Biology subjects

Chang, C.

Publications and source records attributed to Chang, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Spatial compartmentalization of signalling imparts source-specific functions on secreted factors

Efficient regeneration requires multiple cell types acting in a coordination. To better understand the intercellular networks involved and how they change when regeneration fails, we profiled the transcriptome of hematopoietic, stromal, myogenic, and endothelial cells over 14 days following acute muscle damage. A time-resolved computational model of interactions was generated, and VEGFA-driven endothelial engagement was identified as a key differentiating feature in models of successful and failed regeneration. In addition, it revealed that the majority of secreted signals, including VEGFA, are simultaneously produced by multiple cell types. To test whether the cellular source of a factor determines its function, we deleted VEGFA from two cell types residing in close proximity, stromal and myogenic progenitors. By comparing responses to different types of damage, we found that myogenic and stromal VEGFA have distinct functions in regeneration. This suggests that spatial compartmentalization of signaling plays a key role in intercellular communication networks. HighlightsO_LILigand-receptor signaling redundancy during skeletal muscle regeneration C_LIO_LIInflammatory cells, and muscle and fibro/adipogenic progenitors produce VEGFA C_LIO_LIVEGFA from muscle progenitors control their proliferation after muscle damage C_LIO_LIVEGFA from FAP controls angiogenesis only after ischemic damage C_LI eTOC blurbGroppa et al. performed a novel time-resolved bioinformatics analysis that revealed extensive ligand-receptor redundancy among the cell types contributing to skeletal muscle regeneration. They focused on one of these pathways, and showed that VEGFA from different cell types has distinct roles in regeneration.

cell biology↗

bioRxiv2022

DNA repair strategy sets transposon mobilization rates in Caenorhabditis elegans

Transposons are parasitic nucleic acids that threaten genome integrity in all cells. In the metazoan model organism Caenorhabditis elegans, DNA transposons are active in the soma where they are reported to exhibit mobilization rates {cong}1000 fold higher than in germ cells. How and why DNA transposons might be so highly active in the C. elegans soma is a mystery. To better understand this question, we constructed reporter genes that label cells in which Tc1 has mobilized with fluorescent protein. The reporters recapitulate the known properties of DNA transposons in C. elegans and allow transposon activity to be monitored in intact, living animals. Using these reporters, we identify cytoplasmic and nuclear factors that limit transposition in the germline. Interestingly, none of these factors limit transposition in the soma. Rather, we identify a gene (nhj-1/scb-1), which we show is required for 99.9% of Tc1 mobilization events in somatic tissues, but does not influence mobilization in the germline. nhj-1/scb-1 encodes a nematode-specific component of the non-homologous end joining (NHEJ) DNA repair machinery. Mutations in the other components of the NHEJ machinery (cku-70, cku-80, and lig-4) also suppress Tc1 mobilization in the C. elegans soma by {cong}1000 fold. The data show that the use of NHEJ to repair transposon-induced DNA breaks in the soma dramatically increases the rate of transposon mobilization in this tissue. And because C. elegans germ cells use homology-based repair, and not NHEJ, to fix transposon-induced breaks, we propose that the 1000-fold difference in transposon mobility reported for the C. elegans soma and germline can, in large part, be explained by tissue-specific differences in DNA repair strategy. Author SummaryTransposons are common parasitic genetic elements that threaten all genomes. For example, half of the human genome is made up of transposons. Transposon mobilization can disrupt gene function, causing disease, so transposon activity needs to be tightly regulated to prevent harm to the host. Transposons are typically less active in the soma than in the germline, because somatic transposition benefits neither host or transposon. Surprisingly, in the nematode model organism Caenorhabditis elegans, transposons are reported to be 1000-fold more active in the soma than the germline. Here, we develop a system to investigate transposon regulation in an intact live animal, and show that, in large part, tissue-specific differences in transposon activity in C. elegans is due to the use of different DNA repair pathways by these tissues, highlighting the importance of DNA repair strategy in determining outcomes of transposon excision events. Given that DNA repair factors have been linked to transposon regulation in other eukaryotes, we propose that DNA repair choice likely contributes to transposon mobilization in all eukaryotes.

genetics↗

bioRxiv2022

A community driven GWAS summary statistics standard

Summary statistics from genome-wide association studies (GWAS) represent a huge potential for research. A challenge for researchers in this field is the access and sharing of summary statistics data due to a lack of standards for the data content and file format. For this reason, the GWAS Catalog hosted a series of meetings in 2021 with summary statistics stakeholders to guide the development of a standard format. The key requirements from the stakeholders were for a standard that contained key data elements to be able to support a wide range of data analyses, required low bioinformatics skills for file access and generation, to have easily accessible metadata, and unambiguous and interoperable data. Here, we define the specifications for the first version of the GWAS-SSF format, which was developed to meet the requirements discussed with the community. GWAS-SSF consists of a tab-separated data file with well-defined fields and an accompanying metadata file.

bioinformatics↗

bioRxiv2022

Deep learning segmentation of the nucleus basalis of Meynert on 3T MRI

The nucleus basalis of Meynert (NBM) is a key subcortical structure that is important in arousal, cognition, brain network modulation, and has been explored as a deep brain stimulation target. It has also been implicated in several disease states, including Alzheimers disease, Parkinsons disease, and temporal lobe epilepsy (TLE). Given the small size of NBM and variability between patients, NBM is difficult to study; thus, accurate, patient-specific segmentation is needed. We investigated whether a deep learning network could produce accurate, patient-specific segmentations of NBM on commonly utilized 3T MRI. It is difficult to accurately segment NBM on 3T MRI, with 7T being preferred. Paired 3T and 7T MRI datasets of 21 healthy subjects were obtained, with 6 completely withheld for testing. NBM was expertly segmented on 7T MRI, providing accurate labels for the paired 3T MRI. An external dataset of 14 patients with TLE was used to test the model on brains with neurological disorders. A 3D-Unet convolutional neural network was constructed, and a 5-fold cross-validation was performed. The model was evaluated on healthy subjects using the held-out test dataset and the external dataset of TLE patients. The model demonstrated significantly improved dice coefficient over the standard probabilistic atlas for both healthy subjects (0.68MEAN{+/-}0.08SD vs. 0.47{+/-}0.06, p=0.0089, t-test) and TLE patients (0.63{+/-}0.08 vs. 0.38{+/-}0.19, p=0.0001). Additionally, the centroid distance was significantly decreased when using the model in patients with TLE (1.22{+/-}0.33mm, 3.25{+/-}2.57mm, p=0.0110). We developed the first model, to our knowledge, for automatic and accurate patient-specific segmentation of the NBM.

neuroscience↗

bioRxiv2022

Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade

Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+ CH25H+ IL-21+ PD-1+ CD4 T helper cells (CXCL13+ Th) and Granzyme K+ PD-1+ effector-like CD8 T cells, whereas terminally exhausted CD39hi TOXhi PD-1hi CD8 T cells dominated in non-responders. Strikingly, most T cell receptor (TCR) clones that expanded post-treatment were found in pre-treatment biopsies. Notably, PD-1+ TCF-1+ progenitor-like CD8 T cells were present in tumors of responders and non-responders and shared clones mainly with effector-like cells in responders or terminally differentiated cells in non-responders, suggesting that local CD8 T cell differentiation occurs upon ICB. We found that these progenitor CD8 T cells interact with CXCL13+ Th cells within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". Receptor-ligand analysis revealed unique interactions within these triads that may promote the differentiation of progenitor CD8 T cells into effector-like cells upon ICB. These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ Th cells control the differentiation of tumor-specific progenitor CD8 T cell clones in patients treated with ICB.

immunology↗

bioRxiv2022

Reversible and gain modulation of neuronal responses and sensorimotor behavior by mid-infrared stimulation

Neuromodulation serves as a cornerstone for brain sciences and clinical applications. Mid-infrared stimulation (MIRS) has been recently reported to cause non-thermal modulation of brain functions. However little knowledge of mechanisms hampers its application. Here we bridge across ion channels, neuronal signals, and behavioral performances associated with sensorimotor transformation to provide evidence of how the alternation of neuronal activity by MIRS guides the change of behavioral performance in awake-behaving pigeons. We compared effects on visually-guided eye movements by applying MIRS and electrical stimulation (ES) in the pretectal nucleus lentiformis mesencephali (nLM). Distinct from ES, we found a specific gain modulation of MIRS to alter behavior in a manner of the strength of visual inputs. Our simultaneous extracellular recordings showed that MIRS can excite and inhibit the neuronal activity in the same pretectal neuron based on its ongoing sensory responsiveness levels in awake-behaving animals. We further applied computational simulations and found that MIRS can modulate the carbonyl group (-C=O) enriched on the potassium channel to resonate, and could affect action potential generation, alter neuronal responses to sensory inputs and then guide behavior. Our findings suggest that MIRS could be a promising approach for brain researches and neurological diseases, with gene free manipulation.

neuroscience↗

bioRxiv2022

COP I and II dependent trafficking controls ER-associated degradation

Misfolded proteins and components of the endoplasmic reticulum (ER) quality control and ER associated degradation (ERAD) machineries concentrate in mammalian cells in the pericentriolar ER-derived quality control compartment (ERQC), suggesting it as a staging ground for ERAD. By tracking the chaperone calreticulin and an established ERAD substrate, asialoglycoprotein receptor H2a, we have now determined that the trafficking to the ERQC is reversible and recycling back to the ER is slower than the movement in the ER periphery. The dynamics suggest vesicular trafficking rather than diffusion. Indeed, using dominant negative mutants of ARF1 and Sar1 or the drugs Brefeldin A and H89, we observed that COPI inhibition causes accumulation in the ERQC and increased retrotranslocation and ERAD, whereas COPII inhibition has the opposite effect. Our results suggest that targeting of misfolded proteins to ERAD involves COPII-dependent transport to the ERQC and that they can be retrieved to the peripheral ER in a COPI-dependent manner.

cell biology↗

bioRxiv2022

New system for serial crystallography data collection at SBC APS

Serial synchrotron crystallography enables studies of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed by using a high-performance computing pipeline. Here, the system was applied to two {beta}-lactamases: a class D serine {beta}-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-{beta} -lactamase from Stenotrophomonas maltophilia K279a.

molecular biology↗

bioRxiv2022

Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Phenotyping of single cells has dramatically lagged advances in molecular characterization and remains a manual, subjective, and destructive process. We introduce COSMOS, a platform for phenotyping and enrichment of cells based on deep learning interpretation of high-content morphology data in realtime. By training models on an atlas of >1.5 billion images, we demonstrate enrichment of unlabeled cells up to 33,000 fold. We apply COSMOS to multicellular tissue biopsy samples demonstrating that it can identify malignant cells with similar accuracy to molecular approaches while enriching viable cells for functional evaluation. We show high-dimensional embedding vectors of morphology generated by COSMOS without any need for complex sample pre-processing, gating, or bioinformatics capabilities, which enables discovery of cellular phenotypes, and integration of morphology into multi-dimensional analyses. One sentence summaryA novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.

cell biology↗

bioRxiv2022

High-Throughput Screening for Myelination Promoting Compounds Using Human Stem Cell-derived Oligodendrocyte Progenitor Cells Identifies Novel Targets

Promoting myelination capacity of endogenous oligodendrocyte precursor cells (OPCs) is a promising therapeutic approach for central nervous system demyelinating disorders such as Multiple Sclerosis (MS). To aid in the discovery of myelination promoting compounds, we generated an advanced, genome engineered, human pluripotent stem cell (hPSC) line that consist of three reporters (identification-and-purification tag, GFP, and secreted NanoLuc) driven by the endogenous PDGFR, PLP1 and MBP genes, respectively. Based upon this line, we established a high-throughput drug screening platform and performed a small molecule screen with 2500 bioactive molecules. In addition to a number of previously known pathways, our screening effort identified new pathways whose inhibition enhance oligodendrocyte maturation and myelination. Although further genetic and molecular validation is required, the identified inhibitors could potentially be repurposed to develop remyelination therapy for MS and other demyelinating disorders.

neuroscience↗

bioRxiv2022

Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery

Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoM{Phi}). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.

immunology↗

bioRxiv2021

Robustness of DNA Looping Across Multiple Divisions in Individual Bacteria

DNA looping has emerged as a central paradigm of transcriptional regulation as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing E. coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed ten generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the robustness to division events of memoryless distributions emerges from the competition between fast, multiple re-binding events of repressors and slow initiation rate of the RNA-polymerase. We argue that fast re-binding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations. Significance statementIt is well-established that certain intracellular regulators can stabilize DNA loops to greatly enhance activation or repression of gene transcription. In vitro but also in vivo ensemble measurements have determined that only a few copies of regulators are in fact needed to stably form DNA loops. In view of such a small number, we address the issue of sensitivity of gene regulation by DNA looping to variations of intracellular parameters in individual growing E. coli bacteria. Surprisingly, we find that DNA looping from the lac system is robust to a range of perturbations including divisions during which cells can maintain tight repression over many generations. We propose a mechanism that governs the observed robustness across a range of intracellular perturbations.

biophysics↗

bioRxiv2021

Soil microbes mediate the effects of environmental variability on plant invasion

Many studies indicate that increases in resource variability promote plant invasion. However, it remains unknown to what extent these effects might indirectly be mediated by other organisms. To test this, we grew eight alien species in pot-mesocosms with five different native communities under eight combinations of two nutrient-availability, two nutrient-fluctuation and two soil-microbe treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of alien plants under low nutrient availability, whereas its effect was minimal under high nutrient availability. However, the opposite pattern was found when plants grew in living soil. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the soil fungal pathogen diversity under high nutrient availability, but slightly decreased it under low nutrient availability. Our findings indicate that besides its direct influence, environmental variability could also indirectly affect plant invasion via changes in soil-microbial communities.

ecology↗

bioRxiv2021

PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization

Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, there are currently no adequate molecular design capabilities that inform medicinal chemistry decisions on peptide programs. More specifically, SAR (Structure-Activity Relationship) analysis and visualization of linear, cyclic, and cross-linked peptides containing non-natural motifs, which are widely used in drug discovery. To bridge this gap, we developed PepSeA (Peptide Sequence Alignment and Visualization), an open-source, freely available package of sequence-based tools (https://github.com/Merck/PepSeA). PepSeA enables multi-sequence alignment of non-natural amino acids and enhanced HELM (Hierarchical Editing Language for Macromolecules) visualization. Via stepwise SAR analysis of a ChEMBL peptide dataset, we demonstrate PepSeAs power to accelerate decision making in lead optimization campaigns in pharmaceutical settings. PepSeA represents an initial attempt to expand cheminformatics capabilities for therapeutic peptides and to enable rapid and more efficient design-make-test cycles.

bioinformatics↗

bioRxiv2021

Islet transplantation tolerance in animals with defined histocompatibility and diabetes

Advances in organ transplantation benefit from development of genetically inbred animal strains with defined histocompatibility and cell-specific markers to distinguish donor and host cell subsets. For studies of pancreatic islet transplantation tolerance in diabetes, an invariant method to ablate host {beta} cells and induce diabetes would provide an immense additional advantage. Here we detail development and use of B6 RIP-DTR mice, an immunocompetent line permitting diabetes induction with 100% penetrance. This inbred line is homozygous for the C57BL/6J major histocompatibility complex (MHC) haplotype and expresses the mutant CD45.1 allele in the hematopoietic lineage. {beta} cell-specific expression of a high-affinity receptor for diphtheria toxin (DT) permits experimental {beta} cell ablation and diabetes induction after DT administration. Diabetes reversal for over one year was achieved after transplantation with congenic C57BL/6J islets, but not with MHC-mismatched BALB/c islets, which were rapidly rejected. In summary, the generation of a C57BL/6J congenic line harboring the CD45.1 allele and Ins2-HBEGF transgene should advance studies of islet transplantation tolerance and mechanisms to improve islet engraftment and function, thereby optimizing development of cell replacement strategies for diabetes mellitus.

immunology↗

bioRxiv2021

Metabolic Regulation of Mitochondrial Morphologies in Pancreatic Beta Cells: Bioenergetics-Mitochondrial Dynamics Coupling

Cellular bioenergetics and mitochondrial dynamics are crucial for the secretion of insulin by pancreatic beta cells in response to elevated blood glucose concentrations. To obtain better insights into the interactions between energy production and mitochondrial fission/fusion dynamics, we combine live-cell mitochondria imaging with biophysical-based modeling and network analysis to elucidate the principle regulating mitochondrial morphology to match metabolic demand in pancreatic beta cells. A minimalistic differential equation-based model for beta cells was constructed to include glycolysis, oxidative phosphorylation, simple calcium dynamics, and graph-based fission/fusion dynamics controlled by ATP synthase flux and proton leak flux. The model revealed that mitochondrial fission occurs in response to hyperglycemia, starvation, ATP synthase inhibition, uncoupling, and diabetic condition, in which the rate of proton leak exceeds the rate of mitochondrial ATP synthesis. Under these metabolic challenges, the propensities of tip-to-tip fusion events simulated from the microscopic images of the mitochondrial networks were lower than those in the control group and prevented mitochondrial network formation. The modeling and network analysis could serve as the basis for further detailed research on the mechanisms of bioenergetics and mitochondrial dynamics coupling.

systems biology↗

bioRxiv2021

Emotion Down- and Up-Regulation Act on Spatially Distinct Brain Areas:Interoceptive Regions to Calm Down and Other Affective Regions to Amp Up

Prior studies on emotion regulation identified a set of brain regions specialized for generating and controlling affect. Researchers generally agree that when up- and down-regulating emotion, control regions in the prefrontal cortex turn up or down activity in affect-generating areas. However, the assumption that turning up and down emotions produces opposite effects in the same affect-generating regions is untested. We call this assumption the affective dial hypothesis. Our study tested this hypothesis by examining the overlap between the sets of regions activated during up-regulation and those deactivated during down-regulation in a large number of participants (N=105). We found that up- and down-regulation both recruit regulatory regions such as the inferior frontal gyrus and dorsal anterior cingulate gyrus but act on distinct affect-generating regions. While up-regulation increases BOLD signal in regions associated with emotion such as the amygdala, anterior insula, striatum and anterior cingulate gyrus as well as in regions associated with sympathetic vascular activity such as periventricular white matter, down-regulation decreases signal in regions receiving interoceptive input such as the posterior insula and postcentral gyrus. These findings indicate that up- and down-regulation do not generally exert opposing effects on the same affect-generating regions. Instead, they target different brain circuits. Significance StatementMany contexts require modulating ones own emotions. Identifying the brain areas implementing these regulatory processes should advance understanding emotional disorders and designing potential interventions. The emotion regulation field has an implicit assumption we call the affective dial hypothesis: that both emotion up- and down-regulation modulate the same emotion-generating brain areas. Countering the hypothesis, our findings indicate that up- and down-modulating emotions target different brain areas. Thus, the mechanisms underlying emotion regulation differ more than previously appreciated for up- versus down-regulation. In addition to their theoretical importance, these findings are critical for researchers attempting to target activity in particular brain regions during an emotion regulation intervention.

neuroscience↗

bioRxiv2021

LRP-1 Commands Two Parallel Signalling Mechanisms to Support Constitutive Tumour Cell Motility in the Absence of Blood Supply

Tumour cells often face the stress of ischemic (nutrient paucity and hypoxia) environment and must act self-sufficient to migrate toward the nearest blood supply or die. The mechanism that supports the constitutive motility of tumour cells under stress is poorly understood. We and others have previously shown that the low-density lipoprotein receptor-related protein 1 (LRP-1) plays a critical role in tumour cell migration and invasion in vitro and tumour formation in mice. Herein we show that depletion of LRP-1 completely abolishes the self-supported and serum-independent tumour cell motility. More intriguingly, we demonstrate that LRP-1 commands the full tumour cell motility by connecting with two independent cell surface signalling pathways. First, LRP-1 mediates secreted Hsp90 signalling via the "Hsp90 > LRP-1 receptor autocrine loop" for a half of tumour cell motility. Second, LRP1 stabilizes constitutively activated EGFR signalling that contributes the other half of tumour cell motility. Only combined inhibitions of the secreted Hsp90 autocrine and the EGFR signalling reproduces the effect of LRP1 down-regulation on constitutive tumour cell motility. This study reveals a novel mechanism of how tumour cells migrate in the absence of blood support.

cell biology↗