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Song, M.

Publications and source records attributed to Song, M..

At least 91 records · Page 5Linked to original sources
bioRxiv2020

HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

HiChIP and PLAC-seq are emerging technologies for studying genome-wide long-range chromatin interactions mediated by protein of interest, enabling more sensitive and cost-efficient interrogation of protein-centric chromatin conformation. However, due to the unbalanced read distribution introduced by protein immunoprecipitation, existing reproducibility measures developed for Hi-C data are not appropriate for the analysis of HiChIP and PLAC-seq data. Here, we present HPRep, a stratified and weighted correlation metric derived from normalized contact counts, to quantify reproducibility in HiChIP and PLAC-seq data. We applied HPRep to multiple real datasets and demonstrate that HPRep outperforms existing reproducibility measures developed for Hi-C data. Specifically, we applied HPRep to H3K4me3 PLAC-seq data from mouse embryonic stem cells and mouse brain tissues, as well as H3K27ac HiChIP data from human lymphoblastoid cell line GM12878 and leukemia cell line K562, showing that HPRep can more clearly separate among pseudo-replicates, real replicates, and non-replicates. Furthermore, in an H3K4me3 PLAC-seq dataset consisting of 11 samples from four human brain cell types, HPRep demonstrates expected clustering of data which could not be achieved by existing methods developed for Hi-C data, highlighting the need of a reproducibility metric tailored to HiChIP and PLAC-seq data.

genomics↗
bioRxiv2020

Soluble Spike DNA vaccine provides long-term protective immunity against SAR-CoV-2 in mice and nonhuman primates

The unprecedented and rapid spread of SARS-CoV-2 has motivated the need for a rapidly producible and scalable vaccine. Here, we developed a synthetic soluble SARS-CoV-2 spike (S) DNA-based vaccine candidate, GX-19. In mice, immunization with GX-19 elicited not only S-specific systemic and pulmonary antibody responses but also Th1-biased T cell responses in a dose-dependent manner. GX-19 vaccinated nonhuman primate seroconverted rapidly and exhibited detectable neutralizing antibody response as well as multifunctional CD4+ and CD8+ T cell responses. Notably, when the immunized nonhuman primates were challenged at 10 weeks after the last vaccination with GX-19, they did not develop fever and reduced viral loads in contrast to non-vaccinated primates as a control. These findings indicate that GX-19 vaccination provides durable protective immune response and also support further development of GX-19 as a vaccine candidate for SARS-CoV-2 in human clinical trials.

immunology↗
bioRxiv2020

The mouse cortico-basal ganglia-thalamic network

The cortico-basal ganglia-thalamic loop is one of the fundamental network motifs in the brain. Revealing its structural and functional organization is critical to understanding cognition, sensorimotor behavior, and the natural history of many neurological and neuropsychiatric diseases. Classically, the basal ganglia is conceptualized to contain three primary information output channels: motor, limbic, and associative. However, given the roughly 65 cortical areas and two dozen thalamic nuclei that feed into the dorsal striatum, a three-channel view is overly simplistic for explaining the myriad functions of the basal ganglia. Recent works from our lab and others have subdivided the dorsal striatum into numerous functional domains based on convergent and divergent inputs from the cortex and thalamus. To complete this work, we generated a comprehensive data pool of [~]700 injections placed across the striatum, external globus pallidus (GPe), substantia nigra pars reticulata (SNr), thalamic nuclei, and cortex. We identify 14 domains of SNr, 36 in the GPe, and 6 in the parafascicular and ventromedial thalamic nuclei. Subsequently, we identify 6 parallel cortico-basal ganglia-thalamic subnetworks that sequentially transduce specific subsets of cortical information with complex patterns of convergence and divergence through every elemental node of the entire cortico-basal ganglia loop. These experiments reveal multiple important novel features of the cortico-basal ganglia network motif. The prototypical sub-network structure is characterized by a highly interconnected nature, with cortical information processing through one or more striatal nodes, which send a convergent output to the SNr and a more parallelized output to the GPe; the GPe output then converges with the SNr. A domain of the thalamus receives the nigral output, and is interconnected with both the striatal domains and the cortical areas that filter into its nigral input source. This study provides conceptual advancement of our understanding of the structural and functional organization of the classic cortico-basal ganglia network.

neuroscience↗
bioRxiv2020

Molecular mechanism of SARS-Cov-2 components caused ARDS in murine model

COVID-19 has become a major challenge to global health, and until now, no efficient antiviral agents have been developed. The SARS-CoV-2 infection is characterized by pulmonary and systemic inflammation in severe patients, and acute respiratory distress syndrome (ARDS) caused respiratory failure contributes to most mortalities. There is an urgent need for developing effective drugs and vaccines against SARS-CoV-2 and COVID-19 caused ARDS. However, most researchers cannot perform SARS-CoV-2 related researches due to lacking P3 or P4 facility. We developed a non-infectious, highly safety, time-saving SARS-CoV-2 components induced murine model to study the SARS-CoV-2 caused ARDS and cytokine storm syndrome (CSS). We also investigated mAbs and inhibitors which potentially neutralize the pro-inflammatory phenotype of COVID-19, and found that anti-IL-1, anti-IL-6, anti-TNF, anti-GM-CSF mAbs, p38 inhibitor, and JAK inhibitor partially relieved CSS. Besides, anti-IL-6, anti-TNF, anti-GM-CSF mAbs and inhibitors of p38, ERK, and MPO somewhat reduced neutrophilic alveolitis in the lung. In all, we established the murine model mimic of COVID-19, opening a biosafety and less time-consuming avenue for clarifying the mechanism of ARDS and CSS in COVID-19 and developing the therapeutic drugs.

pathology↗
bioRxiv2020

Spontaneous retinal waves generate long-range horizontal connectivity in visual cortex

In the primary visual cortex (V1) of higher mammals, long-range horizontal connections (LHCs) are observed to develop, linking iso-orientation domains of cortical tuning. It is unknown how this feature-specific wiring of circuitry develops before eye opening. Here, we show that LHCs in V1 may originate from spatio-temporally structured feedforward activities generated from spontaneous retinal waves. Using model simulations based on the anatomy and observed activity patterns of the retina, we show that waves propagating in retinal mosaics can initialize the wiring of LHCs by co-activating neurons of similar tuning, whereas equivalent random activities cannot induce such organizations. Simulations showed that emerged LHCs can produce the patterned activities observed in V1, matching topography of the underlying orientation map. We also confirmed that the model can also reproduce orientation-specific microcircuits in salt-and-pepper organizations in rodents. Our results imply that early peripheral activities contribute significantly to cortical development of functional circuits. HighlightsO_LIDevelopmental model of long-range horizontal connections (LHCs) in V1 is simulated C_LIO_LISpontaneous retinal waves generate feature-specific wiring of LHCs in visual cortex C_LIO_LIEmerged LHCs induce orientation-matching patterns of spontaneous cortical activity C_LIO_LIRetinal waves induce orientation-specific microcircuits of visual cortex in rodents C_LI Significance statementLong-range horizontal connections (LHCs) in the primary visual cortex (V1) are observed to emerge before the onset of visual experience, selectively connecting iso-domains of orientation maps. However, it is unknown how such tuning-specific wirings develop before eye-opening. Here, we show that LHCs in V1 originate from the tuning-specific activation of cortical neurons by spontaneous retinal waves during early developmental stages. Our simulations of a visual cortex model show that feedforward activities from the retina initialize the spatial organization of activity patterns in V1, which induces visual feature-specific wirings of V1 neurons. Our model also explains the origin of cortical microcircuits observed in rodents, suggesting that the proposed developmental mechanism is applicable universally to circuits of various mammalian species.

neuroscience↗
bioRxiv2020

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis

Lineage-specific epigenomic changes during human corticogenesis have previously remained elusive due to challenges with tissue heterogeneity and sample availability. Here, we analyze cis-regulatory chromatin interactions, open chromatin regions, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational human brain samples. We show that chromatin looping underlies transcriptional regulation for lineage-specific genes, with transcription factor motifs, families of transposable elements, and disease-associated variants enriched at distal interacting regions in a cell type-specific manner. A subset of promoters exhibit unusually high degrees of chromatin interactivity, which we term super interactive promoters. Super interactive promoters are enriched for critical lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of cell type-specific transcription. Finally, we present CRISPRview, a novel approach for validating distal interacting regions in primary cells. Our study presents the first characterization of cell type-specific 3D epigenomic landscapes during human corticogenesis, advancing our understanding of gene regulation and lineage specification during human brain development.

genomics↗
bioRxiv2020

Projection of orthogonal tiling from the retina to the visual cortex

In higher mammals, the primary visual cortex (V1) is organized into diverse tuning maps of visual features such as orientation, spatial frequency and ocular dominance. The topography of these maps is observed to intersect orthogonally, implying that a developmental principle for efficient tiling of sensory modules may exist. However, it remains unclear how such a systematic relationship among cortical tuning maps could develop. Here, we show that the orthogonal organization of tuning modules already exist in retinal ganglion cell (RGC) mosaics, and that this provides a blueprint of the orthogonal organization in V1. Firstly, from the analysis of multi-electrode recording data in V1, we found that the ON-OFF subregion distance of receptive fields varies periodically across the cortical surface, strongly correlated to ocular dominance and spatial frequency in the area. Further, the ON-OFF alignment angle, that is orthogonal to the ON-OFF distance, appears to correlate with orientation tuning. These suggest that the orthogonal organization in V1 may originate from the spatial organization of the ON-OFF receptive fields in the bottom-up projections, and this scenario was tested from analysis of the RGC mosaics data in monkeys and cats. We found that the ON-OFF RGC distance and ON-OFF angle of neighbouring RGCs are organized into a topographic tiling across mosaics, analogous to the orthogonal intersection of cortical tuning maps. These findings suggest that the regularly structured ON-OFF patterns mirrored from a retina may initiate efficient tiling of functional domains in V1. HighlightsO_LIOrthogonal organization of visual tuning maps are observed in both V1 and the retina C_LIO_LICortical tuning maps are correlated with the profile of ON-OFF feedforward projections C_LIO_LIThe profile of ON-OFF receptive fields varies periodically across the V1 surface C_LIO_LIRegularly structured RGC patterns initiate the orthogonal tiling of sensory modules in V1 C_LI

neuroscience↗
bioRxiv2019

Spontaneous generation of face recognition in untrained deep neural networks

Face-selective neurons are observed in the primate visual pathway and are considered the basis of facial recognition in the brain. However, it is debated whether this neuronal selectivity can arise spontaneously, or requires training from visual experience. Here, we show that face-selective neurons arise spontaneously in random feedforward networks in the absence of learning. Using biologically inspired deep neural networks, we found that face-selective neurons arise under three different network conditions: one trained using non-face natural images, one randomized after being trained, and one never trained. We confirmed that spontaneously emerged face-selective neurons show the biological view-point-invariant characteristics observed in monkeys. Such neurons suddenly vanished when feedforward weight variation declined to a certain level. Our results suggest that innate face-selectivity originates from statistical variation of the feedforward projections in hierarchical neural networks.

neuroscience↗
bioRxiv2019

Spontaneous generation of innate number sense in untrained deep neural networks

Number-selective neurons are observed in numerically naive animals, but it was not understood how this innate function emerges in the brain. Here, we show that neurons tuned to numbers can arise in random feedforward networks, even in the complete absence of learning. Using a biologically inspired deep neural network, we found that number tuning arises in three cases of networks: one trained to non-numerical natural images, one randomized after trained, and one never trained. Number-tuned neurons showed characteristics that were observed in the brain following the Weber-Fechner law. These neurons suddenly vanished when the feedforward weight variation decreased to a certain level. These results suggest that number tuning can develop from the statistical variation of bottom-up projections in the visual pathway, initializing innate number sense.

neuroscience↗
bioRxiv2019

Classification of columnar and salt-and-pepper organization in mammalian visual cortex

In mammalian visual cortex, neural tuning to stimulus orientation is organized in either columnar1 or salt- and-pepper2 patterns across species. This is often considered to reflect disparate mechanisms of cortical development across mammalian taxa. However, it is unknown whether different cortical architectures are generated by species-specific mechanisms3,4, or simply originate from the variation of biological parameters within a universal principle of development5-8. We analysed neural parameters in eight mammalian species and found that cortical organization is predictable by a single factor: the retino-cortical mapping ratio. We show that a Nyquist sampling model explains parametric division of the patterns with high accuracy and that simulations of controlled mapping conditions reproduce both types of organization. Our results explain the origin of distinct cortical circuits under a universal development process.

neuroscience↗
bioRxiv2019

Hierarchy of connectivity-function relationship of the human cortex revealed through predicting activity across functional domains

Many studies showed that anatomical connectivity supports both anatomical and functional hierarchies that span across the primary and association cortices in the cerebral cortex. However, it remains unclear whether a hierarchy of connectivity-function relationship (CFR) exists across the human cortex as well as how to characterize the hierarchy of this CFR if it exists. We first addressed whether anatomical connectivity could be used to predict functional activations across different functional domains using multilinear regression models. Then we characterized the CFR by predicting activity from anatomical connectivity throughout the cortex. We found that there is a hierarchy of CFR across the human cortex. Moreover, this CFR hierarchy was correlated to the functional and anatomical hierarchy reflected in functional flexibility, functional variability, and the myelin map. Our results suggest a shared hierarchical mechanism in the cortex, a finding which provides important insights into the anatomical and functional organization of the human brain.

neuroscience↗
bioRxiv2019

Global variability of the human IgG glycome

Immunoglobulin G (IgG) is the most abundant serum antibody and is a key determinant of the humoral immune response. Its structural characteristics and effector functions are modulated through the attachment of various sugar moieties called glycans. IgG N-glycome patterns change with the age of individual and in different diseases. Variability of IgG glycosylation within a population is well studied and is affected by a combination of genetic and environmental factors. However, global inter-population differences in IgG glycosylation have never been properly addressed. Here we present population-specific N-glycosylation patterns of whole IgG, analysed in 5 different populations totalling 10,482 IgG glycomes, and of IgGs fragment crystallisable region (Fc), analysed in 2,530 samples from 27 populations sampled across the world. We observed that country of residence associates with many N-glycan features and is a strong predictor of monogalactosylation variability. IgG galactosylation also strongly correlated with the development level of a country, defined by United Nations health and socioeconomic development indicators. We found that subjects from developing countries had low IgG galactosylation levels, characteristic for inflammation and ageing. Our results suggest that citizens of developing countries may be exposed to country-specific environmental factors that can cause low-grade chronic inflammation and the apparent increase in biological age.

biochemistry↗
bioRxiv2019

Low-dose IFN-γ induces tumor cell stemness in tumor microenvironment of non-small cell lung cancer

Interferon-{gamma} (IFN-{gamma}) is conventionally recognized as an inflammatory cytokine that play a central role in antitumor immunity. Clinically, although has been used clinically to treat a variety of malignancies, low-level IFN-{gamma} in the tumor microenvironment (TME) increases the risk of tumor metastasis during immunotherapy. Accumulating evidence has suggested that IFN-{gamma} can induce cancer progression. The mechanisms underlying the controversial role of IFN-{gamma} regulating tumor development remain unclear. Herein, we firstly revealed a dose-dependent effect of IFN-{gamma} in inducing tumor stemness to accelerate cancer progression in patients with a variety of cancer types. Mechanically, low-level IFN-{gamma} endowed cancer stem-like properties via the intercellular adhesion molecule-1 (ICAM1)-PI3K-Akt-Notch1 axis, whereas high-level IFN-{gamma} activated the JAK1-STAT1-caspase pathway to induce apoptosis in non-small cell lung cancer (NSCLC). Inhibition of ICAM1 abrogated the stem-like properties of NSCLC cells induced by the low dose of IFN-{gamma} both in vitro and in vivo. Our study first defines the role of low-level IFN-{gamma} in conferring tumor stemness and clearly elucidate the distinct signaling pathways activated by IFN-{gamma} in a dose-dependent manner, providing new insights into cancer treatment, particularly patients with low-level IFN-{gamma} expression in the TME.

cancer biology↗
bioRxiv2018

cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders

Mutations in gene regulatory elements have been associated with a wide range of complex neurological disorders. However, due to their inherent cell type-specificity and difficulties in characterizing their regulatory targets, our ability to identify causal genetic variants has remained limited. To address these constraints, we perform integrative analysis of chromatin interactions using promoter capture Hi-C (pcHi-C), open chromatin regions using ATAC-seq, and transcriptomes using RNA-seq in four functionally distinct neural cell types: iPSC-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus (DG)-like neurons, and primary astrocytes. We identify hundreds of thousands of long-range cis interactions between promoters and distal promoter-interacting regions (PIRs), enabling us to link regulatory elements to their target genes and reveal putative pathways that are dysregulated in disease. We validate several novel PIRs using CRISPR techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP, and DRD2 are transcriptionally regulated by physically linked enhancers. Finally, we show that physical chromatin interactions mediate genetic interactions in autism spectrum disorder (ASD). Our study illustrates how characterizing the 3D epigenome elucidates novel regulatory relationships in the central nervous system (CNS), shedding light on previously unknown functions for noncoding variants in complex neurological disorders.

genomics↗
bioRxiv2018

Intake of dietary fiber, fruits, and vegetables, and risk of diverticulitis

Background & AimsAlthough low fiber intake has been considered a risk factor for diverticulitis, prospective evidence is limited and conflicting, with little known about variation in the protective effects according to food sources. We assessed the associations of intakes of fiber and major food sources of fiber including fruits and vegetables with risk of diverticulitis.\n\nMethodsWe followed 50,019 women in the Nurses Health Study (1990-2014) and 48,292 men in the Health Professionals Follow-up Study (1986-2014) who were free of diverticulitis, cancer, and inflammatory bowel disease at baseline. Incident diverticulitis was identified through self-report with validity confirmed by review of medical records.\n\nResultsDuring a mean follow-up time of 22 years, we documented 4,343 incident cases of diverticulitis in women and 1,142 cases in men. Compared to participants in the lowest quintile, the multivariable HRs (95% CIs) of diverticulitis in the highest quintile of total fiber intake were 0.86 (0.78-0.95; P-trend=0.002) among women and 0.63 (0.51-0.79; P-trend<0.001) among men. Fiber from different food sources, except for vegetable fiber in women, was associated with a decreased risk of diverticulitis. Furthermore, total whole fruit intake was associated with reduced risk of diverticulitis in both cohorts with a multivariable HR for diverticulitis of 0.95 (0.92-0.98; P-trend<0.001) in women and 0.91 (0.86-0.96; P-trend<0.001) in men for every serving increase of total whole fruit intake per day.\n\nConclusionsHigher intake of dietary fiber and fiber from different food sources are associated with a lower risk of diverticulitis. A greater intake of whole fruit is also associated with reduced risk.

epidemiology↗
bioRxiv2018

Adopting Literature-based Discovery on Rehabilitation Therapy Repositioning for Stroke

Stroke is a common disabling disease severely affecting the daily life of the patients. There is evidence that rehabilitation therapy can improve the movement function. However, there are no clear guidelines that identify specific, effective rehabilitation therapy schemes, and the development of new rehabilitation techniques has been fairly slow. One informatics translational approach, called ABC model in Literature-based Discovery, was used to mine an existing rehabilitation candidate which is most likely to be repositioned for stroke. As in the classic ABC model originated from Don Swanson, we built the internal links of stroke (A), assessment scales (B), rehabilitation therapies (C) in PubMed relating to upper limb function measurements for stroke patients. In the first step, with E-utility we retrieved both stroke related assessment scales and rehabilitation therapies records, and complied two datasets called Stroke_Scales and Stroke_Therapies, respectively. In the next step, we crawled all rehabilitation therapies co-occurred with the Stroke_Theapies, named as All_Therapies. Therapies that were already included in Stroke_Therapies were deleted from All_Therapies, so that the remaining therapies were the potential rehabilitation therapies, which could be repositioned for stroke after subsequent filtration by manual check. We identified the top ranked repositioning rehabilitation therapy following by subsequent clinical validation. Hand-arm bimanual intensive training (HABIT) ranked the first in our repositioning rehabilitation therapies list, with the most interaction links with Stroke_Scales. HABIT showed a significant improvement in clinical scores on assessment scales of Fugl-Meyer Assessment and Action Research Arm Test in the clinical validation on upper limb function for acute stroke patients. Based on the ABC model and clinical validation of the results, we put forward that HABIT as a promising rehabilitation therapy for stroke, which shows that the ABC model is an effective text mining approach for rehabilitation therapy repositioning. The results seem to be promoted in clinical knowledge discovery.\n\nAuthor SummaryIn the present study, we proposed a text mining approach to mining terms related to disease, rehabilitation therapy, and assessment scale from literature, with a subsequent ABC inference analysis to identify relationships of these terms across publications. The clinical validation demonstrated that our approach can be used to identify potential repositioning rehabilitation therapy strategies for stroke. Specifically, we identified a promising rehabilitation method called HABIT previously used in pediatric congenital hemiplegia. A subsequent clinical trial confirmed this as a highly promising rehabilitation therapy for stroke.

bioinformatics↗
bioRxiv2018

Fibroblast growth factor is predicted to dominate MAPK activation by pro-angiogenic factors

Angiogenesis is important in physiological and pathological conditions, as blood vessels provide nutrients and oxygen needed for tissue growth and survival. Therefore, targeting angiogenesis is a prominent strategy in both tissue engineering and cancer treatment. However, not all of the approaches to promote or inhibit angiogenesis lead to successful outcomes. Angiogenesis-based therapies primarily target pro-angiogenic factors such as vascular endothelial growth factor-A (VEGF) or fibroblast growth factor (FGF) in isolation, and there is a limited understanding of how these promoters combine together to stimulate angiogenesis. Thus, more quantitative insight is needed to understand their interactions. In this study, we have trained and validated a detailed mathematical model to quantitatively characterize the crosstalk of FGF and VEGF intracellular signaling. The model focuses on FGF- and VEGF-induced mitogen-activated protein kinase (MAPK) signaling and phosphorylation of extracellular regulated kinase (ERK), which promote cell proliferation. We apply the model to predict the dynamics of phosphorylated ERK (pERK) in response to the stimulation by FGF and VEGF individually and in combination. The model predicts that FGF plays a dominant role in promoting ERK phosphorylation, compared to VEGF. The modeling predictions show that VEGFR2 density and trafficking parameters significantly influence the level of VEGF-induced pERK. The model matches experimental data and is a framework to synthesize and quantitatively explain experimental studies. Ultimately, the model provides mechanistic insight into FGF and VEGF interactions needed to identify potential targets for pro-or anti-angiogenic therapies.

systems biology↗
bioRxiv2018

Universality of the developmental origins of diverse functional maps in the visual cortex

The primary visual cortex of higher mammals is organized into diverse functional maps of correlated topography, implying an efficient tiling of functional domains. However, no fundamental principle is available on how systematic organization of the maps could develop initially in various species. Here, we propose that diverse functional maps are seeded from a common framework of retinal afferents, and that this universality of development explains the observed topographical correlations among the maps. From the simulation of retinal ganglion cell mosaics, we successfully developed all four cortical maps observed so far. We validated our model prediction of inter-map relationships from analysis of map data in evolutionarily divergent mammalian species. Our key prediction, the hexagonal periodicity of every functional map, was validated from analysis of the map data in diverse mammalian species. Our results provide new insight into a universal mechanism for the development and evolution of the visual cortex.

neuroscience↗