Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

47 records · Page 3Linked to original sources

bioRxiv2017

Metabolite profile and mitochondrial energetics characterize poor early recovery of muscle mass following hind limb unloading in old mice

The progression of age-related sarcopenia can be accelerated by impaired recovery of muscle mass following periods of disuse due to illness or immobilization. The molecular underpinnings of poor recovery of aging muscle following disuse remain largely unknown. However, recent evidence suggests that mitochondrial energetics may play an important role. Here, we report that 22-24 month old mice with low muscle mass and insulin resistance display poor early recovery of muscle mass following 10 days of hind limb unloading. We took an unbiased approach to identify changes in energy metabolism gene expression and metabolite pools and show for the first time that persistent mitochondrial dysfunction, dysregulated fatty acid {beta}-oxidation and elevated H2O2 emission underlie poor early recovery of muscle mass following a period of disuse in old mice. Importantly, this is linked to more severe whole-body insulin resistance. The findings suggest that muscle fuel metabolism and mitochondrial energetics should be a focus for mining therapeutic targets to improve recovery of muscle mass following periods of disuse in older animals.

physiology↗

bioRxiv2017

Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease

We use deep sequencing to identify sources of variation in mRNA splicing in the dorsolateral prefrontal cortex (DLFPC) of 450 subjects from two prospective cohort studies of aging. Hundreds of aberrant pre-mRNA splicing events are reproducibly associated with Alzheimers Disease (AD). We also generate a catalog of splicing quantitative trait loci (sQTL) effects in the human cortex: splicing of 3,198 genes is influenced by genetic variation. sQTLs are enriched among those variants influencing DNA methylation and histone acetylation. In assessing known AD loci, we report that altered splicing is the mechanism for the effects of the PICALM, CLU, and PTK2B susceptibility alleles. Further, we leverage our sQTL catalog to identify genes whose aberrant splicing is associated with AD and mediated by genetics. This transcriptome-wide association study identified 21 genes with significant associations, many of which are found in AD GWAS loci, but 8 are in novel AD loci, including FUS, which is a known amyotrophic lateral sclerosis (ALS) gene. This highlights an intriguing shared genetic architecture that is further elaborated by the convergence of old and new AD genes in autophagy-lysosomal-related pathways already implicated in AD and other neurodegenerative diseases. Overall, this study of the aging brains transcriptome provides evidence that dysregulation of mRNA splicing is a feature of AD and is, in some genetically-driven cases, causal.

genomics↗

bioRxiv2017

Systematic mapping of chromatin state landscapes during mouse development

Embryogenesis requires epigenetic information that allows each cell to respond appropriately to developmental cues. Histone modifications are core components of a cells epigenome, giving rise to chromatin states that modulate genome function. Here, we systematically profile histone modifications in a diverse panel of mouse tissues at 8 developmental stages from 10.5 days post conception until birth, performing a total of 1,128 ChIP-seq assays across 72 distinct tissue-stages. We combine these histone modification profiles into a unified set of chromatin state annotations, and track their activity across developmental time and space. Through integrative analysis we identify dynamic enhancers, reveal key transcriptional regulators, and characterize the role of chromatin-based repression in developmental gene regulation. We also leverage these data to link enhancers to putative target genes, revealing connections between coding and non-coding sequence variation in disease etiology. Our study provides a compendium of resources for biomedical researchers, and achieves the most comprehensive view of embryonic chromatin states to date.

genomics↗

bioRxiv2017

Systems-level identification of transcription factors critical for mouse embryonic development

Dynamic changes in the transcriptional regulatory circuit can influence the specification of distinct cell types. Numerous transcription factors (TFs) have been shown to function through dynamic rewiring during embryonic development but a comprehensive survey on the global regulatory network is still lacking. Here, we performed an integrated analysis of epigenomic and transcriptomic data to reveal key regulators from 2 cells to postnatal day 0 in mouse embryogenesis. We predicted 3D chromatin interactions including enhancer-promoter interactions in 12 tissues across 8 developmental stages, which facilitates linking TFs to their target genes for constructing genetic networks. To identify driver TFs particularly those not necessarily differentially expressed ones, we developed a new algorithm, dubbed as Taiji, to assess the global importance of TFs in development. Through comparative analysis across tissues and developmental stages, we systematically uncovered TFs that are critical for lineage-specific and stage-dependent tissue specification. Most interestingly, we have identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress and differentiation. Not only does our analysis provide the first comprehensive map of transcriptional regulatory circuits during mouse embryonic development, the identified novel regulators and the predicted 3D chromatin interactions also provide a valuable resource to guide further mechanistic studies.

bioinformatics↗

bioRxiv2017

An exact transformation of convolutional kernels applied directly to DNA/RNA sequences

MotivationConvolutional neural network (CNN) has been widely used in functional motifs identification for large-scale DNA/RNA sequences. Currently, however, the only way to interpret such a convolutional kernel is a heuristic construction of a position weight matrix (PWM) from fragments scored highly by that kernel.\n\nResultsInstead of using heuristics, we developed a novel, exact kernel-to-PWM transformation whose equivalency is theoretically proven: the log-likelihood of the resulting PWM generating any DNA/RNA sequence is exactly the sum of a constant and the convolution of the original kernel on the same sequence. Importantly, we further proved that the resulting PWMs performance on sequence classification/regression can be exactly the same as the original kernels under popular CNN frame-works. In simulation, the exact transformation rivals or outperforms the heuristic PWMs in terms of classifying sequences with sequence- or structure-motifs. The exact transformation also faithfully reproduces the output of CNN models on real-world cases, while the heuristic one fails, especially on the case with little prior knowledge on the form of underlying true motifs. Of note, the time complexity of the novel exact transformation is independent on the number of input sequences, enabling it to scale well for massive training sequences.\n\nAvailabilityPython scripts for the transformation from kernel to PWM, the inverted transformation from PWM to kernel, and a proof-of-concept for the maximum likelihood estimation of optimal PWM are available through https://github.com/gao-lab/kernel-to-PWM.\n\nContactgaog@mail.cbi.pku.edu.cn

bioinformatics↗

bioRxiv2017

Genetic context and proliferation determine contrasting patterns of copy number amplification and loss for 5S and 45S ribosomal DNA arrays in cancer

The multicopy 45S ribosomal DNA (45S rDNA) array gives origin to the nucleolus, the first discovered nuclear organelle, site of Poll I 45S rRNA transcription and key regulator of cellular metabolism, DNA repair response, genome stability, and global epigenetic states. The multicopy 5S ribosomal DNA array (5S rDNA) is located on a separate chromosome, encodes the 5S rRNA transcribed by Pol III, and exhibits concerted copy number variation (cCNV) with the 45S rDNA array in human blood. Here we combined genomic data from >700 tumors and normal tissues to provide a portrait of ribosomal DNA variation in human tissues and cancers of diverse mutational signatures. We show that most cancers undergo coupled 5S rDNA array amplification and 45S rDNA loss, with abundant inter-individual variation in rDNA copy number of both arrays, and concerted modulation of 5S-45S copy number in some but not all tissues. Analysis of genetic context revealed associations between the presence of specific somatic alterations, such as P53 mutations in stomach and lung adenocarcinomas, and coupled 5S gain / 45S loss. Finally, we show that increased proliferation rates along cancer lineages can partially explain contrasting copy number changes in the 5S and 45S rDNA arrays. We suggest that 5S rDNA amplification facilitates increased ribosomal synthesis in cancer, whereas 45S rDNA loss emerges as a byproduct of transcription-replication conflict in highly proliferating tumor cells. Our results highlight the tissue- specificity of concerted copy number variation and uncover contrasting changes in 5S and 45S rDNA copy number along rapidly proliferating cell lineages.\n\nLay SummaryThe 45S and 5S ribosomal DNA (rDNA) arrays contain hundreds of rDNA copies, with substantial variability across individuals and species. Although physically unlinked, both arrays exhibit concerted copy number variation. However, whether concerted copy number is universally observed across all tissues is unknown. It also remains unknown if rDNA copy number may vary in tissues and cancer lineages. Here we showed that most cancers undergo coupled 5S rDNA array amplification and 45S rDNA loss, and concerted 5S-45S copy number variation in some but not all tissues. The coupled 5S amplification and 45S loss is associated with the presence of certain somatic genetic variations, as well as increased cancerous cell proliferation rate. Our research highlights the tissue- specificity of concerted copy number variation and uncover contrasting changes in rDNA copy number along rapidly proliferating cell lineages. Our observations raise the prospects of using 5S and 45S ribosomal DNA states as indicators of cancer status and targets in new strategies for cancer therapy.

genomics↗

bioRxiv2017

An Efficient Platform For Astrocyte Differentiation From Human Induced Pluripotent Stem Cells

Growing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of replicative astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate. Using this method, we generated hiPSC-derived astrocyte populations (hiPSC-astrocytes) from 42 NPC lines (derived from 30 individuals) with an average of [~]90% S100{beta}-positive cells. Transcriptomic analysis demonstrated that the hiPSC-astrocytes are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state. hiPSC-astrocytes respond to inflammatory stimulants, display phagocytic capacity and enhance microglial phagocytosis. hiPSC-astrocytes also possess spontaneous calcium transient activity. Our novel protocol is a reproducible, straightforward (single media) and rapid (<30 days) method to generate homogenous populations of hiPSC-astrocytes that can be used for neuron-astrocyte and microglia-astrocyte co-cultures for the study of neuropsychiatric disorders.\n\nABBREVIATIONS

neuroscience↗

bioRxiv2017

Poly(A) Binding Protein Nuclear 1 regulates the polyadenylation of key synaptic plasticity genes and plays a role in homeostatic plasticity

Polyadenylation is a nuclear process that involves the endonucleolytic cleavage of RNA transcripts and the addition of poly(A) tails. The cleavage often takes place at different positions within the same RNA transcript, generating alternative 3ends. Polyadenylation regulates mRNA localization, stability and translation and is likely to regulate complex processes such as synapse formation, synaptic plasticity and memory. Here we examined whether PolyA Binding Protein Nuclear 1 (Pabpn1), an RNA binding protein known to regulate alternative polyadenylation and polyA tail length in other systems, regulates neuronal mRNA function. Using immunocytochemistry we determined that Pabpn1 is present in both hippocampal slices and cultured hippocampal neurons. Applying shRNAs to knock-down Pabpn1 we discovered that Pabpn1 regulates the mRNA abundance and localization of key synaptic plasticity genes including Calcium/Calmodulin Dependent Protein Kinase II Alpha (Camk2a) and Glutamate Ionotropic Receptor AMPA Type Subunit 2 (Gria2). Furthermore, Pabpn1 knock-down prevented the homeostatic scaling of synaptic transmission elicited by bicuculline. These data demonstrate a link between Pabpn1, polyadenylation and neuronal plasticity.

neuroscience↗

bioRxiv2017

Vegetally Localized Vrtn Functions As A Novel Repressor To Modulate bmp2b Transcription During Dorsoventral Patterning In Zebrafish

The vegetal pole cytoplasm represents a critical source of maternal signals for patterning the primary dorsoventral axis of the early embryo. Vegetally localized dorsal determinants are essential for the formation of the Spemann organizer, which expresses both bone morphogenetic proteins and their antagonists. The extracellular regulation of BMP signalling activity has been well characterized, however, transcriptional regulation of bmp genes along the dorsoventral axis remains largely unknown. Here, we report a novel mode of maternal regulation of BMP signalling in the lateral and ventral regions by analyzing the unexpected dorsalizing effect following vegetal yolk ablation experiment. We identified Vrtn as a novel vegetally localized maternal factor displaying dorsalizing activity. It functions as a novel transcriptional repressor to regulate bmp2b expression in the marginal region. Mechanistically, Vrtn binds bmp2b upstream sequence and inhibits its transcription independently of maternal Wnt/{beta}-catenin signalling. By creating vrtn loss-of-function mutation and analyzing maternal-zygotic mutant embryos, we further showed that Vrtn is required for the formation of dorsoventral axis. Our work thus unveils a novel maternal mechanism regulating BMP gradient during dorsoventral specification.

developmental biology↗

bioRxiv2017

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients

Immunocompromised individuals are at high risk of developing Clostridium difficile-associated disease (CDAD). Fecal microbiota transplantation (FMT) is a highly effective therapy for refractory or recurrent CDAD and, despite safety concerns, has recently been offered to immunocompromised patients. We investigated the genomics of bacterial composition following FMT in immunocompromised patients over a 1-year period. Metagenomic, strain and gene-level bacterial dynamics were characterized in two CDAD-affected hematopoietic stem cell (HCT) recipients following FMT. We found alterations in gene content, including loss of virulence and antibiotic resistance genes. These alterations were accompanied by long-term bacterial divergence at the species and strain levels. Our findings suggest limited durability of the specific bacterial consortium introduced with FMT and indicate that alterations of the functional potential of the microbiome are more complex than can be inferred by taxonomic information alone. Our observation that FMT alone cannot induce long-term donor-like alterations of the microbiota of HCT recipients suggests that FMT cannot indefinitely supersede environmental and/or host factors in shaping bacterial composition.

genomics↗

bioRxiv2017

Significance estimation for large scale untargeted metabolomics annotations

The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate. Relying on estimations of false discovery rates, we explore the effect of different spectrum-spectrum match criteria on the number and the nature of the molecules annotated. We show that the spectral matching settings needs to be adjusted for each project. By adjusting the scoring parameters and thresholds, the number of annotations rose, on average, by +139% (ranging from -92% up to +5705%) when compared to a default parameter set available at GNPS. The FDR estimation methods presented will enable a user to define the scoring criteria for large scale analysis of untargeted small molecule data that has been essential in the advancement of large scale proteomics, transcriptomics, and genomics science.

bioinformatics↗