Biology subjects

Lin, S.

Publications and source records attributed to Lin, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Novel COX-2 Targeted Nanobodies for Molecular Endoscopic Imaging of Colorectal Adenomas

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality in men and women. Timely detection and diagnosis are key to management of CRC, which is under-diagnosed because colorectal aberrant crypt foci, hyperplastic polyps, and microadenomas are often missed with conventional colonoscopy. The enzyme cyclooxygenase-2 (COX-2) is overexpressed in early stages of colorectal carcinogenesis and plays an important regulatory role in the process, suggesting that it could be a valuable target for enhanced imaging of nascent disease. Thus, we have generated an alpaca-derived library of 73 COX-2-specific nanobody clones. Here, we describe one such nanobody, F9-K45Q-K77Q-ROX, in which two native lysine residues have been mutated followed by conjugation to a fluorophore at the N-terminus with retention of COX-2-selective binding. The site of fluorophore conjugation and COX-2 binding affinity of F9-K45Q-K77Q-ROX were determined by proteomic and microscale thermophoretic analyses, respectively. In cell culture studies using 1483 human head and neck squamous cell carcinoma cells, F9-K45Q-K77Q-ROX accumulated inside cells and bound to intracellular COX-2, as visualized by fluorescence microscopy. In vivo pharmacokinetic, and toxicological analyses revealed that F9-K45Q-K77Q-ROX is detectable in circulation with a plasma half-life of 17.9 min and there is no short-term toxicity associated with single injections of 10 mg/kg, 20 mg/kg, or 40 mg/kg doses at 24 h post-administration. Noninvasive in vivo fluorescence endoscopic imaging validated tumor-specific accumulation of F9-K45Q-K77Q-ROX in azoxymethane/dextran sodium sulfate-induced colorectal adenomas in mice. This work demonstrates the first COX-2-targeted nanobodies including a fluorescent derivative that offers significant promise for targeted endoscopic imaging of COX-2-expressing neoplasms. Significance StatementCurrent colorectal cancer screening procedures, such as white-light colonoscopy, chromoendoscopy, and narrow-band imaging aim to detect solid colon tumors and precursor lesions. However, these methods tend to detect only raised solid tumors and mature cancers, whereas precursor lesions, such as aberrant crypt foci, hyperplastic polyps, and small adenomas are frequently missed. To address the need for better visualization of early lesions, we developed a library of alpaca-derived nanobodies targeted to cyclooxygenase-2 (COX-2), an enzyme that is overexpressed in colorectal adenomas. COX-2-targeted nanobodies bearing a fluorescent tag accumulate and are retained in colonic adenomas, facilitating their endoscopic visualization. This novel COX-2-targeted nanobody platform may also be valuable for early detection of other neoplastic diseases in which COX-2 overexpression occurs. (Word counts 119, limit 120)

bioengineering↗

bioRxiv2026

Molecular and Morphological Evidence Reveals Cryptonema producta in Shui Hau, Hong Kong, Previously Misidentified as Anomalocardia flexuosa

For over four decades, the bivalve Anomalocardia flexuosa has been recorded in Hong Kong coastal waters. However, the known native distribution of this heavily exploited commercial species is restricted to the Atlantic coast of South America, raising questions about the biogeographical validity of the Hong Kong populations. By employing an integrative taxonomic approach combining morphological re-evaluations and molecular phylogenetic analysis of the COI gene, we confirm that the species in Shui Hau, Hong Kong, China, has been historically misidentified. The population belongs to Cryptonema producta (syn. Anomalocardia producta).

zoology↗

bioRxiv2026

H2O: A Foundation Model Bridging Histopathology to Spatial Multi-Omics Profiling

Spatial omics technologies have revolutionized the molecular profiling of tissues but remain constrained by high costs and limited scalability. While hematoxylin and eosin (H&E) staining is ubiquitous, it lacks molecular specificity. Here, we present H2O (Histopathology to Omics), a generalist AI framework that bridges the modality gap between histopathology and spatial multi-omics, enabling the direct inference of spatial transcriptomics (ST) and proteomics (SP) landscapes from routine H&E images. H2O integrates Vision Transformers (ViT) with Large Language Models (LLM) via contrastive learning to align histological morphology with semantic molecular knowledge. This cross-modal approach allows the model to incorporate spatial expression profiles into histological pattern recognition, effectively decoding the molecular heterogeneity underlying tissue morphology. Trained on a pan-tissue dataset of 1.3 million paired H&E-spatial patches across 25 organs and cancer types, H2O predicts spatial omics expression from histology with high concordance to sequenced measurements and consistently outperforms state-of-the-art models across three cancer benchmarks. Notably, H2O recovers the MIF-CD74/CD44 signaling axis directly from H&E images, highlighting its capacity to infer biologically meaningful cell-cell communication without molecular profiling. Applying on three additional public cohorts covering fetal and paediatric thymus tissues, human metastatic lymph node, and breast cancer, encompassing human development, 3D spatial frameworks, and integrative multi-omics, H2O yields biologically concordant insights, demonstrating superior accuracy, robustness, and generalizability across real-world applications in diverse scenarios. H2O converts routine histopathology into a portal for spatially resolved multi-omics profiling by computationally generating transcriptomic and proteomic landscapes, thereby enhancing tissue phenotyping and enabling scalable, integrative tissue-atlas construction.

bioinformatics↗

bioRxiv2026

BioClaw: Human-Bot Research Collaboration Ecosystems in Group Chats

Day-to-day research discussions in group chats often generate hypotheses, analysis requests, and interpretation decisions, yet executing those analyses still requires researchers to leave the conversation and rely on fragmented local tools, databases, visualization software, and literature search engines. In this work, we present BioClaw, a human-bot research collaboration ecosystem that converts natural-language requests in group conversations into tool-grounded analyses executed within isolated Docker containers. Deployed across 8 messaging platforms, BioClaw turns each group chat into a persistent execution workspace. Its design combines multi-channel orchestration, per-group state and workspace management, and isolated containerized execution for reliable shared use over long-lived conversations. To support practical research workflows, BioClaw combines containerized execution with preinstalled 31 biomedical tools and 95+ skills. The application of BioClaw spans various biomedical domains (e.g., genomics, clinics, structural biology) and data modalities (e.g., sequencing data, EHR data, protein structure data). These results establish the viability of embedding executable, tool-rich agent workflows within shared digital workspaces, positioning group chats as a transformative paradigm for collaborative scientific discovery and innovation.

bioinformatics↗

bioRxiv2026

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

cancer biology↗

bioRxiv2026

VesSynth: Tubes Are All You Need for Robust Cross-Scale Cross-Modal 3D Vessel Segmentation

The cerebral vasculature is central to brain function, with alterations linked to numerous cerebrovascular and neurological disorders. Yet, no single imaging modality can capture the entire cerebral vascular network in humans. Instead, an array of techniques are sensitized to different spatial scales, while trading off resolution for coverage. Magnetic Resonance Imaging (MRI) typically resolves only large pial vessels, while high-resolution microscopy allows micrometer-scale vessels to be mapped over limited spatial extents. These techniques must therefore be combined to obtain a complete mapping of the cerebral angioarchitecture, which underscores the need for automatic, cross-modal vessel segmentation. Here, we introduce VesSynth, a flexible vessel segmentation framework that achieves state-of-the-art accuracy across multiple modalities and spatial resolutions (MR, optical and X-ray imaging), despite being trained entirely on synthetic data. By enabling consistent vascular mapping across scales, this framework paves the way to comprehensive investigation of cerebrovascular organization and its role in health and disease.

bioengineering↗

bioRxiv2026

RNASTOP: A Deep Learning Framework for mRNA Chemical Stability Prediction and Optimization

Messenger RNA (mRNA) vaccines offer promising therapeutics for combating various diseases, yet their inherent chemical instability hampers their long-term efficacy. Although several methods have been developed to predict mRNA degradation, they exhibit limited accuracy and lack the capability for rational sequence optimization. Here, we propose RNASTOP, a novel framework integrating deep learning with heuristic search to simultaneously predict and optimize mRNA chemical stability. RNASTOP achieves a 13% accuracy improvement over the top-performing model on the Stanford OpenVaccine competition dataset and demonstrates robust generalization in predicting full-length mRNA degradation. Applied to mRNA codon optimization, RNASTOP reduces the minimum free energy of the Varicella-Zoster Virus vaccine sequence by 75.73% while maintaining high translation efficiency. Overall, RNASTOP serves as a powerful tool for predicting and optimizing mRNA chemical stability, poised to expedite the development of mRNA therapeutics. The source code of RNASTOP can be accessed at https://github.com/xlab-BioAI/RNASTOP.

bioinformatics↗

bioRxiv2026

Phosphorylation-driven Targeted Protein Degradation of Oncogenic β-catenin

Therapeutic strategies to inhibit the Wnt signalling pathway for cancer treatment have, so far, failed to advance to the clinic. Induced-proximity drugs are revolutionizing our ability to tackle targets previously considered undruggable. Here, we used an unbiased genome-scale approach to identify induced-proximity protein candidates that inhibit the central Wnt signalling effector {beta}-catenin in colorectal cancer cells. While the identification of several E3 ubiquitin ligases validated our approach, we uncovered that inducing proximity to members of the Casein kinase I (CSNK1) family leads to {beta}-catenin degradation and inhibits the growth of colorectal cancer cells harbouring Wnt pathway mutations. We show that {beta}-catenin degradation induced by CSNK1 proximity is kinase activity- and proteasome-dependent. We propose that the formation of a neo-degron, through kinase recruitment, can expand induced-proximity drug targeting strategies.

molecular biology↗

bioRxiv2026

Antibody recycling via FcRn drives atherosclerotic plaque vulnerability

Atherosclerotic plaques accumulate low-density lipoprotein (LDL) together with antibodies targeting LDL and its apolipoprotein B (apoB) component. Given the association between IgG and plaque vulnerability, we hypothesized that apoB-specific immune complexes actively promote plaque destabilization. Using immunohistochemistry in carotid endarterectomy specimens, we quantified antibody deposition across morphologically defined plaque regions, and measured apoB reactivity and immune complex levels in matched plaque and plasma samples. IgG deposition was strongly associated with thin fibrous caps, reduced collagen content, and higher overall plaque vulnerability. Symptomatic patients exhibited increased apoB-specific IgG and reduced apoB-IgG immune complexes within plaques, indicating enhanced IgG recycling and heightened inflammatory activity. The neonatal Fc receptor (FcRn) was predominantly expressed by CD163+ macrophages, and mediated antibody recycling, LDL uptake, and production of tumor necrosis factor (TNF) and matrix metalloproteinase-9 (MMP-9) in vitro. Plaque FcRn expression increased with age and correlated with mediators of vulnerability, including collagen-degrading enzymes and pro-inflammatory cytokines. Ex vivo treatment of human plaques with a clinically used FcRn-blocking monoclonal antibody reduced IgG recycling and suppressed TNF and MMP-9 production. These findings identify FcRn-dependent antibody recycling as a contributor to inflammatory plaque vulnerability and highlight FcRn as a potential therapeutic target in atherosclerosis.

immunology↗

bioRxiv2026

Intrinsic dataset features drive mutational effect prediction by protein language models

Protein language models (pLMs) are commonly used for predicting protein fitness landscapes, but their wide range of performance across datasets remains poorly understood. We evaluated supervised transfer learning on 41 viral and 33 cellular deep-mutational-scanning (DMS) datasets using embeddings from multiple pLMs. We observed consistently lower predictive performance on viral datasets compared to cellular datasets, independent of model architecture or transfer learning strategy. Surprisingly, a simple baseline model that predicted site mean fitness matched or outperformed supervised models on many datasets, highlighting the dominant role of site effects. Analysis of site variability using two metrics, relative variability of site means (RVSM) and fraction of highly variable sites (FHVS), revealed that patterns of fitness variation within and among sites constrain model performance and largely explain the observed differences between viral and cellular datasets. Moreover, splitting training and test data by site, rather than pooling, revealed that supervised models often rely on site effects rather than capturing broader mutational patterns. These findings highlight limitations of current pLMs for mutational effect prediction and suggest that dataset composition, rather than model architecture or training, is the primary driver of predictive success. Significance StatementMutational effects prediction with protein language models tends to vary widely in prediction accuracy, depending on the dataset considered. While poor performance is commonly equated with poor model quality, we show here that intrinsic dataset features, such as the variability of fitness values within and among sites, are critical predictors of model performance. Moreover, we show that many existing benchmarks overestimate model performance, by allowing training data to leak into the test set. In fact, in many cases, protein language models barely outperform a naive predictor relying entirely on mean fitness values at individual sites. In aggregate, our study reveals that protein language models are not as reliable for predicting mutational effects as is commonly thought.

bioinformatics↗

bioRxiv2026

Focal Transcranial Magnetic Stimulation of the Rat Anterior Cingulate Cortex Inhibits Incubation of Opioid Craving after Voluntary Abstinence

Relapse remains a major challenge in opioid addiction treatment, underscoring the need for innovative therapies. Progress in neuromodulation therapies has been limited by insufficient mechanistic understanding of stimulation engagement and disease-related changes in the brain. We used a novel, focal transcranial magnetic stimulation (TMS) system to deliver high-density theta burst stimulation (hdTBS) combined with resting-state fMRI to test whether anterior cingulate cortex (ACC) stimulation reduces relapse-like behavior and alters functional circuitry in a rodent model of opiate dependence. The coil focality and stimulation parameters approximate human TMS protocols, and the targeted region represents a functional homolog of the human ACC. We trained rats to self-administer oxycodone intravenously for 14 days. We then introduced an electric barrier for 13 days, which caused cessation of drug self-administration. We assessed relapse to oxycodone seeking immediately after training (early abstinence) and after electric-barrier exposure (late abstinence). We administered daily hdTBS or sham stimulation for 7 days before the late-abstinence test. Sham-treated rats showed a time-dependent increase in oxycodone seeking during abstinence (incubation of oxycodone craving) and reduced ACC functional connectivity. In contrast, hdTBS prevented the incubation of oxycodone craving and restored ACC connectivity with the dorsal and ventral striatum. Tracer-based axonal-projection data further showed that stimulation-induced effects aligned with regions receiving dense projections from the stimulation site, suggesting that the projection architecture is critical to the propagation of focal stimulation across distributed networks. These findings identify ACC-centered circuits as mechanistically informed targets for TMS-based interventions that aim to reduce opioid relapse during abstinence. One sentence SummaryPrefrontal TMS stimulation reduced relapse-like behavior and restored corticostriatal circuits, highlighting translational targets for addiction treatment.

neuroscience↗

bioRxiv2026

Metformin Stabilizes the Abdominal Aorta in Aneurysm by Restoring VSMC Mitochondrial Homeostasis via the AMPK-SIRT1-PGC-1α Axis

BACKGROUNDAbdominal aortic aneurysm (AAA) is a life-threatening condition with >80% mortality upon rupture and no effective pharmacotherapy available. Despite epidemiological evidence linking metformin use to reduced AAA progression, its mechanism remains elusive. Notably, peroxisome proliferator-activated receptor {gamma} coactivator 1 (PGC-1, encoded by Ppargc1a) is downregulated in human AAA, yet its functional role in metformins protection is unknown. METHODSWe employed porcine pancreatic elastase (PPE)-induced murine AAA, VSMC-specific Ppargc1a knockout (Ppargc1aVSMC-KO), primary VSMC senescence models, and pharmacological inhibition (Compound C for AMPK; Ex-527 for SIRT1) to define the AMPK-SIRT1-PGC-1 axis. RESULTSMetformin significantly inhibited AAA expansion, suppressed VSMC senescence (p53/p21{downarrow}, SA-{beta}-gal{downarrow}), and preserved contractile phenotype (SMTN{uparrow}, IL-6/TNF-{downarrow}). Crucially, all benefits were abrogated in Ppargc1aVSMC-KO mice, which exhibited accelerated aneurysm growth, mitochondrial fragmentation, ATP depletion, and ROS accumulation. Mechanistically, metformin activated AMPK/SIRT1 to upregulate PGC-1; AMPK or SIRT1 inhibition blocked this cascade and reversed protection. CONCLUSIONMetformin restrains AAA by restoring VSMC mitochondrial homeostasis via the AMPK/SIRT1[->]PGC-1 axis, positioning PGC-1 as a non-redundant, cell-autonomous guardian against vascular degeneration. These findings provide a mechanistic foundation for repurposing metformin and developing PGC-1-targeted therapies in AAA.

cell biology↗

bioRxiv2026

HDAC1/2-mediated repression of Wnt receptor expression orients asymmetric division polarity in C. elegans.

Asymmetric cell division generates distinct daughter cells essential for tissue development, yet the mechanisms orienting division polarity within tissues remain incompletely understood. Here, we uncover a role for chromatin-mediated transcriptional repression in controlling polarity orientation during asymmetric division of C. elegans epidermal stem cells, known as the seam cells. We show that tissue- specific loss of the class I histone deacetylase hda-1, homologous to mammalian HDAC1/2, causes reversals in division polarity and reduces molecular asymmetry between daughter cells. Using Targeted DamID to profile HDA-1 genomic occupancy, we identify the Wnt receptors lin-17/Frizzled and cam-1/Ror as key targets. Single- molecule FISH reveals that these receptors display striking expression gradients along the body axis, with cam-1 enriched anteriorly and lin-17 posteriorly. In hda-1 mutants, both receptors are upregulated so that differences between seam cells are flattened. Overexpression of either receptor alone is sufficient to reproduce the polarity reversals observed in hda-1 mutants, and their co-overexpression produces additive defects. The polarity phenotype is independent of the canonical NuRD and SIN3 complexes, suggesting that HDA-1 acts through an alternative mechanism to regulate Wnt receptor expression. Our findings establish a direct link between histone deacetylase activity and Wnt receptor expression and support a model in which graded expression of Wnt receptors provides positional cues that orient asymmetric division polarity in response to Wnt signals.

developmental biology↗

bioRxiv2026

Laminin-α2 is required for the maintenance of the myotendinous junction in vivo

The myotendinous junction (MTJ) is a critical interface between muscle fibers and tendons, essential for force transmission between muscle and bone. Laminin-2, a key extracellular matrix (ECM) component, is strongly enriched at this interface. Mutations in the LAMA2 gene cause LAMA2-related muscular dystrophy (LAMA2 MD), an early-onset severe congenital muscular dystrophy. Here, we examined the MTJ in dyW/dyWmice, a mouse model for LAMA2 MD. We find a strong disruption of MTJ morphology, including altered muscle fiber tips, collagen XXII mislocalization, and reduced muscle tendon interface. As MTJ loading is altered in dyW/dyW mice and MTJ maintenance requires loading and unloading, we also examined MTJ structures upon denervation-induced unloading. While muscle fiber tip morphology resembled that of dyW/dyW mice, collagen XXII distribution was not affected and the muscle-tendon interface was preserved. Finally, proteomic profiling via laser capture microdissection and mass spectrometry revealed significant regional and global shifts in MTJ protein composition in dyW/dyW and denervated mice. Across both models, we identified integrin-associated remodeling as a shared response linked to the perturbed muscle fiber tip morphology. These findings demonstrate that laminin-2 is required for MTJ stability, and that mechanical unloading contributes to the observed phenotype. Importantly, our results suggest that disruptions in MTJ structure and protein composition may contribute to the pathology observed in LAMA2 MD.

molecular biology↗

bioRxiv2026

Time perception follows Weber's law in Drosophila

The ability to perceive time is essential for adaptive behavior, enabling organisms to respond to change, coordinate actions, and predict future events in dynamic environments and during social interactions. However, its evolutionary origins and underlying neural mechanisms remain poorly understood. Here, we demonstrate that the fruit fly, Drosophila melanogaster, can perceive time intervals ranging from sub-second to a few seconds and use them to predict the location of potential food sources. Using a behavioral paradigm in which flies learn to associate temporal patterns of sound with food rewards, we show that their ability to discriminate between two time intervals depends on the ratio of their durations rather than their absolute difference. This proportional relationship follows Webers law, a fundamental principle of sensory discrimination. Moreover, flies can generalize learned temporal rules to novel stimuli and across sensory modalities, suggesting they form an abstract representation of time. Finally, we identify the mushroom body as a critical neural circuit for temporal learning. These findings reveal unexpected timing capabilities in Drosophila, providing new insights into the evolutionary origin of temporal cognition and establishing Drosophila as a genetically tractable model for investigating the neural basis of time perception.

neuroscience↗

bioRxiv2026

Molecular basis of BET family protein inhibition by four clinical-stage small-molecule inhibitor drugs

The bromodomain and extra-terminal (BET) family proteins are critical epigenetic readers involved in various diseases, making them attractive therapeutic targets. This study elucidates the molecular basis of inhibition by four clinical-stage BET inhibitors (ZEN-3694, INCB054329, PLX51107, and INCB057643) through detailed structural comparison and analysis. Using X-ray crystallography, we determined their complex structures with the second bromodomain of human BRD2 at 1.4-1.5 [A] resolution. All inhibitors occupy the conserved acetyl-lysine binding pocket via extensive hydrophobic interactions. This hydrophobic network is further coupled with hydrogen-bond contacts for inhibitor-binding stabilization. A common feature is the formation of at least one hydrogen bond with a conserved residue of N429. Notably, INCB057643 exhibits an enhanced polar network, forming additional hydrogen bonds with residues D377 and N429, which may contribute to its improved pharmacological profile. These structures reveal a shared competitive inhibition mechanism by occluding the acetyl-lysine binding site, providing a rational basis for their transcriptional repression and guiding future inhibitor design.

biophysics↗

bioRxiv2026

Methionine metabolism and the NOP2 methyltransferase are essential for MYC-Driven liver tumorigenesis.

Hepatocellular carcinoma (HCC) represents the third leading cause of cancer-related death worldwide and has been increasing in developed nations.1,2 The MYC oncogene or its paralogs are frequently amplified or overexpressed in subtypes of cancer associated with stem cell-like features and worse clinical outcomes,3,4 including in liver cancer.5 Unfortunately, selective inhibitors that target MYC or its transcriptional program are not yet clinically available for therapy of HCC. Here, we identified methionine metabolism as a selective vulnerability for MYC but not RAS-driven liver cancers. MYC-driven liver cancer cells are methionine dependent, with markedly diminished tumor growth when mice are fed a methionine low diet. While RAS-driven liver cancer was resistant to a low methionine diet. S-adenosylmethionine (SAM), the predominant methyl donor, partially rescues cell proliferation following methionine depletion, suggesting that methylation processes are especially critical in the context of MYC high tumor cells. Heavy isotope methionine tracing in MYC high cells identified increased levels of m5C nucleotides. We found NOP2, an rRNA m5C-methyltransferase, was regulated by both MYC overexpression and methionine abundance linking the two processes. Methionine depletion reduced methylation of multiple 28S rRNA residues as did NOP2 knockdown. Depletion of NOP2 selectively inhibited MYC liver cancer cell proliferation and in vivo tumor growth. Thus, methionine catabolism is critical for MYC-driven liver tumorigenesis and the rRNA methyltransferase NOP2 may serve as a new therapeutic target in liver cancer.

cancer biology↗

bioRxiv2026

Dual-inactivation of Regnase-1 and SOCS1 rewires exhausted CD8+ T cell fate to enhance anti-tumor functionality

The solid tumor microenvironment inhibits the functionality of tumor infiltrating T cells recognizing cognate tumor antigen, driving their differentiation towards terminal exhaustion. Interventions are sought to enhance the anti-tumor functionality of tumor-reactive T cells for clinical benefit. The functional genome regulating CD8+ T cell function against solid tumors was mapped by performing genome-wide, focused, and combination in vivo CRISPR/Cas9 screens using OT1 and PMEL TCR transgenic T cells in B16-OVA, MC38-gp100 and EG7-OVA syngeneic tumor models. The ability of the top single hits and combinations, which include Regnase-1 and SOCS1, to enhance CD8+ T cell anti-tumor function was evaluated in the OT1/B16-OVA model with large and established tumors, the disseminated PMEL/B16F10 tumor model, and in a novel murine TIL syngeneic model. The impact of Regnase-1 and SOCS1 single and dual-inactivation on the differentiation of exhausted CD8+ T cell subsets and on long-term persistent memory following tumor clearance was evaluated in OT1 CD8+ T cells in the B16-OVA model. The impact of single and dual-inactivation of Regnase-1 and SOCS1 on the anti-tumor function of experimental human T cell therapeutics was characterized in CRISPR/Cas9-engineered human TIL derived in vitro and in mesothelin-targeting CAR-Ts in vivo. NF-{kappa}B and cytokine signaling were identified as the top pathways regulating CD8+ T cell anti-tumor function, with Regnase-1 and Suppressor of Cytokine Signaling 1 (SOCS1) the top single and combination edits regulating the accumulation of tumor-specific TCR transgenic CD8+ T cells in syngeneic tumor models. Dual-inactivation of Regnase-1 and SOCS1 cooperated through non-redundant mechanisms to strongly expand intermediate (Texint) and effector (Texeff) exhausted CD8+ T cells within lymphoid tissues and tumor, with CD8+ T cells rewired to display an enhanced effector state and suppressed expression of TOX. Dual-edited persistent T effector memory cells (Tem) were formed following tumor clearance. Lastly, Regnase-1 and SOCS1 inactivation enhanced human Tumor Infiltrating Lymphocyte (TIL) and chimeric antigen receptor T cells (CAR-T) therapy functionality. Collectively, this study systematically mapped pathways regulating CD8+ T cell anti-tumor functionality, with Regnase-1 and SOCS1 dual-inactivation found to maximize anti-tumor function through non-redundant mechanisms.

immunology↗