Biology subjects

Lee, J.

Publications and source records attributed to Lee, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Translation fidelity mechanisms and their changes in aging

Protein errors (amino acid misincorporations) are associated to protein misfolding and misfunction, and lower levels correlate with longer lifespan. Despite their prevalence, proteome-wide tracking of misincorporations in eukaryotes is challenging, with most insights being recent and coming from the mining of extensive proteomics data sets. These experimental challenges have precluded the direct in vivo probing and full understanding of the bases of fidelity in higher eukaryotes, and their influence in complex processes such as aging. Here we measured proteome-wide misincorporation frequencies in two experimentally tractable eukaryotic systems, yeast and mouse, using mass spectrometry. We find translation fidelity is organism and organ specific. The measured error frequencies correlate with codon:anticodon pairing thermodynamics and tRNA pool composition, which can have synergistic or opposing effects on fidelity depending on organism or tissue type. Most identified protein errors carry a negative fitness burden. Aging experiments in our two systems reveal that, with age, error frequencies increase in post-mitotic cells, but not so in mitotic ones. These changes correlate with remodeling of the tRNA pool, which we identify as a crucial regulator of translation fidelity during lifespan.

molecular biology↗

bioRxiv2026

Clonal hematopoiesis-associated DNMT3A mutations derepress bivalent Polycomb target genes and enhance macrophage migration

Somatic mutations in the de novo DNA methyltransferase DNMT3A are frequent in clonal hematopoiesis, but how they alter the function of differentiated myeloid cells remains unclear. Here, we used isogenic human embryonic stem cell-derived macrophage models to define the consequences of DNMT3A dysfunction during myeloid differentiation. DNMT3A-mutant macrophages selectively upregulated bivalent Polycomb target genes, accompanied by DNA hypomethylation, reduced H3K27me3 and increased promoter accessibility. Despite broad epigenetic changes across bivalent promoters, transcriptional derepression occurred at a subset of loci characterized by lower baseline DNA methylation and higher H3K27me3, identifying pre-existing chromatin state as a determinant of transcriptional response. This Polycomb-associated program was conserved in murine macrophages and enriched for genes involved in cell migration and wound repair. DNMT3A-mutant macrophages exhibited enhanced migration and preferential early recruitment to injured tissue. These findings link clonal hematopoiesis-associated epigenetic alterations to selective transcriptional reprogramming and altered function of differentiated myeloid cells.

cell biology↗

bioRxiv2026

Metabolic-epigenetic coupling between leucine catabolism and glycolysis drives CDK4/6 inhibitor resistance

Resistance to CDK4/6 inhibitors limits the durability of therapy for ER+ breast cancer. Despite the identification of mechanisms that regulate resistance, the metabolic adaptations that enable therapeutic escape remain poorly understood. Here, we identify a metabolic-epigenetic circuit that drives resistance by coordinately rewiring amino acid and glucose metabolism. CDK4/6 inhibitor-resistant ER+ tumor cells upregulate the leucine transporter SLC7A5, enhancing leucine uptake. SLC7A5 overexpression is sufficient to confer palbociclib resistance across ER+ cell lines, patient-derived organoids and xenografts. Stable isotope tracing in cell lines and in xenograft tumors revealed that leucine is catabolized through BCAT2 and HMGCL to increase acetyl-CoA levels, and elevated acetyl-CoA promotes H3K27 acetylation at the GLUT1 promoter, upregulating GLUT1 expression and glycolytic activity. Disrupting leucine transport, catabolism, or availability suppresses GLUT1 expression and restores therapeutic sensitivity in resistant models. In patients receiving palbociclib-based therapy, high SLC7A5 expression and coordinated SLC7A5-GLUT1 co-expression are associated with shorter progression-free survival. Together, these findings define a metabolic-epigenetic mechanism linking branched-chain amino acid catabolism to glycolysis and identify a biomarker-associated metabolic vulnerability in advanced ER+ breast cancer.

cancer biology↗

bioRxiv2026

Pkn1 kinase is a critical regulator of cell division in Chlamydia trachomatis

Chlamydia trachomatis is an obligate intracellular, developmentally regulated pathogen with a reduced genome as a consequence of adapting to the host cell environment. Despite possessing only eight transcription factors, its developmental cycle is tightly regulated. Hence, we hypothesize that factors like post-transcriptional and post-translational modifications play significant roles in controlling developmental progression. Chlamydia encodes serine/threonine kinases, including an ortholog of Pkn1. In this study, we characterized the function of Pkn1 in chlamydial biology and revealed its role as a cell division regulator. We designed an anhydrotetracycline (aTc)-inducible construct encoding Pkn1 tagged with six histidines at the C-terminus (Pkn1_6xH). Wild-type Pkn1 localized primarily at the division septum whereas a kinase-null Pkn1 isoform localized in the cytosol. To further explore the association of Pkn1 with the divisome, we designed a plasmid encoding an aTc-inducible CRISPRi system targeting pkn1(pkn1KD). Intriguingly, decreased pkn1 transcript levels resulted in enlarged chlamydial cells with irregular coccoid shapes akin to penicillin-treated cells, indicating a block in cell division when pkn1 transcripts are reduced. These effects were complemented by expressing an additional wild-type copy, but not a kinase-null copy, of pkn1 during knockdown. Using a bacterial two hybrid system, we identified an interaction between Pkn1 and MreB, a cytoskeletal protein forming a ring at the septum in Chlamydia. We showed the co-localization of these proteins in Chlamydia and that inhibition of MreB function disrupts Pkn1 localization. Overall, our data indicate an essential function for Pkn1 activity in regulating cell division in Chlamydia.

microbiology↗

bioRxiv2026

In vivo Quantitative Tomography of 225Ac Daughters in a Prostate Cancer Mouse Model with a Compton Camera

Targeted alpha therapy with 225Ac is a promising modality for cancer treatment, as shown in recent preclinical and clinical studies. Preclinical imaging of 225Ac is essential to fully understand the biokinetics of developmental 225Ac radiopharmaceuticals. Although single photon emission computed tomography (SPECT) is typically used to achieve this in vivo, conventional preclinical scanners struggle to provide high contrast and accurate quantification for 225Ac imaging due to the very low injected activities (below 1 kBq/g), the unfavorable gamma-ray branching ratios (<26%), and its complex decay chain with several gamma-ray emissions. In this work, we employ a compact CZT-based Compton camera to achieve quantitative tomography of 225Ac daughters in live mice at 18.5 kBq (0.5 Ci) injected activities. Three mice bearing 22Rv1 prostate cancer subcutaneous xenografts were scanned in a single bed position for 30 minutes following intravenous administration of 18.5 kBq of the Anti-CD46 225Ac-Macropa-PEG4-YS5 conjugate. We successfully visualized the in vivo biodistributions of the 225Ac daughters 221Fr and 213Bi, distinguishing between the tumor xenograft and the central organs. Quantification of the tumor uptake from the images revealed an activity as low as 1.1 kBq. In vivo activity quantification computed from the images was compared to ex vivo biodistribution measurements using a gamma counter after harvesting the tissue, showing strong agreement.

bioengineering↗

bioRxiv2026

MAPK signaling links BRD2 chromatin occupancy to PI3K/AKT inhibitor sensitivity

Bromodomain and extra-terminal (BET) proteins, BRD2, BRD3, BRD4, and BRDT, couple histone acetylation to transcription by recruiting elongation and transcription factor complexes to chromatin. Although BET proteins are promising therapeutic targets, the functions of individual family members remain incompletely understood. We identify BRD2 as a co-targetable vulnerability with PI3K/AKT inhibition in breast cancer. Pan-BET inhibition and BRD2 knockout synergized with PI3K pathway inhibitors in breast cancer cell lines, patient-derived organoids, and in vivo models. BRD2 knockout impaired proliferation of triple-negative breast cancer cells and upregulated signaling and stress-response pathways, including the DNA damage response. Mechanistically, BRD2 is phosphorylated at Ser37 by the mitogen- and stress-activated kinases MSK and RSK, and Ser37 phosphorylation is required for chromatin binding and reader function. Finally, mechanistic digital twin modeling identified BETi-PI3Ki regimens that maintained efficacy while reducing drug exposure. Together, these findings identify BRD2 as a phosphorylation-dependent, co-targetable vulnerability in PI3K-inhibited breast cancer.

cancer biology↗

bioRxiv2026

Harmine Plus Exendin-4 Enhances Remission of Recent-Onset Type 1 Diabetes Following Anti-CD3 Therapy

Type 1 diabetes (T1D) results from autoimmune destruction of pancreatic {beta}-cells. While anti-CD3 therapy can delay disease progression and preserve residual {beta}-cell function, disease reversal will likely require both immune modulation and {beta}-cell regeneration. We found that the combination of harmine and exendin-4 (H+E) reduced inflammation-induced human {beta}-cell apoptosis, suppressed cytokine signaling and immunogenicity pathways, and improved {beta}-cell function. Although H+E alone did not reverse diabetes in NOD mice, low-dose anti-CD3 followed by H+E normalized blood glucose, increased insulin levels, improved glucose tolerance, expanded {beta}-cell mass, and enhanced diabetes remission. These effects were associated with reduced pro-inflammatory T-cell responses, increased regulatory T cells, and greater expression of exhaustion-related T-cell markers, without broad lymphocyte depletion. Similar immunomodulatory effects were observed in activated human PBMCs. Transcriptomic analyses identified the lncRNA SNHG6 as a key mediator of H+E action; SNHG6 protected {beta}-cells from cytokine-induced stress, apoptosis, and immunogenicity. Together, these findings demonstrate that H+E promotes {beta}-cell recovery and resilience while reducing {beta}-cell immunogenicity, enabling remission of recent-onset T1D when combined with anti-CD3 therapy. SNHG6 emerges as a novel regulator of {beta}-cell protection during inflammation.

cell biology↗

bioRxiv2026

Cascaded Nano-ring Dialyzer for Continuous Regenerative Peritoneal Dialysis

End-stage kidney disease (ESKD) requires lifelong kidney replacement therapy, yet conventional hemodialysis and peritoneal dialysis remain limited by intermittent treatment, restricted mobility, and repeated dialysate exchange. Here, we developed a continuous regenerative peritoneal dialysis platform based on a nano-ring-assisted nanoelectrokinetic dialyzer for portable artificial kidney applications. We first identified key geometric and electrokinetic parameters governing the removal performance of nano-ring meshes, including mesh dimension, nano-ring coating thickness, the number of cascaded nano-rings, and the relative orientation between fluid flow and the applied electric field. We then developed a single nano-ring dialyzer operating at 1.33 mL/min and scaled the treatment capacity to approximately 10 mL min/min through parallel integration of multiple modules. In a canine model, the closed-loop system achieved approximately 10 % reduction in circulating uremic toxin levels during continuous treatment. We further improved the biocompatibility of the regenerated dialysate by integrating plate-type electrodes, activated carbon, bicarbonate buffering, and UV-C treatment. In an unanesthetized canine model, the improved system sustained continuous toxin removal for 4 h while major hepatic and inflammatory markers remained within recoverable ranges. These results demonstrate that cascaded nano-ring enables continuous dialysate regeneration with scalable throughput, reduced dependence on fresh dialysate, and in vivo control of uremic toxins, providing a technological foundation for portable or wearable regenerative peritoneal dialysis systems.

bioengineering↗

bioRxiv2026

PREpiBind: Protein Representation-integrated Epitope--MHC Class II Binding Prediction

Accurate prediction of peptide-MHC class II (pMHC-II) binding remains challenging because of extensive MHC polymorphism and context-dependent peptide recognition, and it is unclear which protein representation best captures these determinants when the downstream model is held fixed. Here, we present PREpiBind, a pMHC-II prediction method based on a dual-stream, joint-attention framework that integrates MHC and epitope representations. We integrated ten protein representations spanning substitution-matrix, structure-prediction-derived, and protein language model (PLM) families and evaluated them under a common downstream architecture and identical splits across Qualitative, mass spectrometry (MS), and thresholded IC50 datasets. Overall, PREpiBind with PLM representations yielded higher performance than the evaluated reference methods in the Qualitative and MS datasets, whereas NetMHCIIpan-4.3 was higher on the thresholded IC50 datasets using its binding-affinity head. In pooled evaluations, PLM representations yielded the highest ROC-AUC values among the tested representations. ESM3 Large led the Qualitative dataset with an AUC value of 0.927 +/- 0.002, and PLMs also led on the MS and thresholded IC50 datasets. This advantage remained, but narrowed in allele-wise and leave-one-molecule-out evaluations, where structure-prediction-derived Chai-1 was competitive with the leading PLM representations. Under cross-species H2-out transfer, PLMs led when all H2 rows were pooled, whereas Chai-1 led when the eight H2 molecules were weighted equally. The small H2 panel did not support a stable ordering among these leading representations. The results indicate that protein representation choice should depend on the intended prediction scenario rather than on a single global ranking. PREpiBind is an openly available pMHC-II prediction framework with modular and flexible protein representations.

bioinformatics↗

bioRxiv2026

Mitochondrial perturbation adapts the proteome from early to advanced immune responses

Dysregulated immunity, a hallmark of many human diseases, co-occurs with mitochondrial dysfunction and is commonly associated with misprimed primary immune signaling. While transcriptionally well-characterized, the impact of mitochondria on the host response at the protein level is less clear. Using in vitro and in vivo approaches including proteotranscriptomics, our data suggest that OXPHOS promotes expression of early, cell autonomous immune proteins whereas mitochondrial perturbation favors mediators of cell extrinsic responses like inflammation. This response is independent of immune cues, time-dependent, conserved, and occurs across tissues in mouse models of mitochondrial dysfunction. These data illustrate unappreciated roles for mitochondrial state in adapting host responses at the protein level, which have implications for complex disease etiology and the ancestral origins for eukaryotic immune sensing.

immunology↗

bioRxiv2026

A Wireless Wearable Platform for Intravenous Drug Self-Administration in Freely Behaving Rats

Studying how drugs act on neuronal circuits requires delivering them with temporal precision while behavior proceeds undisturbed, a combination that tethered infusion systems cannot provide. We developed WEARIT (Wireless Equipment for Autonomous Rat Infusion Tasks), a wearable, tetherless infusion platform that gives freely moving rats intravenous access under either remote or closed-loop operant control. The device houses a reservoir, miniaturized pump, rechargeable battery and Bluetooth circuitry in a 3D-printed enclosure worn on the back. By measuring spontaneous locomotion, amphetamine-induced hyperlocomotion and food-reinforced operant responding, we show that WEARIT leaves these behaviors unchanged. Remotely triggered fentanyl infusions yielded reliable delivery with physiological responses confirmed by pulse oximetry, and self-administration acquisition and dose-response functions were comparable to conventional tethered systems. WEARIT removes a longstanding constraint on intravenous pharmacology, opening self-administration paradigms to naturalistic and enriched environments and to concurrent imaging or optogenetic manipulation of the circuits engaged by drug reinforcement.

neuroscience↗

bioRxiv2026

Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence

Alternative splicing greatly expands the diversity of gene products encoded by the human genome. Single-cell transcriptomic atlases have characterized human cell types through gene-level expression, but short-read sequencing has limited the ability to resolve full-length isoforms and their functional consequences. Here, we present a cross-tissue single-cell long-read isoform atlas spanning 26 human tissues. We identify hundreds of thousands of novel isoforms along with their cell-type-specific usage, and discover that over one-third of expressed isoforms are absent from existing reference databases. We further demonstrate that isoform usage is a structured, measurable axis of cellular identity that is distinct from gene expression. Applying this framework to cellular senescence, we resolve p16INK4a and p14ARF transcripts from the CDKN2A locus in individual cells and uncover cell-type-dependent isoform remodeling associated with the p16INK4a senescence program. This isoform-resolved single-cell atlas offers a versatile framework to dissect the cellular logic of isoform regulation in senescence and beyond.

genomics↗

bioRxiv2026

De novo Rubisco design with protein language models

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) fixes the majority of carbon dioxide globally but is challenged with low specificity for CO2 versus O2 and low catalytic efficiencies. Traditional engineering efforts have remained difficult because folding, assembly, specificity, and catalysis are tightly coupled, hampering efforts to explore sequence space. Therefore, we leveraged recent advances in protein large language models (PLMs) to generate sequences beyond those observed in nature, using both ProGen-2 that was fine-tuned on a limited dataset of non-Form I Rubiscos and an ESM-2 discriminator. With this approach, we generated 5.6 million novel Rubisco-like sequences and identified 21 highly diverse candidates predicted to be active that occupy regions of Rubisco phylogenetic space not previously observed in nature. Six designs were soluble in Escherichia coli, and five were shown to produce quantifiable 3PGA. One design produced an apparent CO2/O2 specificity estimate beyond the range of the natural representative Rubiscos assayed. We also solved the crystal structure of one de novo design that reproduced the predicted dimer and active-site geometry with sub-angstrom C agreement. Sequence-only generation followed by independent structural filtering therefore recovered soluble, active Rubiscos from regions of sequence space that are not represented in genomic databases. Together, these results establish a scalable strategy for accessing previously unexplored Rubisco sequence space, providing a broadly accessible path toward generating de novo Rubiscos that may have activity and specificity parameters needed to address longstanding limitations in biological carbon fixation.

biochemistry↗

bioRxiv2026

Oral Actinobacteria sense and defend against parasitic epibionts

Bacteria contend with a wide range of antagonistic interactions from neighboring microbes. One widespread but poorly understood threat is posed by Patescibacteria, which proliferate by colonizing host bacteria surfaces and extracting cellular resources. Despite the ubiquity of Patescibacteria in the environment, how hosts defend against these epibionts remains unknown. Here we show that Actinomycetota fend off Patescibacteria using the Esx secretion system. We identify a secreted effector protein that mediates this defensive behavior and demonstrate that Esx induction is part of a multifaceted, epibiont-specific response that includes multiple predicted cell surface modifications. Finally, we show that this response occurs at the transcriptional level and is mediated by a previously undescribed threat sensing pathway whose activation leads to threonine phosphorylation of an FHA domain-containing output protein. Together with bioinformatic evidence linking this threat sensing pathway to Esx across Actinomycetales, our experimental findings establish a functional role for the elusive and broadly distributed Esx pathway in defense against epibionts. Furthermore, they help resolve the ecological relationship between Patescibacteria and their hosts as one of antagonism, not mutualism.

microbiology↗

bioRxiv2026

Unlocking Sensitive Data with SPHERE in the Age of AI

Sensitive human data underpin discoveries across medicine, biology and the social sciences, yet privacy regulation often prevents sharing them with collaborators or artificial intelligence (AI) systems. We introduce SPHERE, a model-free method that makes sensitive datasets directly usable by AI and shareable for open science as a synthetic twin, while the original records never leave the local environment. Across 33 datasets spanning five scientific domains, SPHERE protects individual privacy against adversarial re-identification attacks while preserving the data's statistical structure: means, variances and correlations are reproduced exactly, effect size and P value in linear statistical analysis is numerically identical, nonlinear machine-learning utility is retained, and each twin is generated in seconds on a laptop. Frontier AI agents running on the twin reach the same scientific conclusions as on the original records. Analyses of the twin reproduce genome- and proteome-wide results at UK Biobank scale and recover the findings of landmark studies across three independent cohorts and consortia. The approach also extends to deep-learning embeddings across language, vision and time-series, with minimal utility loss. We make the Stanford Alzheimer's Disease Research Center cohort openly available for the first time, as a SPHERE twin spanning nine modalities that any registered researcher can analyze without an approval process. We release SPHERE with certification of each twin's privacy and fidelity, and an AI agent that autonomously executes research tasks on sensitive data without ever accessing it. Sensitive datasets that are currently closed to research could thus become routine inputs to open science and AI to enable key discoveries.

bioinformatics↗

bioRxiv2026

AGC kinase homology requires and enables co-targeting for CNS regeneration

Axon regrowth in the central nervous system (CNS) is constrained by robust regulatory networks. Here we show that optimal neurite outgrowth in rodent and human CNS neurons is achieved by co-inhibition of kinases across four closely related clades within the protein kinase A, G, and C (AGC) family. The kinases derive from ancestral regulators of cytoskeletal dynamics, resource allocation, and polarized cell growth. Their shared domain architecture makes polypharmacology (co-engagement by a single small molecule) feasible. Phenotype-guided optimization of a tool compound with established efficacy in mouse spinal cord injury models yielded TMP-316, a drug candidate engaging these AGC kinases with selectivity against the broader kinome. A single intrathecal dose of TMP-316 produced sustained motor recovery in a rat cervical hemicontusion model. These findings reveal conditions under which polypharmacology is simultaneously required and enabled by shared evolutionary origins, illuminating a therapeutic discovery principle for pathologies governed by functionally overlapping targets.

neuroscience↗

bioRxiv2026

Opposing Experiences Shape Parvalbumin Interneuron Plasticity through Distinct Molecular Programs

Life experiences profoundly influence brain function, yet how opposing experiences are encoded remains unclear. Here, we show that opposing experiences, chronic stress (CS) and voluntary running (VR), induce largely distinct molecular programs rather than a simple bidirectional modulation of a shared molecular program in parvalbumin interneurons (PVIs). PVI-specific translational profiling across frontal cortex and dorsal and ventral hippocampus reveals that experience-dependent gene expression is organized into brain region-specific architectures, which are further structured into distinct co-expression modules. We uncovered CS-induced upregulation of histone acetyltransferase KAT6A and H3K23 acetylation specifically in PVIs of the frontal cortex accompanied by altered genome-wide redistribution of acetylated H3K23, including genes implicated in neuropsychiatric disorders. Targeted elevation of KAT6A in PVIs recapitulates CS-induced morphological and behavioral alterations. Together, our findings reveal that opposing experiences engage distinct and region-specific molecular programs in PVIs and identify a stress-responsive epigenetic pathway underlying inhibitory circuit plasticity.

neuroscience↗

bioRxiv2026

Descending somatosensory and motor cortical inputs shape auditory processing in the midbrain

Integrating multisensory and behavioral information is essential for sensory perception. In the auditory system, multisensory and behavioral influences emerge early in subcortical structures. Descending projections from non-auditory cortical areas are well positioned to convey such signals, yet how they shape subcortical auditory processing remains poorly understood. Here, we investigated corticocollicular projections from the primary somatosensory (S1) and motor (M1) cortices to the inferior colliculus (IC), a principal integration center in the auditory midbrain. We found that trunk- and limb-related regions of S1 and M1 form prominent monosynaptic projections to the IC, and that optogenetic activation of these projections robustly drives IC activity. Notably, a substantial population of cortical-responsive neurons did not respond to sound. In sound-responsive neurons, concurrent cortical stimulation enhanced sound-evoked responses, whereas cortical activation preceding sound onset suppressed them. Furthermore, both cortical-responsive IC neurons and deep-layer S1 and M1 neurons exhibited locomotion-related modulation and anticipatory activity prior to movement onset, suggesting that these descending pathways convey movement-related signals to the IC. Together, our findings identify a descending sensorimotor circuit that integrates body- and movement-related information with auditory processing in the auditory midbrain.

neuroscience↗