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Han, J.

Publications and source records attributed to Han, J..

At least 235 records · Page 13Linked to original sources

Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation

Histone acetylation is a key component in the consolidation of long-term fear memories. Epigenetic enzymes involved in histone acetylation, including histone acetyltransferases and deacetylases, have been put forward as potential pharmacological targets in the treatment of pathological fear memories, such as those that underlie post-traumatic stress disorder (PTSD). However, these enzymes typically play a ubiquitous role in gene regulation, which precludes the clinical use of systemic manipulations. Recently, we have found that a nuclear-localized metabolic enzyme, Acetyl-coA synthetase 2 (Acss2), modulates histone acetylation during learning and memory. Loss of Acss2 is well-tolerated in mice, with no impact on general health or baseline behavior. Here, we show that an Acss2 null mouse model shows reduced acquisition of long-term fear memories in assays of contextual and cued fear conditioning. We find that loss of Acss2 leads to consolidation-specific reductions in both histone acetylation and the expression of critical learning and memory-related genes in the dorsal hippocampus. Further, we show that systemic administration of blood-brain-barrier (BBB)-permeable Acss2 inhibitors during the consolidation window reduces fear memory formation in mice and rats, and also reduces anxiety in a predator-scent-stress (PSS) paradigm. Our findings suggest that Acss2 plays a critical role in the formation of fear memories, and represents a potential pharmacological target in the treatment of PTSD.

neuroscience↗

Extensive mosaicism by somatic L1 retrotransposition in normal human cells

Over the course of an individuals lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape by retrotranspositions of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 892 single-cell clones established from various tissues collected from 28 individuals. Remarkably, 88% of colorectal epithelial cells acquired somatic L1 retrotranspositions (soL1Rs), carrying [~]3 events per cell on average with substantial intra- and inter-individual variances, which was accelerated at least 10-fold during tumourigenesis. Breakpoints of soL1Rs suggested that a few variant mechanisms can be involved in the L1 retrotransposition processes. Fingerprinting of donor L1s using source-specific unique sequences revealed 34 hot L1s, 44% of which were newly discovered in this study, and many ultra-rare hot L1s in the human population showed higher retrotransposition potential in somatic lineages than common sources. Multi-dimensional analysis of soL1Rs with early embryonic developmental relationships, genome-wide methylation, and gene expression profiles of the clones demonstrated that (1) soL1Rs occur from early embryogenesis at a substantial rate, (2) epigenetic activation of hot L1s is stochastically acquired during the wave of early global epigenomic reprogramming, rather than by the sporadic loss-of-methylation at the late stage, and (3) most L1 transcripts in the cytoplasm do not generate soL1Rs in somatic lineages. In summary, this study provides insights into the retrotransposition dynamics of L1s in the human genome and the resultant somatic mosaicism in normal human cells.

genomics↗

Musashi1 and its short C-terminal variants regulate pluripotency states in embryonic stem cells

Musashi1 (MSI1) is a marker for adult stem cells, but little is known for its expression and function in pluripotent stem cells (PSCs). Here we report that MSI1 is expressed in embryonic stem cells (ESCs) and is required for pluripotency maintenance. We found that there exit short c-terminal MSI1 variants (MSI1-C, hMSI1272-362 or mMSI1138-362) in naive but not primed ESCs. When overexpressed, MSI1 and MSI1-C variants facilitate primed-to-naive pluripotency transition by elevating the pluripotency of primed hESCs toward a formative-like state, enable better survival of hESCs in human-mouse interspecies cell completion, and enhance the ability of blastoid formation of hESCs after naive induction. Mechanistically, we show that the MSI1-C variants, though lacking RNA recognition motifs, bind to RNAs, enhance stress resistance and upregulate DNA damage repair genes. Thus, this study demonstrates that ESCs utilize MSI1 and the newly identified short MSI1-C proteins as double swords to regulate pluripotency states.

developmental biology↗

Helminth egg derivatives as pro-regenerative immunotherapies

The immune system is increasingly recognized as an important regulator of tissue repair. We developed a regenerative immunotherapy from the helminth Schistosoma mansoni soluble egg antigen (SEA) to stimulate production of interleukin (IL)-4 and other type 2-associated cytokines without negative infection-related sequelae. The regenerative SEA (rSEA) applied to a murine muscle injury induced accumulation of IL-4 expressing T helper cells, eosinophils, and regulatory T cells, and decreased expression of IL-17A in gamma delta ({gamma}{delta}) T cells, resulting in improved repair and decreased fibrosis. Encapsulation and controlled release of rSEA in a hydrogel further enhanced type 2 immunity and larger volumes of tissue repair. The broad regenerative capacity of rSEA was validated in articular joint and corneal injury models. These results introduce a new regenerative immunotherapy approach using natural helminth-derivatives. One-Sentence SummaryHelminth-derived soluble egg antigen regenerative immunotherapies promote tissue repair in multiple injury models.

bioengineering↗

Neural Implementation of Precise Temporal Patterns in Motor Cortex

One of the most concerned problems in neuroscience is how neurons communicate and convey information through spikes. There is abundant evidence in sensory systems to support the use of precise timing of spikes to encode information. However, it remains unknown whether precise temporal patterns could be generated to drive output in the primary motor cortex (M1), a brain area containing ample recurrent connections that may destroy temporal fidelity. Here, we used a novel brain-machine interface that mapped the temporal order and precision of motor cortex activity to the auditory cursor and reward to guide the generation of precise temporal patterns in M1. During the course of learning, rats performed the "temporal neuroprosthetics" in a goal-directed manner with increasing proficiency. Precisely timed spiking activity in M1 was volitionally and robustly produced under this "temporal neuroprosthetics", demonstrating the feasibility of M1 implementing temporal codes. Population analysis showed that the local network was coordinated in a fine time scale as the overall excitation heightened. Furthermore, we found that the directed connection between neurons assigned to directly control the output ("direct neurons") was strengthened throughout learning, as well as connections in the subnetwork that contains direct neurons. Network models revealed that excitatory gain and strengthening of subnetwork connectivity transitioned neural states to a more synchronous regime, which improved the sensitivity for coincidence detection and, thus, the precision of spike patterns. Therefore, our results suggested the recurrent connections facilitate the implementation of precise temporal patterns instead of impairing them, which provided new perspectives on the fine-timescale activity and dynamics of M1.

neuroscience↗

Synaptic wiring motifs in posterior parietal cortex support decision-making

The posterior parietal cortex (PPC) exhibits choice-selective activity during perceptual decision-making tasks. However, it is not known how this selective activity arises from the underlying synaptic connectivity. Here, we combined virtual reality behavior, two-photon calcium imaging, high throughput electron microscopy, and circuit modeling to analyze how synaptic connectivity between neurons in PPC relates to their selective activity. We found that excitatory pyramidal neurons preferentially target inhibitory interneurons with the same selectivity. In turn, inhibitory interneurons preferentially target pyramidal neurons with opposite selectivity, forming an opponent inhibition motif. Using circuit models, we show that opponent inhibition amplifies selective inputs and induces competition between neural populations with opposite selectivity, thereby improving the encoding of trial-type information. These results provide evidence for how synaptic connectivity in cortical circuits supports a learned decision-making task.

neuroscience↗

Cell-specific regulation of gene expression using splicing-dependent frameshifting.

Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, sequence conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED vectors can leverage the strong expression of constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. We generated SLED vectors to selectively target all neurons, photoreceptors, or excitatory neurons, and demonstrated that specificity was retained in vivo when delivered using AAVs. We further demonstrated the utility of SLED by creating what would otherwise be unobtainable research tools, specifically a GluA2 flip/flop reporter and a dual excitatory/inhibitory neuronal calcium indicator. Finally, we show the translational potential of SLED by rescuing photoreceptor degeneration in Prph2rds/rds mice and by developing an oncolytic vector that can selectively induce apoptosis in SF3B1 mutant cancer cells. The flexibility of SLED technology enables new avenues for basic and translational research.

molecular biology↗

Microbial dysbiosis and metabolic disorders promote rheumatoid arthritis progression across successive stages

BackgroundRheumatoid arthritis (RA) is a chronic inflammatory disease that typically progresses through four stages, from mild stiffness to severe disability. The critical involvement of gut microbial dysbiosis in promoting RA has been intriguing. The aim of this study was to investigate stage-specific roles of microbial dysbiosis and metabolic disorders in pathogenesis across successive stages of RA. MethodsIn this multi-omics cohort study, fecal metagenomic, plasma metabolomic data were collected from 76 patients grouped into four RA stages, 19 patients with osteoarthritis, and 27 healthy individuals in China. A non-redundant gene catalogue was constructed, functionally annotated, and clustered into metagenomic species (MGS). Leave-one-out analysis was performed to determine the MGS that most drove the microbial dysfunctions with RA across stages. Random forest algorithm was performed to investigate diagnostic potential of microbial or metabolic features for each stage. Additionally, to verify the bacterial invasion of the joint synovial fluid, we conducted 16S rRNA gene sequencing, bacterial isolation, and scanning electron microscopy on joint synovial fluid from another cohort of 271 RA patients grouped into four RA stages. FindingsWe found that microbial dysbiosis and metabolic disorders had stage-specific effects on RA progression. For instance, arginine succinyltransferase pathway was elevated mainly in the second and third stages of RA (p=1{middle dot}4x10-3), which was driven by Escherichia coli, and it was correlated with the increase of the rheumatoid factor (p=1{middle dot}35x10-3). Considerable elevation of methoxyacetic acid (p=1{middle dot}28x10-8) and cysteine-S-sulfate (p=4{middle dot}66x10-12) might inhibit osteoblasts in the second stage and enhance osteoclasts in the third stage, respectively. Moreover, fecal microbes Eggerthella lenta and Bifidobacterium longum that were exclusively elevated in the fourth stage, were also detected in the joint synovial fluid. InterpretationOur findings elucidate for the first time the stage-specific roles of microbial dysbiosis and metabolic disorders across successive stages of RA, which open up new avenues for RA prognosis and therapy. We demonstrate the buildup of these effects might induce microbial invasion of the joint synovial fluid in the fourth stage of RA.

microbiology↗

PDR6-mediated camalexin efflux and disease resistance are regulated through direct phosphorylation by the kinases OXI1 and AGC2-2

Plant immune signaling largely relies on post-translational modifications to establish a rapid and appropriate defense response to different pathogen types and infection pressure. Specific pleiotropic drug resistance (PDR) transporters can transport secondary metabolites to contribute to pathogen invasion resistance. However, the establishment of the post-translational regulation of PDR transporters that efflux secondary metabolites is unclear. In this study, by detecting the camalexin contents on the leaf surfaces of mutants and overexpression lines, two AGC kinases, namely, OXI1 and its closest homologue AGC2-2, were found to be related to extracellular camalexin secretion. The overexpression of OXI1 or AGC2-2 resulted in an increase in camalexin contents on the leaf surface and a decrease in camalexin contents in the leaf interior. These effects increased the resistance of the transgenic lines to surface-inoculated Pseudomonas syringae and Botrytis cinerea. Through in vitro kinase assay and in vivo phosphorylation level detection, we confirmed that the two kinases were related to the phosphorylation modification of PDR6. Pull-down assays, bimolecular fluorescence complementation, and rapamycin-dependent delocalization assays indicated the existence of direct protein-protein interaction between the two kinases and PDR6. By using LC-MS/MS, we also identified the PDR6 phosphorylation sites that were modified by the two kinases in vitro. Through the expression of the dephosphorylated variants of PDR6 in the mutant background, the action site S31 of OXI1 and the action sites S33 and S827 of AGC2-2 were found to have positive effects on the efflux activity of PDR6. In addition, T832, the action site of OXI1, may contribute to the stability of PDR6 on the plasma membrane.

plant biology↗

Identification and characterization of the HERV-K (HML-8) group of human endogenous retroviruses in the genome

Human endogenous retroviruses (HERV) could vertically transmit in a Mendelian fashion and stable maintenance in the human genome which are estimated to comprise about 8%. HERVs affect human physiology and pathology based on the effect of the provirus-encoded protein or LTR elements. The characterization of the genomic distribution is an essential step to understanding the relationship between endogenous retrovirus expression and diseases. However, the poorly characterization of HML-8 hinders a detailed understanding of the expression regulation of this family in human health and its actual impact on host genomes. In the light of this, the definition of a precise and updated HERV-K HML-8 genomic map is urgently needed. Here we report a comprehensive analysis of HERV-K HML-8 sequences presence and distribution within the human genome, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements were characterized with a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor binding sites, and primer binding site feature. The integration time results showed that the HML-8 elements found in the human genome have been integrated in the primate lineage between 23.5 and 52 million years ago (mya). Overall, the results have finally clarified the composition of HML-8, providing an exhaustive background for subsequent functional studies. Highlights[tpltrtarr] A comprehensive characterization of the HERV-K (HML-8) in human genome. [tpltrtarr]There is an apparent preference of HML-8 into intergenic regions and introns. [tpltrtarr]There are two distinct clusters for the env region of the HML-8 elements. [tpltrtarr]The average time of HML-8 integration in human is 37.1 mya.

microbiology↗

Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2

Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to their poor stability, most current mRNA delivery platforms need to be stored at -20{degrees}C or -70{degrees}C, which severely limits their distribution. Herein, we present lyophilized SARS-CoV-2 mRNA-lipid nanoparticle vaccines, which can be stored at room temperature with long-term thermostability. In the in vivo Delta virus challenge experiment, lyophilized Delta variant mRNA vaccine successfully protected mice from infection and cleared the virus. Lyophilized omicron mRNA vaccine enabled to elicit both potent humoral and cellular immunity. In booster immunization experiments in mice and old monkeys, lyophilized omicron mRNA vaccine could effectively increase the titers of neutralizing antibodies against wild-type coronavirus and omicron variants. In humans, lyophilized omicron mRNA vaccine as a booster shot could also engender excellent immunity and had less severe adverse events. This lyophilization platform overcomes the instability of mRNA vaccines without affecting their bioactivity, and significantly improved their accessibility, particularly in remote regions.

immunology↗

The Emergence of the Metabolic Signaling of the Nucleoredoxin-like Genes during Evolution

The nucleoredoxin-like genes NXNL1 and NXNL2 were identified through the biological activity of rod-derived cone viability factors (RdCVF and RdCVF2), the alternatively spliced variants produced by intron retention, that mediate signaling between rod and cone photoreceptors by stimulating glucose uptake. These therapeutic genes for inherited retinal degenerations also produce by splicing thioredoxin-like proteins that reduce oxidized cysteines in photoreceptor proteins. The first NXNL genes date from the first animal phyla. Intron retention produces an active RdCVF protein in the tentacles of Hydra vulgaris, a species without eyes. A Scallop RdCVF protein is produced by ciliated photoreceptors of the retina and binds its receptor, BSG1. In the lamprey, a descendent of early vertebrates, RdCVF metabolic signaling between rod and cones is fully established. In the mouse, the production of BSG1 by photoreceptors is regulated by cell-specific splicing inhibition. RdCVF signaling predates photoreceptors and evolved through two alternative splicing events.

evolutionary biology↗

When self comes to a wandering mind: Brain representations and dynamics of self-generated concepts in spontaneous thought

AO_SCPLOWBSTRACTC_SCPLOWSelf-relevant concepts are major building blocks of spontaneous thought, and their dynamics in a natural stream of thought are likely to reveal ones internal states important for mental health. Here we conducted an fMRI experiment (n = 62) to examine brain representations and dynamics of self-generated concepts in the context of spontaneous thought using a newly developed free association-based thought sampling task. The dynamics of conceptual associations were predictive of individual differences in general negative affectivity, replicating across multiple datasets (n = 196). Reflecting on self-generated concepts strongly engaged brain regions linked to autobiographical memory, conceptual processes, emotion, and autonomic regulation, including the medial prefrontal and medial temporal subcortical structures. Multivariate pattern-based predictive modeling revealed that the neural representations of valence became more person-specific as the level of perceived self-relevance increased. Overall, this study provides a hint of how self-generated concepts in spontaneous thought construct inner affective states and idiosyncrasies.

neuroscience↗

Intracranial Electric Field Recording During Multichannel Transcranial Electrical Stimulation

BackgroundMultichannel transcranial electrical stimulation (tES) modeling and optimization have been widely studied in recent years. Its theoretical bases include quasi-static assumption and linear superposition. However, there is still a lack of direct in vivo evidence to validate the simulation model and theoretical assumptions. MethodsWe directly measured the multichannel tES-induced voltage changes with implanted stereotactic-electroencephalographic (sEEG) electrodes in 12 epilepsy subjects. By combining these measured data, we investigate the linear superposition and prediction accuracy of simulation models for multi-electrode stimulation and further compare the induced EF differences between transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS). ResultsOur in vivo measurements demonstrated that the multi-electrode tES-induced voltages were almost equal to the sum of the voltages generated independently by bipolar stimulation. Both measured voltages and electric fields obtained in vivo were highly correlated with the predicted values in our cohort (Voltages: r = 0.92, p < 0.001; electric fields: r = 0.74, p < 0.001). Under the same stimulation intensity, the tDCS-induced peak-zero voltages were highly correlated with the values of tACS (r = 0.99, p < 0.001; s = 0.99). ConclusionsThe in vivo measurements provides confirmatory results for linear superposition and quasi-static assumption within the human brain. Furthermore, we found that the individualized simulation model reliably predicted the multi-electrode tES-induced electric fields.

biophysics↗

Amino acid availability determines plant immune homeostasis in the rhizosphere microbiome

Microbes possess conserved microbe-associated molecular patterns (MAMPs) such as flagellin that are recognized by plant receptors to induce immunity. Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome indicating they must suppress or evade host immunity. The beneficial bacteria Pseudomonas capeferrum WCS358 can suppress Arabidopsis root immunity via acidification by secreting gluconic acid. While gluconic acid is sufficient to suppress immunity, we found that it is not necessary in a second beneficial strain Pseudomonas simiae WCS417, which produces more gluconic acid than WCS358. To uncover mechanisms that contribute to the suppression of Arabidopsis immunity, we performed a forward genetic screen in EMS-mutagenized P. simiae WCS417 using a flagellin-inducible CYP71A12pro:GUS reporter as an Arabidopsis immune readout. We identified a mutant that cannot suppress flagellin-elicited CYP71A12pro:GUS expression or acidify the rhizosphere. Next generation sequencing revealed a mutation in the catabolic site of an ornithine carbamoyltransferase argF, which is required for arginine biosynthesis. The mutant could be complemented by expression of argF from a plasmid, and a {Delta}argF mutant could not suppress immunity. Fungal pathogens can use alkalization through production of ammonia and glutamate, the arginine biosynthetic precursors, to promote their own growth and virulence. Therefore, we hypothesized that the biosynthesis of specific amino acids may be necessary to reduce levels of ammonia and glutamate to prevent rhizosphere alkalization and bacterial overgrowth. Genetically blocking arginine, glutamine, or proline biosynthesis, or by adding corresponding exogenous amino acids, resulted in rhizosphere alkalization. Interestingly, exogenous amino acids caused bacterial overgrowth in a gluconic acid-deficient mutants. Our findings show that bacterial amino acid biosynthesis contributes to acidification by preventing accumulation of glutamate precursors and the resulting alkalization. Collectively this work shows that by regulating nutrient availability, plants have the potential to regulate their immune homeostasis in the rhizosphere microbiome.

microbiology↗

Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understand the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthogs genome to adapt the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. Combining with large-scale sequencing data of 123 pigs from all over the world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

genetics↗

Predictive profiling of SARS-CoV-2 variants by deep mutational learning

The continual evolution of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the emergence of variants that show resistance to vaccines and neutralizing antibodies (1-4) threaten to prolong the coronavirus disease 2019 (COVID-19) pandemic (5). Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine learning-guided protein engineering technology, which is used to interrogate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as omicron (B.1.1.529), thus supporting decision making for public heath as well as guiding the development of therapeutic antibody treatments and vaccines for COVID-19.

synthetic biology↗

A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike

Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that [~]82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells ([~]0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. A proportion of memory B cells, comprising switched ([~]0.05%) and unswitched B cells ([~]0.04%), was also reactive with S and some of these cells were reactive with ADAMTS13, which is associated with thrombotic thrombocytopenia. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.

immunology↗