Search bioRxiv⌕ Search

Biology subjects

Huang, Z.

Publications and source records attributed to Huang, Z..

At least 271 records · Page 15Linked to original sources

Long-term reliable neural decoding based on flexible implantable microelectronics and machine learning for seizure prediction application

Neural decoding is useful for understanding brain functions and developing neural interface applications. However, neural interfaces based on rigid electronics often suffer from recording instability due to the foreign body responses caused by their mechanical mismatch with soft tissues, limiting the longitudinal accuracy of neural decoding methods. Herein, it is reported that flexible electronics can be integrated with machine learning algorithms to achieve long-term reliable neural decoding. Wet-spun conductive polymer microfibers showed mechanical robustness and flexibility, low impedance, and chronic biocompatibility, enabling intracerebral neural recordings in epileptic mice at a high signal-to-noise ratio eight weeks after implantation. When the signals recorded by the flexible electrodes were used in machine learning analyses with diverse complex algorithms, they consistently showed higher prediction accuracy for epileptic seizures than stiff metal electrode signals, particularly in the case of using long-term recordings for testing or small-sample datasets for training. A real-time warning system based on the flexible neural electrodes was built that predicted seizures eight minutes in advance with a low false alarm rate. Our work bridges flexible electronics and artificial intelligence for neural decoding applications such as long-term treatment of chronic neurological disorders.

bioengineering↗

Rescue of Auditory Function by a Single Administration of AAV-TMPRSS3 Gene Therapy in Aged Mice of Human Recessive Deafness DFNB8

AbstractsPatients with mutations in the TMPRSS3 gene suffer from recessive deafness DFNB8/DFNB10 for whom cochlear implantation is the only treatment option. Poor cochlear implantation outcomes are seen in some patients. To develop biological treatment for TMPRSS3 patients, we generated a knock-in mouse model with a frequent human DFNB8 TMPRSS3 mutation. The Tmprss3A306T/A306T homozygous mice display delayed onset progressive hearing loss similar to human DFNB8 patients. Using AAV2 as a vector to carry a human TMPRSS3 gene, AAV2-hTMPRSS3 injection in the adult knock-in mouse inner ears results in TMPRSS3 expression in the hair cells and the spiral ganglion neurons. A single AAV2-hTMPRSS3 injection in aged Tmprss3A306T/A306T mice leads to sustained rescue of the auditory function, to a level similar to the wildtype mice. AAV2-hTMPRSS3 delivery rescues the hair cells and the spiral ganglions. This is the first study to demonstrate successful gene therapy in an aged mouse model of human genetic deafness. This study lays the foundation to develop AAV2-hTMPRSS3 gene therapy to treat DFNB8 patients, as a standalone therapy or in combination with cochlear implantation.

neuroscience↗

LCP1 Regulates Cell Motility in Chondrosarcoma and Correlates with Metastatic Potential and Poor Patient Outcomes

Chondrosarcoma (CSA) is the second most common primary malignancy of bone, whose aggressive potential and chemo-resistant nature result in extremely poor outcomes in patients with advanced disease. Grading and prognostication of these tumors remain a significant challenge for pathologists, and medical oncologists have no effective therapies to prevent or treat metastatic disease. In the present study, we sought to explore the pathogenesis and aggressive progression of chondrosarcoma by comparing gene expression differences from metastasizing and non-metastasizing CSA tumors. We hypothesized that metastasizing tumors have inherent differences that may be attributed to the dysregulation of specific oncogenic cell signaling pathways. RNA-Seq analysis from patient-derived low-passage cell lines of metastasizing and non-metastasizing tumors pinpointed the gene LCP1 (lymphocyte cytosolic protein 1) as upregulated in CSA cells from metastasizing tumors. Analysis of a large clinical cohort of CSA demonstrated that increased expression of LCP1 correlated with poor patient survival. In vitro analyses confirmed the ability of LCP1 to promote migration and invasion of CSA cells. These data support the key role of LCP1 on metastatic potential and poor prognosis in CSA. In conclusion, we confirm the ability of LCP1 to drive metastatic behavior and correlate with poor outcomes in patients.

cancer biology↗

Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin

The sodium channel NaV1.6 is widely expressed in neurons of the central and peripheral nervous systems, which plays a critical role in regulating neuronal excitability. Dysfunction of NaV1.6 has been linked to epileptic encephalopathy, intellectual disability and movement disorders. Here we present cryo-EM structures of human NaV1.6/{beta}1/{beta}2 alone and complexed with a guanidinium neurotoxin 4,9-anhydro-tetrodotoxin (4,9-ah-TTX), revealing molecular mechanism of NaV1.6 inhibition by the blocker. In the apo-form structure, two potential Na+ binding sites were revealed in the selectivity filter, suggesting a possible mechanism for Na+ selectivity and conductance. In the 4,9-ah-TTX-bound structure, 4,9-ah-TTX binds to a pocket similar to the tetrodotoxin (TTX) binding site, which occupies the Na+ binding sites and completely blocks the channel. Molecular dynamics simulation results show that subtle conformational differences in the selectivity filter affect the affinity of TTX analogues. Taken together, our results provide important insights into NaV1.6 structure, ion conductance, and inhibition.

biophysics↗

SunTag-PE: a modular prime editing system enables versatile and efficient genome editing

Prime editing (PE) holds tremendous potential in the treatment of genetic diseases because it can install any desired base substitution or local insertion/deletion. However, the full-length PE effector size (6.3-kb) was beyond the packaging capacity of adeno-associated virus (AAV), hindering its clinical transformation. Various splitting strategies have been used to improve its delivery, but always accompanied by compromised PE efficiency. Here, we developed a modular and efficient SunTag-PE system that splits PE effectors into GCN4-nCas9 and single-chain variable fragment (scFv) tethered reverse transcriptase (RT). We observed that SunTag-PEs with 1xGCN4 in the N terminus of nCas9 was the most efficient configuration rather than multiple copies of GCN4. This SunTag-PE strategy achieved editing levels comparable to canonical fused-PE and higher than other split-PE strategies (including sPE and MS2-PE) in both PE2 and PE3 forms with no increase in insertion-deletion (indel) byproducts. Moreover, we successfully validated the modularity of SunTag-PE system in the Cas9 orthologs of SauCas9 and FrCas9. Finally, we employed dual AAVs to deliver SunTag-ePE3 and efficiently corrected the pathogenic mutation in HBB mutant cell line. Collectively, our SunTag-PE system provides an efficient modular splitting strategy for prime editing and further facilitate its transformation in clinics.

bioengineering↗

Retrieving the near-complete genome of a threatened bird from wild frozen samples

Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Collecting samples from frozen dead animals in the wild provides an alternative approach to obtaining high-quality nucleic acids. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) of a recent death found in the mountainous region in Gansu, China. We generated a near-complete genome assembly (OTswu) having only 18 gaps scattering in 8 out of the 40 assembled chromosomes. Unlikely most other bird genome assemblies, OTswu contains complete chromosome models (2n = 80). We demonstrated that the great bustard genome likely retained the ancestral avian karyotype. We also characterized the DNA methylation landscapes of OTswu which are strongly correlated with GC content and gene expression. Our phylogenomic analysis suggested Otidiformes and Musophagiformes were sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard was found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriching for metabolism. Finally, we identified an extremely young evolutionary stratum on the sex chromosome, a rare case among Neoaves. Together, our study combining long-read sequencing and RNA-seq technology provides a working strategy for conducting multi-omic analyses for threatened species by retrieving high-quality nucleic acids from dead animals frozen in the wild.

genomics↗

O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors

In mammals, interactions between the bone marrow (BM) stroma and hematopoietic progenitors contribute to bone-BM homeostasis. Perinatal bone growth and ossification provide a microenvironment for the transition to definitive hematopoiesis; however, mechanisms and interactions orchestrating the development of skeletal and hematopoietic systems remain largely unknown. Here, we establish intracellular O-linked {beta}-N-acetylglucosamine (O-GlcNAc) modification as a posttranslational switch that dictates the differentiation fate and niche function of early BM stromal cells (BMSCs). By modifying and activating RUNX2, O-GlcNAcylation promotes osteogenic differentiation of BMSCs and stromal IL-7 expression to support lymphopoiesis. In contrast, C/EBP{beta}-dependent marrow adipogenesis and expression of myelopoietic stem cell factor (SCF) is inhibited by O-GlcNAcylation. Ablating O-GlcNAc transferase (OGT) in BMSCs leads to impaired bone formation, increased marrow adiposity, as well as defective B-cell lymphopoiesis and myeloid overproduction in mice. Thus, the balance of osteogenic and adipogenic differentiation of BMSCs is determined by reciprocal O-GlcNAc regulation of transcription factors, which simultaneously shapes the hematopoietic niche.

physiology↗

Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3

High-voltage-activated R-type CaV2.3 channel plays pivotal roles in many physiological activities and is implicated in epilepsy, convulsions, and other neurodevelopmental impairments. Here, we determine the high-resolution cryo-electron microscopy (cryo-EM) structure of human CaV2.3 in complex with the 2{delta}1 and {beta}1 subunits. The VSDII is stabilized in the resting state. Electrophysiological experiments elucidate that the conformational change of VSDII in response to variation in membrane potential is not required for channel activation, whereas the other VSDs are essential for channel opening. The intracellular gate is blocked by the W-helix. A pre-W-helix adjacent to the W-helix can significantly regulate closed-state inactivation (CSI) by modulating the association and dissociation of the W-helix with the gate. Electrostatic interactions formed between the negatively charged domain on S6II, which is exclusively conserved in the CaV2 family, and nearby regions at the alpha-interacting domain (AID) and S4-S5II helix are identified. Further functional analyses indicate that these interactions are critical for the open-state inactivation (OSI) of CaV2 channels.

biophysics↗

MC1R drives cutaneous repair by promoting angiogenesis and lymphangiogenesis

Cutaneous healing results in scarring with significant functional and psychological sequelae, while chronic non-healing wounds represent repair failure often with devastating consequences, including amputation and death. Due to a lack of effective therapies, novel interventions addressing scarring and chronic wounds are urgently needed. Here, we demonstrate that harnessing melanocortin 1 receptor with a selective agonist (MC1R-Ag) confers multifaceted benefits to wound repair. MC1R-Ag accelerates wound closure and re-epithelialization while improving wound bed perfusion and lymphatic drainage by promoting angiogenesis and lymphangiogenesis. Concomitant reductions in oxidative stress, inflammation and scarring were also observed. To evaluate the therapeutic potential of targeting MC1R in pathological healing, we established a novel murine model that recapitulates the hallmarks of human non-healing wounds. This model combines advanced age and locally elevated oxidative stress. Remarkably, topical application of MC1R-Ag restored repair, whereas disrupting MC1R signalling exacerbated the chronic wound phenotype. Our study highlights MC1R agonism as a promising therapeutic approach for scarring and non-healing wound pathologies, and our chronic wound model as a valuable tool for elucidating ulcer development mechanisms.

pathology↗

Epigenetic and Signaling Determinants of Blood-Brain Barrier-Regulatory Genetic Networks

The blood-brain barrier (BBB) controls the movement of molecules into and out of the central nervous system (CNS). Since a functional BBB forms by mouse embryonic day E15.5, we reasoned that gene cohorts expressed in CNS endothelial cells (EC) at E13.5 contribute to BBB formation. In contrast, adult gene signatures reflect BBB maintenance mechanisms. Supporting this hypothesis, transcriptomic analysis revealed distinct cohorts of EC genes involved in BBB formation and maintenance. Here, we demonstrate that epigenetic regulators histone deacetylase 2 (HDAC2) and polycomb repressive complex 2 (PRC2) control EC gene expression for BBB development and prevent Wnt/{beta}-catenin (Wnt) target genes from being expressed in adult CNS ECs. Low Wnt activity during development modifies BBB genes epigenetically for the formation of functional BBB. As a Class-I HDAC inhibitor induces adult CNS ECs to regain Wnt activity and BBB genetic signatures that support BBB formation, our results inform strategies to promote BBB repair.

neuroscience↗

The Neural Correlates of Arousal: The Ventral Posterolateral Nucleus-Global Transient Co-Activation

Arousal and awareness are two components of consciousness whose the neural mechanisms remain unclear. Spontaneous increases of global (brain-wide) blood-oxygenation-level-dependent (BOLD) signal has been found to be sensitive to changes in arousal. By contrasting BOLD datasets with altered arousal levels, we found that the activation of ventral posterolateral nucleus (VPL) decreased during transient increase in the global signal (top 17% data) in low arousal and awareness states (non-rapid eye movement sleep and anesthesia) as compared to wakefulness, and even in eye-closed (compared with eyes-open) in healthy awake-states, while this activation remained unchanged in patients with unresponsive wakefulness syndrome characterized by high arousal without awareness. These results demonstrate that co-activation of the VPL and global activity is critical to arousal, but not to awareness. One-Sentence SummaryThe VPL nucleus-global brain transient co-activation is related to physiological arousal but not to perceptual awareness.

neuroscience↗

The first host-associated anaerobic isolate of Psychrilyobacter provides insights into its potential roles in the abalone gut

Gut bacteria are essential to their hosts, but few studies have focused on marine animals. Psychrilyobacter is frequently related to various marine animals, but the relationship with host remains unknown due to lack of host-associated isolate or genomic information. Here, we combined of high-throughput sequencing, isolating and genomic analyses to uncover its potential role in host abalone. The high-throughput sequencing and literature compiling results indicated that Psychrilyobacter is widely distributed in marine and terrestrial ecosystems with both host-associated and free-living lifestyles. It showed a strong preference for the guts of marine invertebrates, especially abalone, which generally persisted with high relative abundances. By mimicking the gut inner environment for enrichment, the first host-related pure culture of Psychrilyobacter was isolated from the abalone intestine. Phylogenetic, physiological and biochemical characterizations suggested that it represents a novel species named Psychrilyobacter haliotis B1. Carbohydrate utilization experiments and genomic evidence indicated that B1 is good at fermenting diverse host-food-related monosaccharides and disaccharides but not polysaccharides, implying its critical roles in downstream fermentation instead of upstream food degradation in the gut. Furthermore, this strain showed potential to colonize the gut and benefit the host via different strategies, such as short-chain fatty acids (SCFAs) generation by fermenting carbohydrates and amino acids, and the production of diverse vitamins and antibiotics to support the host growth and antipathogenicity. To our knowledge, strain B1 represents the first host-related pure culture of Psychrilyobacter, acting as a potential probiotic gut anaerobe dominating in diverse marine invertebrates. ImportancePsychrilyobacter is a globally distributing bacterial genus and with an inhabiting preference for guts of marine invertebrates. Due to the difficulty of cultivation and the limited genomic information, its role in host remains largely unknown. We isolated the first host-associated Psychrilyobacter species from abalone gut and uncovered its functional potentials to the host through different mechanisms. Our findings provide some insights into the understanding of host-microbe interactions on a core taxon with the marine invertebrates, and the isolate has an application prospect as a probiotic in protection of marine animals.

microbiology↗

Canonical and Non-Canonical Psychedelic Drugs Induce Common Network Changes in Human Cortex

AO_SCPLOWBSTRACTC_SCPLOWThe neurobiology of the psychedelic experience is not fully elucidated. Identifying common brain network changes induced by both canonical (i.e., acting at the 5-HT2 receptor) and non-canonical psychedelics would provide mechanistic insight into state-specific characteristics. We analyzed whole-brain functional connectivity based on resting-state fMRI data in humans, acquired before and during the administration of nitrous oxide, ketamine, and lysergic acid diethylamide. We report that, despite distinct molecular mechanisms and modes of delivery, all three psychedelics reduced within-network functional connectivity and enhanced between-network functional connectivity. More specifically, all drugs tested increased connectivity between right temporoparietal junction and bilateral intraparietal sulcus as well as between precuneus and left intraparietal sulcus. These regions fall within the posterior cortical "hot zone," posited to mediate the content of consciousness. Thus, both canonical and non-canonical psychedelics modulate networks within an area of known relevance for conscious experience, identifying a biologically plausible candidate for their subjective effects.

neuroscience↗

Proteomics of resilience to Alzheimer's disease identifies brain regional soluble Aβ levels, actin filament processes, and response to injury

Resilience to Alzheimers disease (RAD) is an uncommon combination of high disease burden without dementia that may provide critical insights into limiting the clinical impact of this incurable disease. In this study, we used mass spectrometry-based proteomics to quantify regional protein differences that characterize RAD. Starting with over 700 brain donations, we identified 43 extensively annotated research participants who met stringent inclusion exclusion criteria and analyzed matched isocortical regions, hippocampus, and caudate nucleus. Differential expression analysis of 7,115 soluble proteins identified lower isocortical and hippocampal soluble A{beta} peptide levels as a significant feature of RAD. Protein co-expression analysis revealed a group of 181 densely-interacting proteins significantly associated with RAD that were enriched for actin filament-based process, cellular detoxification, and wound healing in isocortex and hippocampus. We further support our findings using data from 689 human isocortical samples from four independent external cohorts that were the closest approximations of our clinico-pathologic groups. The molecular basis of RAD, a widely replicated state in older adults for which there is no experimental model, likely holds important insights into therapeutic interventions for Alzheimers disease.

neuroscience↗

Cryo-EM structure of the type III-E CRISPR-Cas effector gRAMP in complex with TPR-CHAT

The type III-E CRISPR-Cas effector protein, named gRAMP, is the largest single-unit CRISPR-Cas effector. A caspase-like peptidase (TPR-CHAT) gene often co-occurs with gRAMP gene clusters. However, the exact mechanism of the recognition and cleavage of target RNA of Sb-gRAMP, as well as the molecular architecture of the CRISPR-guided caspase complex, remains unclear. Here, we report the cryo-EM structures of the type III-E effector Sb-gRAMP-crRNA in a complex with TPR-CHAT, with and without target ssRNA at 3.0 and 2.9 [A], respectively. The overall structure of the gRAMP-crRNA-ssRNA-TPR-CHAT complex adopts an "L"-shaped conformation, consisting of a copy of gRAMP, a copy of TPR-CHAT, a 37-nt crRNA, and an 18-nt target ssRNA. The data presented in this manuscript reveal the mechanism of recognition of crRNA and target ssRNA by gRAMP, also, this work reports the structure of the CRISPR type III-E effector in complex with the binding partner TPR-CHAT, which provides vital clues for elucidating the functional relation between the CRISPR-Cas system and caspase peptidase.

biochemistry↗

Reactivation-induced memory integration prevents proactive interference in perceptual learning

We acquire perceptual skills through experience to adapt ourself to the changing environment. Accomplishing an effective skill acquisition is a main purpose of perceptual learning research. Given the often observed learning effect specificity, multiple perceptual learnings with shared parameters could serve to improve the generalization of the learning effect. However, the interference between the overlapping memory traces of different learnings may impede this effort. Here, we trained human participants on an orientation discrimination task. We observed a proactive interference effect that the first training blocked the second training at its untrained location. This was a more pronounced effect than the well-known location specificity in perceptual learning. We introduced a short reactivation of the first training before the second training and successfully eliminated the proactive interference when the second training was inside the reconsolidation time window of the reactivated first training. Interestingly, we found that practicing an irrelevant task at the location of the second training immediately after the reactivation of the first training could also restore the effect of the second training but in a smaller magnitude, even if the second training was conducted outside of the reconsolidation window. We proposed a two-level mechanism of reactivation-induced memory integration to account for these results. The reactivation-based procedure could integrate either the previously trained and untrained locations or the two trainings at these locations, depending on the activated representations during the reconsolidation process. The findings provide us with new insight into the roles of long-term memory mechanisms in perceptual learning.

neuroscience↗

Why are G-quadruplexes good at preventing protein aggregation?

Maintaining a healthy protein folding environment is essential for cellular function. Recently, we found that nucleic acids, and G-quadruplexes in particular, are potent chaperones for preventing protein aggregation. With the aid of structure-function and NMR analyses of two G-quadruplex forming sequences, PARP-I and LTR-III, we uncovered several contributing factors that affect G-quadruplexes in preventing protein aggregation. Notably, three factors emerged as vital in determining holdase activity of G-quadruplexes: their structural topology, structural dynamics, and oligomerization state. These factors together appear to largely dictate whether a G-quadruplex is able to prevent partially misfolded proteins from aggregating. Understanding the genesis of G-quadruplexes power as chaperones is an important facet to elucidating various protein aggregation diseases. Key Points- How nucleic acids act as protein chaperones is currently unknown. - G-quadruplexes are excellent at preventing protein aggregation, and here we describe basic tenets of this activity. - This activity could help design treatments for multiple neurodegenerative diseases.

biophysics↗

Dysfunction of the Polycomb protein RYBP and of 5-methylcytosine oxidases leads to widespread CpG island hypermethylation and cell transformation

DNA hypermethylation is a hallmark of cancer and predominantly affects CpG island regions. Although this phenomenon was first described more than three decades ago, its mechanisms have remained unknown. Since CpG island hypermethylation is strongly biased towards Polycomb target genes, we reasoned that dysfunction of Polycomb repression complexes (PRCs) may underlie CpG island hypermethylation. We observed that a few genes coding for components of the PRC1 complex are downregulated in many cancer types. We focused on RYBP, a key activator of variant PRC1 complexes responsible for H2AK119 monoubiquitylation. We inactivated RYBP in nontumorigenic bronchial epithelial cells and observed a limited extent of DNA hypermethylation. Considering that tumors are deficient in 5-methylcytosine oxidase (TET protein) function as documented by substantially reduced levels of 5-hydroxymethylcytosine in all solid tumors, we then inactivated TET1, TET2, and TET3 in bronchial cells, individually and in combination. Using quadruple knockouts of RYBP and all three TET proteins, we observed widespread hypermethylation of H2AK119Ub1-marked CpG islands affecting almost 4,000 target genes. This hypermethylation closely mirrored the DNA hypermethylation landscape observed in human lung tumors. These cells showed aberrant methylation and dysregulation of several cancer-relevant pathways including cell cycle control genes, defects in the Hippo pathway and overexpression of AP-1 transcription factor genes. As a result, the quadruple knockout bronchial cells acquired properties of a transformed phenotype, including efficient growth in soft agar and formation of squamous cell carcinomas in immune-compromised mice. Our data provide a long- sought mechanism for DNA hypermethylation in cancer and explain how such hypermethylation leads to cell transformation. Cancer formation, therefore, is achievable by misregulation of two epigenetic pathways without introduction of cancer driver mutations.

cancer biology↗