Biology subjects

Qi, S.

Publications and source records attributed to Qi, S..

49 records · Page 3Linked to original sources

bioRxiv2020

Transient high glucose causes delayed wound healing by the DNMT1-mediated Ang-1/NF-κB pathway

The progression of diabetic complications does not halt despite termination of hyperglycemia, suggesting a "metabolic memory" phenomenon. However, whether metabolic memory exists in and affects the healing of diabetic wounds, as well as the underlying molecular mechanisms, remain unclear. In this study, we found that wound healing was delayed and angiogenesis was decreased in diabetic mice, despite normalization of glycemic control. Thus, we hypothesized that transient hyperglycemic spikes may be a risk factor for diabetic wound healing. We showed that transient hyperglycemia caused persistent damage to the vascular endothelium. Transient hyperglycemia directly upregulated DNMT1 expression, leading to the hypermethylation of Ang-1 and reduced Ang-1 expression, which, in turn, induced long-lasting activation of nuclear factor (NF)-{kappa}B and subsequent endothelial dysfunction. An in vivo study further showed that inhibition of DNMT1 promoted angiogenesis and accelerated diabetic wound healing by regulating the Ang-1/NF-{kappa}B signaling pathway. These results highlight the dramatic and long-lasting effects of transient hyperglycemic spikes on wound healing and suggest that DNMT1 is a novel target for diabetic vascular complications.

cell biology↗

bioRxiv2020

Structural Basis of RNA Cap Modification by SARS-CoV-2 Coronavirus

The novel severe acute respiratory syndrome coronoavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused over 2 million infections worldwide in four months. In SARS coronaviruses, the non-structural protein 16 (nsp16) methylates the 5-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of full-length nsp16 and nsp10 of SARS-CoV-2 in the presence of cognate RNA substrate and a methyl donor, S-adenosyl methionine. The nsp16/nsp10 heterodimer was captured in the act of 2-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We reveal large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This structure provides new mechanistic insights into the 2-O methylation of the viral mRNA cap. We also discovered a distantly located ligand-binding site unique to SARS-CoV-2 that may serve as an alternative target site for antiviral development.

biophysics↗

bioRxiv2020

Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a

A massive intronic hexanucleotide repeat (GGGGCC) expansion in C9ORF72 is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryo-EM structure of the human C9ORF72-SMCR8-WDR41 complex at a resolution of 3.2 [A]. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72-SMCR8-WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72-SMCR8-WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72-SMCR8 resembles that of the FLNC-FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72-SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex. Significance StatementC9ORF72, together with SMCR8 and WDR41, has been shown to form a stable complex that participates in the regulation of membrane trafficking. We report the cryo-EM structure of the C9ORF72-SMCR8-WDR41 complex at atomic resolution. Notably, the stoichiometry of the three subunits in the C9ORF72-SMCR8-WDR41 complex is 2:2:2. Interestingly, the C-termini of C9ORF72 and the DENN domain of SMCR8 mediate the dimerization of the two C9ORF72-SMCR8-WDR41 protomers in the complex. Moreover, WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix without direct contact with C9ORF72. Most importantly, the C9ORF72-SMCR8 complex works as a GAP for Rab8a and Rab11a in vitro, and the Arg147 of SMCR8 is the arginine finger.

biochemistry↗

bioRxiv2020

Ultra-high-order ICA: fine overlapping functional parcellations and spatiotemporal reconfiguration

Our recent findings show that functional organizations evolve spatially over time, highlighting the importance of considering within-subject spatial variations and dynamic functional parcellations in brain functional analyses. Meanwhile, a considerable level of multi-functionality suggests the need for overlapping brain parcellations. In this work, we used ultra-high-order ICA to identify fine overlapping functional dynamic parcellations of the brain. The preliminary result of this work was presented at the organization for human brain mapping workshop (OHBM 2019)1.

neuroscience↗

bioRxiv2020

Discovery of peculiar cells in the peri-tumoral regions and peripheral blood of glioblastoma patients by single cell RNA-sequencing

The glioblastoma (GBM) recurrence rate is high, despite multimodal treatment including surgery, radiotherapy, chemotherapy, and immunotherapy. Most recurrences occur at the resection margin that is located outside the GBM contrast-enhancing region (C region) of magnetic resonance imaging. However, the nature of the GBM cells that lie outside the C region is unclear. We used single-cell RNA sequencing (scRNA-seq) to compare 12 samples taken from inside and outside the C region from four patients with GBM and identified a cluster of GBM cells outside the C region that exhibited fragmented CNVs in chromosomes such as 1, 10, 12 and 19 (herein termed CNV 4). A transcription factor-transcription cofactor interaction network was constructed to uncover the transcriptional regulatory mechanism of these CNV 4 GBM cells that had prognostic significance (p < 0.05). Furthermore, a sub-cluster of these CNV 4 GBM cells possessed stem cell-like properties and had tumorigenic potential. In parallel, we analyzed peripheral blood mononuclear cells (PBMCs) from four patients with GBM, three patients with epilepsy and three healthy volunteers by scRNA-seq. We identified a novel subtype of proliferative immune cells only in patients with GBM. Overall, our findings indicate that CNV 4 cells might contribute to GBM recurrence and proliferative circulating immune cells are specific to patients with GBM. This study sheds light on a neglected aspect of GBM, and opens new avenues to explore GBM recurrence and immunotherapy. SignificanceWe show that a subset of GBM cells outside the C region possess the properties of stem cell and tumorigenesis potential, which might be responsible for cancer recurrence. Besides, proliferative lymphocytes are specific to the PBMCs of patients with GBM, which could help to develop novel immunotherapy.

cancer biology↗

bioRxiv2019

Loss of cerebellar function selectively affects intrinsic rhythmicity of eupneic breathing

Respiration is controlled by central pattern generating circuits in the brain stem, whose activity can be modulated by inputs from other brain areas to adapt respiration to autonomic and behavioral demands. The cerebellum is known to be part of the neuronal circuitry activated during respiratory challenges, such as hunger for air, but has not been found to be involved in the control of unobstructed breathing at rest (eupnea). Here we applied a measure of intrinsic rhythmicity, the CV2, which evaluates the similarity of subsequent intervals and is thus sensitive to changes in rhythmicity at the temporal resolution of individual respiratory intervals. The variability of intrinsic respiratory rhythmicity was reduced in a mouse model of cerebellar ataxia compared to their healthy littermates. Irrespective of that difference, the average respiratory rate and the average coefficient of variation (CV) were comparable between healthy and ataxic mice. We argue that these findings are consistent with a proposed role of the cerebellum in the coordination of respiration with other rhythmic orofacial movements, such as fluid licking and swallowing.

animal behavior and cognition↗

bioRxiv2019

Parallel Group ICA + ICA: Joint Estimation of Linked Functional Network Variability and Structural Covariation with Application to Schizophrenia

There is growing evidence that rather than using a single brain imaging modality to study its association with physiological or symptomatic features, the field is paying more attention to fusion of multimodal information. However, most current multimodal fusion approaches that incorporate functional magnetic resonance imaging (fMRI) are restricted to second-level 3D features, rather than the original 4D fMRI data. This trade-off is that the valuable temporal information is not utilized during the fusion step. Here we are motivated to propose a novel approach called \"parallel group ICA+ICA\" that incorporates temporal fMRI information from GICA into a parallel ICA framework, aiming to enable direct fusion of first-level fMRI features with other modalities (e.g. structural MRI), which thus can detect linked functional network variability and structural covariations. Simulation results show that the proposed method yields accurate inter-modality linkage detection regardless of whether it is strong or weak. When applied to real data, we identified one pair of significantly associated fMRI-sMRI components that show group difference between schizophrenia and controls in both modalities. Finally, multiple cognitive domain scores can be predicted by the features identified in the linked component pair by our proposed method. We also show these multimodal brain features can predict multiple cognitive scores in an independent cohort. Overall, results demonstrate the ability of parallel GICA+ICA to estimate joint information from 4D and 3D data without discarding much of the available information up front, and the potential for using this approach to identify imaging biomarkers to study brain disorders.

bioinformatics↗

bioRxiv2018

Delivery of GalNAc-conjugated splice-switching ASOs to non-hepatic cells through ectopic expression of asialoglycoprotein receptor

Splice-switching antisense oligonucleotides (ASOs) are promising therapeutic tools to target various genetic diseases, including cancer. However, in vivo delivery of ASOs to orthotopic tumors in cancer mouse models or to certain target tissues remains challenging. A viable solution already in use is receptor-mediated uptake of ASOs via tissue-specific receptors. For example, the asialoglycoprotein receptor (ASGP-R) is exclusively expressed in hepatocytes. Triantennary GalNAc (GN3)-conjugated ASOs bind to the receptor and are efficiently internalized by endocytosis, enhancing ASO potency in the liver. Here we explore the use of GalNAc-mediated targeting to deliver therapeutic splice-switching ASOs to cancer cells that ectopically express ASGP-R, both in vitro and in tumor mouse models. We found that ectopic expression of the major isoform ASGP-R1 H1a is sufficient to promote uptake and increase GN3-ASO potency to various degrees in all tested cancer cells. We show that cell-type specific glycosylation of the receptor does not affect its activity. In vivo, GN3-conjugated ASOs specifically target subcutaneous xenograft tumors that ectopically express ASGP-R1, and modulate splicing significantly more strongly than unconjugated ASOs. Our work shows that GN3-targeting is a useful tool for proof-of-principle studies in orthotopic cancer models, until endogenous receptors are identified and exploited for efficiently targeting cancer cells.

molecular biology↗

bioRxiv2018

Role of anterograde motor Kif5b in clathrin-coated vesicle uncoating and clathrin-mediated endocytosis

Kif5b-driven anterograde transport and clathrin-mediated endocytosis (CME) are responsible for opposite intracellular trafficking, contributing to plasma membrane homeostasis. However, whether and how the two trafficking processes coordinate remain unclear. Here, we show that Kif5b directly interacts with clathrin heavy chain (CHC) at a region close to that for uncoating catalyst (Hsc70) and preferentially localizes on large clathrin-coated vesicles (CCVs). Uncoating in vitro is decreased for CCVs from the cortex of kif5b conditional knockout (mutant) mouse and facilitated by adding CHC-binding Kif5b fragments, while cell peripheral distribution of CHC or Hsc70 keeps unaffected by Kif5b depletion. Furthermore, cellular entry of vesicular stomatitis virus that internalized into large CCV is inhibited in cells by Kif5b depletion or introducing a dominant-negative Kif5b fragment. These findings showed a new role of Kif5b in CCV uncoating and CME, indicating Kif5b as a molecular knot connecting anterograde transport to CME.

cell biology↗

bioRxiv2018

Reversible inhibition of specific transcription factor-DNA interactions using CRISPR

The control of gene expression by transcription factor binding sites frequently determines phenotype. However, it has been difficult to assay the function of single transcription factor binding sites within larger transcription networks. Here, we developed such a method by using deactivated Cas9 to disrupt binding to specific sites on the genome. Since CRISPR guide RNAs are longer than transcription factor binding sites, flanking sequence can be used to target specific sites. Targeting deactivated Cas9 to a specific Oct4 binding site in the Nanog promoter blocked Oct4 binding, reduced Nanog expression, and slowed division. Multiple guide RNAs allows simultaneous inhibition of multiple binding sites and conditionally-destabilized dCas9 allows rapid reversibility. The method is a novel high-throughput approach to systematically interrogate cis-regulatory function within complex regulatory networks.

molecular biology↗

bioRxiv2018

Attentional set to safety recruits the medial prefrontal cortex

During threat assessment, the early detection of danger is highly adaptive, yet the fast orientation towards safety is also key to survival. The present study aimed to explore how the human brain searches for safety by manipulating subjects attentional set to cues associated with shock probability. Subjects were asked to judge random dots motion (RDM) direction and could be shocked for incorrect responses (RDM task) while keeping alert in detecting the shock probability cues (cue detection task). In contrast to the safe condition, where subjects searched for cues associated with no shock probability, incorrect responses to dangerous+ (D+) cues would increase the shock probability and correct responses to dangerous- (D-) cues would decrease shock probability. In the RDM task, results showed that relative to the D+, the safe attentional set resulted in stronger activation in the ventral medial prefrontal cortex (vmPFC), a core region involved in flexible threat assessment and safety signalling. The vmPFC was also recruited by the D-compared to the D + attentional set. In the cue detection task, shorter response times and greater accuracy were observed for D+ compared to D- and safe cues. Correspondingly, at the neural level D+ cues induced increased activity in the frontoparietal attention network including the inferior parietal lobule and intraparietal sulcus. Overall, our findings demonstrate that attentional set for searching safety recruits the vmPFC, while detection of threat elicits activity in the frontoparietal attention network, suggesting a new role for these regions in human defensive survival circuitry.\n\nSignificance StatementWhile early detection of threat is highly adaptive, the fast orientation towards safety is also key to survival. However, little is known about neural mechanisms underlying attentional set to safety. Using a novel dots motion paradigm combined with fMRI, we explored how human brain prepares for safety searching by manipulating subjects attentional set to cues associated with shock probability. Relative to the dangerous attentional set associated with increasing shock probability, the safe attentional set resulted in stronger activity in the ventral medial prefrontal cortex, a core region involved in flexible threat assessment and safety signalling, suggesting a new role for this region in human defensive survival system in encoding stimuli with survival significance.

neuroscience↗

bioRxiv2017

Endodermal differentiation is reconstructed by coordination of two parallel signaling systems derived from the stele in roots

The plant roots represent the exquisitely controlled cell fate map in which different cell types undergo a complete status transition from stem cell division and initial fate specification, to the terminal differentiation. The endodermis is initially specified in meristem but further differentiates to form Casparian strips (CSs), the apoplastic barrier in the mature zone for the selective transport between stele and outer tissues, and thus is regarded as plant inner skin. In the Arabidopsis thaliana root the transcription factors SHORTROOT (SHR) regulate asymmetric cell division in cortical initials to separate endodermal and cortex cell layer. In this paper, we utilized synthetic approach to examine the reconstruction of fully functional Casparian strips in plant roots. Our results revealed that SHR serves as a master regulator of a hierarchical signaling cascade that, combined with stele-derived small peptides, is sufficient to rebuild the functional CS in non-endodermal cells. This is a demonstration of the deployment of two parallel signaling systems, in which both apoplastic and symplastic communication were employed, for coordinately specifying the endodermal cell fate.

plant biology↗

bioRxiv2017

How Cognitive and Reactive Fear Circuits Optimize Escape Decisions in Humans

Flight initiation distance (FID), the distance at which an organism flees from an approaching threat, is an ecological metric of cost-benefit functions of escape decisions. We adapted the FID paradigm to investigate how fast or slow attacking virtual predators constrain escape decisions. We show that rapid escape decisions rely on reactive fear circuits in the periaqueductal gray and midcingulate cortex (MCC), while protracted escape decisions, defined by larger buffer zones, were associated with cognitive fear circuits which include posterior cingulate cortex, hippocampus and the ventromedial prefrontal cortex, circuits implicated in strategic avoidance and behavioral flexibility. Using a Bayesian Decision Model, we further show that optimization of escape decisions under rapid flight were localized to the MCC, a region involved in adaptive motor control, while the hippocampus is implicated in optimizing decisions that update and control slower escape initiation. These results demonstrate an unexplored link between defensive survival circuits and their role in adaptive escape decisions.\n\nSignificanceHumans, like other animals, have evolved a set of circuits whose primary function is survival. In the case of predation, these circuits include reactive fear circuits involved in fast and immediate escape decisions and cognitive fear circuits that are involved in the conscious feeling of threat as well as slow strategic escape. Using neuroimaging combined with computational modeling, we support this differentiation of fear circuits by showing that fast escape decisions are elicited by the periaqueductal gray and MCC, regions involved in reactive flight. Conversely, slower escape decisions rely on the hippocampus, posterior cingulate cortex and prefrontal cortex, a circuit implicated in behavioral flexibility. These results support the role of the defensive survival circuitry in escape decisions and a separation of fear into reactive and cognitive circuits.

neuroscience↗