Biology subjects

Huang, Z.

Publications and source records attributed to Huang, Z..

At least 217 records · Page 12Linked to original sources

bioRxiv2024

Conditional knockout of Shank3 in the ventral CA1 by quantitative in vivo genome-editing impairs social memory

Individuals with autism spectrum disorder (ASD) have a higher prevalence of social memory impairment. A series of our previous studies revealed that hippocampal ventral CA1 (vCA1) neurons possess social memory engram and that the neurophysiological representation of social memory in the vCA1 neurons is disrupted in ASD-associated Shank3 knockout mice. However, whether the dysfunction of Shank3 in vCA1 causes the social memory impairment observed in ASD remains unclear. In this study, we found that vCA1-specific Shank3 conditional knockout (cKO) by the adeno-associated virus (AAV)- or specialized extracellular vesicle (EV)-mediated in vivo gene editing was sufficient to recapitulate the social memory impairment in male mice. Furthermore, the utilization of EV-mediated Shank3-cKO allowed us to quantitatively examine the role of Shank3 in social memory. Our results suggested that there is a certain threshold for the proportion of Shank3-cKO neurons required for social memory disruption. Thus, our study provides insight into the population coding of social memory in vCA1, as well as the pathological mechanisms underlying social memory impairment in ASD.

neuroscience↗

bioRxiv2024

Psilocybin Promotes Cell-Type-Specific Changes in the Orbitofrontal Cortex Revealed by Single-Nucleus RNA-seq

Recent clinical breakthroughs hold great promise for the application of psilocybin in the treatments of psychological disorders, such as depression, addiction, and obsessive-compulsive disorder. Psilocybin is a psychedelic whose metabolite, psilocin, is a 5-HT2A receptor agonist. Nevertheless, the underlying mechanisms for the effects of psilocybin on the brain are not fully illustrated, and cell type-specific and circuit effects of psilocybin are not fully understood. Here, we combined single-nucleus RNA-seq with functional assays to study the long-term effects of psilocybin on the orbitofrontal cortex (OFC), a brain region vulnerable to psychological disorders such as depression. We showed that a single dose of psilocybin induced long-term genetic and functional changes in neurons of the OFC, and excitatory and inhibitory neurons collectively reduced circuit activity of the brain region. Knockdown of 5-HT2A receptor in deep layer excitatory neurons abated psilocybin-induced functional changes and the anti-depressant effect. Together, these results showed the cell type-specific mechanisms of psilocybin and shed light on the brain region difference in the effect of psychedelics.

neuroscience↗

bioRxiv2024

Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms

Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with [~]30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.

genomics↗

bioRxiv2023

A highly contiguous hexaploid wheat genome assembly facilitates analysis of 1RS translocation and mining of a new adult plant resistance locus to yellow rust disease

High-quality genome information is essential for efficiently deciphering and improving crop traits. Here we report a highly contiguous hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against rust diseases. By using HiFi and Hi-C sequencing reads, a 14.75 Gb genome assembly, with contig N50 and scaffold N50 values reaching 70.94 and 735.11 Mb, respectively, was developed. Comparison with 16 previously sequenced common wheat cultivars revealed unique chromosomal structural features in Zhou8425B. Notably, the 1RS translocation in Zhou8425B was apparently longer and carried more genes encoding AP2/ERF-ERF and B3 transcription factors relative to its counterpart in several genome sequenced 1BL/1RS varieties and rye lines. Aided by Zhou8425B genome assembly, a new APR locus (i.e., YrZH3B) against yellow rust (YR) disease was finely mapped to a 1 - 2 Mb interval on chromosome 3BS. Analysis with 212 Zhou8425B derivative varieties showed that pyramiding of YrZH3B with two other APR loci (YrZH22 and YrZH84) significantly decreased YR severity and enhanced grain yield, with triple combination (YrZH3B/YrZH22/YrZH84) having the highest effects. Our data demonstrate the high value of Zhou8425B assembly in studying wheat genome and agronomically important genes.

genomics↗

bioRxiv2023

Suppression of piriform cortex alters brain-wide dynamics and alleviates seizures in temporal lobe epilepsy

BackgroundTemporal lobe epilepsy (TLE) involves aberrant changes in the brain at molecular, cellular and circuitry levels, leading to recurrent seizures. Approximately one-third of patients develop drug resistance. Circuit-based interventions show promise for alleviating the drug-resistant seizures. This study explored the efficacy of chemogenetic stimulation on specific neuronal populations in piriform cortical microcircuits in a mouse TLE model. ObjectiveThe anterior piriform cortex (APC) is a limbic area closely associated with TLE but is understudied. Our previous study demonstrated that in the APC, parvalbumin-expressing (PV+) interneurons provide strong inhibition and help maintain excitation-inhibition balance. Here, we examined whether and how APCPV neurons can ameliorate seizure symptoms in TLE. MethodsWe used a chronic intrahippocampal kainic acid (IHKA) mouse model that develops hippocampal pathology and spontaneous recurrent seizures (SRSs). APCPV neurons were chemogenetically activated, and local field potentials were recorded longitudinally from multiple regions. Seizure metrics, spectral power and functional connectivity were compared between APCPV-activated and control samples. ResultsLoss of PV+ synapses emerged in the APC during epileptogenesis. Selective activation of APCPV neurons reduced the frequency and duration of hippocampal SRSs and modified long-range dynamics, with region- and frequency-specific changes in interictal band power and functional connectivity. ConclusionAPCPV chemogenetic activation exerts a robust anti-seizure effect and identifies the APC as a promising cortical node for seizure network control. The associated spectral and connectivity signatures suggest that targeted modulation of APC microcircuits can rebalance distributed seizure networks and lower seizure recurrence.

neuroscience↗

bioRxiv2023

Short-chain carboxylates facilitate the counting of yeasts in Sub-high temperature Daqu.

Sub-high temperature Daqu is a traditional solid fermenting agent that produces Chinese strong-aroma Baijiu. It is abundant in various microorganisms, including bacteria, yeasts, molds, and actinomycetes, of which yeasts play a crucial role in ethanol production and flavor formation. Counting yeasts in Daqu is difficult due to the interference of molds and bacteria. Antibiotics are employed to inhibit bacterial growth, but there is no effective way to suppress molds without affecting the growth of yeasts. In this study, short-chain carboxylates (C1-C6) were added to the culture medium at various pH conditions to investigate their effects on the growth of molds and yeasts. Results showed that they have distinct inhibitory effects in a pH-and concentration-dependent manner. A few of these tested short-chain carboxylates effectively suppress mold growth in agar plates without affecting yeast growth. Herein, a simple and feasible method for improving the efficiency of yeast isolation and counting in Daqu has been proposed, which may be useful for studying yeasts from complex habitats.

microbiology↗

bioRxiv2023

Comprehensive Assessment of Ischemic Stroke in Nonhuman Primates: Neuroimaging, Behavioral, and Serum Proteomic Analysis

Ischemic strokes, prevalence and impactful, underscore the necessity of advanced research models closely resembling human physiology. O integrating n ur study in nonhuman primates (NHPs) offers a comprehensive exploration of ischemic stroke, integrating neuroimaging data, behavioral outcomes, and serum proteomics to elucidate the complex interplay of factors involved in stroke pathophysiology. We observed a consistent pattern in infarct volume, peaking at 1-month post-middle cerebral artery occlusion (MCAO) and stabilizing thereafter. This trend was closely correlated with notable changes in motor function and working memory performance. Using diffusion tensor imaging (DTI), we detected significant alterations in fractional anisotropy (FA) and mean diffusivity (MD) values, indicative of microstructural changes in the brain. These findings were strongly correlated with the observed neurological and cognitive deficits, highlighting the sensitivity of DTI metrics in stroke assessment. Behaviorally, the monkeys exhibited a reliance on their unaffected limb for compensatory movements, a response commonly observed in stroke impairment. This adaptation, alongside the consistent findings in DTI metrics, suggests a substantial impact of stroke on motor function and spatial perception. Proteomic analysis through MS/MS functional enrichment revealed two distinct groups of proteins with significant changes post-MCAO. Notably, MMP9, THBS1, MB, PFN1, and YWHAZ emerged as potential biomarkers and therapeutic targets in ischemic stroke. Our findings underscore the complex nature of stroke and the potential of an integrated approach, combining neuroimaging, behavioral studies, and proteomics, for advancing our understanding and treatment of this condition.

neuroscience↗

bioRxiv2023

Age-Related Changes of Dopamine D1 and D2 Receptors Expression in Parvalbumin-Positive Cells of the Orbitofrontal and Prelimbic Cortices of Mice

Dopamine (DA) plays a pivotal role in reward processing, cognitive functions, and emotional regulation. The prefrontal cortex (PFC) is a critical brain region for these processes. Parvalbumin-positive (PV+) neurons are one of the major classes of inhibitory GABAergic neurons in the cortex, they modulate the activity of neighboring neurons, influencing various brain functions. While DA receptor expression exhibits age-related changes, the age-related changes of these receptors in PV+ neurons, especially in the PFC, remains unclear. To address this, we investigated the expression of DA D1 (D1R) and D2 (D2R) receptors in PV+ neurons within the orbitofrontal (OFC) and prelimbic (PrL) cortices at different postnatal ages (P28, P42, P56, and P365). We found that the expression of D1R and D2R in PV+ neurons showed both age- and region-related changes. PV+ neurons in the OFC expressed a higher abundance of D1 than those in the PrL, and those neurons in the OFC also showed higher co-expression of D1R and D2R than those in the PrL. In both the OFC and PrL, D1R in PV+ neurons increased from P28 and reached a plateau at P42, then receded to express at P365. Meanwhile, D2R did not show significant age-related changes in both regions. These results showed dopamine receptors in the prefrontal cortex exhibit age- and region-specific changes, which may contribute to the difference of these brain regions in reward-related brain functions.

neuroscience↗

bioRxiv2023

Targeted protein degradation systems to enhance Wnt signaling

Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETSTM) to drive tissue-specific degradation of ZNRF3/RNF43 E3-ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody-RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1 and ASGR1/2 specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate binding site. Both antibodies enhanced Wnt-activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.

synthetic biology↗

bioRxiv2023

Connecting single neuron transcriptomes to the projectome in mouse visual cortex

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neurons role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morphoelectric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

neuroscience↗

bioRxiv2023

Development of a Next Generation SNP Genotyping Array for Wheat

High throughput genotyping arrays have provided a cost effective, reliable and interoperable system for genotyping hexaploid wheat and its related germplasm pool. Existing, highly cited arrays including our 35K Axiom Wheat Breeders genotyping array and the Illumina 90K iSelect array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in sequencing wheat varieties and landraces has given us access to a vast pool of SNP diversity, whilst technological improvements in array design has allowed us to fit significantly more probes onto a 384-well format Axiom array than was previously possible. Here we describe a novel High Density Axiom genotyping array, the Triticum aestivum Next Generation array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins "Core Collection". We use a novel "minimal marker" optimisation approach to select up to six SNPs in each 1.5 MB region of the wheat genome with the highest combined varietal discrimination potential. A design iteration step allowed us to test and replace skim-sequence derived SNPs which failed to convert to reliable Axiom markers, resulting in a final design, designated TaNG1.1 with 43,372 SNPs derived from a haplotype-optimised combination of novel SNPs, DArTAG-derived and legacy wheat Axiom markers. We show that this design has an even distribution of SNPs across chromosomes and sub-genomes compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous Axiom array. We also demonstrate the improved performance of TaNG1.1 for Genome Wide Association Studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available, and the marker annotations, initial genotyping results and software used to generate the optimised marker sets are freely available.

genomics↗

bioRxiv2023

Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data

RNA Velocity, as an extension of trajectory inference, is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. Nevertheless, existing RNA velocity methods are limited by the batch effect because they cannot directly correct for batch effects in the input data, which comprises spliced and unspliced matrices in a proportional relationship. This limitation can lead to incorrect velocity graphs. This paper introduces VeloVGI, which addresses this issue innovatively in two key ways. Firstly, it employs an optimal transport (OT) and mutual nearest neighbor (MNN) approach to construct neighbors in batch data. This strategy overcomes the limitations of existing methods that are affected by the batch effect. Secondly, VeloVGI improves upon VeloVIs velocity estimation by incorporating the graph structure into the encoder for more effective feature extraction. The effectiveness of VeloVGI was demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb, as well as on several public datasets. The results showed that VeloVGI outperformed other methods in terms of metric performance. Significance StatementRNA Velocity is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. This paper introduces VeloVGI, which addresses this batch effect issue for existing RNA velocity methods. The effectiveness of VeloVGI was demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb, as well as on several public datasets. The results showed that VeloVGI outperformed other methods in terms of metric performance.

bioinformatics↗

bioRxiv2023

Genome assembly and genomic architecture of a prominent cold-resistant rapeseed germplasm

Graphical AbstractThe genomic landscape of cold-tolerant winter rapeseed (Brassica napus, L) has been poorly characterized. We assembled a high-quality reference genome of a prominent cold-tolerant winter rapeseed cultivar, NTS57, and performed phylogenetic and pan-genomic analyses by integrating other reported Brassica napus accessions. The transcriptome analysis revealed that microtubule-associated biological pathways were much more active in NTS57 under cold stress than in the cold-sensitive variety. Whole genome methylation data analysis revealed that DNA demethylation on protein-coding genes and repetitive elements, especially at CHH sites, is essential for cold response in winter rapeseed.

genomics↗

bioRxiv2023

Dynamic Responses of Striatal Cholinergic Interneurons Control the Extinction and Updating of Goal-Directed Learning

Striatal cholinergic interneurons (CINs) regulate behavioral flexibility, but their exact contribution to this process remains elusive. In this study, we report that extinction learning enhances acetylcholine (ACh) release. Mimicking this enhancement by optogenetically inducing CIN burst firing promotes extinction learning. CINs receive excitatory thalamic inputs, and we observed that extinction training augmented thalamic activity. Optogenetically stimulating these thalamic inputs caused CIN burst firing and enhanced ACh release, strengthening extinction learning. Notably, CIN burst firing is usually followed by a pause in firing. We found that disrupting this pause through continuous optogenetic stimulation reversibly impaired the updating of goal-directed behaviors. Furthermore, excessive alcohol consumption reduced thalamus-induced burst-pause firing in CINs and impaired the reversal of goal-directed learning. In summary, thalamic-driven CIN burst firing promotes extinction learning, while the pause is pivotal for reversing goal-directed behavior, a process impacted by excessive alcohol. These findings shed light on how CINs dynamic responses affect behavioral flexibility. HighlightsH1. Burst firing of CINs promotes extinction learning H2. Thalamic-CIN excitation enhances extinction learning H3. Pause of CIN is critical for the reversal of goal-directed learning H4. Chronic alcohol consumption reduces the burst-pause of CINs and impairs the reversal of goal-directed learning.

neuroscience↗

bioRxiv2023

LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand. One-Sentence SummaryLARP1 directly binds free ribosomal subunits to repress TOP mRNAs

molecular biology↗

bioRxiv2023

Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma

Myeloid cells are abundant and plastic immune cell subsets in the liver, to which pro-tumorigenic, inflammatory and immunosuppressive roles have been assigned in the course of tumorigenesis. Yet several aspects underlying their dynamic alterations in hepatocellular carcinoma (HCC) progression remain elusive, including the impact of distinct genetic mutations in shaping a cancer-permissive tumor microenvironment (TME). Here, we generated somatic HCC mouse models bearing clinically-relevant oncogenic driver combinations and subsequent pathway activation that faithfully recapitulated different human HCC subclasses. We identified cancer genetics specific and stage-dependent alterations of the liver TME associated with distinct histopathological and malignant HCC features. These models ranged from T cell-rich, more indolent HCC to aggressive tumors exhibiting heightened myeloid cell infiltration. Interestingly, MAPK-activated, NrasG12D-driven tumors presented a mixed phenotype of prominent inflammation and immunosuppression in a T cell-excluded TME, contrasting with NrasG12V HCC, enriched in adaptive immune cells. Mechanistically, we identified a NrasG12D cancer cell-driven, MEK-ERK1/2-SP1-dependent GM-CSF secretion enabling the accumulation of immunosuppressive and proinflammatory monocyte-derived Ly6Clow cells. GM-CSF blockade curbed the accumulation of this myeloid cell subset, reduced inflammation, induced cancer cell death and prolonged animal survival. Furthermore, the anti-tumor effect of GM-CSF neutralization synergized with the clinically-approved inhibition of the vascular endothelial growth factor (VEGF) to inhibit HCC outgrowth. These findings underscore the striking alterations of the myeloid TME consequential to MAPK pathway activation intensity and the potential of GM-CSF inhibition as a myeloid-centric therapy tailored to subsets of HCC patients.

cancer biology↗

bioRxiv2023

ATR promotes mTORC1 activation via de novo cholesterol synthesis in p16-low cancer cells

DNA damage and cellular metabolism exhibit a complex interplay characterized by bidirectional feedback mechanisms. Key mediators of the DNA damage response and cellular metabolic regulation include Ataxia Telangiectasia and Rad3-related protein (ATR) and the mechanistic Target of Rapamycin Complex 1 (mTORC1), respectively. Previous studies have established ATR as a regulatory upstream factor of mTORC1 during replication stress; however, the precise mechanisms by which mTORC1 is activated in this context remain poorly defined. Additionally, the activity of this signaling axis in unperturbed cells has not been extensively investigated. Here, we demonstrate that ATR promotes mTORC1 activity across various cellular models under basal conditions. This effect is particularly enhanced in cells following the loss of p16, which we have previously associated with hyperactivation of mTORC1 signaling and here found have increased ATR activity. Mechanistically, we found that ATR promotes de novo cholesterol synthesis and mTORC1 activation through the upregulation of lanosterol synthase (LSS), independently of both CHK1 and the TSC complex. Furthermore, the attenuation of mTORC1 activity resulting from ATR inhibition was rescued by supplementation with lanosterol or cholesterol in multiple cellular contexts. This restoration corresponded with enhanced localization of mTOR to the lysosome. Collectively, our findings demonstrate a novel connection linking ATR and mTORC1 signaling through the modulation of cholesterol metabolism.

cancer biology↗

bioRxiv2023

Effects of non-retinal inputs in visual thalamus depend on visual responsiveness and stimulus context

In the dorsolateral geniculate nucleus (dLGN) of the thalamus, stimulus-driven signals are combined with modulatory inputs such as corticothalamic (CT) feedback and behavioural state. How these shape dLGN activity remains an open question. We recorded extracellular responses in dLGN of awake mice to a movie stimulus, while photosuppressing CT feedback, and tracking locomotion and pupil size. To assess the relative impact of stimulus and modulatory inputs, we fit single neuron responses with generalized linear models. While including CT feedback and behavioural state as predictors significantly improved the models overall performance, the improvement was especially pronounced for a subpopulation of neurons poorly responsive to the movie stimulus. In addition, the observed impact of CT feedback was faster and more prevalent in the absence of a patterned visual stimulus. Finally, for neurons that were sensitive to CT feedback, visual stimuli could be more easily discriminated based on spiking activity when CT feedback was suppressed. Together, these results show that effects of modulatory inputs in dLGN depend on visual responsiveness and stimulus type.

neuroscience↗