and P0 Ucp1-Cre;Ift88+/+ pups. Embryos examined at E14.5 and E18.5 also showed no discernible differences in size, morphology, or histology. However, P0 Ucp1-Cre;Ift88flox/flox pups exhibited neonatal lethality caused by defective thermogenesis, despite preserved Ucp1 expression. These mice displayed markedly reduced ketone body levels in both BAT and serum, accompanied by downregulation of Hmgcs2, a key enzyme in ketogenesis. Loss of primary cilia in BAT suppressed ketogenesis and increased ROS production through HMGCS2 downregulation, ultimately impairing non-shivering thermogenesis. Remarkably, neonatal lethality of Ucp1-Cre;Ift88flox/flox pups was completely rescued by thermoneutral housing or {beta}-hydroxybutyrate supplementation. Our findings identified a previously unrecognized mechanism by which primary cilia regulate non-shivering, UCP1-independent thermogenesis via ketogenesis.

cell biology↗

bioRxiv2025

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

DNA methylation (5mC) is an epigenetic mark that plays a critical role in defining cell fate. Following fertilisation, DNA methylation inherited from gametes must be reprogrammed to establish totipotency and enable the parental-to-zygotic transition. To accomplish this, non-mammalian vertebrates such as zebrafish and medaka subtly reprogram maternal 5mC profiles while maintaining high methylation levels throughout embryogenesis. In contrast, eutherian mammals such as mouse and human undergo global 5mC erasure in both embryonic and extraembryonic lineages. However, while embryonic 5mC is rapidly re-established to high levels upon implantation, the trophectoderm, which gives rise to the placenta, displays sustained and conserved DNA hypomethylation, suggesting that this drastic 5mC erasure may be functionally linked to complex placentation in mammals. To clarify whether extensive post-fertilisation 5mC erasure co-evolved with placentation, we explored embryonic methylation dynamics in marsupials, a lineage of therian mammals with a short-lived placenta. We produced a near complete telomere-to-telomere (T2T) genome and generated detailed epigenome maps of embryonic development for an Australian marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata). We found the dunnart embryo exhibits genome wide DNA demethylation at the blastocyst stage, but these changes occur in the trophectoderm only, suggesting that 5mC erasure in the placenta is an ancestral state in therian mammals. Furthermore, the T2T-level dunnart genome assembly enabled identification of sex chromosomes, uncovering extensive hypomethylation of the paternally-inherited inactive X chromosome in females and revealing the previously unannotated master regulator of X chromosome inactivation, lncRNA Rsx. Our data indicate that while the use of genome-wide 5mC erasure differs between eutherian and marsupial lineages, 5mC erasure in extraembryonic tissue is ancestral to therian mammals and may be necessary to support placental development. HIGHLIGHTSO_LIFirst embryonic DNA methylation maps in an Australian marsupial C_LIO_LIExtensive global erasure of DNA methylation in the trophectoderm C_LIO_LIMaintenance of high DNA methylation in the embryonic lineage C_LIO_LIHypomethylated paternal X chromosome with methylated escapee genes C_LI

developmental biology↗

bioRxiv2025

T-Cell Synaptosomes Orchestrate Long-Term Anti-Tumor Immunity via Proliferative and Metabolic Reprogramming

A defining feature of T-cell activation is its dependence on physical contact with antigen-presenting cells (APCs). During this interaction, activated T cells release microvesicles, known as T-cell immunological synaptosomes (TIS), onto the surface of APCs. While TIS are known to activate APCs, their broader in vivo functions remain largely unexplored. Here, we show that TIS are primarily phagocytosed by macrophages and dendritic cells, persist intracellularly for several days, and reprogram these cells in a manner distinct from LPS. TIS upregulate genes involved in metabolism, proliferation, and anti-inflammatory responses, and promote immune cell recruitment, including eosinophils. Notably, TIS induce minimal immune activation upon initial exposure but trigger a rapid and robust response upon secondary administration, indicating a priming effect reminiscent of adaptive immunity. In an MC38 colon cancer model, TIS treatment resulted in near-complete tumor suppression and durable protection upon rechallenge, highlighting their potential as a potent and long-lasting immunotherapeutic platform.

immunology↗

bioRxiv2025

Functional divergence of Capicua isoforms explains differential tissue vulnerability in neurological disease

Many neurological diseases impact specific brain regions despite widespread expression of the disease-related protein. Spinocerebellar ataxia type 1 (SCA1) primarily affects the cerebellum, though Ataxin-1 (ATXN1) is widely expressed. We previously showed that intensified interaction between mutant ATXN1 and Capicua (CIC) drives SCA1 pathogenesis in the cerebellum, whereas ATXN1 loss augments amyloid beta production in the hippocampus and cortex. CIC, however, forms a complex with ATXN1 and its paralog, Ataxin-1-like (ATXN1L)--yet knockout of either yields completely different phenotypes. To determine whether this could be due to CIC having two isoforms, we generated mice bearing either the long (CIC-L) or short (CIC-S) isoform. Loss of CIC-L led to cognitive deficits, whereas loss of CIC-S caused perinatal lethality, phenocopying, ATXN1 and ATXN1L knockout mice, respectively. Furthermore, CIC-L preferentially interacts with ATXN1, and CIC-S with ATXN1L. Our data underscore the importance of isoform-paralog interplay in studying regional vulnerability in neurodegenerative diseases.

molecular biology↗

bioRxiv2025

Over-expression of Cyclic Nucleotide-Gated Ion Channel 2 (CNGC2) triggers 1 hypersensitivity to virulent pathogens and elevated Ca2+

The Arabidopsis Cyclic Nucleotide-Gated Ion Channel 2 (CNGC2), also known as Defense No Death 1 (DND1), is the most extensively studied plant CNGC and has been implicated in diverse physiological processes, including floral transition, responses to heat and humidity, and hormone signaling. Its role in immunity has received particular attention due to the autoimmunity phenotype observed in the cngc2/dnd1 knockout mutants. Interestingly, despite this hyperactivation of immunity, the mutant also exhibits impaired hypersensitive cell death--a hallmark of effector-triggered immunity (ETI)--as well as reduced reactive oxygen species (ROS) production and diminished Ca{superscript 2} influx in response to pathogen-associated molecular patterns (PAMPs) such as the bacterial flagellin peptide flg22. These contradictory phenotypes highlight the complex biological functions of CNGC2. To date, most studies have focused on loss-of-function mutants. In this study, we performed a detailed characterization of CNGC2 overexpression lines to gain deeper insight into its role in immunity. Remarkably, overexpression of CNGC2 led to heightened susceptibility to two taxonomically distinct pathogens, despite the plants displaying wild-type morphology. Overexpression of CNGC2 rescued several cngc2 mutant phenotypes, including morphological defects and delayed flowering, yet these plants were also hypersensitive to elevated external Ca{superscript 2} levels. Furthermore, they exhibited attenuated responses to flg22, suggesting that CNGC2 does not act as a simple positive or negative regulator of immunity. Our findings reveal an essential role for CNGC2 where a balanced expression level is critical for maintaining Ca{superscript 2} homeostasis between the apoplast and cytosol, thereby influencing the generation of Ca{superscript 2} signals essential for immune responses.

plant biology↗

bioRxiv2025

Somatic copy number mutations contribute to fitness in transplantation models of spontaneous human breast cancer metastasis

The contribution of somatic gene dosage mutations (CNA) to breast cancer metastasis remains poorly defined. Using 9 transplantable human neoadjuvant-naive triple-negative breast cancer xenografts, we studied the fitness of copy number clones in spontaneous metastasis from orthotopic transplant sites. Metastatic site preference was strongly patient-dependent, and the emergence of metastases exhibited a general trend toward slower growth at the orthotopic site. In our models, single-cell whole-genome sequencing of primary and metastatic sites showed that distant metastases were most often the result of minor prevalence clones at the orthotopic site, suggesting that some metastatic phenotypes may be weakly negatively fit at the primary site. We validated the existence of a fitness hierarchy of copy number clones using a previously established paradigm of remixing and retransplanting clones. Single-cell clone analysis of competitive repopulation and re-emergence of metastases showed that CNAs arising in cancer evolution can mediate metastatic fitness. Moreover, some clones displaying strong metastatic tendency exhibited weaker survival at the primary site, consistent with the notion that metastatic phenotypes could have a fitness cost at the primary site. Finally, we conducted RNA-seq analysis combined with DriverNet analysis to dissect the contribution of CNA-mediated versus genome-independent transcriptional states. CNA mutations appeared to contribute strongly to transcriptional differences between clones. Among clones of high metastatic potential, we observed CNA-mediated and CNA-independent convergence on pathways such as epithelial-mesenchymal transition (EMT), established as mediators of metastatic cell survival at distant sites. Taken together, our data point to a contribution of CNA-mediated cancer evolution to metastatic states and identify distant-site context as a key determinant of CNA-mediated fitness.

cancer biology↗

bioRxiv2025

Grip and grasp: lizard claw inspired robotic manipulators

This paper considers the selection of a lizard claw to apply as an end effector on a bioinspired robotic manipulator, to improve grasping efficiency. Our work draws on morphological parameters that influence mechanical grip. By considering geometrical ratios that are built on parameters such as the arm-to-tip angle, the claw inner radius, and the slip distance, our research identifies optimal parameters that influence grip strength and stability. We demonstrate that these parameters, when combined to form two specific indices (the geometric mean, IGM, and the arithmetic mean of deviations, IAMD), provide a basis for more extensive comparisons between the different claw morphologies researched. The claw of Crotaphytus collaris is deduced as being the most suitable candidate for application as a bioinspired end effector in a robotic manipulator used for grasping objects, as it closely aligns with our optimal design criteria. To practically demonstrate gripping and grasping, we use a lightweight ping pong ball as well as larger and heavier objects such as an abalone shell, boxing mitts and a printer spool. Our robotic manipulator integrates dual grasping strategies. These include pinching for delicate objects and scooping for larger, irregular objects, thus enhancing its versatility across different environments and for different applications. Overall, this paper offers valuable new insights into biomimetic manipulator design using claws as end effectors, highlighting the importance of lizard claw selection based on morphology.

bioengineering↗

bioRxiv2025

Isoflurane and Surgical Stress Disrupt Fatty Acid and Carbon Metabolism Leading to Cardiomyopathy

Aging alters cardiac resilience to anesthetic and surgical stress, yet the molecular basis of these effects remains poorly understood. To define age-dependent cardiac transcriptional responses to isoflurane exposure and operative (ISO/OP) stress, we analyzed gene expression profiles across young adult (3m), late middle-aged (17m), and geriatric mice (27m) following short-term 2 h ISO/OP exposure. At 24 h after cessation, all age groups exhibited distinct cardiac transcriptional signatures separating ISO/OP from sham controls. In young adult hearts, transcriptional alterations 24 hours after cessation of ISO/OP were characterized by dysregulation of small molecule catabolic processes, fatty acid metabolism, disruptions to protein processing in endoplasmic reticulum and cytoskeletal organization. Late middle-aged mice displayed amplified perturbations in lipid metabolism alongside suppression of muscle system and calcium signaling pathways, while old mice showed robust activation of PPAR and AMPK signaling and downregulation of genes governing contractility and morphogenesis. In contrast, geriatric mice showed upregulation of fatty acid metabolic pathways, robust activation of PPAR and AMPK signaling, coupled with suppression of muscle differentiation and actin organization following ISO exposure, indicating a maladaptive metabolic reprogramming. Overlapping DEGs across all age groups converged on pathways regulating oxidative stress, Ca2+ handling, hypertrophy, and energy metabolism, suggesting a conserved but age-intensified cardiac stress response. Longitudinal profiling in aged mice revealed persistent transcriptomic remodeling five weeks after stress. Crucially, this remodeling was observed even after ISO exposure alone, indicating that general anesthesia is a primary driver of this long-term effect. This persistent signature was marked by mitochondrial dysfunction and dysregulation of genes associated with diabetic cardiomyopathy, extracellular matrix integrity, and neurodegenerative signaling. Together, these findings identify isoflurane exposure as a potent inducer of persistent, age-dependent metabolic and structural reprogramming in the heart, implicating impaired lipid utilization and mitochondrial homeostasis as central mechanisms linking the perioperative period, and specifically anesthetic exposure, to long-term cardiovascular vulnerability.

pharmacology and toxicology↗

bioRxiv2025

Mutation-Agnostic Base Editing of the Progerin Farnesylation Site Rescues Hutchinson-Gilford Progeria Syndrome Phenotypes in Neuromuscular Organoids

Hutchinson Gilford progeria syndrome (HGPS) is a fatal premature aging disorder caused by pathogenic farnesylated lamin A variants that disrupt nuclear architecture and DNA repair. Current therapies, including farnesyltransferase inhibitors, provide only modest survival benefits and lack molecular specificity, while mutation-specific genome-editing strategies cannot address atypical laminopathies. Here, we develop Farnesylation Amino acid Targeted Editing (FATE), a mutation-agnostic base-editing platform that selectively disrupts the LMNA farnesylation motif without affecting other farnesylated proteins. Using isogenic human pluripotent stem cell derived neuromuscular organoids (NMOs), we reveal muscle-specific progerin accumulation that sequesters 53BP1 and abolishes DNA damage foci formation. FATE eliminates perinuclear progerin, restores 53BP1 mobility, reconstitutes DNA repair foci, and normalizes heterochromatin architecture. Importantly, transient delivery of FATE mRNA conjugated with lipid nanoparticles to HGPS NMOs achieves efficient base editing and phenotypic rescue. These findings establish FATE as a mutation-independent therapeutic strategy targeting a fundamental pathogenic mechanism in HGPS and provide a proof-of-concept for RNA-based in situ genome editing in progeroid disease.

pathology↗

bioRxiv2025

Unique structural and ligand binding properties of the Staphylococcus aureus serine hydrolase FphE

Staphylococcus aureus is a human pathogen capable of forming biofilms that complicate treatment and facilitate chronic infections. A family of S. aureus serine hydrolases are important regulators of virulence and biofilm formation. Among these, FphE is highly specific to S. aureus and therefor a viable target for both imaging and therapy. Here, we present bioinformatic and structural evidence that FphE may be involved in aromatic compound metabolism. In addition, twelve distinct crystal forms reveal that FphE exists as a highly unusual but stable and flexible, cross-subunit homodimer, unique to the large alpha/beta hydrolase superfamily. Substrate engagement favors retention of the dimeric state, which is a more catalytically active form of the enzyme and small angle X-ray scattering (SAXS) confirms the dimeric architecture occurs in solution. High-resolution co-crystal structures of FphE covalently bound to two chemically distinct ligands reveal different modes of active site engagement, supporting an atypical structural plasticity of the dimer interface. Together, these findings establish FphE as a structurally unique alpha/beta hydrolase and provide a foundation for structure-guided development of S. aureus specific inhibitors and imaging probes.

microbiology↗

bioRxiv2025

A Physically-Realistic Simulator and Cosine-Based Decoder for MERFISH Spatial Transcriptomics

Imaging-based spatial transcriptomics technologies have opened new avenues for studying cellular organization and gene expression within intact tissues. However, the accuracy of downstream analyses depends critically on the decoding step that reconstructs barcodes from fluorescence patterns and maps them to gene identities. Despite a growing number of decoding methods, systematic benchmarking has been limited. Here, we introduce Serval, a modular framework for developing and benchmarking decoding methods across diverse spatial transcriptomics platforms. Serval separates key decoding stages into independently configurable modules, enabling flexible integration of alternative algorithms. Using this framework, we develop the Cosine decoder, a novel method that improves transcript recovery by optimizing cosine similarity to known barcodes. We evaluate Cosine and baseline methods on synthetic and real MERFISH datasets, showing that Cosine achieves higher transcript recovery and superior correlation with expression references compared to existing methods. Furthermore, we demonstrate that the Serval framework generalizes beyond MERFISH. By extending to the DART-FISH platform, we show that Cosine improves transcript recovery, clustering stability and supports more direct annotation of complex biological structures such as the human primary motor cortex. These results establish that modular decoding frameworks facilitate robust, platformagnostic benchmarking, ultimately supporting more accurate spatial transcriptomics analysis across diverse biological samples.

bioinformatics↗

bioRxiv2025

Mapping disease critical spatially variable gene programs by integrating spatial transcriptomics with human genetics

Spatial gene expression patterns underlie tissue organization, development, and disease, yet current methods for detecting spatially variable genes (SVGs) lack the flexibility to capture multi-scale structure, ensure robustness across platforms, and integrate with genetic data to assess disease relevance. We present Spacelink, a unified framework that models spatial variability of a gene at both whole-tissue and cell-type resolution using an adaptive mixture of data-driven spatial kernels and summarizes it using an Effective Spatial Variability (ESV) metric. Spacelink achieved up to 3.2x higher detection power over eight existing global SVG and cell-type SVG methods while showing consistently superior FDR control across 34 different simulation settings and also showed superior cross-platform concordance in matched tissue Visium and CosMx datasets. Applied to 3 healthy CosMx human tissues (brain cortex, lymph node, liver), Spacelink revealed that SVGs are highly informative for 113 complex traits and diseases (average GWAS sample size = 340,406). Spacelink showed up to 2.2x higher disease informativeness over competing methods in tissue-relevant complex diseases and traits, conditional on putative non-spatial expression-level confounders. Applied to a mouse organogenesis Stereo-seq atlas (8 developmental stages), Spacelink identified 145 genes with stage-associated ESV within brain independent of mean expression, that are enriched in pathways like Wnt signaling and Rap1 signaling characterizing early and late development, respectively. Integration with in vivo Perturb-seq targeting 35 de novo ASD risk genes revealed that perturbations in excitatory neurons and astrocytes preferentially altered spatially structured downstream gene programs (1.7-2.2x higher average ESV across stages than other cell types), many of which were enriched for polygenic autism GWAS loci. In neurodegeneration, analysis of 32 Visium dorsolateral prefrontal cortex samples spanning Alzheimers disease (AD) pathology stages identified 334 genes with decreasing ESV along amyloid burden (enriched for glycolysis) and 216 genes with decreasing ESV along tau tangle accumulation (enriched for apoptotic pathways). Several AD risk genes (PKM, CLU, GPI) showed conserved reductions in spatial variability with AD pathology in both human and 5xFAD mouse, with PKM linking to a colocalized splicing QTL and amyloid burden QTL variant. These results highlight the utility of Spacelink in decoding spatially variable gene programs that connect tissue architecture to disease genetics.

genomics↗

bioRxiv2025

Fusobacterium nucleatum produces previously unappreciated AHR-activating metabolites and promotes CRC cell proliferation via the AHR-TERT axis

Fusobacterium nucleatum (Fn) is prevalently enriched in colorectal cancer (CRC), promoting CRC progression. However, Fn-derived small molecules and their host target pathways in CRC remain largely underexplored. Here, we identify that Fn produces previously unrecognized three indole-containing metabolites, fusotrisindoline (FTIN), streptindole (STIN), and trisindoline (TIN). Using AHR reporter, CYP1A1 mRNA induction, CYP1A enzyme assay, photoaffinity AHR-ligand competition, and in silico docking, we establish that these metabolites are bona fide agonists of the aryl hydrocarbon receptor (AHR), with FTIN being the most potent AHR ligand (EC50 [~]41 nM in HepG2 cells). Genetic and pharmacological perturbations demonstrate that FTIN-activated AHR promotes proliferation, migration, and invasion in EGFR blockade-responsive CRC cell lines, such as SNU-C4, but not in EGFR blockade-resistant cell lines, such as HCT116. We show that FTIN-activated AHR signaling is critical for Fn-mediated promotion of CRC cell growth. A {Delta}tnaA mutant defective in indole production lacked FTIN/STIN/TIN production and was unable to activate AHR or enhance CRC cell growth in vitro and SNU-C4 xenograft growth in vivo. RNA-seq and follow-up functional validation identified TERT as a key downstream effector of FTIN-activated AHR signaling. FTIN upregulated TERT transcription and telomerase activity, and TERT knockdown abrogated FTIN-promoted CRC cell proliferation. FTIN production was conserved across Fn subspecies, as well as other Fusobacterium species, and detected in additional CRC- associated genera. In 30 patient pairs of CRC-matched normal colon tissues, FTIN was quantifiable in most CRC tissues and significantly enriched relative to matched normal colon tissues, whereas STIN/TIN were undetectable. Our findings reveal a metabolite-centered FTIN-AHR-TERT axis by which intratumoral bacteria, such as Fn, accelerate CRC growth and uncover FTIN as a potential biomarker in CRC.

microbiology↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Purine nucleotides are competitive inhibitors of apo-GOT1

The malate-aspartate shuttle (MAS) plays a key role in cellular metabolism by transferring electrons from cytosolic NADH into the mitochondrial matrix, thereby supporting oxidative phosphorylation, in addition to the citric acid cycle and amino acid metabolism. Here, we sought to identify allosteric regulatory metabolites of the MAS enzymes cytosolic glutamic-oxaloacetic transaminase 1 (GOT1) and mitochondrial GOT2. Using the Atavistik Metabolite Proprietary Screening platform, we identified several structurally similar metabolite hits-- most notably deoxyadenosine monophosphate (dAMP) and deoxyguanosine monophosphate (dGMP)--as candidate interactors with GOT1. Follow-up thermal shift assays revealed that dAMP and dGMP destabilize GOT1 in the absence of its cofactor, pyridoxal 5-phosphate (PLP), but have no destabilizing effect when PLP is present. Crystallographic analysis confirmed that dAMP and dGMP bind in the PLP pocket of GOT1, suggesting competitive binding. Together, these results indicate that nucleotide metabolites can interact with GOT1, offering potential insights into MAS regulation and therapeutic intervention strategies.

molecular biology↗