Biology subjects

He, M.

Publications and source records attributed to He, M..

171 records · Page 10Linked to original sources

bioRxiv2018

Radial glial lineage progression and differential intermediate progenitor amplification underlie striatal compartments and circuit organization

The circuitry of the striatum is characterized by two organizational plans: the division into striosome and matrix compartments, thought to mediate evaluation and action, and the direct and indirect pathways, thought to promote or suppress behavior. The developmental origins of and relationships between these organizations are unknown, leaving a conceptual gap in understanding the cortico-basal ganglia system. Through genetic fate mapping, we demonstrate that striosome-matrix compartmentalization arises from a lineage program embedded in lateral ganglionic eminence radial glial progenitors mediating neurogenesis through two distinct types of intermediate progenitors (IPs). The early phase of this program produces striosomal spiny projection neurons (SPNs) through fate-restricted apical IPs (aIPSs) with limited capacity; the late phase produces matrix SPNs through fate-restricted basal IPs (bIPMs) with expanded capacity. Remarkably, direct and indirect pathway SPNs arise within both aIPS and bIPM pools, suggesting that striosome-matrix architecture is the fundamental organizational plan of basal ganglia circuitry organization.

neuroscience↗

bioRxiv2017

Cell size and growth rate are modulated by TORC2-dependent signals

The size of all cells, from bacteria to vertebrates, is proportional to the growth rate set by nutrient availability, but the underlying mechanisms are unknown. Here, we show that nutrients modulate TORC2 signaling, and that cell size is proportional to TORC2 signaling in budding yeast. The TORC2 network controls production of ceramide lipids, which play roles in signaling. We discovered that ceramide-dependent signals control both growth rate and cell size. Thus, cells that can not make ceramides fail to modulate their growth rate or size in response to changes in nutrients. PP2A associated with the Rts1 regulatory subunit (PP2ARts1) is embedded in a feedback loop that controls TORC2 signaling and plays an important role in mechanisms that modulate TORC2 signaling in response to nutrients. Together, the data suggest a model in which growth rate and cell size are mechanistically linked by ceramide-dependent signals arising from the TORC2 network.

cell biology↗

bioRxiv2017

FACT sets a barrier for cell fate reprogramming in C. elegans and Human

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/185116_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (59K):\norg.highwire.dtl.DTLVardef@15ae7aaorg.highwire.dtl.DTLVardef@11f5c08org.highwire.dtl.DTLVardef@1d32442org.highwire.dtl.DTLVardef@f1808f_HPS_FORMAT_FIGEXP M_FIG C_FIG The chromatin regulator FACT (Facilitates Chromatin Transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using C. elegans we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACTs role as a reprogramming barrier is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts into stem cells and neurons. Such activity of FACT is unexpected since known reprogramming barriers typically repress gene expression by silencing chromatin. In contrast, FACT is a positive regulator of gene expression suggesting an unprecedented link of cell fate maintenance with counteracting alternative cell identities. This notion is supported by ATAC-seq analysis showing that FACT depletion results in decreased but also increased chromatin accessibility for transcription factors. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection.

developmental biology↗

bioRxiv2017

Discovery of Resistance Pathways to Fibroblast Growth Factor Receptor inhibition in Bladder Cancer

BackgroundAberrant fibroblast growth factor receptor (FGFR) signaling drives the growth of many bladder cancers. NVP-BGJ398 is a small molecule with potent inhibitory activity of FGFRs 1, 2, and 3, and has been shown to selectively inhibit the growth of bladder cancer cell lines that over-express FGFR3 or have oncogenic FGFR3 fusions. As with many agents targeting receptor tyrosine kinases, resistance is known to develop.\n\nObjectiveWe sought to identify potential mechanisms of resistance to NVP-BGJ398 in cell culture models of bladder cancer.\n\nMethodsRT-112 bladder cancer cell lines were derived that were resistant to growth in 3uM NVP-BGJ398. RNA-sequencing was performed on resistant and parental cell lines to identify potential resistance mechanisms and molecular experiments were carried out to test these predictions.\n\nResultsRNA-seq demonstrated decreased expression of FGFR3 and increased expression of FGFRs 1 and 2 in resistant cell lines. Over-expression of FGFR3 in NVP-BGJ398 resistant cells decreased their proliferation. Pathway analysis of RNA-seq data also implicated PIM kinase signaling, among other pathways, as a potential mediator of resistance. Treatment of BGJ398 resistant cells with the PIM kinase inhibitor SGI-1776 reduced the growth of the cells.\n\nConclusionsOur results suggest that altered FGFR expression and PIM kinase activity could mediate resistance to NVP-BGJ398. These pathways should be investigated in samples from patients resistant to this drug.

cancer biology↗

bioRxiv2017

An insula-central amygdala circuit for behavioral inhibition

Predicting which substances are suitable for consumption during foraging is critical for animals to survive. While food-seeking behavior is extensively studied, the neural circuit mechanisms underlying avoidance of potentially poisonous substances remain poorly understood. Here we examined the role of the insular cortex (IC) to central amygdala (CeA) circuit in the establishment of such avoidance behavior. Using anatomic tracing approaches combined with optogenetics-assisted circuit mapping, we found that the gustatory region of the IC sends direct excitatory projections to the lateral division of the CeA (CeL), making monosynaptic excitatory connections with distinct populations of CeL neurons. Specific inhibition of neurotransmitter release from the CeL-projecting IC neurons prevented mice from acquiring the \"no-go\" response, while leaving the \"go\" response largely unaffected in a tastant (sucrose/quinine)-reinforced \"go/no-go\" task. Furthermore, selective activation of the IC-CeL pathway with optogenetics drove unconditioned lick suppression in thirsty animals, induced aversive responses, and was sufficient to instruct conditioned action suppression in response to a cue predicting the optogenetic activation. These results indicate that activity in the IC-CeL circuit is necessary for establishing anticipatory avoidance responses to an aversive tastant, and is also sufficient to drive learning of such anticipatory avoidance. This function of the IC-CeL circuit is likely important for guiding avoidance of substances with unpleasant tastes during foraging in order to minimize the chance of being poisoned.\n\nSignificance StatementThe ability to predict which substances are suitable for consumption is critical for survival. Here we found that activity in the insular cortex (IC) to central amygdala (CeA) circuit is necessary for establishing avoidance responses to an unpleasant tastant, and is also sufficient to drive learning of such avoidance responses. These results suggest that the IC-CeA circuit is critical for behavioral inhibition in anticipation of potentially poisonous substances during foraging.

neuroscience↗

bioRxiv2017

Buffering Agent Induced Lactose Content Increases via Growth Hormone-Mediated Activation of Gluconeogenesis in Lactating Goats

Dairy goats are often fed a high-concentrate (HC) diet to meet lactation demands; however, long-term concentrate feeding is unhealthy and decreases milk yield and lactose content. Therefore, we tested whether a buffering agent increases the output of glucose in the liver and influences of lactose synthesis. In this study, sixteen lactating goats were randomly assigned to two groups: one group received a HC diets (Concentrate: Forage = 6:4, HG), and the other group received the same diet with a buffering agent added (0.2% NaHCO3, 0.1% MgO, BG) as a treatment for 19-weeks experimental period. The results showed that the total volatile fatty acids and lipopolysaccharide (LPS) declined in the rumen leading to the rumen pH was stabilized in the BG group. Milk yield and lactose content increased. The alanine aminotransferase, aspartate transaminase, alkaline phosphatase, pro-inflammatory cytokines, LPS and lactate content in the plasma was significantly decreased, whereas prolactin and growth hormone levels were increased. The hepatic vein content of glucose was increased. In addition, the expression of pyruvate carboxylase (PC), phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6PC) in the liver was significantly up-regulated. In mammary gland, the glucose transporter type-1, 8, 12 and sodium-glucose cotransporter-1 levels were increased. Cumulatively, the buffering agent treatment increased blood concentrations of glucose via the gluconeogenes and promoting their synthesis in the liver. It may contribute to the increase in milk yield and lactose synthesis of lactating goats.

biochemistry↗

bioRxiv2017

Selective Inhibitory Control Of Pyramidal Neuron Ensembles And Cortical Subnetworks By Chandelier Cells

The neocortex comprises multiple information processing streams mediated by subsets of glutamatergic pyramidal cells (PCs) that receive diverse inputs and project to distinct targets. How GABAergic interneurons regulate the segregation and communication among intermingled PC subsets that contribute to separate brain networks remains unclear. Here we demonstrate that a subset of GABAergic chandelier cells (ChCs) in the prelimbic cortex (PL), which innervate PCs at spike initiation site, selectively control PCs projecting to the basolateral amygdala (BLAPC) compared to those projecting to contralateral cortex (ccPC). These ChCs in turn receive preferential input from local and contralateral CCPCs as opposed to BLAPCs and BLA neurons (the PL-BLA network). Accordingly, optogenetic activation of ChCs rapidly suppresses BLAPCs and BLA activity in freely behaving mice. Thus, the exquisite connectivity of ChCs not only mediates directional inhibition between local PC ensembles but may also shape communication hierarchies between global networks.

neuroscience↗

bioRxiv2017

A Method To Assess Significance Of Differences In RNA Expression Levels Among Specific Groups Of Genes

Genome-wide molecular gene expression studies generally compare expression values for each gene across multiple conditions followed by cluster and gene set enrichment analysis to determine whether differentially expressed genes are enriched in specific biochemical pathways, cellular components, biological processes, and/or molecular functions, etc. This approach to analyzing differences in gene expression enables discovery of gene function, but is not useful to determine whether pre-defined groups of genes share or diverge in their expression patterns in response to treatments nor to assess the correctness of pre-defined gene set groupings. Here we present a simple method that changes the dimension of comparison by treating genes as variable traits to directly assess significance of differences in expression levels among pre-defined gene groups. Because expression distributions are typically skewed (thus unfit for direct assessment using Gaussian statistical methods) our method involves transforming expression data to approximate a normal distribution followed by dividing the genes into groups, then applying Gaussian parametric methods to assess significance of observed differences. This method enables the assessment of differences in gene expression distributions within and across samples, enabling hypothesis-based comparison among groups of genes. We demonstrate this method by assessing the significance of specific gene groups differential response to heat stress conditions in maize.\n\nAbbreviations

bioinformatics↗

bioRxiv2017

HadoopCNV: A Dynamic Programming Imputation Algorithm To Detect Copy Number Variants From Sequencing Data

BACKGROUNDWhole-genome sequencing (WGS) data may be used to identify copy number variations (CNVs). Existing CNV detection methods mostly rely on read depth or alignment characteristics (paired-end distance and split reads) to infer gains/losses, while neglecting allelic intensity ratios and cannot quantify copy numbers. Additionally, most CNV callers are not scalable to handle a large number of WGS samples.\n\nMETHODSTo facilitate large-scale and rapid CNV detection from WGS data, we developed a Dynamic Programming Imputation (DPI) based algorithm called HadoopCNV, which infers copy number changes through both allelic frequency and read depth information. Our implementation is built on the Hadoop framework, enabling multiple compute nodes to work in parallel.\n\nRESULTSCompared to two widely used tools - CNVnator and LUMPY, HadoopCNV has similar or better performance on both simulated data sets and real data on the NA12878 individual. Additionally, analysis on a 10-member pedigree showed that HadoopCNV has a Mendelian precision that is similar or better than other tools. Furthermore, HadoopCNV can accurately infer loss of heterozygosity (LOH), while other tools cannot. HadoopCNV requires only 1.6 hours for a human genome with 30X coverage, on a 32-node cluster, with a linear relationship between speed improvement and the number of nodes. We further developed a method to combine HadoopCNV and LUMPY result, and demonstrated that the combination resulted in better performance than any individual tools.\n\nCONCLUSIONSThe combination of high-resolution, allele-specific read depth from WGS data and Hadoop framework can result in efficient and accurate detection of CNVs.

bioinformatics↗