Biology subjects

Xu, J.

Publications and source records attributed to Xu, J..

At least 343 records · Page 19Linked to original sources

bioRxiv2024

LncCE: Landscape of Cellular-Elevated LncRNAs in Single Cells Across Normal and Cancer Tissues

Long non-coding RNAs (lncRNAs) have emerged as significant players for maintaining the morphology and function of tissues or cells. The precise regulatory effectiveness of lncRNA is closely associated with the spatial expression patterns across tissues and cells. Here, we proposed the Cellular-Elevated LncRNA (LncCE) database to systematically explore cellular-elevated (CE) lncRNAs across normal and cancer tissues in single cells. LncCE encompasses 87,946 CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing (scRNA-seq) datasets, involved in 20 fetal normal tissues, 59 adult normal tissues, as well as 32 adult and 5 pediatric cancer tissues.Two main search options were provided via a given lncRNA name or a cell type. The output results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, co-expression with protein-coding genes as well as their involved in biological functions. For cancers, LncCE particularly provided quantitative figures for exhibiting their expression changes compared to control samples and clinical associations with patient overall survivals. Together, LncCE offers an extensive, quantitative and user-friendly interface to investigate cellular-elevated expression atlas for lncRNAs across normal and cancers tissues at single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.

cancer biology↗

bioRxiv2024

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods to accurately determine the clinical impact of variants of unknown significance (VUS). Towards this goal, the ARSA Critical Assessment of Genome Interpretation (CAGI) challenge was designed to characterize progress by utilizing 219 experimentally assayed missense VUS in the Arylsulfa-tase A (ARSA) gene to assess the performance of community-submitted predictions of variant functional effects. The challenge involved 15 teams, and evaluated additional predictions from established and recently released models. Notably, a model developed by participants of a genetics and coding bootcamp, trained with standard machine-learning tools in Python, demonstrated superior performance among sub-missions. Furthermore, the study observed that state-of-the-art deep learning methods provided small but statistically significant improvement in predictive performance compared to less elaborate techniques. These findings underscore the utility of variant effect prediction, and the potential for models trained with modest resources to accurately classify VUS in genetic and clinical research.

genetics↗

bioRxiv2024

Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells

Although mitochondrial DNA (mtDNA) variants hold promise as endogenous barcodes for tracking human cell lineages, their efficacy as reliable lineage markers is hindered by the complex dynamics of mtDNA in somatic tissues. Here, we utilized computational modeling and single-cell genomics to thoroughly interrogate the origin and clonal dynamics of mtDNA lineage markers across various biological settings. Our findings revealed the majority of purported "clone informative variants (CIVs)" were pre-existing heteroplamies in the first cell instead of de novo somatic mutations during divisions. Moreover, CIVs demonstrated limited discriminatory power among different lineages during normal development; however, certain CIVs with consistently high allele frequencies proved capable of faithfully labeling cell lineages in scenarios of stringent clonal expansion. Inspired by our simulations, we introduced a lineage informative (LI) score, facilitating the identification of reliable mitochondrial lineage markers across different modalities of single-cell genomic data.

bioinformatics↗

bioRxiv2024

Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq

Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seqs exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

biochemistry↗

bioRxiv2024

eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer

The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5 UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant--an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.

cancer biology↗

bioRxiv2024

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat

Error self-correction is a pivotal first step in the analysis of long-read sequencing data. However, most existing methods for this purpose are primarily tailored for noisy sequencing data with error rates exceeding 5%, often collapsing true variants in repeats and haplotypes. Alternatively, some methods are heavily optimized for PacBio HiFi reads, leaving a gap in methods specifically designed for Nanopore R10 reads basecalled with high accuracy or super accuracy models, which typically have error rates below 2%. Here, we introduce DeChat, a novel approach specifically designed for Nanopore R10 reads. DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected. Benchmarking experiments reveal that reads corrected using DeChat exhibit substantially fewer errors, ranging from several times to two orders of magnitude lower, compared to the current state-of-the-art approaches. Furthermore, the application of DeChat for error correction significantly improves genome assembly across various aspects. DeChat is implemented as a highly efficient, standalone, and user-friendly software and is publicly available at https://github.com/LuoGroup2023/DeChat.

bioinformatics↗

bioRxiv2024

Singular Odorant Receptor Expression Orchestrated by Promoter Activation Specificity in Apis Mellifera Olfactory Sensory Neurons

Honeybee, positioned as an outgroup of flies and mosquitos, have exhibited intriguing duplications and expansions of OR genes in genomic studies. However, little is known about how the OR genes are expressed and regulated in honeybee olfactory sensory neurons (OSNs). In this study, we utilized a single-cell multi-omics approach to profile the transcriptome and chromatin accessibility in Apis mellifera antennal nuclei, aiming to elucidate OR gene expression and its underlying regulatory mechanisms. Our systematical analysis unveiled a similar singular expression pattern of ligand-specific receptors in Apis mellifera OSNs, parallel with those observed in Drosophila melanogaster. Mechanistically, we discovered that promoter activation of OR genes orchestrates receptor expression patterns. For instance, although multiple adjacent OR genes are co-expressed with a single active promoter through polycistronic transcription, only the first OR gene could produce functional receptor protein, as supported by transcriptome quantification in OSNs. Additionally, we found that co-expression of receptor proteins might occur only when co-expressed OR genes possess multiple accessible promoters. This scenario is less common than expected, considering the number and evolutionary age of OR genes in Apis mellifera, suggesting a selection favoring the specialization of rapidly expanded OR genes in Apis mellifera. Overall, our study provides significant insights into the insect olfaction system and the regulatory mechanisms of OR genes expression.

neuroscience↗

bioRxiv2024

Mitochondrial Oxidative Phosphorylation Capacity in Skeletal Muscle Measured by Ultrafast Z-Spectroscopy (UFZ) MRI at 3T

BackgroundTo investigate the feasibility of rapid CEST MRI acquisition for evaluating oxidative phosphorylation (OXPHOS) in human skeletal muscle at 3 Tesla, utilizing ultrafast Z-spectroscopy (UFZ) MRI combined with the Polynomial and Lorentzian line-shape Fitting (PLOF) technique. MethodsUFZ MRI on muscle was evaluated with turbo spin echo (TSE) and segmented 3D EPI readouts. Five healthy subjects performed in-magnet plantar flexion exercise (PFE) and subsequent changes of amide, phosphocreatine (PCr) and partial PCr mixed creatine (Cr+) CEST dynamic signals post-exercise were enabled by PLOF fitting. PCr/Cr CEST signal was further refined through pH correction by using the ratios between PCr/Cr and amide signals, named PCAR/CAR, respectively. ResultsUFZ MRI with TSE readout significantly reduces acquisition time, achieving a temporal resolution of <50 seconds for collecting high-resolution Z-spectra. Following PFE, the recovery/decay times ({tau}) for both PCr and Cr in the gastrocnemius muscle of the calf were notably longer when determined using PCr/Cr CEST compared to those after pH correction with amideCEST, namely [Formula] s and{tau} PCr = 98.1 {+/-} 20.4 s versus{tau} CAR =36.4 {+/-} 18.6 s and{tau} PCAR = 43.0 {+/-} 13.0 s, respectively. Literature values of{tau} PCr obtained via 31P MRS closely resemble those obtained from pH-corrected PCr/Cr CEST signals. ConclusionThe outcomes suggest potential of UFZ MRI as a robust tool for non-invasive assessment of mitochondrial function in skeletal muscles. pH correction is critical for the reliable OXPHOS measurement by CEST.

biophysics↗

bioRxiv2024

Ca2+-dependent phosphodiesterase 1 regulates the plasticity of striatal spiny projection neuron glutamatergic synapses

Long-term synaptic plasticity at glutamatergic synapses on striatal spiny projection neurons (SPNs) is central to learning goal-directed behaviors and habits. Although considerable attention has been paid to the mechanisms underlying synaptic strengthening and new learning, little scrutiny has been given to those involved in the attenuation of synaptic strength that attends suppression of a previously learned association. Our studies revealed a novel, non-Hebbian, long-term, postsynaptic depression of glutamatergic SPN synapses induced by interneuronal nitric oxide (NO) signaling (NO-LTD) that was preferentially engaged at quiescent synapses. This form of plasticity was gated by local Ca2+ influx through CaV1.3 Ca2+ channels and stimulation of phosphodiesterase 1 (PDE1), which degraded cyclic guanosine monophosphate (cGMP) and blunted NO signaling. Consistent with this model, mice harboring a gain-of-function mutation in the gene coding for the pore-forming subunit of CaV1.3 channels had elevated depolarization-induced dendritic Ca2+ entry and impaired NO-LTD. Extracellular uncaging of glutamate and intracellular uncaging of cGMP suggested that this Ca2+-dependent regulation of PDE1 activity allowed for local regulation of dendritic NO signaling. This inference was supported by simulation of SPN dendritic integration, which revealed that dendritic spikes engaged PDE1 in a branch-specific manner. In a mouse model of Parkinsons disease (PD), NO-LTD was absent not because of a postsynaptic deficit in NO signaling machinery, but rather due to impaired interneuronal NO release. Re-balancing intrastriatal neuromodulatory signaling in the PD model restored NO release and NO-LTD. Taken together, these studies provide novel insights into the mechanisms governing NO-LTD in SPN and its role in psychomotor disorders, like PD.

neuroscience↗

bioRxiv2024

Calneuron 1 reveals the pivotal roles in schizophrenia via perturbing human forebrain development and causing hallucination-like behavior in mice

Schizophrenia is a highly heritable neurodevelopmental disorder with unknown genetic pathogenic mechanisms. Here, we selected 11 schizophrenia risk genes and generated single-gene-knockout-precise-dorsal/ventral-forebrain-organoids (SKOPOS) via CRISPR-Cas9 system. 90 bulk and 249,430 single-cell RNA-sequencing of SKOPOS revealed that knockout of 11 risk genes lead to different levels of deficits in dorsal/ventral forebrain organoids. Among them, calneuron 1 (CALN1) acts as a pivotal pathogenic gene of schizophrenia via severe disruption of gene expression network, interaction with about 32% (34/106) known schizophrenia risk genes, delayed maturation and impaired spontaneous neural circuit in human developing forebrain. Furtherly, including the spontaneous abrupt burst spiking in cortical neurons and the defects of spatial memory, cognition and social ability, Caln1 KO mice surprisingly displayed spontaneous startle behavior and head-twitch response correlated with hallucination-like behavior, which could be inhibited by antipsychotic drug SEP-363856. In summary, CALN1 is identified as a pivotal pathogenic gene of schizophrenia in forebrain development.

neuroscience↗

bioRxiv2024

InstructPLM: Aligning Protein Language Models to Follow Protein Structure Instructions

Large language models are renowned for their efficacy in capturing intricate patterns, including co-evolutionary relationships, and underlying protein languages. However, current methodologies often fall short in illustrating the emergence of genomic insertions, duplications, and insertion/deletions (indels), which account for approximately 14% of human pathogenic mutations. Given that structure dictates function, mutated proteins with similar structures are more likely to persist throughout biological evolution. Motivated by this, we leverage crossmodality alignment and instruct fine-tuning techniques inspired by large language models to align a generative protein language model with protein structure instructions. Specifically, we present a method for generating variable-length and diverse proteins to explore and simulate the complex evolution of life, thereby expanding the repertoire of options for protein engineering. Our proposed protein LM-based approach, InstructPLM, demonstrates significant performance enhancements both in silico and in vitro. On native protein backbones, it achieves a perplexity of 2.68 and a sequence recovery rate of 57.51, surpassing Protein-MPNN by 39.2% and 25.1%, respectively. Furthermore, we validate the efficacy of our model by redesigning PETase and L-MDH. For PETase, all fifteen designed variable-length PETase exhibit depolymerization activity, with eleven surpassing the activity levels of the wild type. Regarding L-MDH, an enzyme lacking an experimentally determined structure, InstructPLM is able to design functional enzymes with an AF2-predicted structure. Code and model weights of InstructPLM are publicly available*.

bioinformatics↗

bioRxiv2024

Proinflammatory stress activates neutral sphingomyelinase 2 based generation of a ceramide-enriched β cell EV subpopulation

{beta} cell extracellular vesicles (EVs) play a role as paracrine effectors in islet health, yet mechanisms connecting {beta} cell stress to changes in EV cargo and potential impacts on diabetes remain poorly defined. We hypothesized that {beta} cell inflammatory stress engages neutral sphingomyelinase 2 (nSMase2)-dependent EV formation pathways, generating ceramide-enriched EVs that could impact surrounding {beta} cells. Consistent with this, proinflammatory cytokine treatment of INS-1 {beta} cells and human islets concurrently increased {beta} cell nSMase2 and ceramide expression, as well as EV ceramide staining. Direct chemical activation or genetic knockdown of nSMase2, or treatment with a GLP-1 receptor agonist also modulated cellular and EV ceramide. Small RNA sequencing of ceramide-enriched EVs identified a distinct set of miRNAs linked to {beta} cell function and identity. Coculture experiments using CD9-GFP tagged INS-1 cell EVs demonstrated that either cytokine treatment or chemical nSMase2 activation increased EV transfer to recipient cells. Children with recent-onset T1D showed no abnormalities in circulating ceramide-enriched EVs, suggesting a localized, rather than systemic phenomenon. These findings highlight nSMase2 as a regulator of {beta} cell EV cargo and identify ceramide-enriched EV populations as a contributor to EV-related paracrine signaling under conditions of {beta} cell inflammatory stress. Article HighlightsO_ST_ABSa. Why did we undertake this study?C_ST_ABSMechanisms connecting {beta} cell stress to changes in extracellular vesicle (EV) cargo and potential impacts on diabetes are poorly defined. b. What is the specific question we wanted to answer?Does {beta} cell inflammatory stress engage neutral sphingomyelinase 2 (nSMase2)-dependent EV formation pathways to generate ceramide-enriched EVs. c. What did we find?Proinflammatory cytokine treatment of {beta} cells increased {beta} cell ceramide expression, along with EV ceramide in part via increases in nSMase2. Ceramide-enriched EVs housed a distinct set of miRNAs linked to insulin signaling. Both cytokine treatment and nSMase2 activation increase EV transfer to other {beta} cells. d. What are the implications of our findings?Our findings highlight nSMase2 as a regulator of {beta} cell EV cargo and identify ceramide-enriched EV populations as a contributor to EV-related paracrine signaling under conditions of {beta} cell inflammatory stress.

molecular biology↗

bioRxiv2024

Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and variances from genotype-phenotype datasets. Averages and variances are legitimated upon creating distribution density functions obtained through the grouping of data into categories. However, as data from within a given category cannot be differentiated, the investigative power of such methodologies is limited. Genomic Informational Field Theory (GIFT) is a method specifically designed to circumvent this issue. The way GIFT proceeds is opposite to that of GWAS. Whilst GWAS determines the extent to which genes are involved in phenotype formation (bottom-up approach), GIFT determines the degree to which the phenotype can select microstates (genes) for its subsistence (top-down approach). Doing so requires dealing with new genetic concepts, a.k.a. genetic paths, upon which significance levels for genotype-phenotype associations can be determined. By using different datasets obtained in ovis aries related to bone growth (Dataset-1) and to a series of linked metabolic and epigenetic pathways (Dataset-2), we demonstrate that removing the informational barrier linked to categories enhances the investigative and discriminative powers of GIFT, namely that GIFT extracts more information than GWAS. We conclude by suggesting that GIFT is an adequate tool to study how phenotypic plasticity and genetic assimilation are linked. NEW & NOTEWORTHYThe genetic basis of complex traits remains challenging to investigate using classic GWASs. Given the success of gene editing technologies this point needs to be addressed urgently since there can only be useful editing technologies if precise genotype-phenotype mapping information is available initially. GIFT is a new mapping method designed to increase the investigative power of biological/medical datasets suggesting, in turn, the need to rethink the conceptual bases of quantitative genetics.

genetics↗

bioRxiv2024

All-trans retinoic acid induces durable tumor immunity in IDH-mutant gliomas by rescuing transcriptional repression of the CRBP1-retinoic acid axis

Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4+ T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.

cancer biology↗

bioRxiv2024

Archaeal type six secretion system mediates contact-dependent antagonism

Microbial communities are shaped by cell-cell interactions. Even though archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here we report the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time lapse imaging, we show that Halogeometricum borinquense exhibits antagonism towards Haloferax volcanii by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed CISs bound to the cytoplasmic membrane, resembling bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains with antagonistic behavior. Our data provides a mechanistic framework for understanding how archaea may shape microbial communities and impact the food webs they inhabit. TeaserT6SSs are widespread in the archaeal domain and used to kill other archaea.

microbiology↗

bioRxiv2024

Plant Development Drives Dynamic Shifts in the Root Compartment Microbiomes of Wild and Domesticated Finger Millet Cultivars

BackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plants developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages. ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples were Proteobacteria, Actinobacteria, and Bacteroidetes, while the dominant fungal phyla were Ascomycota and Basidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance of Actinobacteria in the endosphere was accompanied by a reduced abundance of Proteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genus Pseudomonas. Moreover, the host plants developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plants developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.

microbiology↗

bioRxiv2024

Transcriptional activation of Bmal1 drives the inflammatory activity of monocytes by modulating mitochondrial unfolded protein response during hypobaric hypoxic stress

BackgroundHypoxic stress-induced inflammation had been considered to play an important role in the onset and progression of altitude-related illnesses, but the origin of inflammatory cytokines, the specific responding cell types, and molecular mechanisms remain unknown. Mitochondria are responsible for oxygen consumption and recently reported to be the master regulators of inflammation, but it is not clear whether and how mitochondrial organelles sense the hypoxic stress and then control the inflammation. MethodsHuman subjects and mouse models were exposed to real or simulated altitude of 5500 m. Bone marrow-derived macrophages (BMDMs) and monocyte RAW264.7 cells were cultured under 1% oxygen hypoxic conditions. Myeloid-specific Bmal1 knock-out mice were generated by crossing Bmal1flox/flox mice with Lyz2-Cre mice. Inflammation was investigated by assessing inflammatory mediators, monocyte activities, and leukocyte infiltrating. Mitochondrial unfolded protein response was examined by measuring stress markers, such as LONP1, AFG3L2, and HSP60. The target molecular mechanisms were identified by performing bioinformatic analyses, ChIP assays, and gain/loss-of-function experiments. Results1) Monocytes in peripheral blood mononuclear cell (PBMCs) were more sensitive and contributed promptly to circulating inflammation in response to acute hypobaric hypoxia. 2) Hypoxic stress triggered the mitochondrial unfolded protein response and then induced the mito-inflammation (NLRP3 inflammasome) in monocytes. 3) Activation of Bmal1 drove mitochondrial stress and mito-inflammation by promoting Fis1-mediated mitochondrial fission in monocytes under hypoxia. 4) BHLHE40, a stress-responsive transcription factor directly targeted by HIF-1, stimulated Bmal1 transcription in monocytes under hypobaric hypoxia. 5) Myeloid-specific Bmal1 deletion alleviated systemic circulating and vascular inflammation under acute hypobaric hypoxia. ConclusionBHLHE40, a transcription factor associated with hypoxia, stimulated Bmal1, which in turn triggered the mitochondrial unfolded protein response and drove the mito-inflammation in monocytes by promoting Fis1-mediated mitochondrial fission. Our work provides a novel mechanism which may develop the circadian targeting drugs for altitude or hypoxia-related diseases.

molecular biology↗

bioRxiv2024

GABAAR-PPT1 palmitoylation homeostasis controls synaptic transmission and circuitry oscillation in CLN1 disease

CLN1 disease, also called infantile neuronal ceroid lipofuscinosis, is a fatal neurodegenerative disease caused by mutations in the CLN1 gene encoding palmitoyl protein thioesterase 1 (PPT1). To identify depalmitoylation substrate of PPT1 is crucial to understand CLN1 disease. In this study, we found that PPT1 depalmitoylates GABAAR 1 subunit at Cystein-260, while binding to Cystein-165 and -179. Mutations of PPT1 or its GABAAR 1 subunit binding site result in enhanced inhibitory synaptic transmission, strengthened and oscillation but disrupted phase coupling in CA1 region and impaired learning and memory in 1- to 2-months-old PPT1-deficient and Gabra1em1 mice. Our study highlights the critical role of PPT1 in maintaining GABAAR palmitoylation homeostasis and reveals a previously unknown molecular pathway in PPT1 induced diseases.

neuroscience↗