Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 361 records · Page 20Linked to original sources

bioRxiv2022

Serum profiles of metabolomic and GDF-15 differentiate idiopathic pulmonary fibrosis from other interstital lung diseases: a preliminary study

Objective1.Explore the differential metabolites and metabolic pathways between different interstitial lung disease (ILD) and healthy controls, so as to find out new biomarkers and metabolic pathways of ILD and provide new biological targets for IPF diagnosis and treatment.2.Detect the levels of serum related fibrosis and metabolic indexes of ILD, explore the relationship between these indexes and the types and general parameters of ILD diseases, and focus on GDF-15 on the basis of metabonomics, explore new metabolic pathways related to ILD, and further expound the pathogenesis of idiopathic pulmonary fibrosis. Method1.According to the inclusion criteria and exclusion criteria, the ILD patients admitted to our hospital from January 1, 2021 to January 1, 2022 were signed with informed consent, and all of them had clear multidisciplinary diagnosis. At the same time, the physical examination in the health management center of our hospital was selected as the healthy control group. General clinical data of ILD patients and healthy controls were collected, including gender, age, onset, clinical manifestations, clinical biochemistry, lung function and other related data. Collect patients peripheral venous blood, keep serum samples, and analyze the serum of ILD patients and healthy controls by liquid chromatography-mass spectrometry (LC-MS) to obtain differential metabolites, metabolic maps and related data. According to the diagnosis, the patients were divided into Idiopathic pulmonary fibrosis (IPF), connective tissue disease-associated interstitial lung disease (CTD-ILD), other interstitial lung disease (ILD) patients and healthy control group. R statistical software was used to observe whether there are differential metabolites in IPF group and healthy control group, CTD-ILD group and healthy control group, other ILD groups and healthy control group, IPF group and CTD-ILD group, IPF group and other ILD groups, CTD-ILD group and other ILD groups by using positive and negative ion flow charts and score charts of orthogonal partial least squares-discriminant analysis. And the potential biomarkers were found through the S-plot diagram of OPLS-DA and the variable weight value VIP>1. ROC curve analysis of differential metabolites was carried out by SPSS21.0 software to analyze the value of differential diagnosis and find out new biomarkers with differential diagnosis significance. Based on KEGG database, the metabolic pathway enrichment analysis of differential metabolites was carried out to find out the main metabolic pathways. 2.Serum levels of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 were detected by Enzyme linked immunosorbent assay (ELISA) in all patients and healthy controls. Using SPSS21.0 statistical software and R statistical software, using T-test, variance analysis or nonparametric test method, according to different diagnoses (IPF/CTD-ILD/ other ILD/ healthy control group, ILD/ healthy control group, IPF/ other), the data were analyzed and compared in subgroups. Pearson correlation analysis was used to analyze the correlation between serum biomarkers and other factors such as lung function, metabolomics and so on. ROC curve was used to analyze the diagnostic efficiency of each index, and the best critical value, sensitivity and specificity were found out. Results1.Analysis of general clinical data and clinical indicators: 26 cases of IPF, 21cases of CTD-ILD, 23 cases of others ILD and 20 cases of healthy control group were included, respectively. There were significant differences in age, sex and smoking history among the four groups (P < 0.05), and the differences were statistically significant. There were statistically significant differences among IPF group, CTD-ILD group and other ILD groups in cough and expectoration symptoms, eosinophil count percentage, creatine kinase, creatine kinase isoenzyme, C-reactive protein and carbon monoxide diffusion capacity (DLco) (P < 0.05). 2. Metabonomics analysis: LC-MC total ion flow chart of serum samples and orthogonal partial least squares discriminant analysis (OPLS-DA) of serum samples showed the difference of ion peak intensity, and there were different metabolites among each group. The OPLS-DA model has good quality evaluation and reliable data analysis. There are 193, 115, 101, 188, 148 and 169 differential metabolites in IPF group and healthy control group, IPF group and CTD-ILD group, CTD-ILD group and other ILD groups, others ILD groups and healthy control group respectively. There is a correlation between the differential metabolites of each ILD subgroup and the healthy control group. The most relevant metabolic pathways in IPF mainly include choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer. The metabolic pathways most related to CTD-ILD and other ILD include choline metabolic pathway and retrograde neural signal metabolic pathway in cancer. Metabolic pathway and linoleic acid metabolic pathway may distinguish IPF from other ILD. Metabolites involved in metabolic pathway are L-Glutamate, PE(18:3(6Z,9Z,12Z)/P-18:0) and PC (18: 2 (9z, 12z)/20: 2 (11z, 14z)), respectively. There are three differential metabolites of linoleic acid pathway, namely 12,13-EpOME, 13S-HODE and PC(18:2(9Z,12Z)/20:2(11Z,14Z)). There are 35 kinds of differential metabolites in IPF group and healthy control group, and the top three places of AUC are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside, ({+/-}14) (15)-EET-SI, with AUC values of 0.985, sensitivity of 100% and specificity of 92.3%. L- acetylcarnitine, 5-hydroxydodecanoate and L-Glutamate are involved in significant enrichment pathways, among which the ROC curve area of L-Glutamate is the largest, with AUC value of 0.921, cutoff value of 40145.490, sensitivity of 80%, specificity of 96%, and participation in metabolic pathways. 3. Serum metabolism-related detection indexes: The six serum detection indexes of IPF group and CTD-ILD group are higher than those of healthy control group, and the difference is statistically significant (P < 0.05), but the difference between IPF group and CTD-ILD group is not statistically significant (P>0.05). The expression of GDF-15 in IPF group and non-IPF ILD group was higher than that in healthy control group, with significant difference, but there was no significant difference between IPF group and non-IPF ILD group. Type I collagen and IL-1{beta} were negatively correlated with DLco. KL-6 is negatively correlated with the measured values of VC and DLco; IGF-1 was negatively correlated with FVC, VC and DLco (all P<0.05). GDF-15 was positively correlated with type I collagen, KL-6, IL-1{beta}, TNF- and IGF-1, and the difference was statistically significant (P < 0.05). ROC curve shows that the area under ROC curve (AUC) of six serum indexes in IPF group is greater than 0.9; In CTD-ILD group, the AUC of IGF-1 was greater than 0.9, the cutoff value was 35.081ng/ml, the sensitivity was 90%, the specificity was 76%, and the area under ROC curve was greater than 0.8, and the difference was statistically significant. In other ILD groups, the ROC curve area of these six indicators ranged from 0.6 to 0.8, among which IGF-1, GDF-15 and TNF- had diagnostic value. In IPF, L-Glutamate was positively correlated with type I collagen, KL-6, IGF-1, IL-1{beta}, TNF- and GDF-15, and the difference was statistically significant (P < 0.05), with the highest correlation with IGF-1. ConclusionIn this study, the serum samples of IPF patients, CTD-ILD patients, other interstitial lung diseases and healthy controls were analyzed by LM-MS and ELISA, and the following conclusions were drawn. 1.There are differences in serum metabolites in different groups. IPF has three main metabolic pathways, namely choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer, among which metabolic pathway and linoleic acid metabolic pathway are different from other groups. There are 35 differential metabolites in IPF and healthy control group with the area under ROC curve larger than 0.80, among which the metabolites with the highest diagnostic value are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside and ({+/-}) 14 (15)-EET-SI. The AUC value of L- glutamic acid is the highest among the metabolites that participate in the enrichment pathway significantly. 2. The expressions of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 are different in different ILDs, which have potential diagnostic and differential diagnostic value, and are correlated with lung function indexes. In IPF, GDF-15 is positively correlated with L-Glutamate, which may be involved in metabolic pathway to further promote pulmonary fibrosis.

molecular biology↗

bioRxiv2022

CMLD-2 Attenuates Myofibroblast Activation and Bleomycin-Induced Pulmonary Fibrosis in Mice through Antagonizing ELAVL1-Mediated Osteopontin mRNA Stabilization

BackgroundFibroblast-myofibroblasts transition (FMT) is one of the hallmark cellular processes in pulmonary fibrosis. This study is to investigate the effects of CMLD-2 in FMT and pulmonary fibrosis, which antagonizes HuR, a supposedly key regulatory RNA binding protein (RBP). MethodsHuR or other deferentially expressed RBPs during TGF-{beta}1-induced FMT were analyzed by transcriptomic methods, and further validated in vitro or in fibrotic lung specimens. The effects of HuR overexpression, down-regulation or inhibition by an antagonist CMLD-2 were analyzed in FMT or bleomycin-induced experimental lung fibrosis. HuR-targeting RNA and their interactions were analyzed by CLIP-seq. ResultsHuR, hnRNPA1, hnRNPE1, TIA1 and TFRC were significantly up-regulated, while ESRP1, ESRP2 and TTP were significantly down-regulated. Cytoplasmic expression of HuR was activated in IPF lung tissue and rat lungs of bleomycin-induced fibrosis. HuR overexpression induced -SMA and collagen I expression, increased the proliferation and migration capacities of fibroblasts with or without the stimulation of TGF-{beta}1. HuR knockdown by shRNA inhibited the proliferation, transition, collagen production and migration properties in fibroblasts or in TGF-{beta}1-stimulated myofibroblasts. Combinative analysis of RNA-seq and CLIP-seq data revealed major HuR binding motifs and several HuR-bound, differentially expressed mRNAs in FMT, specifically SPP1 mRNA encoding osteopontin. HuR-mediated SPP1 mRNA stabilization was further validated by RIP-PCR and half-life analysis using SPP1 mutant transcripts. Inhibiting HuR using CMLD-2 attenuated SPP1/osteopontin expression, TGF-{beta}1-induced FMT in vitro and bleomycin-induced pulmonary fibrosis in mice. Nuclear-cytoplasmic shuttle of HuR was activated in TGF-{beta}1-induced FMT, which was inhibited by p38MAPK (SB203580) or PKC (Go-6976) inhibition, but not associated with phosphorylation of HuR. ConclusionsFibroblast-myofibroblast transition is activated by HuR-SPP1 mRNA interactions, and CMLD-2 is potentiated to be a therapeutic agent targeting HuR for fibroblast-myofibroblast transition and pulmonary fibrosis.

molecular biology↗

bioRxiv2022

Engineering ecologically complementary rhizosphere probiotics using consortia of specialized bacterial mutants

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between inoculated consortia members create conflicts for their survival and functioning. To circumvent this, we used transposon mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth-promotion by assembling consortia of closely related but functionally specialized mutants. While most insertion mutations were harmful, some improved strains plant growth-promotion traits without increasing antagonism between them. Crucially, plant growth-promotion could be improved by applying these specialist mutants as consortia, leading to clear positive relationships between consortia richness, plant root colonization and protection from bacterial wilt disease. Together, our results suggest that increasing intra-species diversity could be an effective way to increase probiotic consortia multifunctionality, leading to more stable plant growth-promotion throughout growth cycle via insurance effects.

ecology↗

bioRxiv2022

STOmicsDB: a database of Spatial Transcriptomic data

Recent technological development in spatial transcriptomics allows researchers to measure gene expression of cells and their spatial locations at the almost single-cell level, which generates detailed biological insight into biological processes. However, specialized spatial transcriptomics databases are rare. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a user-friendly database with multifunctions including search of relevant publications and tools, public dataset visualization, customized specialized databases, new data archive, and online analysis. The current version of STOmicsDB consists of 141 curated spatial transcript datasets covering 12 species, and includes 5,618 spatial multi-omics publications and 674 tools. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.

genomics↗

bioRxiv2022

Structure and function of diadenylate cyclase DacM from Mycoplasma ovipneumoniae

Cyclic diadenosine monophosphate (c-di-AMP) is a second-messenger nucleotide that is produced by many bacteria. C-di-AMP can not only regulate bacterial growth, cell-wall homeostasis, ion transport and gene transcription, but can also be recognized by multiple sensor / receptor proteins in infected host cells to trigger an innate immune response. Mycoplasma ovipneumoniae causes non-progressive pneumonia in both sheep and goats. Here, we analyzed c-di-AMP signaling in M. ovipneumoniae, which is a genome-reduced obligately pathogenic bacterium. Our results demonstrate that these bacteria can produce c-di-AMP, and we could identify the diadenylate cyclase, which was named DacM. The enzyme was found to utilize both ATP and ADP to synthesize c-di-AMP, resembling CdaM from a novel family of diadenylate cyclases first found in Mycoplasma pneumoniae. Furthermore, we present the crystal structures of DacM in the apo state and substrate-bound state at 3 [A] and 1.9 [A] resolution, respectively. Mutation of residues Asp112, Gly113, Tyr128, Phe129, and Arg143 surrounding the active sites to Ala were lethal to DacM enzymatic activity. These structures provide valuable insights into the biochemistry of c-di-AMP, and offer a basis for the structure-based design of new drugs for animal husbandry.

pathology↗

bioRxiv2022

More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction.

SARS-CoV-2 has caused tremendous deaths world wild. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. The relationship between virulence and transmissibility can be simulated. A delicate equilibrium point that optimizing the transmissibility can be numerically obtained. Based on this model, we predict the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. We can also explain the cross-species transmission phenomenon of certain RNA virus based on this model. A small-scale model which simulates the virus packing process is also proposed. It can be explained why a small number of mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.

evolutionary biology↗

bioRxiv2022

The circ_0002538/miR-138-5p/PLLP axis regulates Schwann cell migration and myelination in diabetic peripheral neuropathy

Diabetic peripheral neuropathy (DPN) is the most common complication of diabetes, but the underlying molecular pathogenesis remains unclear. Accumulating evidence indicates that circular RNAs (circRNAs) play vital roles in DPN, while their expressions and functions in Schwann cell (SC) are rarely reported. Here, we performed protein profiling and circRNA sequencing on the peripheral nerves of patients with or without DPN. A total of 265 differentially expressed proteins were identified in DPN by protein profiling, which mainly enrich in myelination according to Gene Ontology analysis. Further, 15637 circRNAs were identified by circRNA sequencing, of which 11 were verified to be dysregulated. Among them, circ_0002538 was found to be downregulated in DPN and chosen for further investigation. Functional experiments revealed that circ_0002538 overexpression promoted SC migration and relieved demyelination in DPN. Mechanistic studies revealed that circ_0002538 could promote PLLP expression by sponging miR-138-5p, while lack of circ_0002538 led to PLLP deficiency, which further suppressed SC migration and caused demyelination. The present research provided novel insights into the pathogenesis of DPN, in which the circ_0002538/miR-138-5p/PLLP axis was suppressed in SCs and hence caused demyelination. These findings expanded the role of circRNAs in DPN and provided potential therapeutic targets for DPN.

neuroscience↗

bioRxiv2022

Genome-wide Association Study Reveals that PvGUX1_1 is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.)

The suture strings is a particularly important pod trait that determines the quality and texture of snap bean (Phaseolus vulgaris L.). The St locus on chromosome 2 has been described as a major locus associated with suture strings. However, the gene and genetic basis underlying this locus remain unknown. Here, we investigated the suture strings of 138 snap bean accessions across two years. A total of 3.66 million single-nucleotide polymorphisms (SNPs) were obtained by deep resequencing. Based on these SNPs, we identified a strong association signal on Chr02 and a promising candidate gene, PvGUX1_1. Further analysis revealed that the 2-bp deletion in exon of PvGUX1_1 was significantly associated with stringlessness. Comparative mapping indicated that PvGUX1_1 was a domesticated locus and diverged from PvGUX1_2 during an early stage. Our study provides important insights into the genetic mechanism of suture string formation and useful information for snap bean improvement.

genetics↗

bioRxiv2022

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

BackgroundMicrobial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data. MethodsHere we present StrainPanDA (Strain-level Pangenome Decomposition Analysis), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of co-existing strains in microbial communities. ResultsWe systematically validate the accuracy and robustness of StrainPanDA using synthetic datasets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization, pathogenicity). ConclusionsStrainPanDA can be applied to metagenomic datasets to detect association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.

bioinformatics↗

bioRxiv2022

AI-Generated Virtual Libraries Could Help Uncover RNA-Specific Regions of Chemical Space

RNAs can recognize small-molecule ligands. However, the extent to which the molecules that they recognize differ from those recognized by proteins remains an open question. Cheminformatics analysis of experimentally validated RNA binders strongly suggests that RNA binders occupy a specific region of chemical space. However, less than 100 validated small molecule ligands are currently known. Here, we demonstrate how structure-based approaches could be used to navigate vast regions of the chemical space specific to ligand binding sites in five highly-structured RNAs. Our method involves using generative-AI to design target- and site-specific virtual libraries and then analyzing them using similar cheminformatics approaches as those used to assess experimentally validated RNA binders. Despite employing a completely orthogonal strategy, our results essentially reproduce the trends observed by analyzing the experimentally validated RNA binders. Large-scale generation of target and site-specific libraries may therefore prove to be helpful in simultaneously mapping the regions of chemical space unique to RNA and generating libraries that could be mined to identify novel RNA binders. TOC IMAGE O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biophysics↗

bioRxiv2022

Keystone species determine the productivity of synthetic microbial biofilm communities

Microbes typically reside in multi-species communities, whose interactions have considerable impacts on the robustness and functionality of such communities. To manage microbial communities, it is essential to understand the factors driving their assemblage and maintenance. Even though the community composition could be easily assessed, interspecies interactions during community establishment remain poorly understood. Here, we combined co-occurrence network analysis with quantitative PCR to examine the importance of each species within synthetic communities (SynComs) of pellicle biofilms. Genome-scale metabolic models and in vitro experiments indicated that the biomass of SynComs was primarily affected by keystone species that are acting either as metabolic facilitators or as competitors. Our study sets an example of how to construct a model SynCom and investigate interspecies interactions.

microbiology↗

bioRxiv2022

Longitudinal Morphological and Functional Characterization of Human Heart Organoids Using Optical Coherence Tomography

Organoids play an increasingly important role as in vitro models for studying organ development, disease mechanisms, and drug discovery. Organoids are self-organizing, organ-like three-dimensional (3D) cell cultures developing organ-specific cell types and functions. Recently, three groups independently developed self-assembling human heart organoids (hHOs) from human pluripotent stem cells (hPSCs). In this study, we utilized a customized spectral-domain optical coherence tomography (SD-OCT) system to characterize the growth of hHOs. Development of chamber structures and beating patterns of the hHOs were observed via OCT and calcium imaging. We demonstrated the capability of OCT to produce 3D images in a fast, label-free, and non-destructive manner. The hHOs formed cavities of various sizes, and complex interconnections were observed as early as on day 4 of differentiation. The hHOs models and the OCT imaging system showed promising insights as an in vitro platform for investigating heart development and disease mechanisms.

bioengineering↗

bioRxiv2022

FRET monitoring of transcription factor activities in living bacteria

Bacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Forster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized in C. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not only complements currently available approaches for DNA-protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria-host interface.

molecular biology↗

bioRxiv2022

AAV11 permits efficient retrograde targeting of projection neurons

Viral tracers that permit efficient retrograde targeting of projection neurons are powerful vehicles for structural and functional dissections of the neural circuit and for the treatment of brain diseases. Recombinant adeno-associated viruses (rAAVs) are the most potential candidates because they are low-toxic with high-level transgene expression and minimal host immune responses. Currently, some rAAVs based on capsid engineering for retrograde tracing have been widely used in the analysis and manipulation of neural circuits, but suffer from brain area selectivity and inefficient retrograde transduction in certain neural connections. Here, we discovered that the recombinant adeno-associated virus 11 (rAAV11) exhibits potent retrograde labeling of projection neurons with enhanced efficiency to rAAV2-retro in some neural connections. Combined with calcium recording technology, rAAV11 can be used to monitor neuronal activities by expressing Cre recombinase or calcium-sensitive functional probe. In addition, we further showed the suitability of rAAV11 for astrocyte targeting. These properties make rAAV11 a promising tool for the mapping and manipulation of neural circuits and gene therapy of some neurological and neurodegenerative disorders. HighlightsO_LINaturally occurring AAV serotype capsid exhibits robust retrograde functionality C_LIO_LIImproved distribution properties and retrograde transport efficiency C_LIO_LICan express Cre recombinase or calcium-sensitive functional probe for neural circuits monitoring C_LIO_LICan specifically target astrocytes C_LI

neuroscience↗

bioRxiv2021

Simultaneous Optimization of Excitation Wavelength and Emission Window for Semiconducting Polymer Nanoparticles to Improve Imaging Quality

Optimized excitation wavelength and emission window are essential for fluorescence imaging with high quality. Semiconducting polymer nanoparticles (SPNs) as fluorescent contrast agents have been extensively studied, but their imaging abilities in the second near-infrared IIb window (NIR-IIb, 1500-1700 nm) with long excitation wavelength have not been reported yet. Herein, as a proof-of-concept, we demonstrate for the first time that an SPN named L1057 nanoparticles (NPs) exhibit intense NIR-IIb signal due to its ultra-high brightness and broad emission spectrum. After screening 915 nm as an optimal excitation wavelength, we applied L1057 NPs to visualize the whole-body vessels, cerebral vessels, gastrointestinal tract, and tumor progression in different stages, achieving superior spatial resolution and signal to background ratio in the NIR-IIb window with respect to NIR-II window (1000-1700 nm). This study reveals that simultaneous optimization of excitation wavelength and emission window is an efficient strategy to enhance imaging quality and that L1057 NPs can serve as a promising NIR-IIb contrast agent for high-resolution and deep-tissue imaging.

bioengineering↗

bioRxiv2021

Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative "low-loss lysis" (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.

genomics↗

bioRxiv2021

Cell free extrachromosomal circular DNA is common in human urine

Cell free extrachromosomal circular DNA (eccDNA) is evolving as a potential biomarker in liquid biopsies for disease diagnosis. In this study, an optimized next generation sequencing-based Circle-Seq method was developed to investigate urinary cell free eccDNA (ucf-eccDNA) from 28 adult healthy volunteers (mean age = 28, 19 males/ 9 females). The genomic distributions and sequence compositions of ucf-eccDNAs were comprehensively characterized. Approximately 1.2 million unique ucf-eccDNAs are identified, covering 14.9% of the human genome. Comprehensive characterization of ucf-eccDNAs show that ucf-eccDNAs contain higher GC content than flanking genomic regions. Most eccDNAs are less than 1000 bp and present four pronounced peaks at 203, 361, 550 and 728 bp, indicating the association between eccDNAs and the numbers of intact nucleosomes. Analysis of genomic distribution of ucf-eccDNAs show that eccDNAs are found in all chromosomes but enriched in chromosomes i.e. chr.17, 19 and 20 with high density of protein-codding genes, CpG islands, SINE and simple repeat elements. Lastly, analysis of sequence motif signatures at eccDNA junction sites reveal that direct repeats (DRs) are commonly found, indicating a potential role of DRs in eccDNA biogenesis. This work underscores the deep sequencing analysis of ucf-eccDNAs and provides a valuable reference resource for exploring potential applications of ucf-eccDNA as diagnostic biomarkers of urogenital disorders in the future. Significance StatementExtrachromosomal circular DNA (eccDNA) is an important genetic element and a biomarker for disease diagnosis and treatment. In this study, we conduct a comprehensive characterization of urinary cell free eccDNA (ucf-eccDNA) in 28 heathy subjects. Over one million ucf-eccDNAs are identified. Ucf-eccDNAs are characterized as high GC content. The size of most ucf-eccDNAs is less than 1000 bp and enriched in four peaks resembling the size of single, double, triple, and quadruple nucleosomes. The genomic distribution of ucf-eccDNAs is enriched in generic regions, protein-coding genes, Alu, CpG islands, SINE and simple repeats. Sequence motif analysis of ucf-eccDNA junctions identified simple direct repeats (DRs) commonly presented in most eccDNAs, suggesting potential roles of DRs in eccDNA biogenesis.

genomics↗

bioRxiv2021

Mapping Consistent, Reproducible, and Transcriptionally Relevant Connectome Hubs of the Human Brain

Human brain connectomes include sets of densely connected regions, known as connectome hubs, which play a vital role in understanding global brain communication, cognitive processing, and brain disorders. However, the consistency and reproducibility of functional connectome hubs anatomical localization have not been established to date and the genetic signatures underlying robust connectome hubs remain unknown. Here, we conduct the first worldwide, harmonized meta-connectomic analysis by pooling resting-state functional MRI data of 5,212 healthy young adults across 61 independent cohorts. We identify highly consistent and reproducible functional connectome hubs in heteromodal and unimodal regions both across cohorts and across individuals. These connectome hubs show heterogeneous connectivity profiles and are critical for both intra- and inter-network communications. Using post-mortem gene expression data, we show that these connectome hubs have a spatiotemporally distinctive transcriptomic pattern dominated by genes involved in the neuropeptide signaling pathway, neurodevelopmental processes, and metabolic processes. These results highlight the robustness of macroscopic connectome hubs and their potential cellular and molecular underpinnings.

neuroscience↗