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Biology subjects

Shen, H.

Publications and source records attributed to Shen, H..

At least 91 records · Page 5Linked to original sources

Learning-induced reorganization of neuronal subnetworks in the primary sensory cortex

Perceptual learning alters the representation of sensory input in primary sensory cortex. Alterations in neuronal tuning, correlation structure and population activity across many subcortical and cortical areas have been observed in previous studies. However, relationships between these different neural correlates - and to what extent they are relevant to specific perceptual tasks - are still unclear. In this study, we recorded activity of the layer 2/3 neuronal populations in the whisker primary somatosensory cortex (wS1) using in vivo two-photon calcium imaging as mice were trained to perform a self-initiated, whisker vibration frequency discrimination task. Individual wS1 neurons displayed learning-induced broadening of frequency sensitivity within task-related categories only during task performance, reflecting both learning-and context-dependent enhancement of category selectivity. Learning increased both signal and noise correlations within pairs of neurons that prefer the same stimulus category ( within-pool), whereas learning decreased neuronal correlations between neuron pairs that prefer different categories ( across-pool). Increased noise correlations in trained animals resulted in less accurate decoding of stimulus categories from population activity but did not affect decoding of the animals decision to respond to stimuli. Importantly, within-pool noise correlations were elevated on trials in which animals generated the learned behavioral response. We demonstrate that learning drives formation of task-relevant like-to-like layer 2/3 subnetworks in the primary sensory cortex that may facilitate execution of learned behavioral responses. Significance StatementWe found that cortical plasticity during perceptual learning alters both neuronal tuning and the structure of pairwise correlations such that they become increasingly aligned to task-related categories, indicating the formation of like-to-like subnetworks in layer 2/3 of sensory cortex. Category-specific increases in signal and noise correlations were induced by learning and only observed during active task performance, which points to top-down feedback as a driver of task-related subnetworks.

neuroscience↗

Extracellular Vesicles from Inflammation-Primed Adipose-Derived Stem Cells Enhance Achilles Tendon Repair by Reducing Inflammation and Promoting Intrinsic Healing

Achilles tendon rupture is a common sports-related tendon injury. Even with advanced clinical treatments, many patients suffer from long-term pain and reduced function. These unsatisfactory outcomes result primarily from an imbalanced injury response with excessive inflammation and inadequate regeneration. Prior studies showed that extracellular vesicles from inflammation-primed adipose-derived stem cells (iEVs) can attenuate inflammation in the early phase of tendon healing. However, the effect of iEVs on tendon inflammation and regeneration in the later phases of tendon healing and the underlying mechanism remain to be determined. Accordingly, this study investigated the mechanistic roles of iEVs in regulating tendon response to injury using a mouse Achilles tendon injury and repair model in vivo and iEV-macrophage and iEV-tendon cell co-culture models in vitro. Results showed that iEVs promoted tendon anti-inflammatory gene expression and reduced mononuclear cell infiltration in the remodeling phase of tendon healing. iEVs also increased injury site collagen deposition and promoted tendon structural recovery. As such, mice treated with iEVs showed less peritendinous scar formation, much lower incidence of postoperative tendon gap or rupture, and faster functional recovery compared to untreated mice. Further in vitro study revealed that iEVs both inhibited macrophage inflammatory response and increased tendon cell proliferation and collagen production. The iEV effects were partially mediated by miR-147-3p, which blocks the toll-like receptor 4/NF-{kappa}B signaling pathway that activates macrophage M1 polarization. The combined results demonstrated that iEVs are a promising therapeutic agent, which can enhance tendon repair by attenuating inflammation and promoting intrinsic healing. Significance statementUsing a clinically relevant mouse Achilles tendon injury and repair model, this study revealed that iEVs, a biological product generated from inflammation-primed adipose-derived stem cells, can directly target both macrophages and tendon cells and enhance tendon structural and functional recovery by limiting inflammation and promoting intrinsic healing. Results further identified miR-147-3p as one of the active components of iEVs that modulate macrophage inflammatory response by inhibiting toll-like receptor 4/NF-{kappa}B signaling pathway. These promising findings paved the road toward clinical application of iEVs in the treatment of tendon injury and other related disorders.

bioengineering↗

Identification of two β-cell subtypes by 7 independent criteria

Despite the recent explosion in surveys of cell-type heterogeneity, the mechanisms that specify and stabilize highly related cell subtypes remain poorly understood. Here, focusing initially on exploring quantitative histone mark heterogeneity, we identify two major sub-types of pancreatic {beta}-cells ({beta}HI and {beta}LO). {beta}HI and {beta}LO cells differ in their size, morphology, cytosolic and nuclear ultrastructure, transcriptional output, epigenomes, cell surface marker, and function. Importantly, {beta}HI and {beta}LO cells can be FACS separated live into CD24+ ({beta}HI) and CD24- ({beta}LO) fractions. From an epigenetic viewpoint, {beta}HI-cells exhibit [~]4-fold higher levels of H3K27me3, more compacted chromatin, and distinct chromatin organization that associates with a specific pattern of transcriptional output. Functionally, {beta}HI cells have increased mitochondrial mass, activity, and insulin secretion both in vivo and ex vivo. Critically, Eed and Jmjd3 loss-of-function studies demonstrate that H3K27me3 dosage is a significant regulator of {beta}HI / {beta}LO cell ratio in vivo, yielding some of the first-ever specific models of {beta}-cell sub-type distortion. {beta}HI and {beta}LO sub-types are conserved in humans with {beta}HI-cells enriched in human Type-2 diabetes. These data identify two novel and fundamentally distinct {beta}-cell subtypes and identify epigenetic dosage as a novel regulator of {beta}-cell subtype specification and heterogeneity. HighlightsO_LIQuantitative H3K27me3 heterogeneity reveals 2 common {beta}-cell subtypes C_LIO_LI{beta}HI and {beta}LO cells are stably distinct by 7 independent sets of parameters C_LIO_LIH3K27me3 dosage controls {beta}HI / {beta}LO ratio in vivo C_LIO_LI{beta}HI and {beta}LO cells are conserved in humans and enriched in Type-2 diabetes C_LI

cell biology↗

Real-Time Quantification of Cell Mechanics and Functions by Double Resonator Piezoelectric Cytometry -Theory and Study of Cellular Adhesion of HUVECs

Cell mechanics is closely associated with cellular structure and function. However, the inability to measure both cellular force and viscoelasticity of statistically significant number of cells noninvasively remains a challenge for quantitative characterizations of various cellular functions and practical applications. Here a double resonator piezoelectric cytometry (DRPC), using AT and BT cut quartz crystals of the same frequency and surface morphology is developed to simultaneously quantify the cells-generated forces ({Delta}S) and viscoelastic moduli (G', G'') of a population of isolated single cells or cells with different degrees of cell-cell interactions in a non-invasive and real time manner. DRPC captures the dynamic mechanical parameters {Delta}S and G', G'' during the adhesions of human umbilical vein endothelial cells (HUVECs) under different ligand densities of adhesion molecules fibronectin or Arg-Gly-Asp (RGD) modified on the gold surfaces of 9 MHz AT and BT cut quartz crystals, and different seeding densities of HUVECs. It is found that both the ligand density and cell seeding density affect the magnitudes of {Delta}S and G', G'' and their correlations are revealed for the first time by DRPC. The validity of DRPC is further verified by mechanical changes of the cells in response to treatments with cytoskeleton regulators.

biophysics↗

Structural variation across 138,134 samples in the TOPMed consortium

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

genomics↗

An efficient context-aware approach for whole slide image classification

Computational pathology for gigapixel whole slide images (WSIs) at slide-level is helpful in disease diagnosis and remains challenging. We propose a context-aware approach termed WSI Inspection via Transformer (WIT) for slide-level classification via holistically modeling dependencies among patches on the WSI. WIT automatically learns feature representation of WSI by aggregating features of all image patches. We evaluate classification performance of WIT along with state-of-the-art baseline method. WIT achieved an accuracy of 82.1% (95% CI, 80.7% - 83.3%) in the detection of 32 cancer types on the TCGA dataset, 0.918 (0.910 - 0.925) in diagnosis of cancer on the CPTAC dataset and 0.882 (0.87 - 0.890) in the diagnosis of prostate cancer from needle biopsy slide, outperforming the baseline by 31.6%, 5.4% and 9.3%, respectively. WIT can pinpoint the WSI regions that are most influential for its decision. WIT represents a new paradigm for computational pathology, facilitating the development of effective tools for digital pathology.

pathology↗

METTL3 maintains epithelial homeostasis through m6A-dependent regulation of chromatin modifiers

The balance between epithelial stemness and differentiation requires the precise regulation of gene expression programs. Epitranscriptomic RNA modifications have been implicated in both epithelial development as well as cancers. However, the underlying mechanisms are poorly understood. Here, we show that deletion of the m6A methyltransferase, METTL3, impairs the m6A-mediated degradation of numerous mRNA transcripts encoding critical chromatin modifying enzymes, resulting in widespread gene expression abnormalities as well as both aberrant cutaneous and oral epithelial phenotypes in vivo. Collectively, these results offer new insights into a new layer of gene regulation within epithelial surface tissues and will inform future epitranscriptomic studies within epithelial cancer and developmental biology.

molecular biology↗

Alveolar epithelial type 1 cells serve as a cell of origin for lung adenocarcinoma with distinct molecular and phenotypic presentation

Lung adenocarcinoma (LUAD) is the most common subtype of cancer arising in the distal lung. LUAD encompasses several pathologic subtypes, each with differing clinical outcomes and biological behaviors. However, the molecular and cellular underpinnings of the different subtypes are largely unknown. Understanding which cell populations in the distal lung contribute to LUAD could provide insights into the marked heterogeneity in pathologic features, clinical presentation and responses to therapy of LUAD. Differential expression analysis of lung adenocarcinoma transcriptomes from The Cancer Genome Atlas revealed distinct alveolar epithelial type 1 (AT1) and alveolar epithelial type 2 (AT2) cell signatures within human LUAD with significantly different survival outcomes between tumors expressing AT2 and AT1 gene signatures, suggesting AT1 cells might contribute to a subset of LUAD cases. To address this, we tested the ability of AT1 cells to give rise to LUAD following induction of KrasG12D, a known oncogenic driver of human LUAD. Activation of KrasG12D in Gram-domain containing 2 (Gramd2)+ AT1 cells gave rise to multiple LUAD lesions, primarily of papillary histology. In contrast, activation of KrasG12D in surfactant protein C (Sftpc+) AT2 cells resulted in LUAD lesions of lepidic histology. Immunohistochemistry established that Gramd2:KrasG12D lesions were of primary lung origin and not metastatic events. Spatial transcriptomic profiling revealed distinct pathway alterations within Gramd2- and Sftpc-derived LUAD. Immunofluorescence confirmed differences observed in the spatial transcriptomic analysis in expression patterns and distribution of cell-specific markers depending on cell of origin, while universal upregulation of the Krt8 intermediate cell state marker was observed. Our results are consistent with Gramd2+ AT1 cells serving as a putative cell of origin for LUAD and suggest that LUAD may be a collection of adenocarcinomas that share a common location within the distal lung but arise from different cells of origin.

cancer biology↗

Utah Array Characterization and Histological Analysis of a Multi-Year Implant in Non-Human Primate Motor and Sensory Cortices

The Utah array is widely used in both clinical studies and neuroscience. It has a strong track record of safety. However, it is also known that implanted electrodes promote the formation of scar tissue in the immediate vicinity of the electrodes, which negatively impacts the ability to record neural waveforms. This scarring response has been primarily studied in rats and mice, which may have a very different response than primate brain. Here, we present a rare nonhuman primate histological dataset (n=1 rhesus macaque) obtained 848 and 590 days after implantation in two brain hemispheres. For 2 of 4 arrays that remained within the cortex, NeuN was used to stain for neuron somata at 3 different electrode depths. Images were filtered and denoised, with neurons then counted in the vicinity of the arrays as well as a nearby section of control tissue. Additionally, 3 of 4 arrays were imaged with a scanning electrode microscope (SEM) to evaluate any materials damage that might be present. Overall, we found a 63% percent reduction in the number of neurons surrounding the electrode compared to control areas. In terms of materials, the arrays remained largely intact with metal and Parylene C present, though tip breakage and cracks were observed on many electrodes. Overall, these results suggest that the tissue response in the nonhuman primate brain shows similar neuron loss to previous studies using rodents. Electrode improvements, for example using smaller or softer probes, may therefore substantially increase the neuronal recording yield in primate cortex.

bioengineering↗

Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M

Plasmodium falciparum causes the most severe malaria in humans. Immunoglobulin M (IgM) serves as the first line of humoral defense against infection and potently activates the complement pathway to facilitate P. falciparum clearance. A number of P. falciparum proteins hijack IgM, leading to immune evasion and severe disease. However, the underlying molecular mechanisms remain unknown. Here, using high-resolution cryo-electron microscopy, we delineate how P. falciparum proteins VAR2CSA, TM284VAR1, DBLMSP, and DBLMSP2 target IgM. Each protein binds IgM in a different manner, and together they present a variety of Duffy-binding-like domain-IgM interaction modes. We further show that these proteins interfere directly with IgM-mediated complement activation, with VAR2CSA exhibiting the most potent inhibitory effect. Structural analyses suggest that VAR2CSA occludes the congregation of the complement C1 complex on IgM. These results underscore the importance of IgM for the adaptation of P. falciparum to humans, and provide critical insights into the immune evasion mechanism of P. falciparum.

biochemistry↗

Molecular evolution of IRG1 shapes itaconate production in metazoans and alleviates the 'double-edged dilemma' of innate immune defense

Itaconate is an innate immune metabolite specifically produced in activated immune cells via the decarboxylation of cis-aconitate, an intermediate of the TCA cycle. By inhibiting succinate-related metabolism, itaconate exerts antimicrobial properties at the expense of potentially disrupting the hosts own central energy metabolism, a double-edged dilemma of immunometabolism. To explore the evolutionary logic of itaconate biosynthesis, we investigated the evolutionary trajectory of IRG1, which encodes for cis-aconitate decarboxylase (CAD), the enzyme responsible for itaconate production. Phylogenetic analysis reveals a putative independent acquisition of metazoan and fungal IRG1 from prokaryotic sources. In metazoans, IRG1 underwent gene duplication and subsequently lost the mitochondrial targeting sequence (MTS), relocating CAD outside the mitochondrial matrix and therefore preventing direct inhibition of energy metabolism. In basal metazoans that contain IRG1, oysters and amphioxus, primitive IRG1 expression is also induced by innate immune stimuli, suggesting an already specialized role of itaconate for innate immune defense in early bilaterians. Our integrated in silico and experimental analysis highlight the molecular adaptations in IRG1, including subcellular relocation, that optimize itaconate production for innate immunity in resolving a fundamental trade-off in immunometabolism.

evolutionary biology↗

PGC-1β maintains mitochondrial metabolism and restrains inflammatory gene expression

Metabolic programming of the innate immune cells known as dendritic cells (DCs) changes in response to different stimuli, influencing their function. While the mechanisms behind increased glycolytic metabolism in response to inflammatory stimuli are well-studied, less is known about the programming of mitochondrial metabolism in DCs. We used lipopolysaccharide (LPS) and interferon-{beta} (IFN-{beta}), which differentially stimulate the use of glycolysis and oxidative phosphorylation (OXPHOS), respectively, to identify factors important for mitochondrial metabolism. We found that the expression of peroxisome proliferator-activated receptor gamma coactivator 1{beta} (PGC-1{beta}), a transcriptional co-activator and known regulator of mitochondrial metabolism, decreases when DCs are activated with LPS, when OXPHOS is diminished, but not with IFN-{beta}, when OXPHOS is maintained. We examined the role of PGC-1{beta} in bioenergetic metabolism of DCs and found that PGC-1{beta} deficiency in DCs indeed impairs mitochondrial respiration. PGC-1{beta}-deficient DCs are more glycolytic compared to controls, likely to compensate for reduced OXPHOS. PGC-1{beta} deficiency also causes decreased capacity for ATP production at steady state and in response to IFN-{beta} treatment. Loss of PGC-1{beta} in DCs leads to increased expression of genes in inflammatory pathways, and reduced expression of genes encoding proteins important for mitochondrial metabolism and function. Collectively, these results demonstrate that PGC-1{beta} is a key positive regulator of mitochondrial metabolism in DCs.

immunology↗

Cell division drives DNA methylation loss in late-replicating domains in primary human cells

DNA methylation undergoes dramatic age-related changes, first described more than four decades ago1-4. Loss of DNA methylation at late-replicating regions of the genome attached to the nuclear lamina advances with age in normal tissues, and is further exacerbated in cancer5-7. We present here the first experimental evidence that this DNA hypomethylation is directly driven by proliferation-associated DNA replication. Loss of DNA methylation at low-density CpGs in A:T-rich, partially methylated domains (PMD solo-WCGWs), tracks cumulative population doublings in primary cell culture. Cell cycle deceleration resulted in a proportional decrease in the rate of DNA hypomethylation. Blocking DNA replication via Mitomycin C treatment halted methylation loss. Loss of methylation continued unabated after TERT immortalization until finally reaching a severely hypomethylated equilibrium. Ambient oxygen culture conditions increased the rate of methylation loss compared to low-oxygen conditions, suggesting that some methylation loss may occur during unscheduled, oxidative damage repair-associated DNA synthesis. Finally, we present and validate a model to estimate the relative cumulative replicative histories of human cells, which we call "RepliTali" (Replication Times Accumulated in Lifetime).

genomics↗

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This MM285 mouse array is widely accessible to the research community, and will accelerate future high sample-throughput studies in this important model organism.

genomics↗

Microglial Piezo1 senses Aβ fibrils stiffness to restrict Alzheimer's disease

The pathology of Alzheimers disease (AD) is associated with the extracellular amyloid-{beta} (A{beta}) plaques that perturb the mechanical properties of brain tissue. Microglia sense and integrate biochemical cues in their local microenvironment, intimate linking with AD progress. However, neither the microglial mechanosensing pathway nor its impact on AD pathogenesis is well studied. Here, we showed that the mechanosensitive ion channel Piezo1 is increased in microglia upon stiffness stimuli of A{beta} fibrils. The upregulation of Piezo1 in A{beta} plaque-associated microglia was observed in AD mouse models and human patients. Microglia lacking Piezo1 disturbed microglial clustering, phagocytosis, and compaction of A{beta} plaques, resulting in the exacerbation of A{beta} and neurodegenerative pathologies in AD. Conversely, pharmacological activation of Piezo1 ameliorated brain A{beta} burden and cognitive impairment in the 5xFAD mouse. Together, our results reveal Piezo1, as a mechanosensor of A{beta} fibrils stiffness in microglia, could represent a promising therapeutic target for AD.

neuroscience↗

STORM-seq Reveals Differentiation Trajectories of Primary Human Fallopian Tube Epithelium

Despite significant advances, current single-cell RNA sequencing (scRNA-seq) technologies often struggle with accurately detecting non-coding transcripts, achieving full-length RNA coverage, and/or resolving transcript-level complexity. Many are also difficult to implement or inaccessible without specialized liquid handlers, further limiting their utility. We present Single-cell TOtal RNA-seq Miniaturized (STORM-seq), a random- hexamer primed, ribo-reduced single-cell total RNA sequencing (sc-total-RNA-seq) protocol using standard laboratory equipment. Adapted as a kit, STORM-seq constructs sequence-ready libraries in one working day, producing the highest complexity scRNA- seq libraries to-date, robustly measuring transcript isoforms and clinically relevant gene fusions in single cells. STORM-seq faithfully reconstructs expression profiles of locus- level transposable elements (TEs), and provides high-resolution profiling of transient, low- abundance enhancer RNAs (eRNAs), offering a powerful tool to dissect single-cell gene regulatory networks in unprecedented detail. Applied to human fallopian tube epithelium, the improved transcriptional resolution reveals a putative progenitor-like population and intermediate cell states, shaped by TEs and non-coding RNAs.

molecular biology↗

Repressor element 1-silencing transcription factor deficiency yields profound hearing loss through Kv7.4 channel upsurge in auditory neurons and hair cells

Repressor element 1-silencing transcription factor (REST) is a transcriptional repressor that recognizes neuron-restrictive silencer elements in the mammalian genomes in a tissue- and cell-specific manner. The identity of REST target genes and molecular details of how REST regulates them are emerging. We performed conditional null deletion of Rest (cKO) in murine hair cells (HCs) and auditory neurons, spiral ganglion neurons (SGNs). Null-deletion of full-length REST resulted in normal HCs and SGNs development but manifested with progressive hearing loss in adulthood. We found that deletion of REST results in an increased abundance of Kv7.4 channels at the transcript, protein, and function levels. Specifically, we found that SGNs and HCs from Rest cKO mice displayed increased Kv7.4 expression and augmented Kv7 currents; SGNs excitability was also significantly reduced. Administration of Kv7.4 channel activator, fasudil, recapitulated progressive hearing loss in mice. In contrast, inhibition of the Kv7.4 channel by XE991 rescued the auditory phenotype of Rest cKO mice. Previous studies identified some loss-of-function mutations within the Kv7.4-coding gene, Kcnq4, as a causative factor for progressive hearing loss in mice and humans. Thus, the present findings revealed that a critical homeostatic Kv7.4 channel level is required for proper auditory functions.

neuroscience↗

Generative pretraining from large-scale transcriptomes: Implications for single-cell deciphering and clinical translation

Exponential accumulation of single-cell transcriptomes poses great challenge for efficient assimilation. Here, we present an approach entitled tGPT towards integration of 22.3 million single-cell transcriptomes by modeling gene expression rankings as generative pretraining task. tGPT is conceptually simple in that it autoregressively models the ranking of a gene in the context of its preceding neighbors. We demonstrated the high performance of tGPT on a range of fundamental single-cell analysis tasks and novel applications on bulk tissues. The single-cell clusters and cell lineage trajectories derived from tGPT are highly aligned with known cell labels and states. The feature patterns of tumor bulk tissues learned by tGPT are associated with a wide range of genomic alteration events, prognosis and treatment outcome of immunotherapy. tGPT represents a new analytical paradigm for integrating and deciphering massive amount of transcriptome data and it will facilitate the interpretation and clinical translation of single-cell transcriptomes.

bioinformatics↗