Biology subjects

Zhou, F.

Publications and source records attributed to Zhou, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Maternal Folate Nutrition Programs Adult Hematopoietic Stem Cell Function Through Mitochondrial Remodeling

Folic acid fortification for the prevention of neural tube defects has been a cornerstone of public health policy for nearly three decades, but its broader consequences for other developing organ systems, particularly the hematopoietic system, are poorly studied. Hematopoietic stem cell (HSC) emergence overlaps developmentally with neural tube closure, and folate-dependent one-carbon metabolism is critical for nucleotide synthesis, cellular methylation, and redox balance, positioning folate as a candidate regulator of HSC programming. Using dietary models of maternal folate deficiency or supplementation in mice, we demonstrate that maternal folate acts as a dose-dependent developmental tuner of hematopoiesis, programming adult offspring HSC function through divergent mitochondrial and chromatin states. Maternal folate deficiency impaired adult HSC self-renewal, associated with mitochondrial defects, disrupted cristae, elevated proteotoxic stress and a stress-adapted chromatin landscape. In contrast, maternal folate supplementation enhanced HSC self-renewal accompanied by improved mitochondrial quality control and CDC42-associated organelle remodeling, and established chromatin states permissive for stem cell maintenance. Fetal HSC metabolomics identified shifts in one-carbon intermediates, pyruvate and lipid pools, suggesting that divergent fetal metabolic states provide substrate-level inputs that drive persistent and opposing chromatin programs in offspring HSCs. Our findings establish maternal folate availability as an unappreciated regulator of lifelong hematopoietic output demonstrating that a single maternal micronutrient, folate, is sufficient to program adult HSC function and regenerative capacity through persistent metabolic and mitochondrial programming.

cell biology↗

bioRxiv2026

METTL3-mediated m6A modification alleviates skeletal muscle atrophy in ALS by regulating ACSL1-dependent triglyceride metabolism

Skeletal muscle-intrinsic defects are increasingly recognized as critical contributors to the pathogenesis of amyotrophic lateral sclerosis (ALS), yet the underlying molecular mechanisms remain poorly understood. N6-methyladenosine (m6A) is the most abundant post-transcriptional RNA modification in mammalian mRNAs that plays important regulatory roles in diverse physiological and pathological processes, however its role in ALS-associated skeletal muscle atrophy remains unknown. Here we found that global m6A methylation and the expression of its methyltransferase METTL3 are reduced in the skeletal muscle of hSOD1G93A transgenic ALS mice. Multi-omics analyses reveal that m6A dysregulation is closely associated with impaired triglyceride metabolism. Functionally, METTL3 promotes triglyceride accumulation in ALS skeletal muscle in an m6A-dependent manner; overexpression of METTL3 in ALS myotubes improves energy supply and alleviates muscle atrophy by promoting triglyceride accumulation. In vivo overexpression of Mettl3 in skeletal muscle attenuates muscle atrophy, improves motor performance, and prolongs survival of ALS mice. Mechanistically, we identify the fatty acid activation enzyme ACSL1 as a key downstream effector of METTL3-mediated regulation of triglyceride metabolism. METTL3-mediated m6A modification promotes the expression of Acsl1 by enhancing its mRNA stability. Further investigation revealed that the regulatory effect of m6A on Acsl1 expression depends on the m6A reader protein IGF2BP2. Collectively, our findings establish m6A modification as a critical regulator of skeletal muscle atrophy in ALS by maintaining triglyceride metabolic homeostasis, highlighting a promising therapeutic target for ALS.

neuroscience↗

bioRxiv2026

A lactate-HIF1-VDR positive feedback loop drives protective SPP1+ macrophage differentiation to inhibit schistosomiasis induced liver fibrosis

Hepatic fibrosis remains a major cause of morbidity and mortality in patients with schistosomiasis without effective therapy. Here we show that vitamin D receptor (VDR) signaling in macrophages is essential for limiting fibrosis, acting through a previously unrecognized metabolic epigenetic circuit. Hepatic macrophages exhibit the highest VDR expression among liver resident cells, and pharmacological VDR activation with paricalcitol selectively expands a protective SPP1+ macrophage subset derived from circulating monocytes. Myeloid specific VDR knockout exacerbates fibrosis and abrogates paricalcitol's hepatoprotective effects, whereas SPP1+ macrophage depletion worsens disease. Mechanistically, VDR activation synergizes with hypoxia and lactate to drive SPP1 expression via glycolytic reprogramming. Moreover, lactate and HIF1alpha cooperatively induce VDR transcription by binding to the Vdr promoter and enhancing histone lactylation, forming a positive feedback loop that amplifies the antifibrotic response. Our findings establish the lactate-HIF1alpha-VDR-SPP1 axis as an endogenous defense mechanism and identify macrophage VDR as a promising therapeutic target for fibrotic liver diseases.

immunology↗

bioRxiv2026

An early-diverging Caladeniinae orchid reveals diversification of terpene and apocarotenoid pathways underlying floral scent evolution

Orchids exhibit extraordinary floral diversity, yet the molecular mechanisms underlying floral scent evolution remain poorly understood. Guided by recent phylogenomic reconstruction of the Australian orchid subtribe Caladeniinae, we used Glossodia major, an earlier-diverging food-deceptive lineage, as an evolutionary anchor for investigating floral volatile diversification. Scent-producing petals showed coordinated expression of terpene synthase (TPS), carotenoid and carotenoid cleavage dioxygenase (CCD) pathways. Functional characterisation identified GmTPS-b3, GmTPS-b4 and GmTPS-a1 as contributors to floral monoterpene and sesquiterpene production, while GmCCD1 produced geranylacetone, the dominant floral volatile, from {zeta}-carotene. GmCCD4 and GmCCD7a showed additional, partially overlapping apocarotenoid-forming activities. Integration of tissue-specific expression, enzyme activity and subcellular localisation linked these pathways to the emitted floral bouquet. Functional comparisons with characterised Caladenia homologues revealed biochemical conservation and catalytic and compartmental specialisation, while expression profiling across 31 species identified pollination strategy-associated regulatory divergence in TPSa1 and TPSb3, consistent with corresponding shifts in terpenoid-rich floral scent. We propose that differential modification and deployment of conserved biosynthetic pathways contributed to the attenuation and re-emergence of terpenoid-rich floral scent during Caladeniinae diversification. More broadly, our findings provide candidate mechanistic links between molecular evolution, pollinator-mediated selection and floral diversification.

plant biology↗

bioRxiv2026

Molecular Editing in Protein Degradation: From a Dual NSD2/GSPT1 Degrader to an NSD2-Selective PROTAC and a GSPT1-Selective Molecular Glue

Both NSD2 and GSPT1 represent compelling targets for anti-cancer drug discovery. Herein, we carried out single-atom modification of LLC0424, an NSD2 degrader with GSPT1 neosubstrate engagement, to yield two structurally analogous molecules with divergent modes of action: 424-ND, an NSD2-selective degrader, and 424-GD, a GSPT1-selective degrader. 424-ND drove selective NSD2 degradation and suppressed androgen receptor (AR) signaling in prostate cancer cells. 424-GD induced selective degradation of GSPT1 and upregulated the integrated stress response markers ATF4 and ATF3. Biolayer interferometry revealed distinct ternary complex cooperativity profiles in the presence of NSD2 or GSPT1, which directly correlate with the observed biased degradation activity. Molecular dynamics and metadynamics simulations showed that the compounds adopt distinct low-energy conformational ensembles with different spatial orientations, likely underlying their divergent cooperativity and selectivity. These findings demonstrate that minimal structural alteration permits precision control over degrader target selectivity, while furnishing selective chemical probes for NSD2 and GSPT1.

cancer biology↗

bioRxiv2026

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates

Large-scale structural variants (SVs) are major drivers of genome evolution and disease susceptibility, shaping lineage-specific gene content, genome architecture, and phenotypic diversity. Yet, their systematic detection across divergent species has been hindered by complex rearrangements and reference bias, limiting our understanding of their evolutionary impact. Here we present LGvar, a divergence-aware tool for identifying SVs in population-scale and cross-species genome assemblies, enabling up to a 7-fold increase in the detection of large deletions, insertions, inversions and complex rearrangements ([≥]10 kbp). Application of LGvar uncovers 112 previously undetected large SVs overlooked by conventional methods and quantifies the effect of evolutionary divergence on SV discovery across primate euchromatic genomes, revealing an approximately 30% overall decline in detection sensitivity with increasing phylogenetic distance. Mapping SVs from comparable syntenic regions onto the primate phylogeny shows that large deletions ([≥]10 kbp) accumulate approximately two-fold faster than insertions and eight-fold faster than inversions, in contrast to the dynamics of smaller SVs (<10 kbp). Integrating structurally divergent regions with the synteny region analysis reveals over 606 previously unreported gene gains and losses in great apes and refined the totals to 134 human-lineage-specific and 51 great-ape-lineage-specific protein coding genes. These results suggest that large SVs follow distinct evolutionary trajectories, with potential selective constraints shaping genome structure. Our study establishes a generalizable strategy for cross-species SV discovery and provides a high-resolution view of how large SVs contribute to genome evolution in primates.

genomics↗

bioRxiv2026

A neurofunctional signature of romantic love predicts rewards on social media, effects of oxytocin and drug-cue reactivity

Romantic love is a selective motivational state supporting pair bonding, yet its neural representation and relation to other affiliative-rewarding experiences remain unclear. Across eight fMRI studies (n=420) spanning naturalistic affiliative-reward, pharmacological and addiction-relevant experiments, we developed and evaluated multivariate whole-brain decoders of romantic love and friendship. Both signatures engaged mesocorticolimbic reward systems and the precuneus, yet were dissociable at the whole-brain level and in their recruitment of social-cognitive systems. The love signature generalized to reward on social media, was specific to positive valence, and did not track sweet-taste or monetary reward, indicating a distinct social-affiliative reward representation. Oxytocin selectively increased love - but not friendship - signature reactivity to the romantic partner. In an independent drug-cue-reactivity dataset, the love signature specifically identified heavy cannabis users. These findings establish a dissociable neurofunctional signature of romantic love in conserved bonding circuits that extend to digital affiliation and are co-opted in addiction.

neuroscience↗

bioRxiv2026

Mutations in SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity in mice

Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) nonstructural protein 1 (Nsp1) dampens the host immune response by shutting off host gene expression, a strategy that has remained evolutionary conserved among a diverse range of coronaviruses (CoVs). Residues important for SARS-CoV-2 Nsp1 mediated host shutoff have been incompletely defined. We have generated and characterized the ability of four Nsp1 mutants to inhibit host gene expression in both plasmid-based overexpression assays and utilized reverse genetic approaches to generate recombinant (r)SARS-CoV-2 expressing each Nsp1 mutant to investigate their impact on viral infection. Infection of K18-hACE2 transgenic mice with the rSARS-CoV-2 Nsp1 mutants resulted in reduced pathogenicity as determined by body weight maintenance and survival, attenuated viral replication in lung and nasal turbinate, distinct immune signatures in lung, and less severe lung pathology in comparison to wild-type (WT) virus-infected mice. Our data suggests amino acid residues in the C-terminal domain, in addition to the linker domain, of SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity as a result of their role in disrupting host gene expression. The reduced pathogenicity of rSARS-CoV-2 Nsp1 mutants highlights the potential for targeting Nsp1 for rational design of viral inhibitors and development of live-attenuated vaccine strategies as effective prophylactic and therapeutic treatments, respectively, to combat SARS-CoV-2 and possibly other CoV infections. IMPORTANCETo mitigate the ongoing public health threat posed by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) and prepare for future coronavirus (CoV) outbreaks, there is an urgent need for effective prophylactic and therapeutic strategies, including vaccines and antivirals. The nonstructural protein 1 (Nsp1) is a conserved CoV virulence factor that suppresses host gene expression and disrupts immune responses. However, the contribution of specific Nsp1 residues to CoV pathogenesis remains unclear. Here, we identify residues within the C-terminal and linker regions of Nsp1 as critical determinants of SARS-CoV-2 pathogenicity in vivo. These findings advance our understanding of CoV host shutoff mechanisms and support Nsp1 as a promising target for the development of live-attenuated vaccines and antiviral therapeutics.

microbiology↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

Multidimensional variation and population stratification across 8000 complete human centromeres

Human centromeres are indispensable for the faithful segregation of chromosomes during cell division, yet their highly repetitive nature has historically precluded comprehensive characterization, leaving fundamental questions about their sequence diversity, evolution trajectories and function dynamics unresolved. Here, we generated 6,312 complete human centromere sequences from 320 phased genome assemblies in Asian Pan-Genome project phase 1. By integrating the assemblies from the Human Pangenome Reference Consortium (HPRC) and Human Genome Structural Variation Consortium (HGSVC), we constructed a multidimensional genetic variation map encompassing over 8,000 gapless centromeres. Centromeric satellite arrays account for 4.19% to 6.01% of the whole genome, with substantial variations in size and architecture across chromosomes. Using a refined alpha satellite clustering approach that captures global diversity, we identified 195 higher-order repeat (HOR) arrays, 56.4% of which are absent from the T2T-CHM13 reference genome. Extensive structural variations across multiple dimensions exhibit population stratification, including centromeric haplotypes (CenHaps), ultra-large pericentric inversions spanning up to 36.6 Mbp, and inter-chromosomal HOR sharing that reflects sequence exchange among chromosomes. Integrating CENP-A CUT&Tag experiments and long-read-based DNA methylation profiles, we demonstrate that 16.8% of centromeres harbor multiple potential kinetochore assembly sites, and CenHap-specific local HOR homogenization is associated with kinetochore positioning. Despite global suppression of recombination at centromeres, we observed asymmetric linkage disequilibrium flanking centromeres and an ancient recombination event within the centromere of chromosome 19. Furthermore, contrary to the prevailing assumption of high mutation rates in centromeres, our estimates based on stringent orthology reveal no significantly higher single-base substitution rates for centromeres relative to flanking pericentromeric regions with substantial variations across chromosomes, despite extraordinary structural plasticity. Collectively, these multi-scale centromeric variations provide a global view of human centromere diversity and population stratification, fundamentally redefine centromere evolution through a dual-track model balancing structural innovation with mutational constraint, and establish an essential resource for investigating centromere biology and a baseline reference for diagnosing centromere-associated disorders.

genomics↗

bioRxiv2026

Transcription factor CCTF1 plays a decisive role in regulating the proteasome activity during archaeal cell division

Archaea of the order Sulfolobales exhibit a highly ordered cell cycle progression similar to that of eukaryotes. It has been demonstrated that degradation of the cell division protein CdvB by the proteasome controls the progression of cell division. However, how the proteasome itself is regulated during the cell cycle is not fully understood. Recently, the cyclically expressed ArsR family transcription factor CCTF1 (cell cycle transcription factor 1) was shown to represses expression of PAN (proteasome-activating nucleotidase) in Sulfolobus acidocaldarius. Here, using biochemical approaches, comparative transcriptomics and proteomics, we provide further insights into the CCTF1 function and show that it regulates PAN expression in Saccharolobus islandicus by binding to an AT-rich palindromic sequence within the pan promoter. We also reassessed the role of the cyclically expressed protein kinase aCcrK in regulation of proteasome activity and conclude that CCTF1, rather than aCcrK, is the primary factor controlling the proteasome activity. These findings advance our understanding of the proteosome-mediated cell cycle regulation in archaea.

microbiology↗

bioRxiv2026

Chronic Mild Stress Impairs Hippocampal Myelination through SOX6-Dependent Dysfunction of Oligodendrocyte Lineage Cells

Chronic stress induces structural and functional changes in the brain, increasing susceptibility to major depressive disorder and other mental illnesses. Myelination deficits are a key pathological feature of stress-related disorders, yet the molecular mechanisms linking chronic stress to oligodendrocyte dysfunction remain poorly understood. Here, we used single-nucleus multiome sequencing to map gene expression and chromatin-accessibility remodeling in the hippocampus of mice exposed to chronic unpredictable mild stress (CUMS), a model that simulates key features of human daily stressors. CUMS induced broad molecular reprogramming across hippocampal cell populations, with stress-responsive gene networks significantly enriched for depression-associated genes. The oligodendrocyte lineage showed heightened vulnerability, with CUMS preferentially disrupting immature OPC/intermediate states and impairing OPC migration, OPC-to-ODC lineage progression, intercellular communication, and myelination. Integrated multiomic analysis identified stage-specific cis-regulatory elements and stress-sensitive gene regulatory networks, converging on SOXD transcription factors, particularly SOX5 and SOX6, as key regulators of OPC dysfunction. SOX6 ChIP-seq confirmed direct SOX6 binding at regulatory elements associated with genes controlling OPC morphogenesis, migration, and glutamatergic signaling. CUMS reduced SOX6 protein levels and SOX6-associated regulatory network activity in OPCs, whereas OPC-specific enhancer-driven restoration of SOX6 rescued stress-induced defects in OPC migration and myelination. Together, these findings define a stress-sensitive SOXD/SOX6 regulatory mechanism linking chronic stress to oligodendrocyte lineage dysfunction and myelination deficits, identifying SOX6 as a functional regulatory node with therapeutic potential for stress-related brain pathology.

neuroscience↗

bioRxiv2026

Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue

Mapping how parenchymal, immune, and stromal cells interact with extended structures such as blood vessels and nerves is challenging using conventional thin-section tissue imaging. Volumetric methods such as light-sheet fluorescence microscopy (LSFM) are ideal in these cases and LSFM is widely used in animal models such as fish and mice. This is enabled by well-established clearing methods, genetically encoded reporters, and vascular dyes. However, LSFM is rarely utilized for human tissue, which is primarily available as formaldehyde-fixed paraffin embedded (FFPE) specimens. Here, we present an approach to volumetric cyclic immunofluorescence (v-CyCIF) that enables 40-plex or greater imaging of immune and other cell types in human specimens up to 1 mm thick. We demonstrate the use of v-CyCIF to study neuroimmune interactions and lymphoid structures in normal and cancer tissues. Following LSFM imaging, specimens can be re-embedded and sectioned to ~50 {micro}m thick for high-resolution confocal imaging of punctate structures and cell-cell junctions. v-CyCIF therefore provides a flexible framework for multi-scale 3D profiling of clinical specimens across imaging formats and resolutions.

cancer biology↗

bioRxiv2026

A distributed neural architecture of sustained affect across external and internal experience

AO_SCPLOWBSTRACTC_SCPLOWSustained affect shapes well-being, yet its neural architecture across externally elicited and internally generated experience remains unclear. Using whole-brain functional connectivity during minutes-long naturalistic movie viewing, we derived positive and negative affective experience signatures and their underlying neural architecture. These signatures predicted valence-specific affective intensity and generalized to independent movie-viewing data and internally generated affect, discriminating sad memory and rumination from neutral distraction while tracking subjective experience. Importantly, their expression showed little relation to vigilance or cognitive demand. Characterization of these signatures revealed coherent community structure and a shared distributed backbone, alongside valence-preferential components, consistent with a partially separable architecture. Extending beyond experimentally evoked states, in four resting-state depression cohorts, these signatures distinguished patients from controls with reduced positive and elevated negative signature expression, and predicted symptom burden and anhedonia. These findings identify a generalizable distributed architecture bridging external and internal affective experience and extending to clinically relevant affective dysregulation.

neuroscience↗

bioRxiv2026

Role of Alanine Transaminase in Retinal Metabolic Homeostasis: Potential therapeutic target in retinal diseases

PurposeAlanine transaminases (ALT), encoded by the GPT gene, catalyzes the reversible conversion of pyruvate and glutamate to alanine and alpha-ketoglutarate, thereby correlating carbohydrate and amino acid metabolism. However, its role in the human neural retina remains unclear. This study aimed to explore the expression, localization, and metabolic function of ALT in the human neural retina and its potential involvement in retinal diseases. MethodsALT1 and ALT2 expression and localization were examined in the retinas of healthy and diabetic retinopathy (DR) donors via immunoblotting and immunofluorescence. ALT function was assessed in ex vivo human retinal explants using pharmacological inhibition with beta-chloro-L-alanine (BCLA), followed by the analyses of enzyme activity, tissue injury, and transcriptomic responses. Stable-isotope tracing with 13C-and 15N-labelled substrates combined with GC-MS was used to define ALT-dependent carbon and nitrogen fluxes in macular and peripheral retinas. Redox level (NADPH/NADP+) was also evaluated under tert-butyl hydroperoxide-induced oxidative stress. ResultsALT1 and ALT2 were both expressed in the human neural retina, with prominent localization in Muller glia and photoreceptor inner segments. ALT1 displayed a diffuse cytoplasmic distribution, whereas ALT2 demonstrated a punctate pattern consistent with mitochondrial localization. In DR retinas, ALT1 expression was spatially disorganized and heterogeneous, while ALT2 remained comparatively preserved. Inhibition of ALT with BCLA markedly reduced ALT activity without causing overt cytotoxicity or major transcriptional changes. Isotope tracing demonstrated that retinal ALT predominantly channels pyruvate-derived carbon into alanine, whereas alanine was minimally contributed to pyruvate production under basal conditions. ALT inhibition suppressed alanine synthesis and release, redirected nitrogen flux towards glutamate, glutamine, and aspartate, and uncovered distinct metabolic adaptations in macular but not peripheral retinas. Under oxidative stress, ALT inhibition induced the decrease of NADP+/NADPH ratio and LDH release, indicating improved redox balance and reduced tissue injury. ConclusionsALT is previously unrecognized as a regulator of carbon and nitrogen partitioner in the human neural retina, contributing to redox homeostasis under stress. The altered distribution of ALT1 in DR retina and the protective metabolic effects of ALT inhibition suggest ALT as a potential contributor to retinal metabolic vulnerability and a candidate therapeutic target in retinal diseases.

neuroscience↗

bioRxiv2026

Integration of proteogenomic analyses in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is still lack of clinically molecular subtyping and effective therapeutic strategies. Herein, a total of 46 paired tissue samples of esophageal squamous cell carcinoma (ESCC) were collected and subjected to a systematic proteogenomic evaluation. Consensus assessment of the ESCC-related transcriptomes and TCGA dataset revealed several consensual modes of gene expression related to ESCC specificity, with 8 plasma-detectable hub proteins that could discriminate ESCC from others. Three ESCC molecular subtypes were defined and validated based on proteome data, including pCC1 with activated immune response and best survival outcome, pCC2 as cell cycle subtype with relative worse outcome, and pCC3 with worst outcome that expressed more cell adhesion related proteins. Furthermore, we proposed potential therapeutic strategies for improving survival outcomes in patients with different ESCC molecular subtypes. This integrative proteogenomic analysis provided a novel view of ESCC-dependent molecular information.

cancer biology↗

bioRxiv2026

Neural cell state modulation by PARK2 and dopaminergic neuroprotection by small molecule Parkin agonism

Parkin, an E3 ubiquitin ligase encoded by PARK2, plays a key role in both hereditary and sporadic Parkinsons disease (PD), yet there are no therapies currently available that can target this important pathway. Here, we show that Parkin is critical for successful neuronal differentiation and survival, and we develop small-molecule Parkin agonists that can protect dopaminergic neurons. Upon differentiation of neural progenitor cells, loss of Parkin results in a reduced capacity to maintain neuronal cell state, dopaminergic neuronal phenotypes, and stress resistance. Moreover, Parkin loss disrupted cell morphology and the stability of neurites. Transcriptional and single-cell analyses reveal that Parkin controls critical pathways regulating stem-like cell transitions and is needed for stable neuronal maturation. We also examined the effects of FB231, a small molecule enhancer of Parkin E3 ligase activity, in models of PD. FB231 reduced pathological -synuclein and enhanced cell survival in human iPSC-derived dopaminergic neurons treated with -synuclein preformed fibrils. Furthermore, FB231 attenuated -synuclein pathology and dopaminergic neurodegeneration in a gut -synuclein murine model of PD. Our findings support that Parkin plays a crucial role in maintaining neuronal homeostasis and that pharmacologic activation of Parkin may be a promising strategy to attenuate neurodegeneration in PD.

neuroscience↗

bioRxiv2026

The structure-interaction model of polymyxin lipopeptides with human oligopeptide transporter 2

Multidrug-resistant (MDR) Gram-negative bacteria pose a critical global health threat, while polymyxins remain a last-line therapy. However, their clinical use is limited by nephrotoxicity. Human oligopeptide transporter 2 (hPepT2) is a membrane transporter mediating the reabsorption of polymyxins in renal cells and contributes to their nephrotoxicity, but the molecular basis of their interaction remains unclear. Here, we investigated the structure-interaction relationship (SIR) of polymyxins with hPepT2 by integrating computational, chemical, and cell biology approaches. Bioinformatic modelling predicted an outward-facing hPepT2 structure and a potential transport pathway, with polymyxins interacting at the lateral opening, particularly E214, D215, D317, D342, and E622. Transporter mutagenesis and molecular analyses confirmed that D215 is critical for polymyxin binding, while other residues influence transporter turnover and/or expression. We subsequently synthesised polymyxin analogues with modifications at Dab1, Dab3, Dab5, and Dab9 of polymyxins, which reduced interactions with hPepT2. Notably, alanine substitution at Dab3 reduced nephrotoxicity in mice while retaining antibacterial activity. Overall, this proof-of-concept study demonstrates that the hPepT2-polymyxin SIR model provides a viable strategy for developing novel, safer lipopeptide antibiotics.

biochemistry↗