Biology subjects

Bai, X.

Publications and source records attributed to Bai, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Chronic kidney disease exacerbates hyperlipidemia and atherosclerosis via miR-148a-3p targeting SIK1/AMPKα1 in liver

BackgroundCardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). As a major risk factor for atherosclerotic cardiovascular disease (ASCVD), hyperlipidemia is a common sequela of CKD, which is linked to increased lipid synthesis, impaired lipoprotein clearance, and maladapted reverse cholesterol transport. Because exosomes can transport miRNAs to modulate intercellular and tissue communication, we hypothesized that exosomal miRNAs can act as endocrine-like molecules to modulate the CKD-associated hyperlipidemia and ASCVD. MethodsSmall RNA-seq and qPCR were used to determine the differential plasma level of exosomal miR-148a-3p in ASCVD patients with and without CKD. RNA-seq and in silico analysis were used to establish the regulation of lipid metabolism via miR-148a-3p/salt-inducible kinase 1 (SIK1)/AMP-activated protein kinase alpha 1 subunit (AMPK1) in the liver. Inhibition of miR-148a-3p or overexpression of SIK1/AMPK1 in ApoE-/- mice with 5/6 nephrectomy was used to elucidate the role of the miR-148a-3p/SIK1/AMPK1 axis in CKD-related hyperlipidemia and atherosclerosis. ResultsThe plasma level of exosomal miR-148a-3p was significantly elevated in patients with ASCVD and CKD (ASCVD/CKD) and ApoE-/- mice with 5/6 nephrectomy. Via circulating exosomes, kidney-generated miR-148a-3p was delivered to the liver, where it targeted SIK1/AMPK1 transcripts, thereby upregulating SREBP2/PCSK9 and reciprocally downregulating LDLR. Levels of SIK1 and AMPK1 were decreased in hepatocytes transfected with miR-148a-3p or treated with plasma exosomes from ASCVD/CKD patients, with attendant SREBP2 activation and attenuated LDL-C binding. The decreased LDL-C binding was rectified by SIK1/AMPK1 or LNA-miR-148a-3p overexpression. LNA-miR-148a-3p or AAV8-SIK1/AMPK administration in 5/6 nephrectomy/ApoE-/- mice significantly ameliorated hyperlipidemia and atherosclerosis. ConclusionIn ASCVD/CKD patients and nephrectomy/ApoE-/- mice, kidney-originating miR-148a-3p targeted hepatic SIK1/AMPK1 mRNA. This exosome-mediated endocrine effect upregulated SREBP2/PCSK9 and reciprocally reduced LDLR level, which elevated plasma LDL-C level and exacerbated ASCVD. These findings underscore a kidney-liver-artery axis involved in cardiovascular-kidney-metabolic syndrome.

pathology↗

bioRxiv2025

Cold sensing by a glutamate receptor drives avoidance behavior in Drosophila larvae

The ability to sense and avoid noxious environments is essential for animal survival; yet, how this is achieved at the behavioral, neuronal, and molecular levels is not well understood. Here, we use Drosophila larvae as a model to investigate how animals sense and avoid cold temperatures. By implementing custom-built thermoelectric devices capable of delivering rapid and precise thermal stimuli, we find that cold delivered to the larval head evokes robust escape behavioral responses. We identify a group of head-located cold-sensitive neurons as necessary and sufficient for such avoidance responses. We further demonstrate that the kainate-type glutamate receptor Clumsy acts as a novel cold sensor required for head cold sensitivity. Knockdown of Clumsy in head cold-sensing neurons suppresses their cold sensitivity. Heterologous expression of Clumsy confers cold sensitivity. Our results show that Drosophila larvae have evolved the capacity to detect and avoid cold temperatures through a previously uncharacterized cold-sensing mechanism.

neuroscience↗

bioRxiv2025

Dual role of GABAB receptor in oligodendrocyte function and immune modulation in experimental multiple sclerosis

GABAB receptors (GABABR) mediate the actions of the inhibitory neurotransmitter GABA in the central nervous system, regulating key processes such as synaptic activity, interneuron communication and excitation-inhibition balance in the brain. Recent studies using the GABABR agonist baclofen have revealed a critical role for these receptors in promoting oligodendroglial differentiation in both health and disease, highlighting their potential as therapeutic targets in demyelinating diseases such as multiple sclerosis (MS). In this study, we identify a dual role for oligodendroglial GABABR in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. Conditional deletion of the GABAB1 subunit in NG2+ cells ameliorates acute disease symptoms while inducing an immune-like phenotype in oligodendrocytes. This immunomodulatory role is further supported by pharmacological activation of GABABR in oligodendrocytes, which reduces the expression of MHC class II in these cells. Notably, baclofen treatment after EAE symptom onset attenuates the course of the disease while enhancing oligodendrocyte progenitor cell differentiation and suppressing T cell infiltration into demyelinating lesions. Moreover, prophylactic baclofen administration delays disease onset and further decreases immune cell recruitment into the spinal cord, underscoring its potent immunomodulatory effect. These data demonstrate that GABABR signaling exerts context-dependent effects on both oligodendrocyte lineage progression and neuroinflammatory responses. Importantly, these compelling findings validate baclofen, a drug already approved for MS-associated spasticity, as a promising candidate for therapies targeting both inflammation and remyelination, advancing our understanding of glial-immune interactions in demyelinating diseases and supporting the translational potential of GABABR modulation in MS.

neuroscience↗

bioRxiv2025

A multimodal human-computer interaction dataset for neurocognitive user state evaluation

We introduce the Simulated Environment for Neurocognitive State Evaluation (SENSE-42), a multimodal dataset collected during user interactions with desktop computers. It is designed for studying spontaneous fluctuations in the neurocognitive state related to the tonic alertness of computer users, with recordings from 42 participants over 2-hour sessions. Within a simulated desktop environment, participants performed real-world routine tasks, including application switching, file management, typing, and web browsing. High-resolution data were recorded across physiological (electroencephalography, electrocardiography, respiration) and subjective modalities of alertness. At five-minute intervals, alertness state was reported using seven questions, addressing sleepiness (Karolinska Sleepiness Scale), mental and temporal demand, perceived performance, effort and frustration (NASA Task Load Index), as well as attentiveness. Behavioural data included keyboard, mouse and webcam inputs. Demographic information, experience metrics, habits, and preferences of computer usage were collected. In addition, individual differences in sleep quality were evaluated using the Pittsburgh Sleep Quality Index and the Epworth Sleepiness Scale. The SENSE-42 dataset can contribute to future research in user state monitoring, behavioural analysis and physiological computing.

neuroscience↗

bioRxiv2025

Systematic Evaluation of Somatic Contamination in Germline Genomes

Large-scale genomic initiatives like the UK Biobank (UKB) have revolutionized our understanding of human disease. These studies typically assume that blood-derived DNA faithfully reflects an individuals germline genome. However, this assumption is challenged by somatic mutations arising from processes like clonal hematopoiesis. Although standard bioinformatics pipelines employ variant allele frequency (VAF)-based filtering to mitigate such contamination, the efficacy of these approaches requires systematic evaluation. By systematically analyzing whole-exome sequencing (WES) and whole-genome sequencing (WGS) data from large cohorts, including the UK Biobank, The Cancer Genome Atlas (TCGA), and the 1000 Genomes Project, we revealed critical limitations in current filtering methodologies. We found that the mutational spectrum of rare "germline" variants is highly similar to that of somatic mutations. Furthermore, we uncovered these variants show significant associations with phenotypes such as age, sex, and smoking status, established drivers of somatic mutagenesis. This persistent somatic contamination introduces substantial confounder effects, potentially generating spurious associations and reverse causality in genetic studies. Our work underscores the urgent reconsideration of two fundamental aspects of genomic research: (1) refinement of variant filtering strategies to better distinguish true germline variants from somatic contaminants, and (2) incorporation of somatic mutagenesis factors as essential covariates in study design. Our findings provide a basic framework for improving the accuracy and interpretability of large-scale genomic studies.

genomics↗

bioRxiv2025

Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases

BackgroundNon-small cell lung cancer (NSCLC) patients with brain metastases (BMET) have a poor prognosis. Cerebrospinal fluid (CSF) is a source of cell free DNA (cfDNA) from the brain and its methylation and fragmentation properties may be an indicator of NSCLC-BMET. MethodsWe applied a nanopore single-molecule sequencing approach to characterize the fragmentation, methylation and hydroxymethylation patterns present in CSF-derived cfDNA from NSCLC-BMET patients (N=15). We compared the cancer cfDNA finding to non-cancer healthy controls (N=11) and their CSF cfDNA. We also compared the fragmentation patterns between CSF-derived cfDNA and plasma-derived cfDNA. ResultsWe observed enriched mono-nucleosome levels and significantly higher mono-/trinucleosome ratios in cancer patients. Comparison with plasma-derived cfDNA further confirmed the unique fragmentation features of CSF-derived cfDNA. Distinct methylation and hydroxymethylation patterns were observed between cancer and control CSF samples. We observed significantly lower degree of hydroxymethylation in cancer patients compared to healthy controls and the affected genes had different pathway profiles. ConclusionsCSF cfDNA in patients with NSCLC-BMET had a distinct profiles of DNA fragmentation, methylation and hydroxymethylation.

genomics↗

bioRxiv2025

Overcoming breeding constraints in polyploid oat from evolutionary insights

Polyploidy provides adaptive advantages in plants by buffering deleterious mutations1,2. While polyploidization can enhance agronomic traits such as increased biomass, known as the gigas effect1-4, increasing genetic gain in polyploid crops remains a critical but difficult goal due to the difficulty in dissecting complex trait inheritance5,6. Here we present chromosome-scale genome assemblies for 26 Avena taxa, spanning diploid, tetraploid, and hexaploid lineages. We traced four independent polyploidization events across the genus, including the formation of A. agadiriana as an allotetraploid (AgAgAg'Ag'), and revealed a reticulate evolutionary history shaped by gene flow involving four subgenomes (A, B, C, D), for example, the hybrid speciation of A. hirtula. Transcriptomic analysis of 286 samples across 11 tissues, combined with deleterious mutation analysis from a cultivated population of 112 accessions, showed that polyploidization led to widespread functional redundancy among homoeologs, supporting a genome-wide buffering effect. However, derived allele frequency analysis revealed that, while disrupting functional genes may yield desirable traits, the buffering effect impedes the fixation of beneficial loss-of-function mutations and thereby limits breeding efficiency. Based on these integrative analyses, we propose breeding strategies to circumvent these limitations by targeting beneficial loss-of-function alleles within the complex polyploid background of oat. Our study highlights broader challenges in the improvement of polyploid crops and provides a foundation for future breeding strategies.

evolutionary biology↗

bioRxiv2025

Changing the initiation unit of nonribosomal peptide synthetases to access underexplored biosynthetic potential

Nonribosomal peptide synthases (NRPSs) are large multimodular enzymes, capable of synthesizing nonribosomal peptides (NRPs) with diverse structures and bioactivities. Genome sequencing revealed a large number of uncharacterized NRPS biosynthetic gene clusters (BGCs) and their products are underexplored. The majority of NRPSs remain silent potentially attributed to factors such as the low activity of the initiation unit or insufficient precursor supply. Exchanging the starter condensation (Cs) domains within initiation unit can change the length of acyl chains of NRPs, hinting at a promising strategy through swapping of a well-studied Cs domain to activate the initiation unit and harness primary metabolites as precursors, which may offer a new option to access silent BGCs. Here, we first pinpointed two highly efficient fusion sites for initiation unit exchanges. Subsequently, they were validated by replacing the initiation region of endopyrrole pathway with a Cs-containing initiation unit for generation of a lipo-endopyrrole derivate. We promptly leveraged this strategy of changing initiation unit to target six previously silent NRPS BGCs, three BGCs were successfully activated and five novel lipopeptides were identified, demonstrating its application to recover silent BGCs. Furthermore, we extended this strategy in more BGCs from different bacteria. Utilizing a heterologous Cs-containing unit to replace the initiation region of chitinimide biosynthetic pathway led to successful incorporation of N-terminal fatty acid chains into chitinimide to create artificial lipo-chitinimides. This study provides a feasible strategy to rationally recover silent BGCs and add fatty acid chains to NRPs, enriching the genome mining and combinatorial biosynthesis approach for bacterial natural products. SignificanceNonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored reservoir for bioactive natural products, but most of them are silent. This study introduces the concept that changing initiation unit to activate and optimize the functional expression of NRPSs, and successfully access three of six previously silent NRPS pathways, providing a feasible complement to the current genome mining approaches. Moreover, the N-terminal lipid chains are crucial for the activity of lipopeptides. We employed a heterologous Cs (starter condensation domain)-containing initiation unit to replace the original initiation region for creation of artificial nonribosomal lipopeptides, ultimately yielding three novel lipo-derivatives. This work presents a groundbreaking approach for activating and optimizing NRPSs and provides profound insight into the exploration of bacterial NRPS pathways.

synthetic biology↗

bioRxiv2025

Bridging Stem Cell Models and Medicine: Integrated 3D Human Cerebral Organoids and Pediatric Serum Reveal Mechanisms and Biomarkers of Anesthetic-Induced Neurotoxicity

BackgroundGeneral anesthetics have been shown to cause acute pathological changes in the developing brain, including neuronal cell death. These effects contribute to long-term cognitive and behavioral impairments observed in animal models. Epidemiological and prospective clinical studies have also reported associations between early-life exposure to anesthesia and neurodevelopmental deficits in children, raising significant concerns about pediatric anesthesia and highlighting the urgent need to understand the molecular mechanisms and biomarkers of anesthetic-induced developmental neurotoxicity (AIDN) using human-relevant models. MethodsThis study employed human induced pluripotent stem cell-derived cerebral organoids that were exposed to varying doses of anesthetic propofol for 1 to 6 hours, including single and repeated exposures. In parallel, serum samples were collected pre- and post-surgery from pediatric patients under 4 years old (n = 10 per group) who underwent either short (<1 hour) or prolonged anesthesia (>3 hours) at the Childrens Hospital of Wisconsin between September 2018 and October 2019. Pathological changes in organoids were assessed using chemical assays, electron microscopy, and western blotting. Brain injury-related proteins in patient serum were quantified via ELISA. Genome-wide expression profiling was conducted on 18,855 mRNAs and 27,427 lncRNAs in organoids and serum using microarray and bioinformatics. ResultsHigher doses, longer duration, and repeated exposures to propofol led to increased apoptosis in organoids. Six-hour exposure induced autophagy as evidenced by LC3-II elevation and led to dysregulation of 553 mRNAs and 792 lncRNAs in organoids, along with their co-expressed signaling networks, affecting pathways related to synaptic integrity, mitochondrial function, and inflammation. ELISA and serum analysis of pediatric patients (<4 years old) exposed to anesthesia (>3 hours) demonstrated elevated brain cell injury-associated proteins (e.g., increased NSE) and brain cell type-specific gene expression changes. Serum findings corroborated organoid data, identifying 21 mRNAs and 12 lncRNAs that were dysregulated in both models and associated with cell injury, neuronal development, inflammation, and learning deficits. ConclusionsThis study represents the first integrative transcriptomic analysis of AIDN using both 3D human cerebral organoids and pediatric patient serum--two complementary, human-relevant models. By identifying consistently dysregulated coding and non-coding RNAs across both platforms, we provide compelling evidence of shared molecular signatures linked to neuronal injury, inflammation, and neurodevelopmental disruption. These findings offer not only mechanistic insights but also lay the groundwork for the development of minimally invasive biomarkers and future therapeutic strategies. This dual-model approach bridges experimental discovery with clinical relevance, advancing the translational understanding of pediatric anesthetic neurotoxicity and supporting efforts to improve long-term neurological outcomes in vulnerable patient populations.

neuroscience↗

bioRxiv2025

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

bioRxiv2025

Nanosecond pulsed electric field precisely manipulates cytoplasmic Ca2+ oscillations during oocyte activation

Oocyte activation deficiency (OAD) is a primary cause of fertilization failure following intracytoplasmic sperm injection (ICSI), a problem that can potentially be overcome through artificial oocyte activation (AOA). However, concerns persist regarding the safety and efficacy of AOA techniques in clinical practice. In this study, nanosecond pulsed electric field (nsPEF) is proposed as a safe and controllable method for oocyte activation in vitro by precisely manipulating Ca2+ signaling in the ooplasm. Mouse oocytes collected from oviducts were exposed to nsPEF stimulation at varying intensities to induce distinct Ca2+ signaling patterns. Subsequently, these oocytes underwent parthenogenetic activation and were cultured to assess developmental potential up to the blastocyst stage. The sperm-initiated physiological Ca2+ oscillations are successfully mimicked by one series of Ca2+ signals induced by nsPEF at low or medium intensities, and improve activation efficiency and developmental potential compared to calcium ionophore A23187. Low-intensity nsPEF pulses mediated repetitive extracellular Ca2+ influx in a non-invasive, electro-permeable manner. Medium-intensity nsPEF stimulation triggered periodic Ca2+ release from the endoplasmic reticulum (ER) via the PIP2-IP3-IP3R pathway, producing physiological-like Ca2+ oscillations. The non-invasive nsPEF method ensures safe oocyte activation by preserving cellular integrity and minimizing stress responses. The efficacy of nsPEF in precisely manipulating Ca2+ signaling patterns was further validated in human unfertilized oocytes. Our findings present a novel AOA approach with enhanced safety and efficacy, especially for patients experiencing repeated fertilization failures. It is anticipated that nsPEF is emerging as a promising technology for addressing male infertility issues, and may offer a potential alternative fertility treatment, bypassing sperm for initiation of oocyte activation.

developmental biology↗

bioRxiv2025

The photoreaction process of a large-Stokes-shift red fluorescence protein-LSSmCherry1

Large Stokes shift red fluorescent proteins are highly valued in fluorescence imaging due to their considerable spectral separation and minimal self-absorption. However, a notable gap remains in our understanding of these proteins excited-state dynamics. Unlocking this knowledge could potentially drive significant advancements in cellular and molecular biology. In this study, we systematically examine the excited-state dynamics of LSSmCherry1, a large Stokes shift red fluorescent protein, under varying isotopic compositions and temperatures. Our aim is to elucidate its distinctive spectral properties. Through steady fluorescence spectral experiments at different temperatures, we demonstrate that the large Stokes shift is significantly reduced by approximately 80 nm at low temperatures compared to room temperature. Using transient fluorescence and absorption spectroscopy, we dissect the excited-state dynamics of LSSmCherry1 in neutral environments. We also investigate the kinetic isotopic effect by comparing spectra in water and heavy water. These analyses allow us to delineate plausible photocyclic pathways. Our results reveal that the excited-state dynamics of LSSmCherry1 follow a model similar to that observed in other fluorescent proteins, such as Green Fluorescent Protein (GFP). Notably, we demonstrate that the excited-state proton transfer (ESPT) process is the primary origin of the large Stokes shift in LSSmCherry1. This ESPT process occurs rapidly, within approximately 365 fs after excitation in the neutral environment. This study provides crucial insights into the mechanisms underlying large Stokes shift fluorescent proteins, potentially paving the way for the development of improved fluorescent probes for biological imaging. TOC GraphicSome journals require a graphical entry for the Table of Contents. This should be laid out "print ready" so that the sizing of the text is correct. Inside the tocentry environment, the font used is Helvetica 8 pt, as required by Journal of the American Chemical Society. The surrounding frame is 9 cm by 3.5 cm, which is the maximum permitted for Journal of the American Chemical Society graphical table of content entries. The box will not resize if the content is too big: instead it will overflow the edge of the box. This box and the associated title will always be printed on a separate page at the end of the document.

biochemistry↗

bioRxiv2025

Structural insights into the ubiquitin independent MIDN-proteasome pathway

The protein midnolin (MIDN) augments proteasome activity in lymphocytes, where it is predominantly expressed in adult mice. MIDN binds both to proteasomes and to substrates, but the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is unknown. Here, we present cryo-electron microscopy structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11. By simultaneously binding to RPN1 with its C-terminal -helix, MIDN positions its substrate-carrying Catch domain above the proteasome channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal -helix must bind to the proteasome for MIDN to stimulate proteasome activity.

biophysics↗

bioRxiv2025

Generalization but not strengthening of negative memories drives the development of depression-like behaviors

Individuals with depression exhibit intensified and generalized negative memories. However, how prior memories actually influence onset and/or progression of depression, particularly whether the strengthening or the generalization of prior memories play a key role, is poorly understood. Here, we introduced behavioral paradigms to differentiate between memory strengthening and generalization, and found that negative experiences that produced memory overgeneralization, but not strengthening, induced depression-like behaviors. Furthermore, we identified that the medial prefrontal cortex (mPFC) to the bed nucleus of the stria terminals (BNST) projection functionally linked memory generalization to depression, together with single-cell calcium imaging which revealed a significant overlap in the mPFCBNST neuronal ensemble encoding depression-like behaviors with that encoding generalized memory, but not memory strength. Circuit-based transcriptomic analysis and chromophore-assisted light inactivation demonstrated that triggering actin remodeling in the mPFCBNST neurons, a memory consolidation mechanism enhanced generalization while reducing memory strength, also induced depression-like behaviors. Collectively, these findings suggest generalization of negative memories as a primary factor that drives depression-like behaviors, highlighting the importance of early identification of individuals at risk for depression who exhibit overgeneralized negative memories, and targeting overgeneralized negative memories in the treatment of depression.

animal behavior and cognition↗

bioRxiv2025

DUSP11 is an intracellular innate immune checkpoint in lung adenocarcinoma

The discovery of immune checkpoints and the rapid growth of immuno-oncology (IO) have sparked tremendous efforts to utilize the immune system to treat a wide range of cancer types/subtypes. While the major focus of IO over the past decades has been to manipulate the adaptive immune system, recent attention has been given to manipulating the innate immune system to treat cancer and/or to enhance adaptive responses. In this work we detail the intracellular protein, Dual Specificity Phosphatase 11 (DUSP11), as an innate immune checkpoint (iIC) in Non-Small Cell Lung Cancer (NSCLC) adenocarcinoma (LUAD). Expression of this atypical phosphatase is correlated with patient survival for multiple cancer types, and we show here that its activity is important for the viability of lung cancer cells in vitro. Specifically, we demonstrate that DUSP11 knockdown in LUAD cells induces apoptosis and an innate immune response capable of activating other cells in vitro, and we provide evidence that these phenotypes are primarily mediated by the pattern recognition receptor, retinoic acid inducible gene I (RIG-I). Finally, we show that expression of DUSP11 is important for tumor engraftment and growth of human LUAD in mice. Overall, these data are the first to establish DUSP11 as an immunosuppressive, pro-neoplastic, and potentially targetable protein in LUAD. In addition, our data suggests that the anti-cancer mechanisms induced by diminishing the activity of DUSP11 are likely to be generalizable to other cancer types such as breast cancer, warranting future investigation and therapeutic development.

cancer biology↗

bioRxiv2024

Association Between Oral Microbiota and Close-Range Proximity in a Primary School

The microbiota is the ensemble of microorganisms inhabiting the human body and it deeply influences human health and well-being. Recent studies showed its interplay with social behavior, suggesting that part of the microbiota might be socially transmissible. In this work, we investigate the association between close-range proximity and the oral microbiota composition in a group of children attending primary school. Unlike most related studies, our cohort comprises non-cohabiting individuals, and we use high-resolution proximity sensors to objectively quantify close-range proximity. Our analysis shows that longer time spent in proximity between pairs of children correlates with a higher similarity between their oral microbiota composition. Building on previous studies on cohabiting individuals, our findings suggest that social contacts beyond the closest social circle may also shape oral microbiota composition, although longitudinal studies are needed to test this hypothesis.

microbiology↗

bioRxiv2024

Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells

BackgroundThe understanding of genetic and epigenetic regulation of gene expression in endothelial and vascular smooth muscle cells remains fragmented with limited experimental validation. MethodsChromatin conformation (Micro-C), DNA methylation (RRBS), chromatin accessibility (ATAC-seq), and transcriptome profiles (RNA-seq) were mapped in human induced pluripotent stem cell (hiPSC)-derived, isogenic endothelial and vascular smooth muscle cells (iECs and iVSMCs). CTCF and RAD21 were depleted to assess the functional relevance of chromatin architecture, and genome editing was used to evaluate the allelic effect of a blood pressure-associated single nucleotide polymorphism (SNP). ResultsSignificant correlations were identified between gene expression levels and chromatin interactions, chromatin accessibility, and DNA methylation in iECs and iVSMCs, with chromatin interactions showing the strongest association. Chromatin contact regions displayed distinct epigenetic landscapes depending on the types of regulatory element interactions involved. Perturbation of CTCF and RAD21 revealed their differential regulatory effects, particularly on the expression of genes overlapping chromatin contacts, with RAD21 exhibiting a broader regulatory impact. SNPs associated with several vascular traits were enriched in chromatin loops or accessible regions in iECs or iVSMCs. Precise genome editing demonstrated allele-dependent effects of SNP rs9833313 on the expression of SHOX2 located 247.4 kbp away but within the same chromatin loops as the SNP. ConclusionThis study provides an extensive epigenetic landscape of vascular cells that may drive novel research on the role of genetic and epigenetic mechanisms of vascular function and disease as demonstrated by our targeted experiments.

genomics↗

bioRxiv2024

H2B.W2, a Spermatocytes-specific Histone Variant, disrupts nucleosome stability and reduces chromatin compaction

Spermatogenesis is a highly regulated process that requires precise chromatin remodeling, which includes the incorporation of testis-specific histone variants. While several of these variants have been characterized, the role of H2B.W2, a member of the H2BW family, remains largely unclear. Here, we showed that H2B.W2 expression occurs mainly in spermatocytes, slightly later than its paralog H2B.W1. Cryo-electron microscopy (cryo-EM) analysis of H2B.W2-containing nucleosomes reveals a more relaxed conformation compared to canonical nucleosomes caused by weakened interactions between the outer DNA turn and the histone core. We pinpointed the N-terminal tail and 2 helix of H2B.W2, specifically residues D85 and Q101, as critical for nucleosome destabilization. Furthermore, we identify G73 within the L1 loop as a key residue involved in disrupting higher-order chromatin structure. Our findings suggest that H2B.W2-mediated nucleosome and chromatin destabilization may play a role in regulating gene expression during spermatogenesis, with potential implications for sperm development and function.

biochemistry↗