Biology subjects

Su, X.

Publications and source records attributed to Su, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2019

Rewired signaling network in T cells expressing the chimeric antigen receptor (CAR)

The chimeric antigen receptor (CAR) directs T cells to target and kill specific cancer cells. Despite the success of CAR T therapy in clinics, the intracellular signaling pathways that lead to CAR T cell activation remain unclear. Using CD19 CAR as a model, we report that, similar to the endogenous T cell receptor (TCR), antigen-engagement triggers the formation of CAR microclusters that transduce downstream signaling. However, CAR microclusters do not coalesce into a stable central supramolecular activation cluster (cSMAC). Moreover, LAT, an essential scaffold protein for TCR signaling, is not required for microcluster formation, immunological synapse formation, and actin remodeling following CAR activation. Meanwhile, CAR T cells still require LAT for the normal production of the cytokine IL-2. Together, these data show that CAR T cells can bypass LAT for a subset of downstream signaling outputs, thus revealing a rewired signaling pathway as compared to native T cells.

immunology↗

bioRxiv2019

Investigating higher order interactions in single cell data with scHOT

Single-cell RNA-sequencing has transformed our ability to examine cell fate choice. For example, in the context of development and differentiation, computational ordering of cells along pseudotime enables the expression profiles of individual genes, including key transcription factors, to be examined at fine scale temporal resolution. However, while cell fate decisions are typically marked by profound changes in expression, many such changes are observed in genes downstream of the initial cell fate decision. By contrast, the genes directly involved in the cell fate decision process are likely to interact in subtle ways, potentially resulting in observed changes in patterns of correlation and variation rather than mean expression prior to cell fate commitment. Herein, we describe a novel approach, scHOT - single cell Higher Order Testing - which provides a flexible and statistically robust framework for identifying changes in higher order interactions among genes. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. We demonstrate the utility of scHOT by studying embryonic development of the liver, where we find coordinated changes in higher order interactions of programs related to differentiation and liver function. We also demonstrate its ability to find subtle changes in gene-gene correlation patterns across space using spatially-resolved expression data from the mouse olfactory bulb. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.

bioinformatics↗

bioRxiv2019

Single-cell dissection of a rare human prostate basal cell carcinoma

As a rare subtype of prostate carcinoma, basal cell carcinoma (BCC) has not been studied extensively and thus lacks systematic molecular characterization. Here we applied single-cell genomic amplification and RNA-Seq to a specimen of human prostate BCC (CK34{beta}E12+/P63+/PAP-/PSA-). The mutational landscape was obtained via whole exome sequencing of the amplification mixture of 49 single cells, and the 5 putative driver genes mutated are CASC5, NUTM1, PTPRC, KMT2C and TBX3. The top 3 nucleotide substitutions are C>T, T>C and C>A, similar to common prostate cancer. The distribution of the variant allele frequency values indicated these single cells are from the same tumor clone. The transcriptomes of 69 single cells were obtained, and they were clustered into tumor, stromal and immune cells based on their global transcriptomic profiles. The tumor cells specifically express basal cell markers like KRT5, KRT14 and KRT23, and epithelial markers EPCAM, CDH1 and CD24. The transcription factor (TF) co-variance network analysis showed that the BCC tumor cells have distinct regulatory networks. By comparison with current prostate cancer datasets, we found that some of the bulk samples exhibit basal-cell signatures. Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells. This study, for the first time, discloses the comprehensive mutational and transcriptomic landscapes of prostate BCC, which lays a foundation for the understanding of its tumorigenesis mechanism and provides new insights into prostate cancers in general.

cancer biology↗

bioRxiv2019

Nanomorphological and mechanical reconstruction of mesenchymal stem cells during early apoptosis detected by atomic force microscopy

Stem cell apoptosis exists widely in embryonic development, tissue regeneration, repair, aging and pathophysiology of disease. The molecular mechanism of stem cell apoptosis has been extensively investigated. However, alterations in biomechanics and nanomorphology have rarely been studied. Therefore, an apoptosis model was established for bone marrow mesenchymal stem cells (BMSCs) and the reconstruction of the mechanical properties and nanomorphology of the cells were investigated in detail. Atomic force microscopy (AFM), scanning electron microscopy (SEM), laser scanning confocal microscopy (LSCM), flow cytometry and Cell Counting Kit-8 analysis were applied to assess the cellular elasticity modulus, geometry, nanomorphology, cell surface ultrastructure, biological viability and early apoptotic signal (phosphatidylserine, PS). The results indicated that the cellular elastic modulus and volume significantly decreased, whereas the cell surface roughness obviously increased during the first 3 h of cytochalasin B (CB) treatment. Moreover, these alterations preceded the exposure of biological apoptotic signal PS. These findings suggested that cellular mechanical damage is connected with the apoptosis of BMSCs, and the alterations in mechanics and nanomorphology may be a sensitive index to detect alterations in cell viability during apoptosis. The results contribute to a further understanding of the apoptosis from the perspective of cell mechanics.

cell biology↗

bioRxiv2019

Draft genome of a porcupinefish, Diodon Holocanthus

The long-spine porcupinefish, Diodon holocanthus (Diodontidae, Tetraodontiformes, Actinopterygii), also known as the freckled porcupinefish, attracts great interest of ecology and economy. Its distinct characteristics including inflation reaction, spiny skin and tetradotoxin, however, have not been fully studied without a complete genome assembly.\n\nIn this study, the whole genome of a single individual was sequenced using single tube-Long Fragment Read co-barcode reads, generating 154.3 Gb of paired-end data (219.8x depth). The gap was further filled using small amount of Oxford Nanopore MinION long read dataset (11.4Gb, 15.9x depth). Taking full use of long, medium, short-range of genome assembly information, the final assembled sequences with a total length of 650.02 Mb obtained contig and scaffold N50 sizes of 2.15 Mb and 8.13 Mb, respectively, despite of high repetitive content. Benchmarking Universal Single-Copy Orthologs captured 95.7% (2,474) of core genes to assess the completeness. In addition, 206.5 Mb (32.10%) of repetitive sequences were identified, and 20,840 protein-coding genes were annotated, among which 18,281 (87.72%) proteins were assigned with possible functions.\n\nThis is the first demonstration of de novo genome of the porcupinefish, which will benefit downstream analysis of ontogeny, phylogeny, and evolution, and improve the exploration of its unique defensive mechanism.

genomics↗

bioRxiv2019

Single-Cell RNA-Seq Reveals Naïve B cells Associated with Better Prognosis of HCC

Hepatocellular Carcinoma (HCC) is a type of malignant solid tumor, causing high morbidity and mortality around the world and the major portion of HCC patients is from China. Cancer immunotherapies have shown some clinical responses in treating some types of cancer but did not shown significant efficiency in HCC treatment. This in part due to the impact of immune cells in the tumor microenvironment. It is commonly believed that HCC is a heterogeneous solid tumor and the microenvironment of HCC plays an important role in tumorgenesis and development. Currently, the residents of the microenvironment of HCC is not well-defined and clarification, especially the immune cells, which we believe that paly pivotal roles in tumorgenesis and development. To depict the landscape of the composition, lineage and functional states of the immune cells in HCC, we performed single-cell RNA sequencing on Diethylnitrosamine (DEN)-induced mouse HCC model. We observed heterogeneity within the immune and hepatocytes both in the precancerous condition of tumorigenesis and cancerous condition of HCC. In this study we found that the disease-associated changes appeared early in pathological progression and were highly cell-type specific. Specific subsets of T and B cells preferentially enriched in HCC, and we identified signature genes for each subset. Additionally, we mapped this group of specific cells to the human TCGA database. We found a cluster of naive B cells characterized by high expression of CD38 associated with better prognosis of human HCC. Our study demonstrates signaling interaction map based on receptor-ligand bonding on the single-cell level could broaden our comprehending of cellular networks in varies status. Our finding provides a new approach for patient stratification and will help further understand the functional states, dynamics and signaling interaction of B cells in hepatocellular carcinoma, and may provide a novel insight and therapeutics for the HCC.

cancer biology↗

bioRxiv2019

Injection molded open microfluidic well plate inserts for user-friendly coculture and microscopy

Open microfluidic cell culture systems are powerful tools for interrogating biological mechanisms. We have previously presented a microscale cell culture system, based on spontaneous capillary flow of biocompatible hydrogels, that is integrated into a standard cell culture well plate, with flexible cell compartment geometries and easy pipet access. Here, we present two new injection molded open microfluidic devices that also easily insert into standard cell culture well plates and standard culture workflows, allowing seamless adoption by biomedical researchers. These platforms allow culture and study of soluble factor communication among multiple cell types, and the microscale dimensions are well-suited for rare primary cells. Unique advances include optimized evaporation control within the well, manufacture with reproducible and cost-effective rapid injection molding, and compatibility with sample preparation workflows for high resolution microscopy (following well-established coverslip mounting procedures). In this work, we present several use cases that highlight the usability and widespread utility of our platform including culture of limited primary testis cells from surgical patients, microscopy readouts including immunocytochemistry and single molecule fluorescence in situ hybridization (smFISH), and coculture to study interactions between adipocytes and prostate cancer cells.

bioengineering↗

bioRxiv2019

Genome analysis and Hi-C assisted assembly of Elaeagnus angustifolia L., a deciduous tree belonging to Elaeagnaceae

Elaeagnus angustifolia L. is a deciduous tree of the Elaeagnaceae family. It is widely used in the study of abiotic stress tolerance in plants and for the improvement of desertification-affected land due to its characteristics of drought resistance, salt tolerance, cold resistance, wind resistance, and other environmental adaptation. Here, we report the complete genome sequencing using the Pacific Biosciences (PacBio) platform and Hi-C assisted assembly of E. angustifolia. A total of 44.27 Gb raw PacBio sequel reads were obtained after filtering out low-quality data, with an average length of 8.64 Kb. And 39.56 Gb clean reads was obtained, with a sequencing coverage of 75x, and Q30 ratio > 95.46%. The 510.71 Mb genomic sequence was mapped to the chromosome, accounting for 96.94% of the total length of the sequence, and the corresponding number of sequences was 269, accounting for 45.83% of the total number of sequences. The genome sequence study of E. angustifolia can be a valuable source for the comparative genome analysis of the Elaeagnaceae family members, and can help to understand the evolutionary response mechanisms of the Elaeagnaceae to drought, salt, cold and wind resistance, and thereby provide effective theoretical support for the improvement of desertification-affected land.

genetics↗

bioRxiv2019

Investigating Fibroblast-Induced Collagen Gel Contraction Using a Dynamic Microscale Platform

Mechanical forces have long been recognized as fundamental drivers in biological processes, such as embryogenesis, tissue formation and disease regulation. The collagen gel contraction (CGC) assay has served as a classic tool in the field of mechanobiology to study cell-induced contraction of extracellular matrix (ECM), which plays an important role in inflammation and wound healing. In a conventional CGC assay, cell-laden collagen is loaded into a cell culture vessel (typically a well plate) and forms a disk-shaped gel adhering to the bottom of the vessel. The decrement in diameter or surface area of the gel is used as a parameter to quantify the degree of cell contractility. In this study, we developed a microscale CGC assay with an engineered well plate insert that uses surface tension forces to load and manipulate small volumes (14 {micro}L) of cell-laden collagen. The system is easily operated with two pipetting steps and the microscale device moves dynamically as a result of cellular forces. We used a straightforward one-dimensional measurement as the gel contraction readout. We adapted a conventional lung fibroblast CGC assay to demonstrate the functionality of the device, observing significantly more gel contraction when human lung fibroblasts were cultured in serum-containing media versus serum-free media (p[≤]0.01). We further cocultured eosinophils and fibroblasts in the system, two important cellular components that lead to fibrosis in asthma, and observed that soluble factors from eosinophils significantly increase fibroblast-mediated gel contraction (p[≤]0.01). Our microscale CGC device provides a new method for studying downstream ECM effects of intercellular cross talk using 7-35 fold less cell-laden gel than traditional CGC assays.

cell biology↗

bioRxiv2019

The rs6505162 C>A polymorphism in the miRNA-423 gene exhibits a protective element of coronary artery in a southern Chinese population with Kawasaki disease

BackgroundManifesting as acute rash, fever and vasculitis, belonging to autoimmune syndrome, Kawasaki disease(KD) is prone to occur in infants and young children. Males and females is affected by KD at a ratio of 1.4 to 1.7: 1. KD is known to own many common clinical manifestations and complications, like coronary artery lesion(CAL) and coronary artery aneurysm(CAA). Polymorphisms of the rs6505162 locus in the miRNA-423 gene are associated with enhancive susceptibility to coronary artery disease and the alterations of the four cytokines IL-4., IL-10, IL-21, IL-22 in the early stages of diabetes. However, no researcher has reported whether rs6505162 is related to KD susceptibility or no. Therefore, we carried out the trial concentrating on the connection between miRNA-423 rs6505162 C>A polymorphism and KD susceptibility.\n\nMethodsTo obtain the genotypes of rs6505162 in objects enrolled by 532 KD children and 623 control, we applied Taqman real-time PCR and all statistical analyses was carried out by SAS.\n\nResultsThe comparison between all cases and all controls hinted that the rs6505162C>A polymorphism has no relationship with KD susceptibility. Nevertheless, a subgroup analysis revealed that the CA/AA genotypes of rs6505162 could reduce the occurrence of CAA (Adjusted age and gender odds ratio=1.30, 95%CI=1.02-1.67, P=0.037) and CAL (Adjusted OR=1.56, 95%CI=1.19-2.03, P=0.001)in KD patients.\n\nConclusionOur final results stated clearly that miRNA-423 rs6505162 polymorphism appears to be a protective element of CAL and CAA in southern Chinese suffers with KD.

genetics↗

bioRxiv2019

A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation: Mapping the Neoantigen to 3D Genome

The high-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate immune response of the T cells. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified neoantigen candidates according to their ability of activating the T cell immuno-response. Numerous prioritization or prediction approaches have been proposed to address this issue but none of them considers the original DNA loci of the neoantigens from the perspective of 3D genome. Here we retrospect the DNA origins of the immune-positive and non-negative neoantigens in the context of 3D genome and discovered that 1) DNA loci of the immuno-positive neoantigens tend to cluster genome-wise. 2) DNA loci of the immuno-positive neoantigens tend to belong to active chromosomal compartment (compartment A) in some chromosomes. 3). DNA loci of the immuno-positive neoantigens tend to locate at specific regions in the 3D genome. We believe that the 3D genome information will help more precise neoantigen prioritization and discovery and eventually benefit precision and personalized medicine in cancer immunotherapy.

bioinformatics↗

bioRxiv2019

A novel thermostable aspartic protease from Talaromyces leycettanus and its specific autocatalytic activation through an intermediate transition state

Aspartic proteases exhibit optimum enzyme activity under acidic condition and have been extensively used in food, fermentation and leather industries. In this study, a novel aspartic protease precursor (proTlAPA1) from Talaromyces leycettanus was identified and successfully expressed in Pichia pastoris. Subsequently, the auto-activation processing of the zymogen proTlAPA1 was studied by SDS-PAGE and N-terminal sequencing, under different processing conditions. TlAPA1 shared the highest identity of 70.3 % with the aspartic endopeptidase from Byssochlamys spectabilis (GAD91729) and was classified into a new subgroup of the aspartic protease A1 family, based on evolutionary analysis. Mature TlAPA1 protein displayed an optimal activity at 60 {degrees}C and remained stable at temperatures of 55 {degrees}C and below, indicating the thermostable nature of TlAPA1 aspartic protease. During the auto-activation processing of proTlAPA1, a 45 kDa intermediate was identified that divided the processing mechanism into two steps: formation of intermediates, and activation of the mature protein (TlAPA1). The former step was completely induced by pH of the buffer, while the latter process depended on protease activity. The discovery of the novel aspartic protease TlAPA1 and study of its activation process will contribute to a better understanding of the mechanism of aspartic proteases auto-activation. IMPORTANCEThe novel aspartic protease TlAPA1 was identified from T. leycettanus and expressed as a zymogen (proTlAPA1) in P. pastoris. Enzymatic characteristics of the mature protein were studied and the specific pattern of zymogen conversion was described. The auto-activation processing of proTlAPA1 proceeded in two stages and an intermediate was identified in this process. These results describe a new subgroup of aspartic protease A1 family and provide insights into a novel mode of activation processing in aspartic proteases.

molecular biology↗

bioRxiv2019

Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive (1). The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.

evolutionary biology↗

bioRxiv2018

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

Concerted examination of multiple collections of single cell RNA-Seq (scRNA-Seq) data promises further biological insights that cannot be uncovered with individual datasets. However, such integrative analyses are challenging and require sophisticated methodologies. To enable effective interrogation of multiple scRNA-Seq datasets, we have developed a novel algorithm, named scMerge, that removes unwanted variation by combining stably expressed genes and utilizing pseudo-replicates across datasets. Analysis of large collections of publicly available datasets demonstrates that scMerge performs well in multiple scenarios and enhances biological discovery, including inferring cell developmental trajectories.

bioinformatics↗

bioRxiv2018

Influence of food and Nosema ceranae infection on the gut microbiota of Apis cerana workers

BackgroundGut microbiota plays an essential role in bees health. To elucidate the effect of food and Nosema ceranae infection on the gut microbiota of honeybee Apis cerana, we used 16S rRNA sequencing to survey the gut microbiota of honeybee workers fed with sugar water or beebread and inoculated with or without N. ceranae.\n\nResultsThe gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was significantly differential by food type. The N. ceranae infection significantly affects the gut microbiota only at bees fed with sugar water. Higher abundance of Lactobacillus, Gluconacetobacter and Snodgrassella and lower abundance of Serratia were found in bees fed with beebread than with sugar water. N. ceranae infection led to higher abundance of Snodgrassella and lower abundance of Serratia in sugar-fed bees. Imputed bacterial KEGG pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho=0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection.\n\nConclusionsBoth food and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread feeding not only provide better nutrition but also help establish a more stabled gut microbiota therefore protect bee in response to N. ceranae infection.\n\nAbstract ImportanceGut microbiota plays an essential role in bees health. Scientific evidence suggests the diet and infection can affect the gut microbiota and modulate the gut health, however the interplay between those two factors and bee gut microbiota is not well known. In this study, we used high-throughput sequencing method to monitor the changes of gut microbiota by both food intake and the Nosema ceranae infection. Our result showed that the gut microbiota composition and diversity of Asia Honeybee was significantly associated with both food intake and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and less mortality than those fed with sugar water when infected by N. ceranae. Those data suggest the potential role of beebread, not only providing better nutrition but also helping establish a more stabled gut microbiota to protect bee against N. ceranae infection.

microbiology↗

bioRxiv2018

A Composition-Dependent Molecular Clutch Between T Cell Signaling Clusters and Actin

Biomolecular condensates play important roles in eukaryotic cells by concentrating molecules into foci without a surrounding membrane. During T cell activation, biomolecular condensates form at the immunological synapse (IS) through multivalency-driven phase separation of the adaptor protein LAT and its binding partners Grb2, Sos1, SLP-76, Nck and WASP. These condensates move radially at the IS, traversing a radially-oriented and then a concentric actin network. To understand the persistent radial movement, we biochemically reconstituted LAT condensates with mobile actomyosin filaments. We found that basic regions of Nck and N-WASP promote strong association and co-movement of LAT condensates with actin. Condensates lacking these components were instead propelled by steric interactions. In cells, LAT condensates lost Nck while traversing the boundary between the two actin networks, and condensates engineered to constitutively bind actin moved aberrantly. We propose that Nck and WASP form a clutch between LAT condensates and actin, and changes in composition enable condensate movement by distinct actin networks in different regions of the IS.

cell biology↗

bioRxiv2018

Bi-clustering interpretation and prediction of correlation between gene expression and protein abundance

Most organisms transcript and protein level only moderately correlate for various reasons, such as regulation of transcription and protein degradation. Better prediction and understanding the correlation between gene expression and protein abundance has been possible by harnessing the matching RNA/protein datasets produced by modern high-throughput RNA-Seq and mass spectrometry methods. In this work, we have utilized some well-studied matching RNA/protein datasets, and explored for the first time a bi-clustering method to cluster genes that have consistent correlation patterns between gene expression and protein abundance. The clustering results have been interpreted from the perspective of both transcriptomic and proteomic features, which show that mRNA half-life, protein half-life and protein structure in concert significantly affect the correlation of gene expression and protein abundance. With these and other carefully selected features, a prediction model based on individual clusters, called Cluster-based Linear prediction Model (CLM), was built and tested on mouse liver mitochondrial, mouse brainstem mitochondrial, Saccharomyces cerevisiae and Danio rerio datasets. CLM could find genes for which protein abundance can be predicted from mRNA data. In summary, based on bi-clustering, feature selection and CLM model, we have established a new and valuable cluster-based protein abundance prediction method.

bioinformatics↗

bioRxiv2017

MapZ forms a stable ring structure that acts as a track for FtsZ treadmilling in Streptococcus mutans

Bacterial binary division requires the accurate placement of the division machinery. FtsZ, the vital component of the division machinery, can assemble into filaments and self-organize into a ring structure (Z-ring) at the proper site for cell division. Thus, understanding how bacteria control the spatiotemporal formation of the FtsZ ring is crucial for small molecule and nanoparticle antibacterial drug discovery. MapZ, a recently identified FtsZ regulator in Streptococcaceae, has been found to localize at the mid-cell and position the FtsZ ring. However, the mechanism is still unclear. Here, by using total internal reflection fluorescence microscopy, super-resolution imaging, and single molecule tracking, we investigated the mechanism by which MapZ regulates the FtsZ ring position. The results show that FtsZ exhibites dynamic treadmilling motion in S. mutans. Importantly, depletion of MapZ leads to an unconstrained movement of treadmilling FtsZ filaments and a shorter lifetime of the constricting FtsZ ring. Furthermore, by revealing that MapZ forms an immobile ring-like nanostructure at the division site, our study suggests that MapZ forms a stable ring that acts as a nanotrack to guide and restrict treadmilling FtsZ filaments in S. mutans, representing a novel way in which bacteria control the division.

microbiology↗