Biology subjects

Tang, F.

Publications and source records attributed to Tang, F..

48 records · Page 3Linked to original sources

bioRxiv2020

Surveying Brain Tumor Heterogeneity by Single-Cell RNA Sequencing of Multi-sector Biopsies

Brain tumors are among the most challenging human tumors for which the mechanisms driving progression and heterogeneity remain poorly understood. We combined single-cell RNA-seq with multisector biopsies to sample and analyze single-cell expression profiles of gliomas from 13 Chinese patients. After classifying individual cells, we generated a spatial and temporal landscape of glioma that revealed the patterns of invasion between the different sub-regions of gliomas. We also used single-cell inferred CNVs and pseudotime trajectories to inform on the crucial branches that dominate tumor progression. The dynamic cell components of the multi-region biopsy analysis allowed us to spatially deconvolute with unprecedented accuracy the transcriptomic features of the core and those of the periphery of glioma at single cell level. Through this rich and geographically detailed dataset, we were also able to characterize and construct the chemokine and chemokine receptor interactions that exist among different tumor and non-tumor cells. This study provides the first spatial-level analysis of the cellular states that characterize human gliomas. It also presents an initial molecular map of the crosstalks between glioma cells and the surrounding microenvironment with single cell resolution.

genomics↗

bioRxiv2019

A MAP of tumor-host interactions in glioma at single cell resolution

Single-cell RNA sequencing is the reference technique to characterize the heterogeneity of tumor microenvironment and can be efficiently used to discover cross-talk mechanisms between immune cells and cancer cells. We present a novel method, single cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand-receptor interactions in glioma using six publicly available human glioma datasets encompassing 71 patients. We provide a comprehensive map of the signalling mechanisms between malignant cells and non-malignant cells in glioma uncovering potential novel therapeutic targets.

bioinformatics↗

bioRxiv2019

Rapid pacing by circulating traveling waves improves maturation of hiPSC-derived cardiomyocytes in self-organized tissue ring

Directed differentiation methods allow acquisition of high-purity cardiomyocytes (CMs) differentiated from human induced pluripotent stem cells (hiPSCs); however, their immaturity characteristic limits their application for drug screening and regenerative therapy. The rapid electrical pacing of cardiomyocytes have been used for efficiently promoting the maturation of cardiomyocytes, here we describe a simple device in modified culture plate on which hiPSC-derived CMs (hiPSC-CMs) can form three-dimensional self-organized tissue rings (SOTRs). Using calcium imaging, we show that within the ring, traveling waves (TWs) of action potential spontaneously originated and ran robustly at a frequency up to 4 Hz. After 2 weeks, SOTRs with TW training showed matured features including structural organization, increased cardiac-specific gene expression, enhanced Ca2+-handling properties, an increased oxygen-consumption rate, and enhanced contractile force. We subsequently used a mathematical model to interpret the origination, propagation, and long-term behavior of the TWs within the SOTRs. This new idea for spontaneous hiPSC-CM maturation also has potential for pacing the electrical excitable cells such as neuron and retina cells for various applications.

bioengineering↗

bioRxiv2019

Enhancing single-cell cellular state inference by incorporating molecular network features

In biological systems, genes function in conjunction rather than in isolation. However, traditional single-cell RNA-seq (scRNA-seq) analyses heavily rely on the transcriptional similarity of individual genes, ignoring the inherent gene-gene interactions. Here, we present SCORE, a network-based method, which incorporates the validated molecular network features to infer cellular states. Using real scRNA-seq datasets, SCORE outperforms existing methods in accuracy, robustness, scalability, data integration and removal of batch effect. When applying SCORE to a newly generated human ileal scRNA-seq dataset, we identified several novel stem/progenitor clusters, including a Cripto-1+ cluster. Moreover, two distinct groups of goblet cells were identified and only one of them tended to secrete mucus. Besides, we found that the recently identified BEST4+OTOP2+ microfold cells also highly expressed CFTR, which is different from their colonic counterparts. In summary, SCORE enhances cellular state inference by simulating the dynamic changes of molecular networks, providing more biological insights beyond statistical interpretations.

bioinformatics↗

bioRxiv2019

Adopting tipping-point theory to transcriptome profiles unravels disease regulatory trajectory

Differentiation involves bifurcations between discrete cell states, each defined by a distinct gene expression profile. Single-cell RNA profiling allows the detection of bifurcations. However, while current methods capture these events, they do not identify characteristic gene signals. Here we show that BioTIP - a tipping-point theory-based analysis - can accurately, robustly, and reliably identify critical transition signals (CTSs). A CTS is a small group of genes with high covariance in expression that mark the cells approaching a bifurcation. We validated its accuracy in the cardiogenesis with known a tipping point and demonstrated the identified CTSs contain verified differentiation-driving transcription factors. We then demonstrated the application on a published mouse gastrulation dataset, validated the predicted CTSs using independent in-vivo samples, and inferred the key developing mesoderm regulator Etv2. Taken together, BioTIP is broadly applicable for the characterization of the plasticity, heterogeneity, and rapid switches in developmental processes, particularly in single-cell data analysis. HighlightsO_LIIdentifying significant critical transition signals (CTSs) from expression noise C_LIO_LIA significant CTS contains or is targeted by key transcription factors C_LIO_LIBioTIP identifies CTSs accurately and independent of trajectory topologies C_LIO_LISignificant CTSs reproducibly indicate bifurcations across datasets C_LI

systems biology↗

bioRxiv2019

Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering

Gene expression in response to external stimuli underlies a variety of fundamental cellular processes. However, how the transcription machinery is regulated under these scenarios is largely unknown. Here, we discover a novel role of nuclear actin in inducible transcriptional regulation using next-generation transcriptome sequencing and super-resolution microscopy. The RNA-seq data reveal that nuclear actin is required for the establishment of the serum-induced transcriptional program. Using super-resolution imaging, we found a remarkable enhancement of RNA polymerase II (Pol II) clustering upon serum stimulation and this enhancement requires the presence of nuclear actin. To study the molecular mechanisms, we firstly observed that Pol II clusters co-localized with the serum-response genes and nuclear actin polymerized in adjacent to Pol II clusters upon serum stimulation. Furthermore, N-WASP and Arp2/3 are reported to interact with Pol II, and we demonstrated N-WASP is required for serum-enhanced Pol II clustering. Importantly, using an optogenetic tool, we revealed that N-WASP phase-separated with the carboxy-terminal domain of Pol II and nuclear actin. In addition to serum stimulation, we found nuclear actin also essential in enhancing Pol II clustering upon interferon-{gamma} treatment. Taken together, our work unveils nuclear actin promotes the formation of transcription factory on inducible genes, acting as a general mechanism underlying the rapid response to environmental cues.

cell biology↗

bioRxiv2019

3D association of ER, PR and Her2 at protein levels to aid sub-grouping of breast cancer patients in routine clinical practice

Treatments of patients with solid tumors frequently rely on the relative and semi-quantitative assessment of tissue protein biomarkers by immunohistochemistry (IHC). The perspective of transition to absolute and quantitative assessment of tissue biomarkers is hindered by lack of a suitable method, especially for Formalin Fixed Paraffin Embedded (FFPE) tissues. In this study, we explored the feasibility of Quantitative Dot Blot (QDB) method as a universal platform to quantitate tissue biomarkers as absolute and continuous variables in FFPE samples by measuring unprecedentedly the protein levels of Estrogen Receptor (ER), Progesterone Receptor (PR), Her2 and Ki67 simultaneously in 1048 FFPE samples. When using measured Her2, ER and PR levels as coordinates to develop 3D scatterplot, we observed a distinct distribution pattern of the samples with natural segregation of three groups as the likely phenotypical projection of known intrinsic subtypes. Thus, we have achieved a major milestone in this transition by identifying the first practice method for daily clinical practice, and one clinical usage in 3D subtyping of samples for prediction and prognosis. This study may serve as basis for a new field of Quantitative Diagnosis where diagnosis, prognosis and prediction are derived from database analysis of protein biomarkers as absolute and continuous variables.

pathology↗

bioRxiv2019

Numerical simulation for behind armor blunt trauma of human torso under non-penetrating ballistic impact

A human torso finite element model with high bio-fidelity was developed to study the behind armor blunt trauma (BABT) of pistol cartridge on human torso with bulletproof composite structure (BCS) and the effect of buffer layer (expandable polyethylene, EPE) on BABT. The bulletproof structure was made of multilayered composite of aluminum alloy (AlSi10Mg) and thermoplastic polyurethanes (TPU), and the ANSYS/LS-DYNA software was used to simulate the blunt ballistic impact process of pistol cartridge on human torso. Results indicated that the BCS could resist the shooting speed of 515 m/s without being broken. During the process of pistol cartridge shooting the BCS, the energy of pistol cartridge was transmitted to the human organs through the BCS, thereby causing human injury. Moreover, the mechanical response parameters of various organs were determined by the distance between the human organs and the impact point. The sternal fracture and liver rupture were not produced based on the threshold stress of sternum and liver injury, no matter whether the buffer layer was added or not. According to the Axelsson injury model, a slight to moderate injury was created when there was no buffer layer, but the injury level was trace to slight caused by the buffer layer with thickness of 1.0 mm, and the buffer layer with thickness of 2.5 mm and 5.0 mm caused subtle BABT. It was concluded that the buffer layer could effectively reduce the BABT, and the reduction was related to the thickness of the buffer layer. This study reveals the mechanism of the BABT, which can provide a theoretical basis for the design of the bulletproof structure and the evaluation of structural bulletproof performance and protection performance.

bioengineering↗

bioRxiv2019

Developing a routine lab test for absolute quantification of Her2 in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tissues using Quantitative Dot Blot (QDB) method

While the transition from current prevailing method of relative and semi-quantitative assessment of solid tumor biomarkers to their absolute quantitation promises improved objectivity, consistency and accuracy in daily clinical practice, this transition is hindered by lacking of suitable technique, especially for Formalin Fixed Paraffin Embedded (FFPE) tissue samples. In this retrospective study, Quantitative Dot Blot (QDB) method was adopted to measure Her2 levels absolutely and quantitatively at protein level using 2X15 m FFPE breast cancer tissue slices collected sequentially and non-selectively from local hospital. Her2 levels measured from 332 samples using two diagnostic antibodies respectively were strongly correlated (r=0.963, p=0.0000). When the result was evaluated with results from IHC or FISH analysis using Receiving Operating Characteristics (ROC) analysis, we were able to achieve 100% sensitivity (95% CI: 95.6% to 100%) and 99.3% specificity (95% CI: 96.14% to 99.98%) with results from IHC analysis using 0.267 nmole/g as cutoff, and 93.02% sensitivity (95%CI: 80.94% to 98.54%) and 93.68% specificity (95% CI: 86.76% to 97.65%) with results from FISH analysis using 0.261 nmole/g as cutoff. Thus, QDB method is demonstrated to provide objective and consistent assessment of Her2 levels in FFPE samples with comparable results from both IHC and FISH analyses. It is also the first method to achieve absolute quantitation of tissue biomarkers in FFPE samples to meet daily clinical need.

pathology↗

bioRxiv2018

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2

Rigorous exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here using multiple knockout mouse models and single-cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2as has a key, complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function, largely independent of Hand2as transcription and transcripts. Full-length deletion of Hand2as in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, resulting in profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose a cis-functional role for the Hand2as locus in dampening HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the need for complementary genetic and single-cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.\n\nImpact statementThe long noncoding RNA Hand2as critically controls the precise expression of its neighboring gene HAND2, thereby balancing cardiac lineages and expression programs that are essential for heart development and function.

developmental biology↗

bioRxiv2018

Single-cell RNA-seq identifies a reversible epithelial-mesenchymal transition in abnormally specified epithelia of p63 EEC syndrome

Mutations in transcription factor p63 are associated with developmental disorders that manifest defects in stratified epithelia including the epidermis. The underlying cellular and molecular mechanism is however not yet understood. We established an epidermal commitment model using human induced pluripotent stem cells (iPSCs) and characterized differentiation defects of iPSCs derived from ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome patients carrying p63 mutations. Transcriptome analyses revealed distinct step-wise cell fate transitions during epidermal commitment; from multipotent simple epithelium to basal stratified epithelia, and ultimately to the mature epidermal fate. Differentiation defects of EEC iPSCs caused by mutant p63 occurred during the specification switch from the simple epithelium to the basal stratified epithelial fate. Single-cell transcriptome and pseudotime analyses identified signatures of embryonic epithelial-mesenchymal transition (EMT) associated with the deviated commitment route of EEC iPSCs. Repressing mesodermal activation reversed the EMT and enhanced epidermal commitment. Our findings demonstrate that p63 is required for specification of stratified epithelia, probably by repressing embryonic EMT during epidermal commitment. This study provides insights into disease mechanisms underlying stratified epithelial defects caused by p63 mutations and suggests potential therapeutic strategies for the disease.\n\nSignificance statementMutations in p63 cause several developmental disorders with defects of epithelial related organs and tissues including the epidermis. Our study is to dissect the unknown cellular and molecular pathomechanism. We utilized human induced pluripotent stem cells (iPSCs) derived from ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome patients carrying p63 mutations and studied transcriptome changes during differentiation of these cells to epidermal cells. Our analyses showed that the specification of the proper epithelial cell fate was affected by p63 EEC mutations, with an abnormal embryonic epithelial-mesenchymal transition (EMT). Repressing mesodermal activation reversed the EMT and enhanced epidermal commitment. This study provides insights into disease mechanisms associated with p63 mutations and suggests potential therapeutic strategies.

developmental biology↗

bioRxiv2018

Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice

Xist is the master regulator of X chromosome inactivation (XCI). In order to further understand the Xist locus in reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) and in somatic cell nuclear transfer (SCNT), we tested transcription-factor-like effectors (TALE)-based designer transcriptional factors (dTFs), which were specific to numerous regions at the Xist locus. We report that the selected dTF repressor 6 (R6) binding the intron 1 of Xist, which did not affect Xist expression in mouse embryonic fibroblasts (MEFs), substantially improved the iPSC generation and the SCNT preimplantation embryo development. Conversely, the dTF activator targeting the same genomic region of R6 decreased iPSC formation, and blocked SCNT-embryo development. These results thus uncover the critical requirement for the Xist locus in epigenetic resetting, which is not directly related to Xist transcription. This may provide a unique route to improving the reprogramming.

developmental biology↗