Biology subjects

Hou, J.

Publications and source records attributed to Hou, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity

Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/Interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded NADases produce signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR sub-classes. Here we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) via ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of di-ADPR or ADPr-ATP allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta. Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.

plant biology↗

bioRxiv2022

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity

Plant nucleotide-binding leucine-rich-repeat receptors (NLRs) with an N-terminal toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded NADase activity for immune signaling. TIR-NLR (TNL) signaling requires conserved helper NLRs NRG1 and ADR1 and the lipase-like protein EDS1 that functions as a heterodimer with each of its paralogs PAD4 and SAG101. We show that TIR-containing proteins catalyze production of 2-(5-phosphoribosyl)-5-adenosine mono-/di-phosphate (pRib-AMP/ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP/ADP. pRib-ADP binding triggers a conformational change in the PAD4 C-terminal domain to allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP/ADP as a missing link in TIR signaling via EDS1-PAD4 and as likely second messengers for plant immunity.

plant biology↗

bioRxiv2022

Optical control of CRISPR-Cas editing with cyclically caged guide RNAs

The CRISPR/Cas system has been proved as one of the most powerful tools for precise gene editing. However, the approaches for precise control over the genome editing and regulatory events are still desirable. Here, we reported a spatiotemporal and efficient CRISPR/Cas9 and Cpf1-mediated editing with photo-sensitive circular gRNAs. This approach relies on only two or three pre-installed photolabile substituents followed by a simple covalent cyclization, which provides a robust synthesize approach in comparison to heavily modified gRNAs. In established cells stably expressing Cas9, the circular gRNA in coordination with light irradiation could direct a precise cleavage of GFP and VEGFA within a pre-defined cutting region. We have also achieved light-mediated MSTN gene editing in embryos, whereas a new bow-knot-type gRNA showed no background editing in the absence of light irradiation. Together, our work provides a significantly improved method to precisely manipulate where and when genes are edited.

biochemistry↗

bioRxiv2022

Bile Acid Restrained T Cell Activation Explains Cholestasis Aggravated Hepatitis B Virus Infection

Cholestasis is a common complication of Hepatitis B Virus (HBV) infection, characterized by increased intrahepatic and plasma bile acid levels. Cholestasis was found negatively associated with hepatitis outcome, however; the exact mechanism by which cholestasis impact on anti-viral immunity and impede HBV clearance remains elusive. Here, we found that cholestatic mice are featured with dysfunctional T cell response, and bile acids inhibit the activation and metabolic reprogramming of CD4+ T cells. Mechanistically, bile acids disrupt intracellular calcium homeostasis via inhibiting mitochondria calcium uptake and elevating cytoplasmic Ca2+ concentration of CD4+ T cells, leading to STIM1 and ORAIL1 decoupling and impaired store-operated Ca2+ entry which is essential for NFAT signaling and T cell activation. Moreover, in a transgenic mouse model of HBV infection, it was confirmed that cholestasis compromised T cells activation resulting in poor viral clearance. Collectively, our results suggest that bile acids play pivotal roles in anti-HBV infection via controlling T cells activation and metabolism, and that targeting regulation of bile acids may be a therapeutic strategy for host virus defense.

immunology↗

bioRxiv2022

A highly attenuated SARS-CoV-2 related pangolin coronavirus variant has a 104nt deletion at the 3'-terminus untranslated region

SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3-terminus untranslated region (3-UTR). We further report the characterization of the GX_P2V variant in in vitro and in vivo infection models. In cultured Vero and BGM cells, the GX_P2V variant produced minimal cell damage and small plaques. The GX_P2V variant infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V variant is highly attenuated in in vitro and in vivo infection models. Attenuation of the variant is likely due to the 104-nt deletion in the HVR in the 3-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2021

Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein

The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. In this study, we predicted several potential T cell epitopes with web-based analytic tools, and narrowed them down from several potential MHC-I and MHC-II epitopes by ELIspot and cytolytic assays to a conserved MHC-I epitope. The epitope is highly conserved in current viral variants including the most recent Omicron and compatible with presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.

immunology↗

bioRxiv2021

Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments

Predicting tumor sensitivity to antineoplastics remains an elusive challenge, with no methods demonstrating predictive power. Joint analysis of tumors--from patients with distinct malignancies who had progressed on multiple lines of therapy--and drug perturbation transcriptional profiles predicted sensitivity to 28 of 350 drugs, 26 of which (93%) were confirmed in low-passage, patient-derived xenograft (PDX) models. Drugs were prioritized based on their ability to either invert the activity of individual Master Regulator proteins, with available high-affinity inhibitors, or of the modules they comprise (Tumor-Checkpoints), based on de novo mechanism of action analysis. Of 138 PDX mice enrolled in 16 single and 18 multi-protein treatment arms, a disease control rate (DCR) of 68% and 91 %, and an objective response rate (ORR) of 12% and 17%, were achieved respectively, compared to 6% and 0% in the negative controls arm, with multi-protein drugs achieving significantly more durable responses. Thus, these approaches may effectively complement and expand current precision oncology approaches, as also illustrated by a case study.

systems biology↗

bioRxiv2021

Single-cell RNA-seq analysis reveals aberrant CSF1 expression in disease-causing synovial fibroblasts of pigmented villonodular synovitis

ObjectivesAlthough the role of the CSF1/CSF1R axis in pigmented villonodular synovitis (PVNS) has been confirmed, the cells that express CSF1 and CSF1R and the underlying mechanism remain unclear. Single-cell RNA sequencing (scRNA-seq) of PVNS obtained through biopsies depicted the cellular diversity of PVNS, revealed specific CSF1/CSF1R-expressing cells and further identified novel gene expression that is associated with the development of PVNS. MethodsscRNA-seq was performed on tissues obtained from the 6 biopsies of 3 patients with PVNS. Flow cytometry, immunofluorescence and western blot validated the transcriptional results, while co-culture systems revealed the cross talk between fibroblasts and macrophages. Results8 subsets of fibroblasts and 5 subsets of macrophages were identified from the synovium of patients with PVNS and were found to be related to distinct signaling pathways. The cellular components of localized and diffuse PVNS are overall similar. Moreover, the synovium and nodule of PVNS share similar composition. The specific cells expressing CSF1/CSF1R were also identified. Other than that, unique CXCL12+CSF1+ fibroblasts were revealed to attract macrophages as disease-causing synovial fibroblasts, leading to the formation of masses in PVNS. ConclusionsPVNS consists of macrophages, fibroblasts, T cells, endothelial cells and mast cells. Among them, the CSF1-expressing fibroblasts appeared to be tumor-like cells that attract macrophages, subsequently forming tumor-like mass in PVNS. This paves the path for novel treatments of PVNS by targeting CXCL12+CSF1+ fibroblasts and the CXCL12-CXCR4 axis.

molecular biology↗

bioRxiv2021

Population-level survey of loss-of-function mutations revealed that background dependent fitness genes are rare and functionally related in yeast

In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared to the reference strain S288C. Out of these 632 genetic background-dependent fitness genes identified, a total of 2/3 show a continuous variation across the population while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear-cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All background-dependent fitness genes tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.

genetics↗

bioRxiv2021

Time Evolution of the Stroke Symptom-Herb Networks Based on TCM Prescriptions

Traditional Chinese Medicine (TCM) has its origins in distant antiquity and has piled up over a long time with much knowledge about diseases, especially stroke. Different combinations of symptom variables yield different combinations of herbs to form a myriad of prescriptions, and they have undergone repeated confirmation and are worthy objects of excavation and analysis. Herbal studies on stroke have developed from genomics to transcriptomics, proteomics and metabolomics, yet more thought is needed on putting time in a wider perspective of the symptoms and herbs for stroke in Chinese medicine. Due to this, we studied the dynamic structure of TCM prescriptions on stroke, using over 270 TCM prescription books containing 2231 prescriptions related to stroke recorded from 341 to 2000 CE. We labeled the functions of the prescriptions with the symptoms based on subject terms in MESH Neurologic Manifestations, then standardized the herbs in the prescriptions, and finally connected the co-occurring symptoms and herbs in the prescriptions to build an undirected complex network. The Stroke Symptom-Herb Networks (SSHNs) can be seen from its network characteristics that it is not a random network and has small-world characteristics. It has experienced two peaks in its nearly 1700-year history, during the Song dynasty, the Ming and Qing dynasties. From 600 years onwards, the core herb cluster has been initially formed. The comparison of sub-network similarities allowed us to identify several symptoms with similar herb clusters. We divided the community based on modularity, and by analyzing the community evolution, we found a more fixed historical evolutionary trend with Hemiplegia and Sialorrhea nodes and their associated symptom and herb nodes. In the time series analysis, we found many symptom-herb combinations that were consistently closely related to historic time depends on assessing the similarity between the symptoms and the herbs. The complex network provides a distinctive perspective for understanding the symptom-herb relationships embedded in TCM prescriptions in remote antiquity.

scientific communication and education↗

bioRxiv2021

Comparison of Wild Type DNA Sequence of Spike Protein from SARS-CoV-2 with Optimized Sequence on The Induction of Protective Responses Against SARS-Cov-2 Challenge in Mouse Model

COVID-19 caused by SARS-CoV-2 has been spreading worldwide. To date, several vaccine candidates moved into EUA or CA applications. Although DNA vaccine is on phase III clinical trial, it is a promised technology platform with many advantages. Here, we showed that the pGX9501 DNA vaccine encoded the spike full-length protein-induced strong humoral and cellular immune responses in mice with higher neutralizing antibodies, blocking the hACE2-RBD binding against live virus infection in vitro. Importantly, higher levels of IFN-{gamma} expression in CD8+ and CD4+ T cell and specific cytotoxic lymphocyte (CTL) killings effect were also observed in the pGX9501-immunized group. It provided subsequent protection against virus challenges in the hACE2 transgenic mouse model. Overall, pGX9501 was a promising DNA vaccine candidate against COVID-19, inducing strong humoral immunity and cellular immunity that contributed to the vaccines protective effects.

immunology↗

bioRxiv2021

Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure

The trimeric spike protein (S) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein through a mass spectrometric approach with HCD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures on S protein. Peptide microarray assays prove that human ppGalNAc-T6 actively participates in O-glycosylation of S protein. Importantly, the upregulation of ppGalNAc-T6 expression can profoundly enhance the O-glycosylation level by generating new O-glycosites and increasing both O-glycan heterogeneity and intensities. Further molecular dynamics simulations reveal that the O-glycosylation on the protomer-interface regions, which are mainly modified by ppGalNAc-T6, can potentially stabilize the trimeric S protein structure. Our work provides deep molecular insights of how viral infection harnesses the host O-glycosyltransferases to dynamically regulate the O-glycosylation level of the viral envelope protein responsible for membrane fusion.

biochemistry↗

bioRxiv2021

Expanding Asgard members in the domain of Archaea shed new light on the origin of eukaryotes

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only six phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe five previously unknown phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Njord- and Balderarchaeota. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Archaea and a new Asgard lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that the Asgard archaea described here have potential to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters except Njordarchaeota, which may possess a heterotrophic lifestyle with capability of peptides and amino acids utilization. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Balderarchaeota and Tyrarchaeota, respectively. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree and sheds new light on the evolution of eukaryotes.

evolutionary biology↗

bioRxiv2021

PEAK3 pseudokinase represents a pro-migratory and -invasive signalling scaffold

The PEAK family of pseudokinases comprises PEAK1 and PEAK2 as well as the recently-identified PEAK3. PEAK1/2 play fundamental roles in regulating tyrosine kinase signal output and oncogenesis, while PEAK3 remains poorly-characterized. Here, we demonstrate that PEAK3 undergoes homotypic association as well as heterotypic interaction with PEAK1/2. PEAK3 also recruits ASAP1/2, Cbl and PYK2 and the adaptors Grb2 and CrkII, with binding dependent on PEAK3 dimerization. PEAK3 tyrosine phosphorylation on Y24 is also dependent on dimerization as well as Src family kinase activity, and interestingly, is decreased via PTPN12 in response to EGF treatment. Y24 phosphorylation is required for binding of Grb2 and ASAP1. Overexpression of PEAK3 in MDA-MB-231 breast cancer cells enhanced cell elongation and cell motility, while knockdown of endogenous PEAK3 decreased cell migration. In addition, overexpression of PEAK3 in PEAK1/2 compound knock-out MCF-10A breast epithelial cells enhanced acinar growth and invasion in 3D culture, with the latter phenotype dependent on PEAK3 tyrosine phosphorylation and binding of Grb2 and ASAP1. These findings characterize PEAK3 as an integral member of the PEAK family with scaffolding roles that promote cell proliferation, migration and invasion.

cancer biology↗

bioRxiv2021

Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data

The creation of scalable single-cell and highly-multiplexed imaging technologies that profile the protein expression and phosphorylation status of heterogeneous cellular populations has led to multiple insights into disease processes including cancer initiation and progression. A major analytical challenge in interpreting the resulting data is the assignment of cells to a priori known cell types in a robust and interpretable manner. Existing approaches typically solve this by clustering cells followed by manual annotation of individual clusters or by strategies that gate protein expression at predefined thresholds. However, these often require several subjective analysis choices such as selecting the number of clusters and do not automatically assign cell types in line with prior biological knowledge. They further lack the ability to explicitly assign cells to an unknown or uncharacterized type, which exist in most highly multiplexed imaging experiments due to the limited number of markers quantified. To address these issues we present Astir, a probabilistic model to assign cells to cell types by integrating prior knowledge of marker proteins. Astir uses deep recognition neural networks for fast Bayesian inference, allowing for cell type annotations at the million-cell scale and in the absence of previously annotated reference data across multiple experimental modalities and antibody panels. We demonstrate that Astir outperforms existing approaches in terms of accuracy and robustness by applying it to over 2.1 million single cells from several suspension and imaging mass cytometry and microscopy datasets in multiple tissue contexts. We further showcase that Astir can be used for the fast analysis of the spatial architecture of the tumour microenvironment, automatically quantifying the immune influx and spatial heterogeneity of patient samples. Astir is freely available as an open source Python package at https://www.github.com/camlab-bioml/astir.

bioinformatics↗

bioRxiv2021

The Human walking kinematic model combined with upper and lower limb movement

The purpose of this study is to build a relatively complete human walking kinematic model. This model is combined with the rolling-foot model (lower limb) and multi-rod swinging model (upper limb) connected by COM. We calculated the velocity of COM and other critical joints of the upper limb by marker point capture experiment using the high-speed camera. This research shows that the hand joint velocity measured through the experiment can achieve high coincidence with that calculated by the theoretical model given specific inputs. Moreover, the common pattern of upper limb angles is also studied for an accurate description. The proposed kinematic model is expected to forecast desired motion intention for better compliance by the rehabilitation and assistive robots.

biophysics↗

bioRxiv2021

Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of life

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only seven phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of Asgard archaea. Here, we describe five novel phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Hoder- and Balderarchaeota. Comprehensive phylogenomic analyses supported a new Asgard lineage Tyrarchaeota was identified as a deeper branching lineage cluster with the eukaryotic nuclear host lineage than Heimdallarchaeota that were previously considered as the closest archaeal relatives of eukaryotes. Metabolic reconstruction of Tyrarchaeota suggests a mixotrophic lifestyle of this archaea, capable of peptides and amino acids utilization while having the potential using the Wood-Ljungdahl pathway for carbon fixation and acetogenesis. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree thus sheds new light on the evolution and geochemical functions of the Asgard archaea.

evolutionary biology↗

bioRxiv2021

Improving deep learning-based protein distance prediction in CASP14

Accurate prediction of residue-residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions (i.e. classifying distances between two residues into two categories: in contact (< 8 Angstrom) and not in contact otherwise) and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the F1 measure. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps.

bioinformatics↗