Biology subjects

Wu, Q.

Publications and source records attributed to Wu, Q..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Next-Generation saRNA Platforms: Systematic Screening and Engineering Enhances Superior Protein Expression and Organ-Specific Targeting for RNA Therapeutics

Self-amplifying RNA (saRNA), derived from alphaviruses, encodes nonstructural proteins (NSP1-4) that form a replicase complex, enabling prolonged and amplified protein expression at lower doses than conventional mRNA. However, its high immunogenicity and limited replication efficiency require optimization for improved protein expression. Here, we systematically optimized a widely used Venezuelan Equine Encephalitis Virus (VEEV)-based saRNA by refining its capping structure, nucleotide modifications, polyA tail length, and regulatory elements, achieving over 10-fold enhancement in protein expression compared to the wild-type. Additionally, we screened 28 alphavirus-derived saRNA constructs in vitro, selecting the top 3 candidates Everglades virus (EVEV), Mosso das Pedras virus (MDPV), and Rio Negro virus (RNV) for in vivo evaluation using SM102 lipid nanoparticle (LNP) formulations and luciferase reporters. These optimized saRNAs demonstrated sustained expression and distinct extrahepatic tissue-specific biodistribution, notably high spleen targeting compared to conventional mRNA. Such organ-specific expression profiles present novel strategies for targeted RNA therapeutics, and further integration with advanced delivery technologies could enhance the precision, efficacy, and therapeutic potential of mRNA-based treatments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/644708v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1eed9bdorg.highwire.dtl.DTLVardef@192815org.highwire.dtl.DTLVardef@196a8e9org.highwire.dtl.DTLVardef@2b6e53_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC figureC_FLOATNO C_FIG

molecular biology↗

bioRxiv2025

High-resolution NMR spectroscopy of proteins in intact mitochondria

Understanding protein structure and function within mitochondria is essential for unraveling the molecular mechanisms underlying cellular energy production, stress response, and disease. Here, we present a novel approach for NMR observation of proteins within intact mitochondria by delivering proteins directly into isolated mitochondria via electroporation. Using this method, we investigate the interaction of -synuclein (-syn) with the mitochondria membrane and examine how post-translational modifications regulate this interaction. Additionally, we assessed the stability of GB1 and the dimerization of its variant within mitochondria, achieving quantitative insights into mitochondrial environmental impact on protein function. This approach offers a valuable framework for exploring mitochondrial related biomolecular events at atomic-resolution within intact mitochondria, paving the way for a more comprehensive understanding of the molecular events governing mitochondrial health and dysfunction.

biochemistry↗

bioRxiv2025

Progressively reduced cerebral oxygen metabolism and elevated plasma NfL levels in the zQ175DN mouse model of Huntington disease

Huntingtons disease (HD) is a progressive neurodegenerative disorder caused by a CAG-repeat expansion in exon-1 of the huntingtin gene. Currently, no disease-modifying therapies are available, with a significant challenge in evaluating therapeutic efficacy before clinical symptoms emerge. This highlights the need for early biomarkers and intervention strategies. Therefore, it is essential to develop and characterize accurate mouse models and identify early biomarkers for preclinical therapeutic development. In this study, we characterized the pathological progression of the heterozygous zQ175 neo-deleted knock in (zQ175DN) mouse model across four age groups: 3, 6, 10, and 16 months to identify human translatable outcome measures. T2-relaxation-under-spin-tagging (TRUST) MRI was used to assess global CMRO2, while T2-weighted MRI was used to analyze brain volumes. Significant brain volume loss was detected as early as 6 months of age, worsening progressively with age in the zQ175 DN mice, resembling HD brain volumetric changes. A decline in CMRO2 was observed in 6-month-old zQ175 DN mice, with significant and progressive reductions in 10- and 16-months old HD mice. Additionally, PHP1-positive mutant huntingtin (mHTT) aggregates were present in the striatum of zQ175 DN mice at all four age groups, with intranuclear localization prior to 6 months, transitioning to both intranuclear and neuropil aggregates in older zQ175 DN mice, suggesting that the localization of mHTT aggregates may reflect the severity of HD pathogenesis. Interestingly, plasma neurofilament light chain (NfL) protein concentrations were significantly elevated at 6 months of age and older zQ175DN mice. These findings provide valuable insights for selecting outcome measures in preclinical evaluations of HD therapies using the zQ175 DN mouse model.

neuroscience↗

bioRxiv2025

Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome

Mass spectrometry (MS)-based proteomics is widely used for quantitative protein profiling and has become a powerful tool for studying protein interactions. However, most current research focuses on single-species proteomics to study protein interactions. Protein interactions within more complex microbiomes, composed of 100s of bacterial species, remain largely unexplored. The human gut microbiome, closely linked to human health and disease, has become a key area of study using metaproteomics. Yet, due to the complexity of the microbiome, the interactions between gut microbes and their host remain largely unknown. In this study, we analyzed peptide abundance correlations within a metaproteomics dataset derived from in vitro cultured human gut microbiomes subjected to various drug treatments. Our analysis revealed that peptides from the same protein or taxon exhibited correlated abundance changes. By using t-SNE for visualization, we generated a peptide correlation map in which peptides from the same taxon formed distinct clusters. Furthermore, peptide abundance correlations enabled genome-level taxonomic assignments for a greater number of peptides. In single-species subsets of the dataset, peptide correlation networks constructed using taxon-based normalized peptide abundance (TNPA) linked peptides from functionally related proteins. These networks also provided insights into the potential functions of previously uncharacterized proteins. Altogether, our study demonstrates that analyzing peptide abundance correlations enhances both taxonomic and functional analyses in human gut metaproteomics research.

microbiology↗

bioRxiv2025

Mutations and structural variants arising during double-strand break repair

Double-strand break (DSB) repair is highly mutagenic compared to normal replication. In budding yeast, repair of an HO endonuclease-induced DSB at MAT can be repaired by using a transcriptionally silent HMR::Kl-URA3 donor. During repair, -1 deletions in homonucleotide runs are strongly favored over +1 insertions, whereas during replication, spontaneous +1 and -1 events are equal. Microhomology-bounded, repair-associated intragenic deletions (IDs) are recovered 12 times more frequently than tandem duplications (TDs). IDs have a mean length of 56 bp, while TDs average 22 bp. These data suggest a picture of the structure of the repair replication fork: IDs and TDs occur within the open structure of a migrating D-loop, where the 3 end of a partly copied new DNA strand can dissociate and anneal with a single-stranded region of microhomology that lies either [~]80 bp ahead or [~]40 bp behind the 3 end. Another major class of repair-associated mutations ([~]10%) are interchromosomal template switches (ICTS), even though the K. lactis URA3 sequence in HMR is only 72% identical (homeologous) with S. cerevisiae ura3-52. ICTS events begin and end at regions of short ([~]7 bp) microhomology; however, ICTS events are constrained to the middle of the copied sequence. Whereas microhomology usage in intragenic deletions is not influenced by adjacent homeology, we show that extensive pairing of adjacent homeology plays a critical role in ICTS. Thus, although by convention, structural variants are characterized by the precise base pairs at their junction, microhomology-mediated template switching actually requires alignment of extensive adjacent homeology. Significance statementDNA synthesis during repair of a double-strand chromosome break by homologous recombination exhibits a high rate of mutation compared to normal replication. Using a genetic system in budding yeast, we isolated thousands of mutations occurring during repair. We conclude that the repair replication fork appears to have the two DNA strands open [~]80 bp ahead of the DNA polymerase, but the strands re-anneal rapidly behind the polymerase. Additionally, we analyzed interchromosomal template switching, in which the partially copied DNA strand dissociates and pairs with a new template at a short stretch of perfectly matching bases (microhomology), and resumes copying. We show that these apparent microhomology-mediated template switching events in fact require the pairing of [~]200 bp of imperfectly matching bases (homeology).

genetics↗

bioRxiv2025

Monocyte control of organismal energy homeostasis

Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing deviations of those parameters and responding accordingly to support tissue function and organismal homeostasis. Here we demonstrate that dysregulation of iron metabolism in parenchyma cells, imposed by the deletion of ferritin H chain, is sensed by monocyte-derived macrophages. In response, macrophages derived from circulating monocytes support tissue function, energy metabolism and thermoregulation, as demonstrated in bone marrow chimeric and parabiotic mice. This salutary effect is contingent on a transcriptional program, controlled in macrophages by the transcription factor A mitochondria. This transcriptional response acts in a non-cell autonomous manner to support the mitochondria of parenchyma cells, irrespectively of mitochondrial transfer. In conclusion, monocyte-derived macrophages cross-regulate Fe and energy metabolism to support tissue function and organismal homeostasis.

immunology↗

bioRxiv2025

Glycogen Engineering Improves the Starvation Resistance of Mesenchymal stem cells and their Therapeutic Efficacy in Pulmonary Fibrosis

Mesenchymal stem cells (MSCs) are widely used in regenerative medicine, including the treatment of pulmonary fibrosis. However, implanted MSCs disappear within days, constraining therapeutic efficacy, which is largely attributed to nutrient deprivation. In this study, we established glycogen metabolism engineering strategies in mammalian cells. By expressing a functionally optimized glycogen synthase (GYSmut), MSCs could accumulate large amounts of glycogen rapidly as a reserve substance. Glycogen engineering significantly improved the survival of MSCs during starvation both in vitro and in vivo, enhancing cell viability post-implantation and their therapeutic efficacy in pulmonary fibrosis. Glycogen-engineered MSCs may serve as chassis cells for further applications. Our research highlights the importance of glucose metabolism regulation in cell-based therapy and demonstrates the great potential for the metabolic engineering of MSCs and other therapeutic cells.

bioengineering↗

bioRxiv2025

AMPK- and cGAS-Mediated Dual Sensing of Glucose and dsDNA Synergizes to Enhance Antitumor Immunity

Intratumoral glucose availability is linked considerably to tumor growth, immune evasion, and metastasis. However, the precise molecular mechanisms by which glucose levels govern cellular and immune responses against tumors remain incompletely understood. Here, we explored the context of tumors of intersections between AMP-activated protein kinase (AMPK) and cGAS-STING signaling, a key pathway initiating antitumor immunity. We unexpectedly found that AMPK activation robustly enhances cGAS-STING signaling within cancer and immune cells, which potently impacts melanoma and colorectal cell senescence, organoid apoptosis, and the infiltration of CD4+ and CD8+ T lymphocytes. Using classic or newly developed AMPK agonist Aldometanib, TBK1S511E/S511E knock-in (KI) mice, glucose metabolic modulator, as well as AMPK1/2 dKO melanoma, we demonstrated that dual sensing of intratumoral glucose and dsDNA integrated by the AMPK-TBK1 cascade is essential for initiating antitumor immunity and suppressing cancer progressions. Notably, novel AMPK agonists or intervening in glucose glycolysis by Lonidamine synergized effectively with STING agonists, substantially inhibiting melanoma growth. Therefore, these findings unravel a concise mechanism integrating glucose metabolism and innate DNA sensing into cancer cell fate and propose an effective therapeutic strategy to enhance antitumor immunity. HIGHLIGHTSO_LIDual and synergistic sensing of glucose and dsDNA facilitates antitumor immunity in melanoma and colorectal cancer; C_LIO_LIAMPK substitutes intratumoral cGAS-STING-IRF3 signaling through TBK1 phosphorylation at S511; C_LIO_LIGlucose deficiency induces cancer cell senescence, apoptosis, and T lymphocyte infiltration via the AMPK-TBK1 cascade; C_LIO_LINewly developed AMPK agonists synergize with STING agonists to retrieve striking tumor suppression. C_LI

cancer biology↗

bioRxiv2025

TransBrain: A computational framework for translating brain-wide phenotypes between humans and mice

Despite remarkable advances in whole-brain imaging technologies, the lack of quantitative approaches to bridge rodent preclinical and human studies remains a critical challenge. Here we present TransBrain, a computational framework enabling bidirectional translation of brain-wide phenotypes between humans and mice. TransBrain improves human-mouse homology mapping accuracy through: (1) a novel detached region-specific deep neural network trained on integrated multi-modal human transcriptomics to improve cortical correspondence (89.5% improvement over the original transcriptome), which revealed two evolutionarily conserved gradients explaining >50% of cortical organizational variance, and (2) random walk-based graph representation learning to construct a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity. We demonstrated TransBrains utility through three cross-species applications: quantitative assessment of resting-state brain organizational features, inferring human cognitive functions from mouse optogenetic circuits, and translating molecular insights from mouse models to individual-level mechanisms in autism. TransBrain enables quantitative cross-species comparison and mechanistic investigation of both normal and pathological brain functions.

neuroscience↗

bioRxiv2025

Iterative acylation on mature lasso peptides by widespread acetyltransferases for lipolasso production

The biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) leverages iterative catalysis to enhance structural and biological diversity. Traditionally, iterative enzymes install multiple post-translational modifications (PTMs) on linear peptides, rather than mature RiPPs with intricate three-dimensional structures, which would require complex changes in substrate binding poses. Here, we present a prolific class of GCN5-related N-acetyltransferases (GNATs) that iteratively and consecutively acylate two Lys residues within the loop and ring motifs of lasso peptides, diverging from the typical iterative modification of linear peptides--an unprecedented function for PTM enzymes. Utilizing high-resolution cryo-electron microscopy and enzymatic reconstitution, we mapped the lasso peptide binding pocket of IatT and pinpointed key residues involved in demarcating the two distinct acetylation steps. Structure-based engineering of IatTs acetyl group recognition site expanded the cavity to accommodate longer-chain acyl groups, leading to the creation of lipolasso peptides, a novel class of ribosomal lipopeptide. This engineering strategy can be applied to any RiPP BGC encoding GNAT, facilitating the efficient diversification of rare ribosomal lipopeptides. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/630886v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1d88af9org.highwire.dtl.DTLVardef@18c1298org.highwire.dtl.DTLVardef@118b9f3org.highwire.dtl.DTLVardef@580a50_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Characterizing Tyrosine Ring Flips in Proteins by 19F NMR

Aromatic ring-flip dynamics are hallmarks of concerted protein "breathing" motions that are essential for biological function. Ring flips occur on a broad range of timescales (ns-s) and have been primarily studied by NMR spectroscopy, typically requiring expensive isotope labeling of aromatic side chains, thereby limiting such studies to a few proteins. Here, we report two novel di-fluorotyrosine probes, 3,5-F2Y and 2,6-F2Y, that can be incorporated into proteins cost-effectively for characterizing and modulating tyrosine ring-flip dynamics. We show that 19F rotating-frame (R1{rho}) relaxation dispersion is powerful for quantifying ring flips on the {micro}s-ms timescale. Importantly, the tyrosine ring-flip rates (kflip) for 3,5-F2Y in GB1 and HPr are comparable to those measured by 1H and 13C NMR studies, validating 3,5-F2Y as a largely non-perturbing, native-like ring-flip probe. In contrast, 2,6-F2Y acts as an effective "brake" on ring flips, enabling direct visualization and quantitative characterization of previously undetected tyrosine ring flips in ubiquitin via 19F lineshape analysis. Furthermore, we use 2,6-F2Y to assess the environmental effects on ring-flip dynamics in crowding reagents and in living X. laevis oocytes. Collectively, our study opens a new avenue for measuring and modulating ring-flip dynamics in vitro and in living cells. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/630691v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@dcf8e1org.highwire.dtl.DTLVardef@1578887org.highwire.dtl.DTLVardef@1c481d0org.highwire.dtl.DTLVardef@268ae0_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

A molecularly defined brain circuit module for regulating the panic-like defensive state

Panic is an episode of strong defensive state, characterized by intense fear and severe physical symptoms such as elevated cardiorespiratory activities. How the brain generates panic state remains poorly understood. Here, we developed a robot-based experimental paradigm to evoke panic-like defensive state in mice. When stimulated by the robot, the mice exhibited jumping escapes and elevated cardiorespiratory activities. With this paradigm, we identified Cbln2-expressing (Cbln2+) neurons in the posterior hypothalamic nucleus (PHN) as a key neuronal population essential for the induction of panic-like defensive state. Activation of Cbln2+ PHN neurons induced behavioral and physical symptoms of panic-like defensive state. These neurons were strongly activated by noxious mechanical stimuli and encode jumping escape vigor. They were synaptically innervated by anxiety-associated brain areas and provoked panic-like defensive state via their projection to the periaqueductal gray. Together, our results reveal a molecularly defined circuit module that regulates the panic-like defensive state in mice.

neuroscience↗

bioRxiv2024

Hepatic Inactivation of Carnitine Palmitoyltransferase 1a Lowers Apolipoprotein B Containing Lipoproteins in Mice

Genome- and epigenome-wide association studies have associated variants and methylation status of carnitine palmitoyltransferase 1a (CPT1a) to reductions in very low-density lipoprotein (VLDL) cholesterol and triglyceride levels. We report significant associations between the presence of CPT1a SNPs and reductions in plasma cholesterol, as well as positive associations between hepatic Cpt1a expression and plasma cholesterol levels across inbred mouse strains. Mechanistic studies show that both wild type and human apolipoprotein B100 (apoB)-transgenic mice with liver-specific deletion of Cpt1a (LKO) display lower circulating apoB levels consistent with reduced LDL-cholesterol (LDL-C) and LDL particle number. Despite a reduction in steady-state plasma lipids, VLDL-triglyceride (VLDL-TG) and cholesterol (VLDL-C) secretion rates are increased, suggesting accelerated clearance of apoB-containing lipoproteins (apoB-LPs) in LKO mice. Mechanistic approaches show greater peroxisome proliferator activated receptor (PPAR) signaling which favors enhanced lipoprotein lipase-mediated metabolism of apoB-LPs, including increases in ApoCII and ApoAIV and reductions in ApoCIII & Angptl3. These studies provide mechanistic insight linking genetic variants and methylation status of CPT1a to reductions in circulating apoB-LPs in humans. HIGHLIGHTSO_LILoss-of-function SNPs in CPT1a associate with reductions in plasma cholesterol in humans C_LIO_LIHepatic Cpt1a expression positively associates with plasma cholesterol levels across inbred strains of mice C_LIO_LILiver-specific Cpt1a deficiency lowers circulating apoB, plasma cholesterol, LDL-C, and LDL particle number C_LIO_LICpt1a ablation activates PPAR and favors clearance of apoB-containing lipoproteins C_LI

physiology↗

bioRxiv2024

Global analysis of protein and small-molecule substrates of ubiquitin-like proteins (UBLs)

AbstractUbiquitin-like proteins (UBLs) constitute a family of evolutionarily conserved proteins that share similarities with ubiquitin in 3D structures and modification mechanisms. For most UBLs including Small-Ubiquitin-like Modifiers (SUMO), their modification sites on substrate proteins cannot be identified using the mass spectrometry-based method that has been successful for identifying ubiquitination sites, unless a UBL protein is mutated accordingly. To identify UBL modification sites without having to mutate UBL, we have developed a dedicated search engine pLink-UBL on the basis of pLink, a software tool for identification of cross-linked peptide pairs. pLink-UBL exhibited superior precision, sensitivity, and speed than "make-do" search engines such as MaxQuant, pFind, and pLink. For example, compared to MaxQuant, pLink-UBL increased the number of identified SUMOylation sites by 50 [~] 300% from the same datasets. Additionally, we present a method for identifying small-molecule modifications of UBLs. This method involves antibody enrichment of a UBL C-terminal peptide following enrichment of a UBL protein, followed by LC-MS/MS analysis and a pFind 3 blind search to identify unexpected modifications. Using this method, we have discovered non-protein substrates of SUMO, of which spermidine is the major one for fission yeast SUMO Pmt3. Spermidine can be conjugated to the C-terminal carboxylate group of Pmt3 through its N1 or also likely, N8 amino group in the presence of SUMO E1, E2, and ATP. Pmt3-spermidine conjugation does not require E3 and can be reversed by SUMO isopeptidase Ulp1. SUMO-spermidine conjugation is present in mice and humans. Also, spermidine can be conjugated to ubiquitin in vitro by E1 and E2 in the presence of ATP. The above observations suggest that spermidine may be a common small molecule substrate of SUMO and possibly ubiquitin across eukaryotic species. HighlightsO_LIA specialized software pLink-UBL enables precise identification of UBL modification sites on protein substrates. C_LIO_LIpFind 3 blind search enables identification of unexpected small-molecule substrates of a UBL protein. C_LIO_LISpermidine is a small molecule substrate of fission yeast SUMO Pmt3 as well as mammalian SUMO proteins. C_LIO_LIThe C-terminal carboxyl group of Pmt3 can be attached to the N1 or likely also the N8 amino group of spermidine in the presence of E1, E2, and ATP, and can be detached by SUMO isopeptidase. C_LI

biochemistry↗

bioRxiv2024

Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing

Adenosine-to-Inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes. Despite its significance, the regulatory mechanisms controlling A-to-I editing remain largely unknown. In this study, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-based RNA EDITing regulator Screening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cell CRISPR-based RNA EDITing sequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations on dozens of selected genes. Through screening 1,350 RNA-binding proteins, we identified a series of known and novel A-to-I editing regulators. Detailed mechanistic investigation revealed DDX39B as a global repressor of A-to-I editing, which functions by preventing double-stranded RNA accumulation through its helicase and ATPase activities. We demonstrate that targeting DDX39B significantly enhances the efficiency of RNA editing-based tools like CellREADR and LEAPER, and represents a promising strategy for anti-HDV therapy by modulating viral genome editing. These technological advances not only expand our understanding of RNA editing regulation but also provide powerful tools for exploring tissue-specific and context-dependent RNA modification mechanisms, with broad implications for therapeutic development.

molecular biology↗

bioRxiv2024

Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection

The gut microbiomes pivotal role in health and disease is well-established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the dysbiosis and aberrant cross-talks between the microbiome and host in SARS-CoV-2 infection. Altogether this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.

microbiology↗

bioRxiv2024

scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity by providing gene expression data at single-cell resolution, uncovering insights into rare cell populations, cell-cell interactions, and gene regulation. Foundation models pretrained on large-scale scRNA-seq datasets have shown great promise in analyzing such data, but existing approaches are often limited to modeling a small subset of highly expressed genes and lack the integration of external genespecific knowledge. To address these limitations, we present sc-Long, a billion-parameter foundation model pretrained on 48 million cells. sc-Long performs self-attention across the entire set of 28,000 genes in the human genome. This enables the model to capture long-range dependencies between all genes, including lowly expressed ones, which often play critical roles in cellular processes but are typically excluded by existing foundation models. Additionally, sc-Long integrates gene knowledge from the Gene Ontology using a graph convolutional network, enriching its contextual understanding of gene functions and relationships. In extensive evaluations, sc-Long surpasses both stateof-the-art scRNA-seq foundation models and task-specific models across diverse tasks, including predicting transcriptional responses to genetic and chemical perturbations, forecasting cancer drug responses, and inferring gene regulatory networks.

bioinformatics↗

bioRxiv2024

In vivo engineered quadrivalent CAR-macrophages break tumor barrier,remodel TME and overcome tumor heterogeneity through antigen spreading

CAR-macrophages have shown promising prospect in treating solid tumors. Ex vivo engineered CAR-macrophages face the challenge of low transfection efficiency, long preparation cycle, and limited cell number. Here, we designed two novel CAR molecules, GPC3-CAR-Super IL-2 and FAP-CAR-{bigtriangleup}TGF{beta}RII from the perspective of targeting tumor cells and improving tumor microenvironment, and generated quadrivalent CAR-macrophages in vivo for treating solid tumors by the LNP-mRNA system. We found that in vivo engineered quadrivalent CAR-macrophages can strongly activate tumor immunity and achieve complete tumor regression without significant side effects. Mechanically, in vivo engineered quadrivalent CAR-macrophages broke down physical barriers around the tumor constructed by CAFs and significantly promoted infiltration and expansion of CD8+ T cells. Moreover, the transiently formed CAR-macrophages in vivo are sufficient to form long-lasting T cell memory which can effectively prevent tumor recurrence. Most importantly, in vivo engineered CAR-macrophages also stimulated T cell memory against antigen-negative tumor cells through antigen spreading, which might effectively prevent the immune escape of heterogeneous tumor cells. Overall, we developed a platform of in vivo CAR-macrophages with dual roles as a tumor-killing effector cell and a recurrence-preventing vaccine.

bioengineering↗