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Biology subjects

Jiang, S.

Publications and source records attributed to Jiang, S..

At least 199 records · Page 11Linked to original sources

Integrating transcription factor abundance with chromatin accessibility in human erythroid lineage commitment

We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance. By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.

genomics↗

Genome-wide annotation of gene regulatory elements linked to cell fitness

Noncoding regulatory elements control gene expression and thus govern nearly all biological processes. Epigenomic profiling assays have identified millions of putative regulatory elements, but systematically determining the function of those regulatory elements remains a substantial challenge. Here we adapt CRISPR screening by epigenetic repression to screen all 111,619 putative non-coding regulatory elements defined by open chromatin sites in human K562 leukemia cells for their role in regulating essential cellular processes and proliferation. In an initial screen containing 1,084,704 gRNAs, we implemented an analysis framework to quantify perturbation effects, and nominate 1,108 regulatory elements that strongly impact cell fitness. We tested 8,845 of the primary screen elements in a secondary screen, evaluated their cell-type specificity in a second cancer cell line, and then used a single-cell RNA-seq CRISPR screen to discover 63 connections between distal regulatory elements and target genes. This comprehensive and quantitative genome-wide map of essential gene regulatory elements presents a framework for extensive characterization of noncoding regulatory elements that drive complex cell phenotypes and for prioritizing non-coding genetic variants that may contribute to common traits and disease risk.

genomics↗

Binocular vs. monocular recovery experience differentially promote recovery from visual deficits in a mouse model of amblyopia

Altered visual experience during monocular deprivation (MD) profoundly changes in ocular dominance (OD) in the developing primary visual cortex (V1). MD-driven changes in OD are an experimental model of amblyopia, where early-life alterations in vision lead visual disruption in adulthood. Current treatments for amblyopia include patching of the dominant eye, and more recently-developed binocular therapies. However, the relative impact of monocular vs. binocular recovery experiences on recovery of function in V1 is not well understood. Using single-unit recording, we compared how binocular recovery [BR] or reverse occlusion [RO] of identical duration and content affects OD and visual response recovery in mouse binocular V1 after a period of MD. We also tested how BR and RO affected MD-driven alterations of parvalbumin expression, and visually-driven expression of cFos in parvalbumin-positive and negative neurons. Finally, we tested how BR and RO affected recovery of normal visual acuity for the two eyes in the context of visually-driven behavior. We find that BR is quantitatively superior with respect to normalization of V1 neurons OD, visually-driven cFos expression, and visual acuity for the two eyes. However, MD-driven changes in the firing rate and response properties of V1 principal neuron and fast-spiking interneuron populations do not recover fully after either BR or RO. Binocular matching of orientation preference also remains disrupted in V1 neurons after both forms of recovery experience. Thus BR and RO, analogs of differing treatment regimens for amblyopia, differentially impact various aspects of visual recovery in a mouse model for amblyopia. Significance StatementAmblyopia resulting from altered childhood eye function is a leading cause of lifelong vision loss. Treatment typically involves patching of the dominant eye (forcing monocular visual experience), and produces only partial recovery of vision. Using a well-established mouse model of amblyopia, we directly compared how two types of visual experiences influence recovery of visual function. Our findings suggest that binocular vs. monocular visual experience differentially effect restoration of normal visual responses in cortical neurons, visually-driven neuronal gene expression, and visual acuity. Understanding how the quality of recovery experience impacts visual system recovery in amblyopia should provide critical insights for clinical strategies for its treatment.

neuroscience↗

Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave

Microglia, the brains resident myeloid cells, play central roles in brain defense, homeostasis, and disease. Using sustained colony-stimulating factor 1 receptor inhibition, we report an unprecedented level of microglial depletion and establish a model system that achieves an empty microglial niche in the adult brain. We identify a myeloid cell that migrates from an important neurogenic niche, the subventricular zone, and associated white matter areas. These cells exhibit tremendous chemotaxis potential, migrating radially and tangentially in a dynamic wave and filling the brain in a distinct pattern, to fully replace the microglial-depleted brain. These repopulating cells are enriched in disease-associated microglia genes and exhibit distinct phenotypic and functional profiles to endogenous microglia. Our findings shed light on the overlapping and distinct functional complexity and diversity of myeloid cells of the CNS and provide new insight into myeloid cell dynamics in an empty microglial niche without contributions from bone marrow-derived cells.

immunology↗

Comparative Chromatin Dynamics of Stem Cell Differentiation in Human and Rat

Differentiation of cell types homologous between species are controlled by conserved networks of regulatory elements driving gene expression. In order to identify conservation of gene expression and chromatin accessibility during cell differentiation in two different species. We collected a daily time-course of gene expression and chromatin accessibility in rat and human to quantify conserved and species-specific chromatin dynamics during embryonic stem cell differentiation to definitive endoderm (DE) as well as to neuronal progenitor cells (NPC). We identify shared and cell-type specific transient differentiation markers in each species, including key transcription factors that may regulate differentiation into each cell-type and their candidate cis-regulatory elements (cCREs). Our analysis shows that DE differentiation has higher conservation of gene expression and chromatin accessibility than NPC differentiation. We provide the first global comparison of transcriptional complexity and chromatin dynamics between human and rat for DE and NPC differentiation.

genomics↗

A Safe and Effective Mucosal RSV Vaccine Consisting of RSV Phosphoprotein and Flagellin Variant

Respiratory syncytial virus (RSV) is a major cause of serious acute lower respiratory tract infection in infants and the elderly. No licensed RSV vaccine available thus far calls for the development of vaccines with new target(s) and vaccination strategies. Here, we constructed a recombinant protein, designated P-KFD1, comprised of RSV phosphoprotein (P) and E. coli K12 strain-derived flagellin variant KFD1. Intranasal (i.n.) immunization with P-KFD1 inhibits RSV replication in both upper and lower respiratory tract, and protects mice against lung disease without vaccine-enhanced disease (VED). The P-specific CD4+ T cells provoked by P-KFD1 i.n. immunization, either reside in or migrate to respiratory tract, mediate protection against RSV infection. Sc-RNA seq and carboxyfluorescein succinimidyl ester (CFSE) labeled cell transfer further characterized the Th1 and Th17 responses induced by P-KFD1. Finally, we found the anti-viral protection depends on either IFN-{gamma} or IL-17A. Collectively, P-KFD1 is promising as a safe and effective mucosal vaccine candidate to prevent RSV infection. HIGHLIGHTSO_LIA new subunit RSV vaccine candidate with new target and vaccination strategy, P-KFD1, is designed and generated C_LIO_LIIntranasal immunization with P-KFD1 protects mice against RSV infection and averts vaccine-enhanced disease C_LIO_LISc-RNA seq and CFSE-labelled cell transfer identified characteristics of the protective CD4+ T cells C_LIO_LILocal and peripheral CD4+ T cells provide protection against RSV infection dependent on either IFN-{gamma} or IL-17A C_LI

immunology↗

Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells

Precision medicine depends critically on developing treatment strategies that can selectively target cancer cells with minimal adverse effects. Identifying unique transcriptional regulators of oncogenic signaling, and targeting cancer-cell-specific enhancers that may be active only in specific tumor cell lineages, could provide the necessary high specificity, but a scarcity of functionally validated enhancers in cancer cells presents a significant hurdle to this strategy. We address this limitation by carrying out large-scale functional screens for pro-growth enhancers using highly multiplexed CRISPR-based perturbation and sequencing in multiple cancer cell lines. We used this strategy to identify 488 pro-growth enhancers in a colorectal cancer cell line and 22 functional enhancers for the MYC and MYB key oncogenes in an additional nine cancer cell lines. The majority of pro-growth enhancers are accessible and presumably active only in cancer cells but not in normal tissues, and are enriched for elements associated with poor prognosis in colorectal cancer. We further identify master transcriptional regulators and demonstrate that the cancer pro-growth enhancers are modulated by lineage-specific transcription factors acting downstream of growth signaling pathways. Our results uncover context-specific, potentially actionable pro-growth enhancers from cancer cells, yielding insight into altered oncogenic transcription and revealing potential therapeutic targets for cancer treatment.

cancer biology↗

Selection and Validation of Reference Genes Desirable for Gene Expression Analysis by qRT-PCR on Seed Germination of Castanea henryi

Seed germination is the beginning of the plants life cycle, and seed biology is one of the most extensively researched areas in plant physiology, however, Castanea henryi as an important seed plant, the stable internal reference gene during germination is not clear. In this study, seven candidate genes (TUA, TUB, TIF, UBC, RPL21, RPL30, RPL34) were screened out from transcriptome data, we analyzed the expression of seven candidate reference genes in C. henryi at different germination stages with RT-qPCR, and using common algorithms including NormFinder, geNorm and BestKeeper to evaluate the candidate genes stability. The results showed that RPL34 and RPL30 were selected as the most stable genes by NormFinder; TIF was the most stable gene identified by BestKeeper; RPL34 and RPL21 were the most stable genes ranked by geNorm, and TUB was the most unstable gene identified by all of the three software. The RPL34 gene was used as the reference gene, to detected the expression trend of two starch synthetase genes SS1 and SS2 during germination by RT-qPCR, the results of RT-qPCR and transcriptome sequencing were basically consistent, which verified the stability of RPL34 candidate gene. Our result is not only showed functional genes for germination of C. henryi seeds and provide useful guidelines for the selection of reliable reference genes for the normalization of RT- qPCR data for germination of seed plants.

molecular biology↗

High-throughput functional characterization of visceral afferents by optical recordings from thoracolumbar and lumbosacral dorsal root ganglions

Functional understanding of visceral afferents is important for developing new treatment to visceral hypersensitivity and pain. The sparse distribution of visceral afferents in dorsal root ganglions (DRGs) has challenged conventional electrophysiological recordings. Alternatively, Ca2+ indicators like GCaMP6f allow functional characterization by optical recordings. Here we report a turnkey microscopy system that enables simultaneous Ca2+ imaging at two parallel focal planes from intact DRG. By using consumer-grade optical components, the microscopy system is cost effective and can be made broadly available without loss of capacity. It records low-intensity fluorescent signals at a wide field of view (1.9 x 1.3 mm) to cover a whole mouse DRG, with a high pixel resolution of 0.7 micron/pixel, a fast frame rate of 50 frames/sec, and the capability of remote focusing without perturbing the sample. The wide scanning range (100 mm) of the motorized sample stage allows convenient recordings of multiple DRGs in thoracic, lumbar, and sacral vertebrae. As a demonstration, we characterized mechanical neural encoding of visceral afferents innervating distal colon and rectum (colorectum) in GCaMP6f mice driven by VGLUT2 promotor. A post-processing routine is developed for conducting unsupervised detection of visceral afferent responses from GCaMP6f recordings, which also compensates the motion artefacts caused by mechanical stimulation of the colorectum. The reported system offers a cost-effective solution for high-throughput recordings of visceral afferent activities from a large volume of DRG tissues. We anticipate a wide application of this microscopy system to expedite our functional understanding of visceral innervations in both health and diseases.

bioengineering↗

The landscape of human brain immune response in patients with severe COVID-19

In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between brain tropism, neuroinflammation and host immune response has not been well characterized. We analyzed 68,557 single-nucleus transcriptomes from three brain regions (dorsolateral prefrontal cortex, medulla oblongata and choroid plexus) and identified an increased proportion of stromal cells and monocytes in the choroid plexus of COVID-19 patients. Differential gene expression, pseudo-temporal trajectory and gene regulatory network analyses revealed microglial transcriptome perturbations, mediating a range of biological processes, including cellular activation, mobility and phagocytosis. Quantification of viral spike S1 protein and SARS-CoV-2 transcripts did not support the notion of brain tropism. Overall, our findings suggest extensive neuroinflammation in patients with acute COVID-19. One Sentence SummarySingle-nucleus transcriptome analysis suggests extensive neuroinflammation in human brain tissue of patients with acute coronavirus disease 2019.

neuroscience↗

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

Recent advances in neuroscience make the extraction of full neuronal morphology at whole brain dataset available. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of more than one thousand neurons including their dendrites and full axons, and detected million scale putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.

neuroscience↗

Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with Ebstein's anomaly

Heart organoids have the potential to generate primary heart-like anatomical structures and hold great promise as in vitro models for cardiac disease. However, their properties have not yet been carefully studied, which hinders a wider spread application. Here we report the development of differentiation systems for ventricular and atrial heart organoids, enabling the study of heart disease with chamber defects. We show that our systems generate organoids comprising of major cardiac cell types, and we used single cell RNA sequencing together with sample multiplexing to characterize the cells we generate. To that end, we also developed a machine learning label transfer approach lever-aging cell type, chamber, and laterality annotations available for primary human fetal heart cells. We then used this model to analyze organoid cells from an isogeneic line carrying an Ebsteins anomaly associated genetic variant, and we successfully recapitulated the diseases atrialized ventricular defects. In summary, we have established a workflow integrating heart organoids and computational analysis to model heart development in normal and disease states.

developmental biology↗

The hybrid nature of task-evoked activity: Inside-out neural dynamics in intracranial EEG and Deep Learning

A.The standard approach in neuroscience research infers from the external stimulus (outside) to the brain (inside) through stimulus-evoked activity. Recently challenged by Buzsaki, he advocates the reverse; an inside-out approach inferring from the brains activity to the neural effects of the stimulus. If so, stimulus-evoked activity should be a hybrid of internal and external components. Providing direct evidence for this hybrid nature, we measured human intracranial stereo-electroencephalography (sEEG) to investigate how prestimulus variability, i.e., standard deviation, shapes poststimulus activity through trial-to-trial variability. We first observed greater poststimulus variability quenching in trials exhibiting high prestimulus variability. Next, we found that the relative effect of the stimulus was higher in the later (300-600ms) than the earlier (0-300ms) poststimulus period. These results were extended by our Deep Learning LSTM network models at the single trial level. The accuracy to classify single trials (prestimulus low/high) increased greatly when the models were trained and tested with real trials compared to trials that exclude the effects of the prestimulus-related ongoing dynamics (corrected trials). Lastly, we replicated our findings showing that trials with high prestimulus variability in theta and alpha bands exhibits faster reaction times. Together, our results support the inside-out approach by demonstrating that stimulus-related activity is a hybrid of two factors: 1) the effects of the external stimulus itself, and 2) the effects of the ongoing dynamics spilling over from the prestimulus period, with the second, i.e., the inside, dwarfing the influence of the first, i.e., the outside. B. Significance StatementOur findings signify a significant conceptual advance in the relationship between pre- and poststimulus dynamics in humans. These findings are important as they show that we miss an essential component - the impact of the ongoing dynamics - when restricting our analyses to the effects of the external stimulus alone. Consequently, these findings may be crucial to fully understand higher cognitive functions and their impairments, as can be seen in psychiatric illnesses. In addition, our Deep Learning LSTM models show a second conceptual advance: high classification accuracy of a single trial to its prestimulus state. Finally, our replicated results in an independent dataset and task showed that this relationship between pre- and poststimulus dynamics exists across tasks and is behaviorally relevant.

neuroscience↗

Life-history dynamics: damping time, demographic dispersion and generation time

Transient dynamics are crucial for understanding ecological and life-history dynamics. In this study, we analyze damping time, the time taken by a population to converge to a stable (st)age structure following a perturbation, for over 600 species of animals and plants. We expected damping time to be associated with both generation time Tc and demographic dispersion{sigma} based on previous theoretical work. Surprisingly, we find that damping time (calculated from the population projection matrix) is approximately proportional to Tc across taxa on the log-log scale, regardless of{sigma} . The result suggests that species at the slow end of fast-slow continuum (characterized with long generation time, late maturity, low fecundity) are more vulnerable to external disturbances as they take more time to recover compared to species with fast life-histories. The finding on damping time led us to next examine the relationship between generation time and demographic dispersion. Our result reveals that the two life-history variables are positively correlated on a log-log scale across taxa, implying long generation time promotes demographic dispersion in reproductive events. Finally, we discuss our results in the context of metabolic theory and contribute to existing allometric scaling relationships.

ecology↗

A framework for predicting potential host ranges of pathogenic viruses based on receptor ortholog analysis

Viral zoonoses are a serious threat to public health and global security, as reflected by the current scenario of the growing number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases. However, as pathogenic viruses are highly diverse, identification of their host ranges remains a major challenge. Here, we present a combined computational and experimental framework, called REceptor ortholog-based POtential virus hoST prediction (REPOST), for the prediction of potential virus hosts. REPOST first selects orthologs from a diverse species by identity and phylogenetic analyses. Secondly, these orthologs is classified preliminarily as permissive or non-permissive type by infection experiments. Then, key residues are identified by comparing permissive and non-permissive orthologs. Finally, potential virus hosts are predicted by a key residue-specific weighted module. We performed REPOST on SARS-CoV-2 by studying angiotensin-converting enzyme 2 orthologs from 287 vertebrate animals. REPOST efficiently narrowed the range of potential virus host species (with 95.74% accuracy).

microbiology↗

Spatially expandable fiber-based probes as a multifunctional deep brain interface

Understanding the cytoarchitecture and wiring of the brain requires improved methods to record and stimulate large groups of neurons with cellular specificity. This requires miniaturized neural interfaces that integrate into brain tissue without altering its properties. Existing neural interface technologies have been shown to provide high-resolution electrophysiological recording with high signal-to-noise ratio. However, with single implantation, the physical properties of these devices limit their access to one, small brain region. To overcome this limitation, we developed a platform that provides three-dimensional coverage of brain tissue through multisite multifunctional fiber-based neural probes guided in a helical scaffold. Chronic recordings from the spatially expandable fiber probes demonstrate the ability of these fiber probes capturing brain activities with a single-unit resolution for long observation times. Furthermore, using Thy1-ChR2-YFP mice we demonstrate the application of our probes in simultaneous recording and optical/chemical modulation of brain activities across distant regions. Similarly, varying electrographic brain activities from different brain regions were detected by our customizable probes in a mouse model of epilepsy, suggesting the potential of using these probes for the investigation of brain disorders such as epilepsy. Ultimately, this technique enables three-dimensional manipulation and mapping of brain activities across distant regions in the deep brain with minimal tissue damage, which can bring new insights for deciphering complex brain functions and dynamics in the near future.

bioengineering↗

The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 homeostasis and is targeted by a bacterial type-III effector

Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogen Ralstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while, after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.

plant biology↗

Is there a need for preoperative α-blocker in patients missed preoperative diagnosis of extra-adrenal retroperitoneal paraganglioma undergoing paraganglioma resection? A retrospective study of 167 cases at a single center

BackgroundPreoperative -adrenergic blockade is believed to decrease perioperative risks and mortality in adrenal pheochromocytoma surgeries. The aim of this study is to evaluate the effects of the preoperative -adrenergic blockade on patients outcomes in extra-adrenal retroperitoneal paraganglioma surgeries. MethodsWe searched our clinical database for the diagnosis extra-adrenal retroperitoneal paraganglioma by postoperative histopathology in the General Hospital of Peoples Liberation Army from 2000 till 2017. And we recorded preoperative status of patients, preoperative medication preparation, intraoperative and postoperative cardiovascular events, intake and output, length of stay in ICU, length of hospital stay, and short time outcomes. ResultsThe intraoperative morbidity of heart rate elevation and highest heart rate were higher in patients undergoing tumor manipulation with preoperative -adrenergic blockade than those without (P<0.05), while there were no significant differences in intraoperative morbidity of blood pressure elevation and SAP decreased following tumorectomy in these two groups (P>0.05). There were no significant differences in postoperative complications and outcomes (P>0.05). ConclusionUnder the current medical techniques, either with or without preoperative medicine, resection of extra-adrenal retroperitoneal paraganglioma could be carried out successfully.

physiology↗