Biology subjects

Huang, W.

Publications and source records attributed to Huang, W..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

CryoSeek identification of glycofibrils with diverse compositions and structural assemblies

Last year, we reported CryoSeek, a research strategy that employs cryo-electron microscopy (cryo-EM) to discover novel bio-entities from any accessible source, supplemented with AI-facilitated data processing and bioinformatic analyses. Here we report CryoSeek characterization of five additional glycofibrils isolated from the Tsinghua Lotus Pond (TLP), named TLP-IPT, TLP-12, TLP-3, TLP-2, and TLP-0, with overall resolutions ranging from 3.0-3.5 [A]. These five glycofibrils, all covered with dense glycoshells, have decreasing ratios of the central protein components, with TLP-0 with no protein at all. IPT (immunoglobulin-like, plexins, transcription factors) refers to the tandem domain that constitutes the central filament of this type of glycofibrils. In TLP-12, the central cylindrical stem is made of a trimer of dodecapeptide repeats that weave to {beta}-sheet ribbons. The central stem of TLP-3 is also a trimer, but of linear tripeptide repeats. TLP-2, similar to our previously reported TLP-4, only has a linear chain of dipeptide repeats, and glycosylation occurs to a phosphoserine in each repeat. Glycan-mediated interactions are essential for the assembly of all five glycofibrils. Our previous and present studies demonstrate the diversity in the high-order structure and folding of glycans.

biophysics↗

bioRxiv2025

Vitamin B12 alleviates Verheij syndrome-like defects via phospholipid remodeling in a C. elegans PUF60 spliceosomopathy model

Verheij syndrome (VRJS) is a rare genetic disorder caused by mutations in the poly(U)-binding splicing factor 60 (PUF60), a core component of the spliceosomal complex. VRJS triggers multiple congenital anomalies, but the underlying pathomechanisms remain poorly understood. Mutation of the Caenorhabditis elegans PUF60 ortholog, rnp-6, recapitulates several hallmarks of VRJS, including growth delay and smaller body size. Here, we demonstrate that developmental defects in rnp-6 mutants are rescued by dietary K12-type Escherichia coli strains. Through complementary genetic screens and multi-omics analyses, we identify vitamin B12 (VB12) as a potent suppressor of these defects, acting via the methionine/S-adenosylmethionine/phosphatidylcholine metabolic axis. Mechanistically, rnp-6 mutation causes aberrant splicing with methionine and phospholipid metabolism-related genes, which cumulatively impair cellular methylation potential, dysregulate phosphatidylcholine metabolism, and induce integrated stress response. We identify intron retention of the nhr-114/HNF4 transcription factor as a primary driver of growth defects, and restoring its splicing robustly suppresses these phenotypes. VB12 supplementation bypasses the aberrant splicing, restores metabolic balance, and activates mTORC1 to rescue developmental phenotypes. Finally, we show that PUF60 deficiency induces aberrant splicing of methionine and phospholipid metabolism-related genes in a human cell line, and is associated with altered plasma methionine and phospholipid levels in VRJS patients. Our findings establish C. elegans as a tractable model for VRJS and uncover SAM/SAH/phospholipid dysregulation as a key mechanism underlying the spliceosomopathy, suggesting VB12 as a potential strategy to mitigate VRJS-related anomalies.

genetics↗

bioRxiv2025

Independent evolution of holocentric centromeres in an early branching apicomplexan parasite

During its asexual cycle, Cryptosporidium parvum (C. parvum) amplifies through three rounds of nuclear division before undergoing cytokinesis to form infectious merozoites. However, chromosome organization and segregation during nuclear division remain unstudied. Here, we visualized H3-histones, including the centromeric histone H3 (CENH3), telomeres, and centrosomes during mitosis. Nuclear division was accompanied by centrosome duplication and elongated microtubules that spanned the dividing nuclei. Surprisingly, C. parvum centromeres detected by CENH3 showed diffuse staining throughout nuclear division, that overlapped with telomeres in the apical nucleus. Analysis of centromeres based on CENH3 capture and DNA sequencing revealed numerous distinct binding sites scattered across all eight chromosomes, including both coding regions and intergenic regions, that were typified by GA rich repeat sequences. The unique holocentric chromosome structure of C. parvum is unlike the single regional centromeres found in related apicomplexans, suggesting it arose independently from other known examples in plants, insects and worms.

microbiology↗

bioRxiv2025

De Novo Design, Directed Evolution and Computational Study of Heme-Binding Helical Bundle Protein Catalysts for Biocatalytic Enantioselective Ge-H Insertion

De novo designed proteins offer a malleable platform for the development of stereoselective transformations not found in biochemistry. Here, we report the de novo design and directed evolution of helical bundle protein catalysts for enantioselective germylation through Ge-H insertion, a transformation not previously achieved by enzymatic catalysis. Comparative computational analysis revealed that, relative to Si-H insertion, the Ge-H insertion reaction proceeds through an earlier and more flexible transition state, introducing distinct challenges for stereocontrol. Using a fully de novo designed truncated four-helix bundle scaffold as the starting point, directed evolution afforded a quadruple mutant that catalyzes Ge-H insertion with high efficiency, enantioselectivity, and broad substrate scope. Molecular dynamics simulations indicated that beneficial mutations introduced from directed evolution enhanced active-site preorganization and modulated local back-bone flexibility, contributing to improved transition-state complementarity with fine-tuned binding pocket size and more stable cofactor positioning regulated by hydrogen bonding interactions. These findings showcase the excellent potential for de novo proteins to achieve stereoselective transformations previously unknown to biocatalysts and underscore the importance of active-site remodeling of de novo protein scaffolds via directed evolution in achieving selective catalysis involving flexible transition states. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/679279v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@11d5beaorg.highwire.dtl.DTLVardef@7d6559org.highwire.dtl.DTLVardef@88d0fborg.highwire.dtl.DTLVardef@501945_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

An SR45-dependent exonic splicing enhancer is essential for regulating alternative splicing in Arabidopsis

Alternative splicing (AS) is a critical gene regulatory mechanism that underpins developmental plasticity and environmental adaptation in eukaryotes. Although numerous cis-elements and trans-factors governing AS have been characterized in animals, their functional roles in plants remain largely unexplored. We previously identified the Arabidopsis sot5 mutant, which exhibits leaf virescence due to a mutation in the conserved 5 splice site (5ss) of intron 7. Here, through characterization of a suppressor of sot5 (E61), we found that E61 harbors a G to A mutation in exon 8 of the SOT5 gene. Interestingly, this mutation creates a synonymous codon but disrupts the exonic splicing enhancer (ESE) motif (AAGAAGA), thereby reducing the splicing efficiency of the adjacent intron 7. Retention of this intron produces a functional protein that rescues the sot5 virescent phenotype. We confirmed the causal role of this ESE by using a cytidine base editor (CBE) to convert the ESE sequence to AAGAAAA or AAAAAAA in sot5. The edited plants phenocopied the suppressor E61. Genetic analyses revealed that mutations of SR45 encoding an RNA-binding protein but not its paralog SR45a similarly rescues the sot5 phenotype by impairing intron 7 splicing. Furthermore, we demonstrated that SR45 directly binds to the ESE motif in vitro, and that mutating the proximal ESEs in intron 2 of another SR45 target, GPDHC1 (Glycerol-3-Phosphate Dehydrogenase C1), recapitulates the splicing defect observed in the sr45 mutant. These findings establish that SR45 specifically recognizes AAG-repeat ESEs to enhance the splicing of adjacent weak introns, revealing a potent strategy for fine-tuning gene expression through targeted editing of splicing regulatory elements for crop improvement.

molecular biology↗

bioRxiv2025

Targeting Amygdala-Brainstem Synapses to Reverse Prepulse Inhibition Deficits

Sensorimotor gating, a fundamental pre-attentive process, can be assessed using the acoustic prepulse inhibition (PPI) assay. PPI deficits are a hallmark endophenotype of schizophrenia and are observed across various neuropsychiatric disorders, often predicting symptoms such as attention impairments, psychosis, and other cognitive/motor dysfunctions. Reversal of PPI deficits is routinely tested in disease models as a preclinical trial for antipsychotic drug screening. However, the cellular and circuit-level mechanisms underlying PPI deficits remain unclear, limiting therapeutic progress. We recently identified an uncharted pathway in mice, by which glutamatergic neurons in the central nucleus of the amygdala (CeA) activate glycinergic neurons in the caudal pontine reticular nucleus (PnC), contributing to PPI regulation. Given the prevalence of amygdala dys-function in disorders associated with PPI deficits, CeA-PnC glutamatergic synapses represent a novel therapeutic target. Here, using "Cal-Light," an in vivo Ca2+-dependent photo-tagging approach, we precisely identified CeA and PnC neurons active during acoustic startle and PPI with high spatiotemporal resolution. Furthermore, we used mice carrying homozygous deficiency in PRODH, a schizophrenia-relevant gene encoding proline dehydrogenase and modulating PPI. While Prodh-/- mice showed aberrant CeA neuronal properties and reduced PPI levels, we restored PPI by photo-activating CeA-PnC glutamatergic synapses, underscoring their involvement in pathological states. These findings provide new mechanistic insights into the amygdala-brainstem circuitry that underlies PPI deficits, offering new potential for therapeutic interventions.

neuroscience↗

bioRxiv2025

Aspartate transaminases are required for blood development

Red blood cells (RBCs) have a limited lifespan of approximately 120 days. This necessitates continuous RBC production, resulting in [~]200 billion new RBCs made per day to maintain oxygen delivery. Despite this enormous biosynthetic demand, the metabolic pathways supporting erythropoiesis are poorly understood. We profiled metabolites across four independent models of elevated erythropoiesis and a consistent increase in aspartate levels emerged when compared to controls. This suggested a potential role for aspartate metabolism in RBC production. To test this, we deleted the aspartate aminotransferases Got1 or Got2 globally or in an erythroid-specific manner. Loss of either enzyme resulted in anemia, with Got2 deficiency producing a more severe phenotype. Individual loss of either Got or dual Got deletion led to an erythroid defect, where early progenitors accumulated. In human and mouse models of erythropoiesis, GOT1 and GOT2 loss had opposing impacts on aspartate despite exhibiting similar anemic phenotypes, suggesting an aspartate-independent function for these enzymes. GOT1 and GOT2 are also components of the malate-aspartate shuttle (MAS), which regulates NAD(H) homeostasis. However, conditional deletion of another MAS enzyme, Mdh1, did not cause anemia, and alleviating NADH reductive stress in GOT2-deficient cells with cytoplasmic bacterial NADH oxidase (LbNOX) failed to restore erythropoiesis. Instead, transcriptomic and epigenetic analyses revealed dysregulation of chromatin histone modifications in GOT-deficient erythroid cells, implicating epigenetic dysfunction as a driver of defective erythropoiesis. Collectively, these findings identify a previously unrecognized role for GOT1 and GOT2 as a central link between metabolism and epigenetic regulation during erythroid development. These insights may inform the development of new therapeutic strategies for anemia.

biochemistry↗

bioRxiv2025

The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart

Trametinib (Trm) is a highly selective MEK inhibitor that potently and persistently abrogates ERK1/2 activation. Trm initially was used to treat BRAF V600E-mutated melanoma but its FDA-approved indications are expanding rapidly. Trm generally is well tolerated but it can cause dose-limiting cardiomyopathy and heart failure. Here we characterize a mouse model of Trm cardiotoxicity using complementary in vitro approaches to show that Trm induces mitochondrial dysfunction in cardiomyocytes and some cancer cell types. In vivo, Trm caused contractile dysfunction within 3 days and heart failure within 2 weeks. High resolution respirometry using isolated cardiac mitochondria revealed that Trm compromises oxidative metabolism, in part through blunted activity of Electron Transport System Complexes. Trm-mediated mitochondrial injury led to the release of mitochondrial Damage-Associated Molecular Patterns including mitochondrial DNA in both mice and humans, triggering activation of canonical innate immune pathways including cGAS-STING. In multiple rodent and human cardiomyocyte platforms, Trm diminished mitochondrial respiratory capacity at nanomolar concentrations but this lesion was reversed by expression of a phosphomimetic STAT3-S727 construct. We also found that Trm induced mitochondrial dysfunction in some but not all cancer cell lines, identifying a previously unrecognized effect that could contribute to Trms anti-cancer efficacy.

physiology↗

bioRxiv2025

Biodegradation of the endocrine-disrupting compound bisphenol F by Sphingobium yanoikuyae DN12

Bisphenol F (BPF) is an emerging environmental pollutant widely present in surface water and wastewater systems. Microbial activity is crucial in driving its degradation, offering a potential avenue for mitigating its environmental impact. Although the degradation pathway for BPF has been identified in various bacteria, the biodegradation mechanisms remain unclear. In this study, we isolated a highly efficient BPF-degrading strain of Sphingobium yanoikuyae DN12, which could utilize BPF as the sole carbon source and energy source for growth, from a river sediment in Anhui Province China. Through Ultra performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS) analysis, we found that oxidation and hydrolysis are key steps for BPF biodegradation. Utilizing whole-genome sequencing, comparative transcriptomics analysis and biochemical identification, a gene cluster bpf was identified to be involved in BPF degradation. BpfAB is a two-component oxidoreductase responsible for converting BPF to 4,4-dihydroxybenzophenone (DHBP). BpfC is a Baeyer-Villiger monooxygenase (BVMO) responsible for converting DHBP to 4-hydroxyphenyl-4-hydroxybenzoate (HPHB). Isotope tracing demonstrated that the oxygen atom incorporated by BpfAB originates from water, whereas that incorporated by BpfC derives from molecular oxygen (O2). BpfD is an /{beta} hydrolase responsible for converting HPHB to 4-hydroxybenzoate (4HB) and 1,4-hydroquinone (HQ). Analysis of the taxonomic and habitat of 325 prokaryotic genomes revealed that BpfA-like homologs are predominantly found in the phylum Pseudomonadota, primarily inhabiting soil and aquatic environments. This study enhances our understanding of the biodegradation mechanism of BPF, and provides guidance for the effective remediation of BPF-contaminated environments. IMPORTANCEBPF is a widely used alternative to bisphenol A and poses a growing threat to ecosystems and human health due to its environmental persistence and endocrine-disrupting effects. Although microbial degradation pathways for BPF have been reported, the key enzymes involved and their catalytic mechanisms remain unclear. This work reports the isolation of a Sphingobium strain capable of mineralizing BPF and the genetic basis for the catabolic pathway. Three enzymes--a two-component oxidoreductase, a Baeyer-Villiger monooxygenase, and an /{beta} hydrolase--were biochemically characterized and shown to catalyze the three critical steps in BPF degradation. These findings provide insights into the biochemical processes involved in the microbial degradation of BPF.

microbiology↗

bioRxiv2025

Core gastric microbiota linked to pathogenesis and preserved across age stratified cohorts

Mounting evidences reveal a complex microbial niche in gastric environment. Nevertheless, the phylogenetic stability of gastric microbiota remains undetermined. Here, using full-length 16S rRNA and ITS amplicon sequencing applied to gastric brushes from a pediatric endoscopic cohort (n=243), we identified a core microbiota comprising 11 genera, which clustered into two antagonistic communities (CST1A and CST1B). CST1A was enriched in healthy subjects, while CST1B correlated with gastroduodenal disease. Notably, this bipartite architecture arose through bacterial interactions, with fungal taxa demonstrating minimal integration. Further stratified analyses revealed that H. pylori infection preferentially depleted CST1A taxa. The subclusters exhibited divergent metabolic profiles, with CST1A specializing in motility processes and CST1B in nucleotide/peptidoglycan synthesis. Cross-cohort validation of six datasets (n=1,183) confirmed the persistent relevance of the CST1A-CST1B structure across disease stages. Collectively, our findings define a core gastric microbiota established in early life, linked to gastric disease risk, and persisting into adulthood. HighlightsO_LIIdentification of a gastric bacterial network established in early life. C_LIO_LIDysbiosis in two subclusters within the core microbiota is associated with pediatric peptic ulcers. C_LIO_LIHelicobacter pylori infection reduces the abundance of the core microbiota, with a particularly greater inhibitory effect on CST1A. C_LIO_LIThe core microbiota is preserved across age stratified cohorts and is associated with gastric cancer. C_LI

microbiology↗

bioRxiv2025

Proteome profiling reveals HES1-driven mitotic catastrophe in ovarian serous carcinoma

Ovarian high-grade serous cancer (HGSC) is an aggressive subtype of epithelial ovarian cancer. Here, we identify BX-912, a phosphoinositide-dependent kinase 1 (PDPK1) inhibitor, as a promising therapeutic agent for HGSC. BX-912 suppressed HGSC growth as a single agent and synergized with olaparib independently of BRCA status. Unexpectedly, BX-912 treatment induced multinucleation, a phenotype not observed with other PDPK1 inhibitors. Proteome Integral Solubility Alteration (PISA) profiling revealed the transcription factor HES1 as a functional target of BX-912. Structural modeling showed that BX-912 binds the Orange domain of HES1, while its WRPW motif mediates interactions with protein partners, including the AP2 endocytic protein complex, coordinating their nuclear accumulation that leads to a mitotic catastrophe. Furthermore, cell cycle analyses showed that BX-912 combined with olaparib synergistically enhanced DNA damage and G2-M arrest. Our study demonstrates the value of proteomics for revealing hidden drug activities. It also identifies potential inhibition strategies for HES1, which is commonly overexpressed in HGSC. Additionally, this study proposes a novel strategy of targeting consecutive cell cycle phases to enhance treatment efficacy in HGSC.

cancer biology↗

bioRxiv2025

Glycemia Shift Pancreatic Islets Rhythmicity via δ-α Cell in vivo, Impairment in Diabetes

Blood glucose homeostasis relies on the well-coordinated rhythmic activity of millions of islets throughout the pancreas. Islet rhythmicity is triggered by glucose elevation and mediated by paracrine interactions. However, the dynamics of islet population rhythmicity in healthy and diabetic pancreases in vivo remain poorly understood. Using simultaneous multi-islet Ca2+ imaging (20-100 islets per experiment) in both live mice and pancreatic tissue slices, we systematically studied how glycemia fluctuations and intra-islet paracrine signaling collectively shape the islet rhythmicity. In this study, we report that a transition from Hyperglycemia to Euglycemia induces a coordinated shift from slow to fast islet Ca2+ oscillations (HESF) in vivo. HESF is conserved in pancreatic tissue slices and isolated islets, however, not dispersed single cells in vitro, suggesting a mechanistic link with paracrine interactions. We found HESF arises from -cell activation, which is inhibited by {delta} cells upon glucose elevation. The autonomous islets mostly differ in phase and period at high glucose level. Diabetic mice with disrupted glycemic stability lost HESF both in vivo and in vitro. Interestingly, HESF is preserved in {beta}-cell knockout Gcgr transgenetic mice, both in vivo and in vitro, suggesting HESFs dependence on Glp1r. Indeed, HESF was restored in semaglutide-treated diabetic mice with stabilized glycemic stability. These findings offer a comprehensive understanding of how {delta} and cells influence islet rhythmicity and precisely maintain the stability of blood glucose.

physiology↗

bioRxiv2025

Expanding the repertoire of chemically induced covalent neoantigens

The ubiquitin-proteasome system generates peptide fragments that are displayed on MHC-I molecules. Recent studies revealed that covalent small molecules can hijack this process, leading to the presentation of hapten-modified peptide fragments, or covalent neoantigens. Here, we report a chemical proteomics platform to systematically investigate this process and harness covalent neoantigens for immune cell recruitment and activation. Using a bioorthogonal cysteine-reactive probe (IA-mTz), we demonstrate that diverse intracellular proteins can be modified, processed, and presented as covalent neoantigens across multiple cell lines. Mass spectrometry confirmed the presence of IA-mTz-modified peptides within the MHC-I immunopeptidome, and structural modeling revealed stable peptide-MHC-I interactions. We further integrated a bioorthogonal strategy that enables immune engagement: IA-mTz-modified cells conjugated with trans-cyclooctene (TCO)-IgG elicited Fc receptor activation in a reporter assay, supporting immune recruitment via antibody-dependent cellular phagocytosis. This approach was extended to additional cysteine-reactive probes and to 2,4-dinitrochlorobenzene (DNCB), a common skin sensitizer, which we show induces covalent neoantigen formation in a cell- and HLA-dependent manner. These findings reveal a previously underappreciated breadth of covalent neoantigen formation and provide a generalizable strategy for immune targeting of covalent neoantigens.

biochemistry↗

bioRxiv2025

Inhibiting Clarinet/CLA-1 restores function to injured motor neurons

To regain function, injured axons need to both regenerate and reform synapses with appropriate postsynaptic cells. We found that inhibiting the scaffolding protein Clarinet/CLA-1, a C. elegans ortholog of Piccolo and Fife, robustly improves axon regeneration. Despite the importance of CLA-1 during synapse development, disrupting the medium isoform of CLA-1 increases the number of axons that regenerate to the neuromuscular junction without significantly influencing synapse reformation. Consequently, the axons that do regenerate are capable of regaining function. Mechanistically, the enhanced axon regeneration observed in cla-1(-) mutants depends on the function of PTRN-1, a microtubule minus-end binding protein. Our data supports a model where loss of CLA-1 promotes PTRN-1 function, which speeds trafficking of injury-related cargo to and from the lesion, thus improving repair. Together, our results reveal a highly conserved synaptic active zone protein that can be manipulated to enhance axon regeneration without sacrificing the function of the repaired axons. HighlightsO_LIClarinet/CLA-1 is a robust inhibitor of C. elegans GABAergic axon regeneration C_LIO_LILoss of CLA-1 function improves both axon regeneration and functional repair C_LIO_LICLA-1 isoforms differentially regulate axon regeneration and synaptic transmission C_LIO_LICLA-1 regulates axon regeneration via microtubule minus-end protein PTRN-1/Patronin C_LIO_LICLA-1 knockdown improves cargo trafficking during the early injury response C_LI

neuroscience↗

bioRxiv2025

Stochastic modelling of prostate progenitor architecture

Prostate cancer is a significant global health concern. Experimental and clinical research have contributed to the improvement of treatment outcomes dramatically in the past decade. However, much of the structure of the prostate and its constituent cell types remains unclear: observations of phenotypic switching between basal and luminal cells, as well as intermediate cell types between them, make classifying the components of the prostate an ongoing challenge. Importantly, a tumours cell type of origin seems to play a role in the aggressiveness and genetic heterogeneity of the cancer. To understand how different structures between cell types impact the emergence and treatment of prostate cancer, we model the emergence of a tumour by a fit mutant arising amongst healthy cells via a compartmental modelling approach. We label cells in different compartments based on their phenotype and allow for phenotypic switching between them. We measure the time until and probability of invasion and extinction of this mutant in healthy prostates through individual-based simulations. We find that less-tight population size regulation of the luminal compartment allows for the explosive population growth associated with cancer. Tumours arising in the basal compartment require more time to spread but are more strongly embedded within the prostate, explaining the longer latency and higher aggressiveness and persistence associated with these tumours. Interestingly, the inclusion of a hybrid compartment does not qualitatively change the observations, raising questions as to what mechanistic role intermediate phenotypes play in prostate cancer emergence, if any. Our model contributes to dissecting the relationship between prostate structure and outcomes for cancers arising therein.

evolutionary biology↗

bioRxiv2025

Self-inactivating AAV-CRISPR at different ages enables sustained amelioration of Huntington's disease deficits in BAC226Q mice

Huntingtons disease (HD) is a monogenic autosomal dominant neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene, yielding a gain-of-toxic-function mutant Huntingtin protein mHTT. CRISPR/Cas9 is a potentially powerful therapeutic tool for treating HD by eliminating mutant HTT (mHTT) gene. We developed a specific SaCas9 guide RNA to target human mHTT, and a self-inactivating gene editing system that abolishes SaCas9 after a short transient expression for high gene editing efficiency and maximal safety to prevent off-target effects. Both conventional and the new self-inactivating gene editing systems achieved successful elimination of mHTT gene, 60-90% mHTT protein and 90% of mHTT aggregation in BAC226Q HD mouse brains, which resulted in significant long-term rescue of neural pathology, motor deficits, weight loss and shortened lifespan. These beneficial effects were observed when gene editing was applied before, at and well after the on-set of pathological and behavioral abnormalities. These proof-of-concept data demonstrate that gene editing can be a highly effective therapeutic approach for HD and other inherited neurodegenerative diseases. One Sentence SummarySelf-inactivating CRISPR for mutant huntingtin in HD mice achieved long-term rescue of neural pathology, motor deficits, weight loss and survival.

neuroscience↗

bioRxiv2025

Decoupled Information Theoretic Feature Selection for Rapid Protein Key Tuning Residue Identification

Rational protein engineering requires identifying residues that modulate function without disrupting functionality, a key challenge in protein engineering. Existing computational methods struggle to distinguish genuine functional sites from positions coevolving due to structural constraints, leading to high false-discovery rates. Here we present an information-theoretic decoupling framework that, without machine learning, isolates key tuning residues by computationally "denoising" sequence data, iteratively removing confounding evolutionary signals to reveal underlying functional sites. We validated this framework across 10 datasets spanning enzymes, fluorescent proteins, and antibodies. In a nanobody-antigen binding case study, our method identified > 25% (6/20) of verified binding-critical residues (p = 0.031), while the best of five benchmarked tools found zero. Performance was consistent across all datasets, with supervised variants achieving large effect sizes (Hedges g > 0.7, p < 0.01) and unsupervised variants also showing gains (g > 0.2, p < 0.05) over benchmarks. This interpretable framework provides a generalizable method to accelerate protein design, from focusing antibody maturation to optimizing biocatalysts.

bioinformatics↗

bioRxiv2025

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗