Biology subjects

Tang, F.

Publications and source records attributed to Tang, F..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert tumor microenvironment and confers resistance to immunotherapy

Immune checkpoint blockade (ICB) has demonstrated clinical success in "inflamed" tumors with significant T-cell infiltrates, but tumors with an immune-desert tumor microenvironment (TME) fail to benefit. The tumor cell-intrinsic molecular mechanisms of the immune-desert phenotype remain poorly understood. Here, we demonstrate that inactivation of the Polycomb-repressive complex 2 (PRC2) core components, EED or SUZ12, a prevalent genetic event in malignant peripheral nerve sheath tumor (MPNST) and sporadically in other cancer types, drives a context-dependent immune-desert TME. PRC2 inactivation reprograms the chromatin landscape that leads to a cell-autonomous shift from primed baseline signaling-dependent cellular responses (e.g., interferon {gamma}) to PRC2-regulated development and cellular differentiation transcriptional programs. Further, PRC2 inactivation reprograms the TME, leads to diminished tumor immune infiltrates and immune evasion through reduced chemokine production and impaired antigen presentation and T-cell priming, and confers ICB primary resistance through blunted T-cell recruitment in vivo. We demonstrate that strategies that enhancing innate immunity via intratumoral delivery of inactivated modified vaccinia virus Ankara (MVA) leads to increased tumor immune infiltrates and sensitizes PRC2-loss tumors to ICB. Our results provide novel molecular mechanisms of context-dependent dysfunctional epigenetic reprogramming that underline the immune-desert phenotype in MPNST and other cancers with PRC2 inactivation. Importantly, our findings highlight genetic-inactivation of PRC2 as a novel context-dependent ICB therapeutic resistance biomarker in cancer, and caution that therapeutic strategies that non-selectively target PRC2 in the host may lead to undesirable context-dependent immune evasion and ICB resistance in tumors. Our studies also point to intratumoral delivery of immunogenic therapeutic viruses as an initial strategy to modulate the immune-desert TME and capitalize on the clinical benefit of ICB.

cancer biology↗

bioRxiv2022

Machine-Learning-Based Olfactometry: Odor Descriptor Clustering Analysis for Olfactory Perception Prediction of Odorant Molecules

Although gas chromatography/olfactometry (GC/O) has been employed as a powerful analytical tool in odor measurement, its application is limited by the variability, subjectivity, and high cost of the trained panelists who are used as detectors in the system. The advancements in data-driven science have made it possible to predict structure-odor-relationship (SOR) and thus to develop machine-learning-based olfactometry (ML-GCO) in which the human panelists may be replaced by machine learning models to obtain the sensory information of GC-separated chemical compounds. However, one challenge remained in ML-GCO is that there are too many odor descriptors (ODs) being used to describe the sensory characteristics of odorants. It is impractical to build a corresponding model for each OD. To solve this issue, we propose a SOR prediction approach based on odor descriptor clustering. 256 representative ODs are firstly classified into 20 categories using a co-occurrence Bayesian embedding model. The categorization effect is explained according to the semantic relationships using a pre-trained Word2Vec model. Various molecular structure features including molecularly parameters, molecular fingerprints, and molecular 2D graphic features extracted by convolutional neural networks, are employed to predict the aforementioned odor categories. High prediction accuracies (Area under ROC curve was 0.800{+/-}0.004) demonstrate the rationality of the proposed clustering scenario and molecular feature extraction. This study makes the ML-GCO models much closer to the practical application since they can be expected as either an auxiliary system or complete replacement of human panelists to perform the olfactory evaluation.

molecular biology↗

bioRxiv2022

Odorant molecular feature mining by diverse deep neural networks for prediction of odor perception categories

The use of an artificial intelligence (AI)-based prediction model of the structure-odor relationship (SOR) has shown great potential in the replacement of human panelists in gas chromatography-olfactometry (GCO). However, the Al-based GCO encounters issues such as poor accuracy, generalization, and practicality, owning to the insufficient feature extraction of odorant molecular structure. The purpose of this study is to the prediction of odor perception categories based on the odorant structure feature extraction by diverse deep neural networks, including molecular graphic convolution neural network (MG-CNN), molecular graph transformer neural network, and atom interaction neural networks. The results of the performance comparison of different feature extractors demonstrate that the MG-CNN model produces the highest accuracy and thus may be most suitable for the SOR prediction. It is hoped that the proposed method can be applied in practice as an auxiliary tool of GCO for the sensory evaluation of key compounds in food ingredients. HighlightsO_LIDifferent deep neural networks were used to predict categorized odor descriptors. C_LIO_LIEnd-to-end-based representation learning was performed for molecular feature extraction. C_LIO_LIMolecular graphs with pre-training of convolution neural networks was most accurate. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/488977v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@10495a2org.highwire.dtl.DTLVardef@1fbf27eorg.highwire.dtl.DTLVardef@1ed3664org.highwire.dtl.DTLVardef@8e1383_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8

Non-coding RNAs exert diverse functions in many cell types. In addition to transcription factors from coding genes, non-coding RNAs may also play essential roles in shaping and directing the fate of germ cells. Here, we report the presence of many long non-coding RNAs (lncRNAs) which were specifically expressed in the germ cells during human gonadal development by single-cell profiling of the reported datasets, and the functional characterization of one divergent lncRNA, LNC1845. Comprehensive bioinformatic analysis of these lncRNAs indicates that divergent lncRNAs occupied the majority of female and male germ cells. Integrating lncRNA expression into the bioinformatic analysis also enhances the cell-type classification of female germ cells. Functional dissection using in vitro differentiation of human pluripotent stem cells to germ cells revealed the regulatory role of LNC1845 on a transcription factor essential for ovarian follicle development, LHX8, by modulating the levels of histone modifications, H3K4me3 and H3K27Ac. Hence, this study provides a comprehensive analysis of lncRNAs in developing germ cells and elucidates how a lncRNA function as a cis regulator during human germ cell development. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/486705v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@31290forg.highwire.dtl.DTLVardef@17ec505org.highwire.dtl.DTLVardef@1b8cd0dorg.highwire.dtl.DTLVardef@19e4de3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIlncRNAs are expressed at significantly higher levels in both male and female germ cells than in somatic cells during human gonadal development. C_LIO_LIDivergent lncRNAs are enriched in the female meiotically and male mitotically arrested germ cells. C_LIO_LILNC1845 regulates the transcriptional expression of LHX8 by modulating H3K4me3 and H3K27Ac levels. C_LI

developmental biology↗

bioRxiv2021

PSEA: A phenotypic similarity ensemble approach for prioritizes candidate genes to aid mendelian disease diagnosis

MotivationNext-generation sequencing (NGS) is increasingly applied to the molecular diagnosis of genetic disorders. However, challenges for the interpretation of NGS data remain given the massive number of variants produced by NGS. Careful assessment is required to identify the most likely disease-causing variants that best match the patients clinical phenotypes, which is highly experience-dependent and of low cost-effectiveness. ResultsThe human phenotype ontology (HPO) together with the information content (IC) are widely used for phenotypic similarity evaluation. Here, we introduce PSEA, a new phenotypic similarity evaluation tool capable of quantifying groups of HPO terms unbiasedly. By comparing with other methods, PSEA show optimal performance and show a higher tolerance to phenotypic noise or incompleteness. We also developed a web server for disease-causing gene prioritization and HPO-gene weighted linkage visualization. AvailabilitySource code and Web service are free available at https://github.com/zhonghua-wang/psea and https://phoenix.bgi.com/psea, respectively. Contactwangzhonghua@genomics.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

Origin, specification and differentiation of a rare supporting-like lineage in the developing mouse gonad

Gonadal sex determination represents a unique model for studying cell fate decisions. However, a complete understanding of the different cell lineages forming the developing testis and ovary remains elusive. Here, we investigated the origin, specification and subsequent sex-specific differentiation of a previously uncharacterized population of supporting-like cells (SLC) in the developing mouse gonads. The SLC lineage is closely related to the coelomic epithelium and specified as early as E10.5, making it the first somatic lineage to be specified in the bipotential gonad. SLC progenitors are localized within the genital ridge at the interface with the mesonephros and initially co-express Wnt4 and Sox9. SLCs become sexually dimorphic around E12.5, progressively acquire a Sertoli- or granulosa-like identity and contribute to the formation of the rete testis and rete ovarii. Finally, we found that WNT4 is a crucial regulator of the SLC lineage and is required for the formation of the rete testis. TeaserDescription of an uncharacterized multipotent gonadal cell lineage involved in testis and ovary development

developmental biology↗

bioRxiv2021

Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2

The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 is an attractive target for COVID-19 vaccine developments, which naturally exists in a trimeric form. Here, guided by structural and computational analyses, we present a mutation-integrated trimeric form of RBD (mutI tri-RBD) as a broadly protective vaccine candidate, in which three RBDs were individually grafted from three different circulating SARS-CoV-2 strains including the prototype, Beta (B.1.351) and Kappa (B.1.617). The three RBDs were then connected end-to-end and co-assembled to possibly mimic the native trimeric arrangements in the natural S protein trimer. The recombinant expression of the mutI tri-RBD, as well as the homo-tri-RBD where the three RBDs were all truncated from the prototype strain, by mammalian cell exhibited correct folding, strong bio-activities, and high stability. The immunization of both the mutI tri-RBD and homo-tri-RBD plus aluminum adjuvant induced high levels of specific IgG and neutralizing antibodies against the SARS-CoV-2 prototype strain in mice. Notably, regarding to the "immune-escape" Beta (B.1.351) variant, mutI tri-RBD elicited significantly higher neutralizing antibody titers than homo-tri-RBD. Furthermore, due to harboring the immune-resistant mutations as well as the evolutionarily convergent hotspots, the designed mutI tri-RBD also induced strong broadly neutralizing activities against various SARS-CoV-2 variants, especially the variants partially resistant to homo-tri-RBD. Homo-tri-RBD has been approved by the China National Medical Products Administration to enter clinical trial (No. NCT04869592), and the superior broad neutralization performances against SARS-CoV-2 support the mutI tri-RBD as a more promising vaccine candidate for further clinical developments.

immunology↗

bioRxiv2021

Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference

Nowadays the advanced technology for single-cell transcriptional profiling enables people to routinely generate thousands of single-cell expression data, in which data from different cell states or time points are derived from different samples. Without transferring such time-stamped cross-sectional data into pseudo-time series, we propose COSLIR (COvariance restricted Sparse LInear Regression) for directly reconstructing the gene regulatory networks (GRN) that drives the cell-state transition. The differential gene expression between adjacent cell states is modeled as a linear combination of gene expressions in the previous cell state, and the GRN is reconstructed through solving an optimization problem only based on the first and second moments of the sample distributions. We apply the bootstrap strategy as well as the clip threshold method to increase the precision and stability of the estimation. Simulations indicate the perfect accuracy of COSLIR in the oracle case as well as its good performance and stability in the sample case. We apply COSLIR separately to two cell lineages in a published single-cell qPCR dataset during mouse early embryo development. Nearly half of the inferred gene-gene interactions have already been experimentally reported and some of them were even discovered during the past decade after the dataset was published, indicating the power of COSLIR. Furthermore, COSLIR is also evaluated on several single-cell RNA-seq datasets, and the performance is comparable with other methods relying on the pseudo-time reconstruction.

bioinformatics↗

bioRxiv2021

The PD-L1 and TLR7 dual-targeting nanobody-drug conjugate exerts potent antitumor efficacy by orchestrating innate and adaptive immune responses

A variety of tumors are insensitive to immune checkpoint blockade (ICB) therapy. We propose that ICB therapy alone is insufficient to fully reactivate antitumor T cells, while effective mobilization of antigen-presenting cells (APCs) to assist adaptive immune cell activation can lead to potent antitumor effects with broad responsiveness. The Toll-like receptor 7 (TLR7) agonist SZU-101 we developed can induce the innate immune response against tumors and increase the immunogenicity of tumors. Interestingly, SZU-101-induced upregulation of programmed death ligand 1 (PD-L1) expression in tumor tissues can further enhance the response rate of the PD-L1 antibody. In addition, PD-L1 nanobodies have better solid tumor penetration ability, and because of this ability, they can be used to precisely deliver SZU-101 to tumor tissues. Therefore, a PD-L1 and TLR7 dual-targeting nanobody-drug conjugate (NDC), a novel drug molecule, was developed. We found that TLR7 agonists and PD-L1 nanobodies act synergistically and that NDC treatment reshapes the tumor immune microenvironment, activates both innate and adaptive immune cells, and exerts antitumor effects in both "hot" and "cold" tumors primarily through CD8+ T cells and natural killer (NK) cells. Our data show that a PD-L1 and TLR7 dual-targeting NDC can exhibit potent antitumor efficacy by orchestrating innate and adaptive immune responses and shows good prospects for clinical development. One Sentence SummaryBased on results showing that TLR7 agonists and PD-L1 nanobodies exert synergistic antitumor effects, a PD-L1 and TLR7 dual-targeting nanobody-drug conjugate that we developed shows good prospects for clinical development because it can orchestrate innate and adaptive immune responses, reshape the tumor immune microenvironment, and exert potent antitumor effects against both "hot" and "cold" tumors.

immunology↗

bioRxiv2021

CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity

Safe, economical and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and halt the pandemic. We have constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains two immunodominant peptides screened from receptor-binding domain (RBD) and is fully chemically synthesized. And the vaccine has optimized nanoemulsion formulation, outstanding stability and safety. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of RBD-specific and protective neutralizing antibodies (NAbs), which were also effective to RBD mutations. CoVac501 was found to elicit the increase of memory T cells, antigen-specific CD8+ T cell responses and Th1-biased CD4+ T cell immune responses in NHPs. More importantly, the sera from the immunized NHPs can prevent infection of live SARS-CoV-2 in vitro. One-Sentence SummaryA novel SARS-CoV-2 vaccine we developed, CoVac501, which is a fully chemically synthesized and self-adjuvanting peptides conjugated with TLR7 agonists, can induce high-efficient humoral and cellular immune responses against SARS-CoV-2.

immunology↗

bioRxiv2020

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19. HIGHLIGHTSO_LILarge-scale scRNA-seq analysis depicts the immune landscape of COVID-19 C_LIO_LILymphopenia and active T and B cell responses coexist and are shaped by age and sex C_LIO_LISARS-CoV-2 infects diverse epithelial and immune cells, inducing distinct responses C_LIO_LICytokine storms with systemic S100A8/A9 are associated with COVID-19 severity C_LI

genomics↗

bioRxiv2020

Chromatin accessibility profiles of castration-resistant prostate cancers reveal novel subtypes and therapeutic vulnerabilities

In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR)-dependence due to lineage plasticity, which has become more prevalent, leads to clinically highly aggressive tumors with few therapeutic options and is mechanistically poorly defined. To identify the master transcription factors (TFs) of CRPC in a subtype-specific manner, we derived and collected 29 metastatic human prostate cancer organoids and cell lines, and generated ATAC-seq, RNA-seq and DNA sequencing data. We identified four subtypes and their master TFs using novel computational algorithms: AR-dependent; Wnt-dependent, driven by TCF; neuroendocrine, driven by ASCL1 and NEUROD1 and stem cell-like (SCL), driven by the AP-1 family. The transcriptomic signatures of these four subtypes enabled the classification of 370 patients. We find that AP-1 co-operates with the inhibitable YAP/TAZ/TEAD pathway in the SCL subtype, the second most common group of CRPC tumors after AR-dependent. Together, this molecular classification reveals new drug targets and can potentially guide therapeutic decisions.

cancer biology↗

bioRxiv2020

Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

By circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs. HighlightsO_LIGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetus C_LIO_LIDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DT C_LIO_LIMeasuring chromatin open regions in single cells with high detectability by METATAC C_LIO_LIIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM C_LI

genomics↗

bioRxiv2020

DNA methylation is indispensable for leukemia inhibitory factor dependent embryonic stem cells reprogramming

Naive pluripotency can be maintained by the 2i/LIF supplements (CHIR99021, PD0325901 and LIF), which primarily affect canonical WNT, FGF/ERK, and JAK/STAT3 signaling. However, whether one of these tripartite supplements alone is sufficient to maintain naive self-renewal remain unclear. Here we show that LIF alone is sufficient to induce reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs) to ESCs with hypermethylated state (L-ESCs). In vitro, upon withdrawal of 2i, 2i/L-ESCs overcome the epigenetic barrier and DNA hypermethylated, which accompanies transcriptional changes and subsequent establishment of epigenetic memory. Global transcriptome features also show that L-ESCs are close to 2i/L-ESCs and in a stable state between naive and primed pluripotency. Notably, our results demonstrate that DNA methylation was indispensable for LIF-dependent mouse ESCs reprogramming and self-renew. LIF-dependent ESCs reprogramming efficiency is significantly increased in serum treatment and reduced in Dnmt3a or Dnmt3l knockout ESCs. Importantly, unlike epiblast and EpiSCs, L-ESCs contribute to somatic tissues and germ cells in chimaeras. Such simple culture system of ESCs is more conducive to clarify the molecular mechanism of ESCs in vitro culture. SignificanceEmbryonic stem cell (ESCs) exhibit naive pluripotency which reflects their ability to contribute to all embryonic lineages upon injection into blastocyst. ESCs were originally derived by co-culture with feeder cells and fetal calf serum. In this manuscript, we took a detailed approach to dissect the roles of LIF alone in ESC reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs). Here, for the first time, we derived stable hypermethylated pluripotent ESCs under culture of LIF alone (L-ESCs). We further assessed L-ESCs properties both in vitro and in vivo, and provide molecular insights to the mechanism which allows LIF alone to maintain pluripotency and a hypermethylated state. We believe these findings are novel and valuable for future ESCs study.

cell biology↗

bioRxiv2020

Somatic cell-derived BMPs induce male germ cell meiosis initiation during embryonic stage via regulating Dazl expression

Germ cell fate is believed to be determined by the signaling from sexually differentiated somatic cell. However, the molecular mechanism remains elusive. In this study, ectopic initiation of meiosis in male germ cells was observed during embryonic stage by over-activating CTNNB1 in Sertoli cells. Somatic cell transcriptome and single germ cell RNA-seq analysis indicated that TGF-{beta} signaling was activated after CTNNB1 over-activation. In vitro and in vivo experiments confirmed somatic cell-derived BMPs played crucial roles in germ cell meiosis initiation. Further studies revealed that Dazl was significantly increased in germ cells of CTNNB1 over-activated testes and induced by BMP signaling. DNMT3a and DNA methylation was also reduced in germ cells of CTNNB1 over-activated testes and increased by BMP signaling inhibitor treatment. Taken together, this study demonstrates that germ cell fate could be reprogrammed after sex determination. BMP signaling pathway is involved in germ cell meiosis initiation via up-regulating Dazl expression.

developmental biology↗

bioRxiv2020

Genome-wide Identification and Analysis of Enhancer Regulated microRNAs Across 31 Human Tissues

Enhancers are cis-regulatory DNA elements that positively regulate the transcription of target genes in a tissue-specific manner and dysregulation in various diseases such as cancer. Recent studies showed that enhancers can regulate miRNAs and participate in the biological synthesis of miRNAs. However, the network of enhancer-regulated miRNAs across multiple cancers is still unclear. Here, a total of 2,418 proximal enhancer-miRNA interactions and 1,280 distal enhancer-miRNA interactions were identified through the integration of genomic distance, co-expression, and 3D genome data in 31 cancers. The results showed that both proximal and distal interactions exhibited significant tissue-specific feature and there was a noteworthy positive correlation between the expression of miRNA and the number of regulated enhancers in most tissues. Furthermore, it was found that there was a high correlation between the formation of enhancer-miRNA pairs and the expression of eRNAs whether in distal or proximal regulation. The characteristics analysis showed that miRes (enhancers that regulated miRNAs) and non-miRes presented significant differences in sequence conservation, GC content and histone modification signatures. Notably, GC content, H3K4me1, H3K36me3 were present differently between distal regulation and proximal regulation, suggesting they might participate in chromosome looping of enhancer-miRNA interactions. Finally, we introduced a case study, enhancer: chr1:1186391-1186507[~]miR-200a was highly relevant to the survival of thyroid cancer patients and a cis-eQTL SNP on enhancer affected the expression TNFRSF18 gene as a tumor suppressor.

bioinformatics↗

bioRxiv2020

Lineage reversion drives WNT independence in intestinal cancer

The WNT pathway is a fundamental regulator of intestinal homeostasis and hyperactivation of WNT signaling is the major oncogenic driver in colorectal cancer (CRC). To date, there are no described mechanisms that bypass WNT dependence in intestinal tumors. Here, we show that while WNT suppression blocks tumor growth in most organoid and in vivo CRC models, the accumulation of CRC-associated genetic alterations enables drug resistance and WNT-independent growth. In intestinal epithelial cells harboring mutations in KRAS or BRAF, together with disruption of p53 and SMAD4, transient TGF{beta} exposure drives YAP/ TAZ-dependent transcriptional reprogramming and lineage reversion. Acquisition of embryonic intestinal identity is accompanied by a permanent loss of adult intestinal lineages, and long-term WNT-independent growth. This work delineates genetic and microenvironmental factors that drive WNT inhibitor resistance, identifies a new mechanism for WNT-independent CRC growth and reveals how integration of associated genetic alterations and extracellular signals can overcome lineage-dependent oncogenic programs.

cancer biology↗

bioRxiv2020

Dissecting endothelial to haematopoietic stem cell transition by single-cell transcriptomic and functional analyses

Haematopoietic stem cells (HSCs) in adults are believed to be born from hemogenic endothelial cells (HECs) in mid-gestational mouse embryos. Due to rare and transient nature, the HSC-competent ECs have never been stringently identified and accurately captured, let alone their genuine vasculature precursors. Here, we firstly used high-precision single-cell transcriptomics to unbiasedly examine relevant EC populations at continuous developmental stages and transcriptomically identified putative HSC-primed HECs. Combining computational prediction and in vivo functional validation, we precisely captured HSC-competent HECs by newly constructed Neurl3-EGFP reporter mouse model, and realized enrichment further by surface marker combination. Surprisingly, endothelial-haematopoietic bi-potential was rarely but reliably witnessed in culture of single HECs. Noteworthy, primitive vascular ECs experienced two-step fate choices to become HSC-primed HECs, resolving several previously observed contradictions. Taken together, comprehensive understanding of endothelial evolutions and molecular programs underlying HSC-primed HEC specification in vivo will facilitate future investigations directing HSC production in vitro.

developmental biology↗