Biology subjects

Velazquez, J. J.

Publications and source records attributed to Velazquez, J. J..

3 recordsLinked to original sources

bioRxiv2023

Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering

Implantation of the human embryo commences a critical developmental stage that comprises profound morphogenetic alteration of embryonic and extra-embryonic tissues, axis formation, and gastrulation events. Our mechanistic knowledge of this window of human life remains limited due to restricted access to in vivo samples for both technical and ethical reasons. Additionally, human stem cell models of early post-implantation development with both embryonic and extra-embryonic tissue morphogenesis are lacking. Here, we present iDiscoid, produced from human induced pluripotent stem cells via an engineered a synthetic gene circuit. iDiscoids exhibit reciprocal co-development of human embryonic tissue and engineered extra-embryonic niche in a model of human post-implantation. They exhibit unanticipated self-organization and tissue boundary formation that recapitulates yolk sac-like tissue specification with extra-embryonic mesoderm and hematopoietic characteristics, the formation of bilaminar disc-like embryonic morphology, the development of an amniotic-like cavity, and acquisition of an anterior-like hypoblast pole and posterior-like axis. iDiscoids offer an easy-to-use, high-throughput, reproducible, and scalable platform to probe multifaceted aspects of human early post-implantation development. Thus, they have the potential to provide a tractable human model for drug testing, developmental toxicology, and disease modeling.

developmental biology↗

bioRxiv2021

Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

A major advantage of single cell RNA-Sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. To date, such ordering was mainly used to group cells and to infer interactions within cells. Here we present TraSig, a computational method for improving the inference of cell-cell interactions in scRNA-Seq studies. Unlike prior methods that only focus on the average expression levels of genes in clusters or cell types, TraSig fully utilizes the dynamic information to identify significant ligand-receptor pairs with similar trajectories, which in turn are used to score interacting cell clusters. We applied TraSig to several scRNA-Seq datasets. As we show, using the ordering information allows TraSig to obtain unique predictions that improve upon those identified by prior methods. Functional experiments validate the ability of TraSig to identify novel signaling interactions that impact vascular development in liver organoid.

bioinformatics↗

bioRxiv2020

Synthetic Maturation of Multilineage Human Liver Organoids via Genetically Guided Engineering

Pluripotent stem cell (PSC)-derived organoids are emerging as novel human-based microphysiological models but display immature phenotypes with limited subsets of endothelial or stromal cells. Here we demonstrate that in vitro manipulation of gene regulatory networks (GRNs) in PSC-derived liver organoids selected either through computational analysis or targeted tissue design can advance tissue maturation in vitro. Through an unbiased comparison with the genetic signature of mature livers, we identify downregulated GRNs in fetal liver organoids compared to adult livers. We demonstrate that overexpression of PROX1 and ATF5, together with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, drives maturation in vitro. Single cell analyses reveal hepatobiliary-, endothelial-, and stellate-like cell populations. The engineered organoids demonstrate enhanced vasculogenesis, capture native liver characteristics (e.g. FXR signaling, CYP3A4 activity), and exhibit therapeutic potential in mice. Collectively, our approach provides a genetically guided framework for engineering developmentally advanced multilineage tissues from hiPSCs. HIGHLIGHTSO_LIIn vitro tissue maturation via genetically encoded molecular programs C_LIO_LIComputational analysis to identify maturation transcription factors in liver organoids C_LIO_LIPromoting vascularization of organoids via genetically encoded molecular programs C_LIO_LISingle cell analysis of parenchymal and non-parenchymal cells C_LIO_LIModeling of native liver functions and in vivo therapeutic potential C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC="FIGDIR/small/087445v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@6ec32aorg.highwire.dtl.DTLVardef@1cf2eeforg.highwire.dtl.DTLVardef@1128748org.highwire.dtl.DTLVardef@16fb5a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗