A5033311273- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- CRISPR and Genetic Engineering
- 3D Printing in Biomedical Research
- Cell Image Analysis Techniques
- Innovative Microfluidic and Catalytic Techniques Innovation
- Congenital heart defects research
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- Microfluidic and Capillary Electrophoresis Applications
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- RNA regulation and disease
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- Renal cell carcinoma treatment
- Cancer Genomics and Diagnostics
- Cancer Cells and Metastasis
- RNA modifications and cancer
The Francis Crick Institute
2021-2024
University of Cambridge
2019-2023
Broad Institute
2017
Imperial College London
2013-2016
Abstract Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro 1–5 , but their developmental potential is substantially extended by interactions with extraembryonic cells, including trophoblast (TS) endoderm (XEN) and inducible XEN (iXEN) 6–11 . Here we assembled cell-derived embryos from mouse ES TS iXEN showed that they recapitulate the development whole natural embryo utero up to day 8.5 post-fertilization. Our model displays headfolds defined forebrain...
Abstract Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction total cellular transcriptome. This precludes detection many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts hinders alternative splicing analysis. We, therefore, developed VASA-seq to detect in single cells, which is enabled by fragmenting tailing all RNA molecules subsequent cell lysis. The method compatible...
Overlap-directed DNA assembly methods allow multiple parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of parts, have become widely adopted synthetic biology, despite being incompatible with a key principle engineering: modularity. To answer this, we present MODAL: Modular Overlap-Directed Assembly Linkers strategy that brings modularity overlap-directed allowing an initial set into variety arrangements one-pot reactions. MODAL is...
The development of mouse embryos can be partially recapitulated by combining embryonic stem cells (ESCs), trophoblast (TS), and extra-embryonic endoderm (XEN) to generate embryo-like structures called ETX embryos. Although transcriptionally capture the gastrula, their ability recapitulate complex morphogenic events such as gastrulation is limited, possibly due limited potential XEN cells. To address this, we generated ESCs transiently expressing transcription factor Gata4, which drives fate,...
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation now key limiting factor. Here, we introduce a microfluidic platform integrates steps in cells to sequence library for up 96 samples and reduces input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture demonstrate supports workflows with arbitrary numbers of reaction clean-up capture steps. By reducing...
Abstract Mammalian embryos sequentially differentiate into trophectoderm and an inner cell mass, the latter of which differentiates primitive endoderm epiblast. Trophoblast stem (TS), extraembryonic (XEN) embryonic (ES) cells derived from these three lineages can self-assemble synthetic embryos, but mechanisms remain unknown. Here, we show that a cell-specific cadherin code drives embryogenesis. The XEN enables sorting layer below ES cells, recapitulating epiblast before implantation. TS...
Abstract Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit scale-up is, however, accompanied by background noise when processing challenging samples and overall RNA capture efficiency is lower. These drawbacks stem from lack strategies to enrich for high-quality material or specific cell types at moment encapsulation absence implementable multi-step enzymatic processes that increase capture. Here we alleviate both...
Abstract To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and accurately quantify their functional effects. A gene exemplifying challenge variant interpretation von Hippel–Lindautumor suppressor ( VHL ). encodes an E3 ubiquitin ligase that regulates cellular response hypoxia. Germline pathogenic in predispose patients tumors including clear cell renal carcinoma (ccRCC) pheochromocytoma, somatic mutations are frequently...
Recently, de novo variants in an 18 nucleotide region the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted affect tens thousands individuals worldwide. non-protein-coding gene transcribed into U4 small nuclear RNA (snRNA) component major spliceosome. syndrome disrupt spliceosome function and alter 5' splice site selection. Here, we performed saturation genome editing (SGE) identify functional clinical impact across entire...
Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), rapid integrated method to link surface proximity environment accessibility transcriptional identity within three-dimensional (3D) disease models. The utilizes steady-state diffusion kinetics...
ABSTRACT To maximize the impact of precision medicine approaches, it is critical to accurately identify genetic variants in cancer-associated genes with functional consequences. Yet, our knowledge rare conferring clinically relevant phenotypes and mechanisms through which they act remains highly limited. A tumor suppressor gene exemplifying challenge variant interpretation VHL . encodes an E3 ubiquitin ligase that regulates cellular response hypoxia. Germline pathogenic predispose patients...
Abstract Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs will provide insight mechanisms underlying mammalian pre-implantation development. Here, we explore this type of regulation by exerting microenvironmental control over mouse stem cells. Microfluidic encapsulation cells agarose microgels stabilizes the naive pluripotency network specifically induces expression...
ABSTRACT In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify termini polyadenylated transcripts capturing only a small fraction total transcriptome. This precludes detection many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts. Additionally, workflows do not sequence full transcript hindering analysis alternative splicing. We...
Abstract Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit scale-up is, however, accompanied by background noise when processing challenging samples and overall RNA capture efficiency is lower. These drawbacks stem from lack strategies to enrich for high-quality material or specific cell types at moment encapsulation absence implementable multi-step enzymatic processes that increase capture. Here we alleviate both...
Abstract Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs could provide insight mechanisms underlying mammalian pre-implantation development. Here, we explore this by exerting microenvironmental control over mouse stem cells (ESCs). Microfluidic encapsulation of ESCs agarose microgels stabilized the naïve pluripotency network specifically induced expression...
Embryo-like structures generated from stem cells can achieve varying developmental milestones, but none have been shown to progress through gastrulation, neurulation, and organogenesis. 1–7 Here, we show that “ETiX” mouse embryos, established embryonic aggregated with trophoblast inducible extraembryonic endoderm cells, develop gastrulation beyond undertake neural induction generate the progenitors needed create entire organism. The head-folds of ETiX embryos anterior expression Otx2,...
Abstract High-throughput single-cell RNA-seq (scRNA-seq) is used to describe complex tissues by characterizing transcriptional states of individual cells. Defining a cell's position, both in regard tissue margins and its social context, essential for understanding the intrinsic extrinsic variables that effect identity Conventional high-throughput scRNA-seq assays, however, decouple cells from their original locations within tissues. In situ hybridization readouts gene expression sequencing...