Biology subjects

Chen, G.

Publications and source records attributed to Chen, G..

At least 307 records · Page 17Linked to original sources

bioRxiv2020

Transcription factor-based gene therapy to treat glioblastoma through direct neuronal conversion

Glioblastoma (GBM) is the most prevalent and aggressive adult primary cancer in the central nervous system (CNS). Therapeutic approaches for glioblastoma are under intense investigation, such as the emerging immunotherapy, but so far only marginal progress has been made due to the heterogeneity and highly invasive nature of glioblastoma. Here, we propose an alternative approach to tackle GBM through reprogramming proliferative GBM cells into non-proliferative neurons. We report efficient neuronal conversion from human GBM cells by overexpressing single neural transcription factor Neurogenic differentiation 1 (NeuroD1), Neurogenin-2 (Neurog2) or Achaete-scute homolog 1 (Ascl1). Subtype characterization reveals that the majority of Neurog2- and NeuroD1-converted neurons are glutamatergic, while Ascl1 favors GABAergic neuron generation. The GBM cell-converted neurons not only express pan-neuronal markers, such as NeuN and MAP2, but also exhibit neuron-specific electrophysiological activities. We further conducted transcriptome analyses to investigate the underlying cell conversion mechanism. Our RNA-seq analyses discover that neuronal genes are activated among glioma cells after overexpression of neural transcription factors, and different signaling pathways are activated by different neural transcription factors. Importantly, the neuronal conversion of GBM cells is accompanied by significant inhibition of GBM cell proliferation in both in vitro and in vivo models. Therefore, these results suggest that GBM cells can be reprogrammed into different subtypes of neurons, leading to a potential alternative approach to treat brain tumor. SignificanceConverting dividing glioblastoma cells into non-dividing neurons may provide an innovative therapeutic approach to treat glioblastoma. HighlightsO_LIEfficient neuronal conversion of human glioblastoma cells achieved by overexpression of neural transcription factors C_LIO_LINeurog2- and NeuroD1-converted neurons are mostly glutamatergic, while Ascl1-converted neurons are mainly GABAergic C_LIO_LITranscriptome analyses reveal the activation of neuronal genes after overexpression of neural transcription factors in glioblastoma cells C_LIO_LIInhibition of cell proliferation during glioblastoma cell conversion both in vitro and in vivo C_LI

neuroscience↗

bioRxiv2020

Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration

Haptic object perception begins with continuous exploratory contacts, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration across time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimation. For this experiment, we designed sixteen haptic stimuli (4 kinds of curve x 4 kinds of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along with the surface twice and to estimate one of the two features--roughness or curvature--dependent on the task instruction. We found that the brain activity in several higher-level regions (e.g., bilateral posterior parietal cortex) linearly increased with curvature through the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase, but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns for haptic roughness estimation in either the contralateral PSC or in the higher-level regions. Together, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, while the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon object features. HighlightsO_LIWe observed the brain activity of haptic object perception using parametric stimuli. C_LIO_LIHaptic curve estimation showed parametric modulation across the cortical hierarchy. C_LIO_LICurve parametric modulation in the sensorimotor cortex showed time dependency. C_LIO_LIRoughness parametric modulation showed very little dependency in any regions of the brain. C_LIO_LIThese findings reflect the nature of time-dependent haptic object processing in the brain. C_LI

neuroscience↗

bioRxiv2020

Fine-scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes

ABSTRACTHan Chinese is the most populated ethnic group across the globe with a comprehensive substructure that resembles its cultural diversification. Studies have constructed the genetic polymorphism spectrum of Han Chinese, whereas high-resolution investigations are still missing to unveil its fine-scale substructure and trace the genetic imprints for its demographic history. Here we construct a haplotype network consisted of 111,000 genome-wide genotyped Han Chinese individuals from direct-to-consumer genetic testing and over 1.3 billion identity-by-descent (IBD) links. We observed a clear separation of the northern and southern Han Chinese and captured 5 subclusters and 17 sub-subclusters in haplotype network hierarchical clustering, corresponding to geography (especially mountain ranges), immigration waves, and clans with cultural-linguistic segregation. We inferred differentiated split histories and founder effects for population clans Cantonese, Hakka, and Minnan-Chaoshanese in southern China, and also unveiled more recent demographic events within the past few centuries, such as Zou Xikou and Chuang Guandong. The composition shifts of the native and current residents of four major metropolitans (Beijing, Shanghai, Guangzhou, and Shenzhen) imply a rapidly vanished genetic barrier between subpopulations. Our study yields a fine-scale population structure of Han Chinese and provides profound insights into the nation’s genetic and cultural-linguistic multiformity.Competing Interest StatementThe authors AL, KK, ST, XW, LW, TL, HW, JD, QZ, XY, and GC work for WeGene (Shenzhen Zaozhidao Technology Co. Ltd. or Shenzhen WeGene Clinical Laboratory).View Full Text

genomics↗

bioRxiv2020

A high-quality genome assembly and annotation of the humpback grouper Cromileptes altivelas

Cromileptes altivelas that belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource for C. altivelas breeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.

genomics↗

bioRxiv2020

Genome-wide identification of long non-coding RNAs in the gravid ectoparasite Varroa destructor

Long non-coding RNAs (lncRNAs) emerge as critical regulators with various biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs are likely to play key roles in cellular processes, genetic information processing and environmental responses. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable pest control.

genomics↗

bioRxiv2020

Single Cell-type Integrative Network Modeling IdentifiedNovel Microglial-specific Targets for the Phagosome inAlzheimer's disease

SummaryLate-Onset Alzheimer’s Disease (LOAD) results from a complex pathological process influenced by genetic variation, aging and environment factors. Genetic susceptibility factors indicate that myeloid cells such as microglia play a significant role in the onset of LOAD. Here, we developed a computational systems biology approach to construct probabilistic causal and predictive network models of genetic regulatory programs of microglial cells under LOAD diagnosis by integrating two independent brain transcriptome and genome-wide genotype datasets from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MAYO) studies in the AMP-AD consortium. From this network model, we identified and replicated novel microglial-specific master regulators predicted to modulate network states associated with LOAD. We experimentally validated three microglial master regulators (FCER1G, HCK and LAPTM5) in primary human microglia-like cells (MDMi) by demonstrating the molecular impact these master regulators have on modulating downstream genomic targets identified by our top-down/bottom-up method and the causal relations among the three key drivers. These master regulators are involved in phagocytosis, a process associated with LOAD. Thus, we propose three new master regulator (key driver) genes that emerged from our network analyses as robust candidates for further evaluation in LOAD therapeutic development efforts.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2020

Genetic Risk Scores for Cardiometabolic Traits in Sub-Saharan African Populations

There is growing support for the use of genetic risk scores (GRS) in routine clinical settings. Due to the limited diversity of current genomic discovery samples, there are concerns that the predictive power of GRS will be limited in non-European ancestry populations. Here, we evaluated the predictive utility of GRS for 12 cardiometabolic traits in sub-Saharan Africans (AF; n=5200), African Americans (AA; n=9139), and European Americans (EA; n=9594). GRS were constructed as weighted sums of the number of risk alleles. Predictive utility was assessed using the additional phenotypic variance explained and increase in discriminatory ability over traditional risk factors (age, sex and BMI), with adjustment for ancestry-derived principal components. Across all traits, GRS showed upto a 5-fold and 20-fold greater predictive utility in EA relative to AA and AF, respectively. Predictive utility was most consistent for lipid traits, with percent increase in explained variation attributable to GRS ranging from 10.6% to 127.1% among EA, 26.6% to 65.8% among AA, and 2.4% to 37.5% among AF. These differences were recapitulated in the discriminatory power, whereby the predictive utility of GRS was 4-fold greater in EA relative to AA and up to 44-fold greater in EA relative to AF. Obesity and blood pressure traits showed a similar pattern of greater predictive utility among EA. This work demonstrates the poorer performance of GRS in AF and highlights the need to improve representation of multiethnic populations in genomic studies to ensure equitable clinical translation of GRS. Key MessagesO_LIGenetic Risk Score (GRS) prediction is markedly poorer in sub-Saharan Africans compared with African Americans and European Americans C_LIO_LITo ensure equitable clinical translation of GRS, there is need need to improve representation of multiethnic populations in genomic studies C_LI

genomics↗

bioRxiv2020

To pool or not to pool: Can we ignore cross-trial variability in FMRI?

In this work, we investigate the importance of explicitly accounting for cross-trial variability in neuroimaging data analysis. To attempt to obtain reliable estimates in a task-based experiment, each condition is usually repeated across many trials. The investigator may be interested in (a) condition-level effects, (b) trial-level effects, or (c) the association of trial-level effects with the corresponding behavior data. The typical strategy for condition-level modeling is to create one regressor per condition at the subject level with the underlying assumption that responses do not change across trials. In this methodology of complete pooling, all cross-trial variability is ignored and dismissed as random noise that is swept under the rug of model residuals. Unfortunately, this framework invalidates the generalizability from the confine of specific trials (e.g., particular faces) to the associated stimulus category ("face"), and may inflate the statistical evidence when the trial sample size is not large enough. Here we propose an adaptive and computationally tractable framework that meshes well with the current two-level pipeline and explicitly accounts for trial-by-trial variability. The trial-level effects are first estimated per subject through no pooling. To allow generalizing beyond the particular stimulus set employed, the cross-trial variability is modeled at the population level through partial pooling in a multilevel model, which permits accurate effect estimation and characterization. Alternatively, trial-level estimates can be used to investigate, for example, brain-behavior associations or correlations between brain regions. Furthermore, our approach allows appropriate accounting for serial correlation, handling outliers, adapting to data skew, and capturing nonlinear brain-behavior relationships. By applying a Bayesian multilevel model framework at the level of regions of interest to an experimental dataset, we show how multiple testing can be addressed and full results reported without arbitrary dichotomization. Our approach revealed important differences compared to the conventional method at the condition level, including how the latter can distort effect magnitude and precision. Notably, in some cases our approach led to increased statistical sensitivity. In summary, our proposed framework provides an effective strategy to capture trial-by-trial responses that should be of interest to a wide community of experimentalists.

neuroscience↗

bioRxiv2020

Regulations of expressions of rat/human sulfotransferases (SULTs) by anti-cancer drug, nolatrexed and micronutrients.

Cancer is a disease related to cellular proliferative-state. Drastically increase in cell-cycle regulations augments cellular folate-pool and folate-metabolism. So, this pathway is targeted therapeutically. A number of drugs are involved in this metabolism i.e. folic-acid/folinic-acid/nolatrexed(NT)/ methotrexate(MTX) for the research and treatment of cancer. Our previous study showed that MTX significantly modulated rat/human SULTs. Present study was an attempt to study the effect of NT (widely used in different cancers) and these micronutrients on the expressions of rat/human SULTs. Male Sprague-Dawley rats were treated with NT (01,10 or 100 mg/Kg) or both sexes were treated to folic acid (100,200 or 400 mg/kg) for 2-weeks and their AST-IV (2-napthol sulfation) and STa (DHEA-sulfation) activities, protein-expression (Western-Blot) and mRNA-expression (RT-PCR) were tested. In cultured HepG2 cells NT (1nM-1.2mM) or folonic-acid (10nM-10M) were applied for 10 days. Folic acid (0-10M) was treated to human hepatocarcinoma (HepG2) cells. PPST (phenol-catalyzing), MPST (dopamine) DHEAST (dehydroepiandrosterone,DHEA) and EST (estradiol-sulfating) protein-expressions (Western-blot) were tested in all HepG2 study. Present results suggest NT significantly increased SULTs expressions in rat (protein/mRNA/activity) and HepG2 cells. Folic acid increased SULTs activity/protein in sex-dependant manner (ASTIV in female/ STa in male). Both folic and folinic acid increased several hSULTs isoforms with varied level of significance (least or no increase at highest-dose) in HepG2 cells pointing its dose-dependent multi-phasic responses. The clinical importance of this study may be furthered in the verification of sulfation-metabolism of several exogenous/endogenous molecules, drug-drug interaction and their influences on the patho-physiological processes. Further studies are necessary in this regard.

pharmacology and toxicology↗

bioRxiv2020

scSTATseq: Diminishing Technical Dropout Enables Core Transcriptome Recovery and Comprehensive Single-cell Trajectory Mapping

The advent of single-cell RNA sequencing has provided illuminating information on complex systems. However, large numbers of genes tend to be scarcely detected in common scRNAseq approaches due to technical dropout. Although bioinformatics approaches have been developed to approximate true expression profiles, assess the dropout events on single-cell transcriptomes is still consequently challenging. In this report, we present a new plate-based method for scRNAseq that relies on Tn5 transposase to tagment cDNA following second strand synthesis. By utilizing pre-amplification tagmentation step, scSTATseq libraries are insulated against technical dropout, allowing for detailed analysis of gene-gene co-expression relationships and mapping of pathway trajectories. The entire scSTATseq library construction workflow can be completed in 7 hours, and recover transcriptome information on up to 8,000 protein-coding genes. Investigation of osteoclast differentiation using this workflow allowed us to identify novel markers of interest such as Rab15. Overall, scSTATseq is an efficient and economical method for scRNAseq that compares favorably with existing workflows.

genomics↗

bioRxiv2020

Long non-coding RNA LINC00152 plays an oncogenic role via targeting STAT3 and c-MYC signaling in esophageal adenocarcinoma

ObjectiveEsophageal cancer remains a threat to public health with an increasing incidence and low survival rate worldwide. In the past thirty years the rates for esophageal adenocarcinoma (EAC) have increased over 500%. Prior studies have linked Barrets esophagus (BE), Low grade dysplasia (LGD), and High grade dysplasia (HGD) as general precursors to EAC. However, the exact pathways by which EAC occurs have not been uncovered. Recent genomic studies have discovered a new family of active RNA species named long non-coding RNAs (lncRNAs). Of which, LINC00152 has been linked to several human cancers and shown to promote cell proliferation in lung, gastric, hepatocellular, colorectal, and clear cell renal carcinoma. This study is to investigate the roles of LINC00152 in EAC using EAC patient data and EAC cell lines. MethodsWe used LINC00152 specific siRNAs to knockdown LINC00152 and used the Gateway cloning method to generate stable overexpression of LINC00152 in Flo, OE19, and OE33 cell lines for in vitro study. The cells were tested for changes in cell proliferation, colony formation, invasion and migration. Real-time PCR assay was used for detecting mRNA expression and Western blot was used for examining altered protein expressions affected by LINC00152. Data analysis were performed using excel and Prism. Statistical differences were assessed using the Students T-test. Survival analysis was done using Kaplan-Meier estimates. ResultsThis study found that high levels of LINC00152 correlated positively with tumor progression, invasive potential, and TNM stage advancement in EAC. LINC00152 knockdown could inhibit cell proliferation, colony formation, and cell invasion. Western blot and Real-time PCR results suggests that LINC00152 may active via STAT3 and c-MYC signaling as both demonstrated changes following knockdown and overexpression experiments. ConclusionsThis study indicated that LINC00152 might be used as both a biomarker and a novel therapeutic target to improve the outcome for EAC patients. Further characterization of LINC00152 as a novel therapeutic target for EAC is warranted.

cancer biology↗

bioRxiv2020

An isothermal method for sensitive detection of Mycobacterium tuberculosis complexes using CRISPR/Cas12a cis- and trans-cleavage

Tuberculosis is still one of the most serious infectious diseases resulting in lethal death worldwide. The traditional method is still not enough to meet the clinical requirements of rapid diagnosis, high specificity and sensitivity. Fast, sensitive and accurate detection of mycobacterium tuberculosis (MTB) is an urgent need for the treatment and control of tuberculosis disease. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated proteins (Cas12a) exhibits strongly nonspecific degradation ability of exogenous single-strand nucleic acid (trans-cleavage) after specific recognition of target sequence. We purified Cas12a protein and selected a proper guide RNA (gRNA) based on conserved sequences of MTB from gRNA library we designed. Then, we proposed a novel method based on recombinase polymerase amplification (RPA) and CRISPR/Cas12a nuclease system for specific and sensitive detection of MTB DNA. The assay based on fluorescence detection pattern showed 4.48 fM of limit of detection (LOD) and good linear correlation of concentration and fluorescence value (R2=0.9775). Also, it showed good performance in distinguishing other bacteria. Furthermore, its clinical performance was evaluated by 193 samples and showed sensitivity of 99.29% (139/140) and specificity of 100% (53/53) at 99% confidence interval, respectively, compared with culture method. The CRISPR/Cas12a system showed good specificity, excellent sensitivity and accuracy for MTB detection, and it meets requirements of MTB detection in clinical samples and has great potential for clinical translation.

molecular biology↗

bioRxiv2020

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

BackgroundThe global dissemination of colistin resistance encoded by mcr-1 has been attributed to extensive use of colistin in livestock, threatening colistin efficacy in medicine. The emergence of mcr-1 in common pathogens, such as Escherichia coli, is of particular concern. Therefore, China banned the use of colistin in animal feed from May 1ST 2017. We investigated subsequent changes in mcr-1 prevalence, and the genomic epidemiology of mcr-1-positive Escherichia coli (MCRPEC). MethodsSampling was conducted pre- (October-December 2016) and post-colistin ban (October-December, 2017 and 2018, respectively). 3675 non-duplicate pig fecal samples were collected from 14 provinces (66 farms) in China to determine intervention-related changes in mcr-1 prevalence. 15193 samples were collected from pigs, healthy human volunteers, colonized and infected hospital inpatients, food and the environment in Guangzhou, to characterize source-specific mcr-1 prevalence and the wider ecological impact of the ban. From these samples, 688 MCRPEC were analyzed with whole genome sequencing (WGS), plasmid conjugation and S1-PFGE/Southern blots to characterize associated genomic changes. FindingsAfter the ban, mcr-1 prevalence decreased significantly in national pig farms, from 45{middle dot}0% (308/684 samples) in 2016, to 19{middle dot}4% (274/1416) in 2018 (p<0{middle dot}0001). This trend was mirrored in samples from most sources in Guangzhou (overall 19{middle dot}2% [959/5003 samples] in 2016; 5{middle dot}3% [238/4489] in 2018; p<0{middle dot}0001). The population structure of MCRPEC was diverse (23 sequence clusters [SCs]); ST10 clonal complex isolates were predominant (247/688 [36%]). MCRPEC causing infection in hospitalized inpatients were genetically more distinct and appeared less affected by the ban. mcr-1 was predominantly found on plasmids (632/688 [92%]). Common mcr-1 plasmid types included IncX4, IncI2 and IncHI2 (502/656 [76.5%]); significant increases in IncI2-associated mcr-1 and a distinct lineage of mcr-1-associated IncHI2 were observed post-ban. Changes in the frequency of mcr-1-associated flanking sequences (ISApl1-negative MCRPEC), 63 core genome SNPs and 30 accessory genes were also significantly different after the ban, consistent with rapid genetic adaptation in response to changing selection pressures. InterpretationA rapid, ecosystem-wide, decline in mcr-1 was observed after banning the use of colistin in animal feed, with associated genetic changes in MCRPEC. Genomic surveillance is key to assessing and monitoring stewardship interventions. FundingNational Natural Science Foundation of China

microbiology↗

bioRxiv2019

Infection risk and extensive parental care govern the molecular evolution of Toll-like receptors in birds.

The arms race between pathogens and the immune system of their hosts is a critical evolutionary force that affects the ecology and life history of organisms. An increased infection risk selects for adaptations in immune genes that encode receptors involved in pathogen recognition and the initiation of innate immune responses, including Toll-like receptor (TLR) genes. Although recent studies assessed the evolution of major histocompatibility complex (MHC) genes, the ecological and evolutionary processes that drive the evolution of immune genes across major phylogenetic lineages remain unstudied. Moreover, trade-offs between immune responses and other energy-demanding vital functions may limit the resource allocation into costly immune functions, and therefore affect the evolution of immune genes. Here we assess the evolutionary patterns of six TLR genes across 121 bird species, covering 95% of extant orders that represent diverse ecologies and life histories. Selection analyses revealed that all six TLR genes show strong signs of purifying selection, while few sites underwent episodic positive selection. Comparative phylogenetic analyses showed that the intensity of positive selection of TLR genes is associated with long-distance migration, extensive parental care (i.e., altricality and prolonged parent-offspring association), and a large body size (a proxy of increased longevity). Together, these results suggest that the evolution of immune genes is characterized by episodic positive selection, and is shaped by an increased inflection risk and extensive parental care that buffers the costs of immune functions.

evolutionary biology↗

bioRxiv2019

Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers

Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here we developed a computational framework to identify risk noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as candidate risk mutations in five major pediatric cancers. We experimentally validated the oncogenic role of CHD4 overexpression via enhancer hijacking in B-ALL. We observed a general exclusivity of coding and noncoding mutations affecting the same genes and pathways. We showed that integrated mutation signatures can help define novel patient subtypes with different clinical outcomes. Our study introduces a general strategy to systematically identify and characterize the full spectrum of noncoding mutations in cancers.

cancer biology↗

bioRxiv2019

In Vivo Neuroregeneration to Treat Ischemic Stroke in Adult Non-Human Primate Brains through NeuroD1 AAV-based Gene Therapy

Stroke is a leading cause of death and disability but most of the clinical trials have failed in the past, despite our increasing understanding of the molecular and pathological mechanisms underlying stroke. While many signaling pathways have been identified in the aftermath of stroke, the majority of current approaches are focusing on neural protection rather than neuroregeneration. In this study, we report an in vivo neural regeneration approach to convert brain internal reactive astrocytes into neurons through ectopic expression of a neural transcription factor NeuroD1 in adult non-human primate (NHP) brains following ischemic stroke. We demonstrate that NeuroD1 AAV-based gene therapy can convert reactive astrocytes into neurons with high efficiency (90%), but astrocytes are never depleted in the NeuroD1-expressed areas, consistent with the proliferative capability of astrocytes. The NeuroD1-mediated in vivo astrocyte-to-neuron (AtN) conversion in monkey cortex following ischemic stroke increased local neuronal density, reduced reactive microglia, and surprisingly protected parvalbumin interneurons in the converted areas. The NeuroD1 gene therapy showed a broad time window, from 10 days to 30 days following ischemic stroke, in terms of exerting its neuroregenerative and neuroprotective effects. The cortical astrocyte-converted neurons also showed Tbr1+ cortical neuron identity, similar to our earlier findings in rodent animal models. Unexpectedly, NeuroD1 expression in converted neurons showed a significant decrease after 6 months of viral infection, suggesting a potential self-regulatory mechanism of NeuroD1 in adult mature neurons of NHPs. These results suggest that in vivo cell conversion through NeuroD1-based gene therapy may be an effective approach to regenerate new neurons in adult primate brains for tissue repair.

neuroscience↗

bioRxiv2019

Regeneration of dorsal spinal cord neurons after injury via in situ NeuroD1-mediated astrocyte-to-neuron conversion

Spinal cord injury (SCI) often leads to impaired motor and sensory functions, partially because the injury-induced neuronal loss cannot be easily replenished through endogenous mechanisms. In vivo neuronal reprogramming has emerged as a novel technology to regenerate neurons from endogenous glial cells by forced expression of neurogenic transcription factors. We have previously demonstrated successful astrocyte-to-neuron conversion in mouse brains with injury or Alzheimers disease by overexpressing a single neural transcription factor NeuroD1 via retroviruses. Here we demonstrate regeneration of dorsal spinal cord neurons from reactive astrocytes after SCI via adeno-associated virus (AAV), a more clinically relevant gene delivery system. We find that NeuroD1 converts reactive astrocytes into neurons in the dorsal horn of stab-injured spinal cord with high efficiency ([~]95%). Interestingly, NeuroD1-converted neurons in the dorsal horn mostly acquire glutamatergic neuronal subtype, expressing spinal cord-specific markers such as Tlx3 but not brain-specific markers such as Tbr1, suggesting that the astrocytic lineage and local microenvironment affect the cell fate of conversion. Electrophysiological recordings show that the NeuroD1-converted neurons can functionally mature and integrate into local spinal cord circuitry by displaying repetitive action potentials and spontaneous synaptic responses. We further show that NeuroD1-mediated neuronal conversion can occur in the contusive SCI model, allowing future studies of evaluating this reprogramming technology for functional recovery after SCI. In conclusion, this study may suggest a paradigm shift for spinal cord repair using in vivo astrocyte-to-neuron conversion technology to generate functional neurons in the grey matter.

neuroscience↗

bioRxiv2019

Interactions between emotion and action in the brain

A growing literature supports the existence of interactions between emotion and action in the brain, and the central participation of the anterior midcingulate cortex (aMCC) in this regard. In the present functional magnetic resonance imaging study, we sought to investigate the role of self-relevance during such interactions by varying the context in which threating pictures were presented (with guns pointed towards or away from the observer). Participants performed a simple visual detection task following exposure to such stimuli. Except for voxelwise tests, we adopted a Bayesian analysis framework which evaluated evidence for the hypotheses of interest, given the data, in a continuous fashion. Behaviorally, our results demonstrated a valence by context interaction such that there was a tendency of speeding up responses to targets after viewing threat pictures directed towards the participant. In the brain, interaction patterns that paralleled those observed behaviorally were observed most notably in the middle temporal gyrus, supplementary motor area, precentral gyrus, and anterior insula. In these regions, activity was overall greater during threat conditions relative to neutral ones, and this effect was enhanced in the directed towards context. A valence by context interaction was observed in the aMCC too, where we also observed a correlation (across participants) of evoked responses and reaction time data. Taken together, our study revealed the context-sensitive engagement of motor-related areas during emotional perception, thus supporting the idea that emotion and action interact in important ways in the brain.

neuroscience↗