Biology subjects

Tam, P. P. L.

Publications and source records attributed to Tam, P. P. L..

9 recordsLinked to original sources

bioRxiv2025

Neural crest cell derived DKK1 modulates Wnt signalling in the second heart field to orchestrate cardiac outflow tract development

Heart morphogenesis is highly complex, and depends on the generation of diverse cell types which interact with each other in an orchestrated manner to remodel the primitive heart tube into a functional organ. Cardiac outflow tract formation critically depends on continued contribution of cardiac progenitor cells from the anterior second heart field to ensure proper growth of the outflow tract. Prior to entering the outflow tract, neural crest cells migrate in close apposition to the second heart field and may play important roles in regulating second heart field growth dynamics, however the molecular mechanisms by which neural crest cells interact with the second heart field have remained elusive. Here, we discover that neural crest cells are a primary source of Dickkopf1 (DKK1), a secreted Wnt signalling inhibitor, which modulates Wnt signalling activity in the second heart field to impose a balance between progenitor maintenance and differentiation. Further, we identify the ubiquitin ligase NEDD4 as a critical regulator of DKK1 levels, with disruption of Nedd4 activity leading to outflow tract defects. In the context of disease pathogenicity, we show a novel human congenital heart disease variant of NEDD4 has lost the ability to ubiquitinate DKK1, and is associated with heart defects in a mouse model of the genetic variant. Our findings point to an unexpected role for neural crest cells acting as a rheostat of Wnt signalling activity in cardiac progenitors, identifying a new molecular pathway underpinning correct outflow tract morphogenesis, and a new causative factor of congenital heart disease.

developmental biology↗

bioRxiv2024

Characterization of the mesendoderm progenitors in the gastrulating mouse embryo

A population of putative mesendoderm progenitor cells that can contribute cellular descendants to both mesoderm and endoderm lineages is identified. These progenitor cells are localized to the anterior primitive streak and the adjacent epiblast of E7.0-E7.5 mid-to late-gastrula stage embryos. Lineage tracing in vivo revealed that putative mesendoderm progenitors that are marked by Mixl1 and Mesp1 activity contribute descendants to the endoderm layer. Analysis of the role of Mixl1 transcription factor in endoderm differentiation of the mouse epiblast stem cells revealed the choice for endoderm or mesoderm cell fate depends on the timing of activation of Mixl1 upon exit from pluripotency, suggesting Mixl1 function may underpin the divergence of the mesendoderm progenitor to mesoderm and endoderm lineages. The knowledge gained on the spatial, temporal, and lineage attribute of mesendoderm progenitors enriches our mechanistic understanding of germ layer allocation and endoderm differentiation of mesendoderm progenitor in embryonic development and lineage allocation of primed state pluripotent stem cells in vitro.

developmental biology↗

bioRxiv2024

Unraveling the Role of MIXL1 Activation in Endoderm Differentiation of Isogenic Human Induced Pluripotent Stem Cells

Human induced pluripotent stem cells (hiPSC) possess the ability to differentiate into a multitude of cell and tissue types but display heterogeneous propensity of differentiation into specific lineage. Characterization of the transcriptome of eleven hiPSC lines showed that activation of MIXL1 at the early stage of stem cell differentiation correlated with higher efficacy in generating definitive endoderm and advancing differentiation and maturation of endoderm derivatives. Enforced expression of MIXL1 in the endoderm-inefficient hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity to generate the requisite stem cell products.

developmental biology↗

bioRxiv2022

An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution

Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across multiple developmental lineage trajectories. In this study, we engineered barcoded iPSCs to generate an atlas of multilineage differentiation from pluripotency, encompassing a time-course of WNT-induced differentiation perturbed using modulators of WNT, BMP, and VEGF signalling. Computational mapping of in vitro cell types to in vivo developmental lineages revealed a diversity of iPSC-derived cell types comprising mesendoderm lineage cell types including lateral plate and paraxial mesoderm, neural crest, and primitive gut. Coupling this atlas of in vitro differentiation with Summary data-based Mendelian Randomisation analysis of human complex traits, we identify the WNT-inhibitor protein TMEM88 as a putative regulator of mesendodermal cell types governing development of diverse cardiovascular and anthropometric traits. Using genetic loss of function models, we show that TMEM88 is required for differentiation of diverse endoderm and mesoderm cell lineages in vitro and that TMEM88 knockout in vivo results in a significant dysregulation of arterial blood pressure. This study provides an atlas of multilineage iPSC differentiation coupled with new molecular, computational, and statistical genetic tools to dissect genetic determinants of mammalian developmental physiology.

genomics↗

bioRxiv2022

Spatial and molecular anatomy of germ layers in the gastrulating primate embryo

During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors and germ layer morphogenesis. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a morphological and molecular survey of spatiotemporal dynamics of cell types populating the non-human primate embryos during gastrulation. We performed serial sections of Cynomolgus monkeys (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21, and reconstructed three-dimensional digital models based on high-resolution anatomical atlas that revealed the dynamic changes in the geography of the mesoderm and primitive streaks. Spatial transcriptomics identified unique gene profiles that correspond to distinct germ layers and cross-species spatiotemporal transcriptome analysis revealed a developmental coordinate of germ layer segregation between mouse and primate. Furthermore, we identified species-specific transcription programs during gastrulation. These results offer important insights into evolutionarily conserved and divergent processes during mammalian gastrulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/474719v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1058f45org.highwire.dtl.DTLVardef@105cborg.highwire.dtl.DTLVardef@12362d7org.highwire.dtl.DTLVardef@2e2346_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LIA high-resolution anatomical atlas of Cynomolgus gastrulation embryos C_LIO_LICreated a three-dimensional digital template from serial sections of five developmental stages C_LIO_LIA two-dimensional spatiotemporal transcriptome of the germ layers of gastrulating embryos C_LIO_LICross-species comparison infers conservation of functional attributes of regulome and signaling activity in germ layer formation C_LI

developmental biology↗

bioRxiv2021

Niche-guided tissue patterning by chemomechanical flow lithography

Stem-cell derived tissue models are commonly cultured under globally-delivered stimuli that trigger histogenesis via self-organizing activity. However, the culture of such tissue models is prone to stochastic behavior, limiting the reproducibility of cellular composition and resulting in non-physiological architectures. To overcome these shortcomings, we developed a method for printing cell niche microenvironments with microstructured cues that mediate local histogenic processes, including mechanosensing and differentiation of selected cell types. Microstructured cues include independently tunable mechano-chemical properties, with conjugated peptides, proteins, and morphogens across a range of Youngs moduli. By rationally designing niches, we mediate the structure of tissues derived from stem-cell-progenitor sources, including a bone-fat assembly from stromal mesenchyme, and embryonic tissues derived from hiPSC. We show that microstructured cues can recapitulate mechano-chemical signals resembling early embryonic histogenesis. This outcome includes a role for niche mechanics in human embryonic organization, where soft niche mechanics bias markers of mesendodermal differentiation and epithelial-to-mesenchymal-transition (EMT), as well as a demonstration of a material-mediated morphogen signaling centers able to induce foci of mesenchymal and EMT differentiation. Thus, microstructured materials can mediate local histogenic processes to enhance the structure and composition of tissue models.

bioengineering↗

bioRxiv2020

TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation

Protein interaction is critical molecular regulatory activity underlining cellular functions and precise cell fate choices. Using TWIST1 BioID-proximity-labelling and network propagation analyses, we discovered and characterized a TWIST-chromatin regulatory module (TWIST1-CRM) in the neural crest cell (NCC). Combinatorial perturbation of core members of TWIST1-CRM: TWIST1, CHD7, CHD8, and WHSC1 in cell models and mouse embryos revealed that loss of the function of the regulatory module resulted in abnormal specification of NCCs and compromised craniofacial tissue patterning. Our results showed that in the course of cranial neural crest differentiation, phasic activity of TWIST1 and the interacting chromatin regulators promote the choice of NCC fate while suppressing neural stem cell fates, and subsequently enhance ectomesenchyme potential and cell motility. We have revealed the connections between TWIST1 and potential neurocristopathy factors which are functionally interdependent in NCC specification. Moreover, the NCC module participate in the genetic circuit delineating dorsal-ventral patterning of neural progenitors in the neuroepithelium.

developmental biology↗

bioRxiv2019

TWIST1 homo- and heterodimers orchestrate specificity control in embryonic stem cell lineage differentiation and craniofacial development

The extensive array of bHLH transcription factors and their combinations as dimers underpin the diversity of molecular function required for cell type specification during embryogenesis. The bHLH factor TWIST1 plays pleiotropic roles during development. However, which combinations of TWIST1 dimers are involved and what impact each dimer imposes on the gene regulation network controlled by TWIST1 remain elusive. In this work, proteomic profiling of human-TWIST1 expressing cell lines and transcriptome analysis of mouse cranial mesenchyme have revealed that TWIST1 homodimer and heterodimers with TCF3, TCF4 and TCF12 E-proteins are the predominant dimer combinations. Dimers formation or their balance are altered by disease-causing mutations in TWIST1 helix domains, which may account for the defective differentiation of the craniofacial mesenchyme observed in patients. Functional analyses of the loss and gain of TWIST1-E-protein dimer activity have revealed previously unappreciated roles in guiding lineage differentiation of embryonic stem cells: TWIST1-E-protein heterodimers activate the differentiation of mesoderm and neural crest cells which is accompanied by epithelial-to-mesenchymal transition, while TWIST1 homodimers maintain the stem cells in a progenitor state and block entry to the endoderm lineage.

developmental biology↗

bioRxiv2018

Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing

Circular RNAs (circRNAs) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). The challenges of detecting a BSJ from short read high throughput sequencing (HTS) data has steered software development to focus primarily on algorithmic methods to accurately capture BSJs. Here we present Ularcirc, the first software tool that provides a complete circRNA workflow from detection, integrated visualization, quality filtering of BSJ and forward splicing junctions (FSJ), through to sequence retrieval and downstream functional analysis. More importantly, Ularcirc uses an innovative method to filter out false positive circRNAs coined read alignment distribution (RAD) score which allows detection of circRNAs independent of gene annotations. We used Ularcirc to characterise circRNAs from public and in-house generated data sets and demonstrate how to discover (i) novel splicing patterns of parental transcripts, (ii) internal splicing patterns of circRNA, and (iii) the complexity of BSJ formation. Furthermore, we identify circRNAs that have potential open reading frames longer than their linear sequence. Finally, we have identified and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple sites within coding exons. Ularcirc can be accessed via https://github.com/VCCRI/Ularcirc.

bioinformatics↗