Biology subjects

Tran, J.

Publications and source records attributed to Tran, J..

At least 19 recordsLinked to original sources

bioRxiv2026

A hyperactivating mutation in formin-like 2 causes brain and vertebrae defects

Formins are a group of proteins that nucleate and polymerize actin monomers into filaments to promote cell morphology and migration. Mutations in formin-encoding genes cause a broad spectrum of human diseases, ranging from kidney disease to non-syndromic intellectual disability. Through a forward genetics screen, we identified a mouse strain (nmf418) with a homozygous mutation in a splice acceptor in Fmnl2 that causes hindlimb motor dysfunction, enlarged midbrain colliculi, cerebellar hypoplasia, and vertebral abnormalities in the thoracolumbar spinal cord. The nmf418 mutation causes skipping of exon 10, which encodes a portion of the diaphanous inhibitory domain (DID) required for FMNL2 autoinhibition, and results in dramatically lower FMNL2 protein levels. Consistent with a gain-of-function mechanism, mutant FMNL2 has altered enrichment at filopodia tips, increased actin polymerization activity, and its expression results in enhanced cell migration in vitro. Furthermore, none of the neural or skeletal phenotypes were recapitulated in Fmnl2 knockout mice. Transcriptomic analysis of the embryonic cerebellum suggests that complete loss of Fmnl2 triggers broad compensatory upregulation of actin regulatory pathways, while expression of mutant FMNL2 is associated with dysregulation of cell migration, motility pathways, and calcium homeostasis pathways. Taken together, these findings suggest that Fmnl2 is largely dispensable for overall mouse development but that its autoregulation is essential for proper formation of the mouse nervous and skeletal systems.

genetics↗

bioRxiv2026

Germinal centers can persist for up to one year with declining somatic hypermutation and ongoing plasma cell output

The total duration of primary germinal center (GC) responses, and how B cell evolution changes as these responses mature, remain poorly defined. Here, longitudinal sampling of rhesus macaques immunized with HIV Envelope protein revealed that a single slow-delivery prime sustained ongoing GCs for nearly a year without additional antigen. Somatic hypermutation (SHM) accumulated throughout these prolonged responses, but its rate declined substantially over time, independent of both priming strategy and boosting. Over the same period, subdominant non-base Env specificities became increasingly represented within the GC response. Delaying boosting until after primary GC contraction increased recruitment of recalled memory B cells into the GC response. Bone marrow plasma cells were generated throughout prolonged GC maturation, with the timing of their generation modulated by booster timing. Together, these findings reveal how GCs evolve across nearly a year and how this prolonged maturation shapes the memory and plasma cell compartments that underpin long-term humoral immunity.

immunology↗

bioRxiv2026

Urban Vietnam at the microbiome transition: Co-existing enterotypes reflect the global industrialization patterns

Vietnam's rapid socioeconomic and dietary transition offers a rare window into how industrialization is reflected in the gut microbiome, yet Vietnamese populations remain underrepresented in global reference datasets. We investigated whether healthy Vietnamese adults in Hanoi harbor microbial community configurations associated with different stages of industrialization. Metagenomic data from stool samples of 183 clinically screened participants in Hanoi were analyzed alongside 629 publicly available metagenomic datasets from populations in low to middle income (LMI) and high income (HI) countries. Species-level taxonomic composition and gene-content-based metabolic pathways were characterized using community clustering and multivariable association analyses. Rather than forming a single population profile, the Vietnamese cohort separated into two enterotypes that mirrored the global industrialization gradient. Enterotype 1 more closely resembled populations from LMICs and showed greater microbial richness and diversity, whereas Enterotype 2 aligned with taxonomic and functional profiles observed in HICs. Both taxonomic and functional potential shows similar trajectories. Diet and lifestyle patterns describe some of the variance between enterotypes, supporting an association between contemporary exposures and microbiome structure without establishing causation. Antibiotic resistance profiles also varied between enterotypes, suggesting that the transition may encompass functions relevant to antimicrobial exposure. Together, these findings position urban Vietnam at a microbiome transition, where community states associated with different levels of industrialization coexist within a single population. This Vietnamese reference cohort expands representation in global metagenomic research and provides a baseline for tracking how rapid socioeconomic change may reshape microbial ecology, metabolic capacity, and antimicrobial resistance.

microbiology↗

bioRxiv2026

Validating a high-throughput in vitro model for culturing antibiotic-altered microbiome communities

The gut microbiome plays a central role in host health, and its disruption is associated with metabolic, infectious, and immune conditions. Stool sampling is frequently used to characterize snapshots of the gut microbiota. To screen microbiota communities in vitro, multi-stage bioreactors have been developed that model distinct physiological environments along the gastrointestinal tract. However, such bioreactors are often operationally complex and provide limited throughput. Stool-derived in vitro communities offer several advantages to study microbiota due to their ease of use, high-throughput nature, and have previously been shown to remain stable following repeat passaging. Yet, prior characterization of stool-derived cultures has relied on 16S rRNA sequencing of unaltered gut microbiota, leaving several key questions unanswered: 1) how closely does in vitro culture recapitulate the functional potential and resistome composition of its inoculum and 2) can these cultures model antibiotic disrupted microbial communities? In this work, we generated stool-derived in vitro cultures from male and female mice with both unaltered and antibiotic altered gut microbiomes and applied shotgun metagenomic sequencing to characterize taxonomic composition, functional pathway capacity, and antimicrobial resistance gene (ARG) content. Antibiotic-altered microbiota communities, dominated by Enterobacteriaceae, were faithfully recapitulated in culture with preservation of both taxonomy and ARGs. By contrast, unaltered communities underwent substantial restructuring in culture, with Bifidobacterium and Enterococcus blooming and driving sex-divergent shifts in functional capacity and a substantial amplification of the resistome. Together, these findings validate a high-throughput stool-derived in vitro culture as a tractable proxy for an antibiotic altered gut microbiome to screen interventions.

microbiology↗

bioRxiv2026

Exploratory multi-omics analysis reveals sex-specific differences in microbial response to antibiotic exposure

Antibiotic exposure is a major driver of microbiome disruption and antimicrobial resistance gene (ARG) expansion. Yet, the role of biological sex in shaping these responses remains poorly understood. Most studies do not stratify antibiotic-induced microbiome changes by sex or integrate multi-omics datasets, limiting our understanding of how microbial, metabolic, and immune responses interact. Therefore, there remains a critical need for an integrative systems-level approach to determine how sex-specific disruptions under antibiotic pressure are paralleled across microbial, metabolic, and host immune layers. The objective of this work was to perform an exploratory study investigating how continuous antibiotic exposure reshaped the gut microbiome across sexual maturation and how these perturbations influenced downstream host responses in a sex-specific manner using an integrative multi-omics framework. Male and female mice that were exposed to continuous antibiotics were profiled over sexual maturation using shotgun metagenomics, untargeted metabolomics, and bulk RNA sequencing of the spleen to assess microbial composition, ARG dynamics, metabolic profiles, and immune responses. Overall, our results demonstrated sex-specific correlations at a systems-level that help provide valuable context to the differences observed in males and females upon antibiotic exposure.

microbiology↗

bioRxiv2026

Whole-genome sequencing data of a diverse grapevine germplasm collection maintained in Bordeaux, France

Grapevine (Vitis vinifera) is one of the worlds most economically important fruit crops and a model species for perennial fruit tree genetics and genomics. The extensive genetic diversity found in cultivated and wild Vitis species provides a valuable resource for studies of domestication, adaptation, trait evolution, and breeding. This article presents a standardized whole-genome variant dataset comprising 547 grapevine accessions maintained in the INRAE Bordeaux grapevine germplasm collection, including 397 domesticated V. vinifera cultivars and 150 wild Vitis accessions. Whole-genome sequencing data were generated at a target sequencing depth of approximately 20x, and sequence variants were identified using a standardized Genome Analysis Toolkit (GATK) workflow against the reference genome PN40024v4 (40X). Variant discovery was carried out simultaneously across the complete sample set to ensure consistent genotype calling. All accessions were sequenced using the same technology and processed using the same reference genome, sequence alignment, variant-calling, and filtering workflow to produce a standardized variant dataset comprising ca. 9.1M SNPs and 0.77M INDELs. The resulting VCF files provide a harmonized genomic resource that can be readily reused for studies of grapevine genetics, germplasm characterization, population genomics, comparative genomics, genome-wide association studies, and the development and benchmarking of bioinformatic methods. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@14f2b12org.highwire.dtl.DTLVardef@94b5acorg.highwire.dtl.DTLVardef@1232f80org.highwire.dtl.DTLVardef@1038e85org.highwire.dtl.DTLVardef@81ec71_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIThis dataset provides whole-genome raw sequencing for 118 wild Vitis accessions originating from North America and Asia and a sequencing-derived variant data for these accessions and 429 Vitis vinifera cultivars and wild accessions from the INRAE Bordeaux germplasm collection, previously published by Dong et al. 2023[1]. The dataset captures genetic variation across a total of 547 grapevine accessions, including domesticated and wild grapevine germplasm using a common variant-calling pipeline, facilitating direct comparisons among accessions. C_LIO_LIThe inclusion of wild Vitis species together with cultivated grapevine accessions provides a resource for studies of grapevine diversity, domestication, phylogenetic relationships, and comparative genomics. The dataset enables the investigation of genetic variation across multiple Vitis species using a standardized set of genomic variants. C_LIO_LIThe variant call format (VCF) file can be reused for population genetics, phylogenetic analyses, genetic diversity assessments, introgression analyses, and the identification of genomic regions of interest. The dataset is compatible with widely used bioinformatics software and can be integrated with other publicly available grapevine genomic resources. C_LIO_LIThis dataset constitutes a genomic resource for grapevine breeding and conservation research. Researchers can use these data to identify genetic diversity in wild relatives, compare allelic variation between cultivated and wild germplasm, investigate candidate loci associated with traits of interest, and support the management and characterization of grapevine germplasm collections. C_LI

genomics↗

bioRxiv2026

Direction of ESCRT-III-dependent membrane bending emerges from bilayer asymmetry

In cells, ESCRT-III is unique in mediating fission of membrane necks from inside, a process called reverse-topology fission. Yet, in vitro, the complex primarily assembles outside membrane necks and mediates fission with normal topology. Here, we show that the direction of ESCRT-mediated membrane deformation emerges from bilayer asymmetry rather than being intrinsically encoded by the ESCRT machinery alone. Using genetic perturbations in budding yeast, we find that disruption of phospholipid asymmetry and sphingolipid homeostasis does not abolish ESCRT-dependent trafficking but renders ILV formation highly sensitive to membrane physical state, leading to inefficient cargo sorting and accumulation of stalled endosomal intermediates. In vitro reconstitution experiments and synthetic in vivo cargo systems demonstrate that asymmetric protein distribution across the membrane is sufficient to bias curvature directionality, with luminal leaflet crowding promoting efficient ILV incorporation and cytosolic crowding inhibiting inward budding. Together, these results support a model in which ESCRT-mediated membrane bending directionality emerges from the intrinsic tension difference between the bilayer leaflets. This tension difference arises from both lipid and cargo crowding-encoded asymmetries within the bilayer, rather than being solely encoded by ESCRT polymer properties.

biophysics↗

bioRxiv2026

Non-plastic gene expression underlies root phenotypes involved in drought adaptation in Vitis spp.

Drought is a major abiotic stress threatening plant productivity and agricultural sustainability, yet the molecular mechanisms underlying adaptive root responses to water deficit in the water use strategies continuum remain insufficiently understood, particularly in perennial crops. In this study, we explored drought responses in nine accessions belonging to three wild Vitis species (V. acerifolia, V. candicans, and V. doaniana) displaying variying drought-response strategies. Plants were subjected to moderate drought stress (40% soil water content) for three weeks under greenhouse conditions. By integrating physiological, metabolic, and transcriptomic analyses, we aimed to identify both conserved and species-specific mechanisms associated with drought adaptation. Differential expression analyses revealed a conserved core set of drought-responsive genes shared among species, including genes involved in abscisic acid signaling, reactive oxygen species detoxification, solute transport, and plant defense. In parallel, each species exhibited distinct transcriptional and metabolic signatures reflecting alternative adaptive strategies related to osmoregulation, and oxidative stress mitigation. Weighted gene co-expression network analysis (WGCNA) further revealed significant associations between constitutive, non-plastic gene expression and root phenotypic traits. Overall, our findings demonstrate that wild Vitis species rely on both conserved stress-responsive pathways and species-specific constitutive regulation to cope with drought stress. These results highlight the importance of root-associated traits and intrinsic regulatory networks in shaping drought adaptation and provide new targets for the development of drought-resilient grapevine rootstocks.

plant biology↗

bioRxiv2026

A biochemical probe for microtubule lattice integrity uncovers motor-caused lattice damage

Microtubules experience mechanical and enzymatic stresses that can compromise lattice integrity, yet where and how lattice damage forms remains poorly understood due to the lack of tools that directly visualize damage as it occurs. Existing approaches infer damage indirectly through repair events or rely on static ultrastructural snapshots, precluding dynamic analysis. Here, we introduce MT-DS (Microtubule Damage Sensor), a damage-selective fluorescent probe that directly labels microtubule lattice openings. MT-DS combines taxane-based microtubule binding with a multivalent protein scaffold to restrict intraluminal diffusion and selectively retain the probe at sites of lattice openings. Using MT-DS, we visualize intrinsic lattice defects in stabilized microtubules, uncover a strong enrichment of damage at annealing sites, and demonstrate that kinesin-1{Delta}6 actively generates de novo lattice damage during motility. By enabling direct, time-resolved detection of microtubule damage, MT-DS establishes lattice integrity as an experimentally accessible parameter and provides a chemical tool to investigate how mechanical stress reshapes the microtubule cytoskeleton.

biochemistry↗

bioRxiv2025

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism

The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex conserved in all domains of life. However, whether membrane fission was an ancestral ESCRT-III activity predating eukaryogenesis remains unknown. Here we show that ESCRT-IIIA from Asgard Heimdallarchaeota, the closest archaeal relatives of eukaryotes, performs membrane fission through an N-terminal amphipathic helix, which we term Hofund. In eukaryotes, Hofund is fragmented across ESCRT-IIIA paralogs, and disrupting these regions causes severe fission defect in yeast. Remarkably, Heimdallarchaeota Hofund restores fission when fused to defective eukaryotic paralogs. These findings suggest that ESCRT-III-mediated fission arose before eukaryogenesis and later diversified to support the regulatory complexity of eukaryotic compartmentalization.

cell biology↗

bioRxiv2025

Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury

The cellular origin of intestinal epithelial homeostasis and regeneration has been a subject of continued debate, with recent models challenging the primacy of WNT-dependent Lgr5 crypt base columnar (CBC) cells as the central intestinal stem cell population. Here, we revisit this question through quantitative integration of single-cell transcriptomic, chromatin accessibility, spatial, and lineage-tracing analyses across the proximal-to-distal axis of the small intestinal epithelium. Our data show that under homeostatic conditions, Lgr5 cells exclusively sustain epithelial self-renewal in nearly all crypt-villus units along the entire length of the small intestine, a process for which R-spondin is indispensable. Following irradiation or chemotoxic injury, surviving Lgr5 cells and their progeny reprogram into transient fetal-like cell states that initiate epithelial repair. Crucially, successful regeneration depends on the reactivation of canonical WNT/{beta}-catenin signaling, as evidenced by increased TCF motif accessibility and upregulation of WNT target genes in newly forming Lgr5+ stem cells. Accordingly, pharmacological inhibition of WNT signaling blocks the reconstitution of Lgr5 cells and crypt regeneration, leading to epithelial collapse. These findings reconcile prior controversies by demonstrating the central role of Lgr5 CBC cells in epithelial self-renewal and regeneration following injury.

cell biology↗

bioRxiv2025

Cardiomyopathy-Associated and Basic Residue Mutations in Myopalladin Alter Actin Binding, Bundling, and Structural Stability

BACKGROUNDMyopalladin (MYPN) is a striated muscle-specific sarcomeric protein belonging to the immunoglobulin (Ig)-domain-containing family of actin regulators. The Ig3 domain of MYPN is indispensable for interacting with and stabilizing actin filaments, and an increasing number of cardiomyopathic (CM)-associated mutations have been identified within this domain, highlighting its importance for normal cardiac function. Despite their clinical significance, the molecular basis of how these variants disrupt MYPN activity remains poorly understood. METHODSTo identify actin-binding sites, we introduced charge-neutralizing alanine substitutions at basic residues in the Ig3 domain and assessed their impact using actin co-sedimentation assays. CM mutations were similarly evaluated for their effect on actin interaction. Wild-type (WT) and mutant MYPN were expressed in Drosophila cardiomyocytes and body wall muscles to assess localization and interaction with actin. The impact of these mutations on protein secondary structure and stability was determined by circular dichroism spectroscopy. In addition, the WT Ig3 domain was further analyzed in co-sedimentation and co-polymerization assays to quantify polymerization of monomeric actin, subsequent bundling and to assess how calcium and salt concentrations modulate MYPN Ig3-actin interactions. RESULTSMYPN-actin binding is electrostatically driven and mediated by conserved basic charge clusters within its Ig3 domain, a mechanism common among many actin-binding proteins. CM mutations disrupted the MYPN-actin interaction, leading to significant loss of actin bundling without broadly altering secondary structure, except in the destabilized P961L variant. Immunostaining and green fluorescent protein (GFP)-tagged constructs revealed that R955W and P961L mutants accumulated into clusters at the Z-discs. WT Ig3 domain assays further showed that MYPN promotes actin polymerization and crosslinking even under non-polymerizing conditions, and actin-binding activity was not modulated by calcium. CONCLUSIONSThese findings demonstrate that CM-linked MYPN Ig3 mutations compromise actin binding and organization, suggesting that disruption of the MYPN-actin interface is a key pathogenic mechanism in cardiomyopathy. What Is Known?O_LIMyopalladin (MYPN) is a striated muscle-specific sarcomeric protein. C_LIO_LIMYPN plays an important role in controlling skeletal muscle growth by regulating actin dynamics and modulating stress-responsive signal transduction and gene expression. C_LIO_LIMutations in MYPN are linked to various inherited cardiomyopathies (CMs), including dilated, hypertrophic, restrictive, and left ventricular noncompaction forms. C_LI What new information does this article contribute?O_LITwo conserved clusters of basic residues on the surface of Ig3 domain were identified as key mediators of actin binding and bundling. C_LIO_LISeveral cardiomyopathy (CM)-associated MYPN mutations localize to this region, where they impair actin interactions and nearly abolish actin bundling activity. C_LIO_LIMutants such as R955W and P961L mislocalize abnormally in Drosophila cardiomyocytes and body wall muscles. C_LI Novelty and SignificanceThe importance of the MYPN gene, which encodes the sarcomeric protein myopalladin (MYPN), was highlighted when 66 mutations in this gene were linked to cardiomyopathies (CMs). MYPN bundles and stabilizes actin filaments and is essential for the organization and maintenance of Z-disc integrity. The C-terminal immunoglobulin (Ig) domains mediate actin interactions, with the Ig3 domain representing the minimal actin-binding unit. Notably, many disease-associated mutations cluster within this actin-binding region and give rise to diverse clinical phenotypes. Despite its clinical relevance, the molecular mechanisms by which different MYPN mutations lead to CM remain poorly understood. Prior mechanistic studies focused mainly on mutations within the cardiac ankyrin repeat protein (CARP) interaction domain of MYPN, which disrupt signaling and nuclear shuttling. In contrast, our study addresses mutations localized to the actin-binding region of MYPN. The effects of these mutations on MYPN-actin interactions had not been previously explored. We show that CM-associated mutations within the Ig3 domain disrupt MYPN-actin interactions, reduce or abolish actin bundling, and induce abnormal subcellular localization patterns in Drosophila cardiac and skeletal muscles. This study provides the first direct evidence that disruption of MYPN-actin interactions represents a distinct and clinically relevant mechanism of cardiomyopathy.

biochemistry↗

bioRxiv2025

Microtubule lattice conformation and integrity regulate α-tubulin acetylation

Microtubule acetylation of lysine 40 of -tubulin is a hallmark of stable microtubules. This luminal modification is catalyzed by -tubulin acetyltransferase 1 (TAT1) and reversed by histone deacetylase 6 (HDAC6). However, acetylation regulation within the microtubule lumen and the influence of lattice architecture on enzymatic activity remain poorly understood. Here, we reconstitute microtubule acetylation in vitro using purified TAT1 and HDAC6 on microtubules assembled with defined lattice conformations. We show that TAT1 overwrites HDAC6 enzymatic activity, but its acetylation efficiency decreases upon microtubule damage. Importantly, TAT1 efficiently acetylates microtubules in expanded lattices and twisted tubulin states, while compacted lattices impede its activity. Our findings reveal that both microtubule integrity and lattice conformation are critical regulators for TAT1 enzymatic activity, suggesting that dynamic lattice transitions modulate the acetylation pattern of microtubules in cells.

cell biology↗

bioRxiv2025

Phase Separation and a Hydrodynamic Instability Localize Proteins at Growing Microtubule Ends

Regulating microtubule dynamics is essential for cellular function, and precise localization of regulatory proteins at microtubule ends is critical. End-binding protein EB3, a key regulator of microtubule growth, accumulates over an extended region at the growing end, forming a comet that gradually fragments into transient droplets along the microtubule shaft. Here, we combine in vitro reconstitution experiments with theoretical analysis to show that surface-mediated condensation of EB3 effectively localizes the protein at microtubule ends. Our results reveal that a Rayleigh-Plateau instability limits the condensates extent, producing a finite comet length and discrete droplets along the shaft. Remarkably, the comet size is independent of the GTP-cap size. This finding is supported by experiments on cells showing that modulation of microtubule growth velocity and hence GTP-cap size do not consistently alter EB3 comet length. Furthermore, our theory shows that rapid droplet evaporation requires a transition of EB3 to a non-phase-separating state. Overall, our work challenges the view that comet length directly reflects GTP-cap size and highlights a novel mechanism for regulating microtubule dynamics.

biophysics↗

bioRxiv2025

Distinguish risk genes functioning at presynaptic or postsynaptic regions and key connectomes associated with pathological α-synuclein spreading

Previous studies have suggested that pathological -synuclein (-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: (1) How many and which connections in the connectome are necessary for predicting the progression of pathological -Syn? (2) How to identify risk gene that affects pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, we addressed these key questions with novel mathematical models. Strikingly, the spreading of pathological -Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. We further explored the genes that are responsible for the selective vulnerability of different brain regions to transmission to distinguish the genes that play roles in presynaptic from those in postsynaptic regions. Those risk genes were significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses were then conducted to identify key drivers of genes responsible for selective vulnerability and overlapping with Parkinsons disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, our study has demonstrated for the first time that these are functionally distinct processes.

neuroscience↗

bioRxiv2025

ACLY promotes NK cell effector function by regulating glycolysis and histone acetylation

Natural Killer (NK) cells are innate immune lymphocytes important for host viral and tumor immunity. We investigated the requirement for ATP citrate lyase (ACLY) in NK cell function using an inducible genetic mouse model. ACLY regulates the citrate-malate shuttle, generating cytosolic acetyl-coenzyme A that is primarily used for acetylation or lipid synthesis. ACLY-deficient NK cells upon IL-15 activation exhibited significant defects in glycolysis, proliferation, cytokine production, and cytotoxicity, without decreased intracellular lipids. Notably, ACLY-deficiency specifically resulted in reduced NK cell responses to activating receptors associated with the adapter proteins DAP10 or DAP12. This is due to decreased DAP12 and increased DAP10 transcript and protein, coupled with epigenetic profiling that demonstrated altered histone acetylation of these genes in ACLY KO. Supplementation of ACLY-deficient NK cells with acetate was sufficient to overcome most functional defects, including restoring DAP10/12 expression and activating receptor function, emphasizing the importance of ACLY-generated cytosolic acetyl-coenzyme A for NK effector functions.

immunology↗

bioRxiv2024

Key Regulatory Elements of the TGFbeta-LRRC15 Axis Predict Disease Progression and Immunotherapy Resistance Across Cancer Types

Transforming growth factor-beta (TGF{beta}) has dual roles in cancer, initially suppressing tumors but later promoting metastasis and immune evasion. Efforts to inhibit TGF{beta} have been largely unsuccessful due to significant toxicity and indiscriminate immunosuppression. Leucine-rich repeat-containing protein 15 (LRRC15) is a TGF{beta}-regulated antigen expressed by mesenchymal-derived cancer cells and cancer-associated fibroblasts (CAFs). In preclinical studies, ablation of TGF{beta}-driven LRRC15+ CAFs increased tumor infiltration of CD8+ T cells. However, the underlying pathobiological mechanisms prompting TGF{beta}s upregulation of LRRC15 expression are unclear. Using an integrated approach combining functional compound screening with single-cell RNA sequencing, we reveal key genomic features regulating TGF{beta}s ability to increase LRRC15 expression on cancer cells. Construction of gene regulatory networks converged our analyses on four key genes--MMP2, SPARC, TGF{beta}R2, and WNT5B--central to TGF{beta}-induced LRRC15 pathobiology. Validation of these genes in cell models and their use in predicting immunotherapy responses highlight their potential in refining immunotherapy strategies and personalizing co-treatment options.

pharmacology and toxicology↗

bioRxiv2024

Perinatal Reduction of Genetically Aberrant Neurons from Human Cerebral Cortex

Human neurons are postmitotic and long-lived, requiring precise genomic regulation to maintain function over a lifetime. Normal neuronal function is highly dependent on gene dosage, with copy number variants (CNVs) and heterozygous point mutations associated with a host of neurodevelopmental and neuropsychiatric conditions [1-5]. Here, we investigated the landscape of somatic CNVs arising in fetal human brains, and how they change over development, to understand the processes that generate normal neuronal genomes. We sequenced 2,158 single neurons from human postmortem brain using two distinct single cell whole genome sequencing (scWGS) approaches. Tn5-transposase based (TbA) scWGS of 1,327 neurons from 16 individuals ranging in age from gestational week 14 to 90 years old resulted in 8,765 CNVs. Primary template amplification (PTA) was used to assess for CNV from 831 neurons from 12 individuals. Up to 46% of neurons in prenatal cortex showed aberrant genomes, characterized by widespread CNVs of multiple chromosomes, but this proportion reduces by 4-5 fold after birth across the two scWGS approaches (p=7.5x10-6, Fisher meta-analysis). We identified micronuclei in the developing cortex in situ, reflecting chromosomal material missegregated during neurodevelopment [6-8]. Neurons with widespread CNVs were eliminated in the perinatal period, while neurons with smaller CNV burden slowly declined during postnatal aging. CNVs in surviving neurons were depleted for genes that are dosage-sensitive or involved in neurodevelopmental disorders (p<0.05), suggesting selective elimination of neurons with CNVs involving these critical genes. We surveyed 44,861 nuclei with 10X Genomics scATAC/RNAseq and determined that neurons with high CNV burdens also showed abnormal expression of synaptic gene sets, suggesting that abnormal synaptic gene regulation contributes to neuronal elimination. Elimination of defective neuronal genomes during synaptogenesis may represent a critical process of genome quality control and a vulnerable target of factors that contribute to neurodevelopmental disease.

neuroscience↗