Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA362615 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To probe the phenotypic heterogeneity found in cell populations, we developed an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA) that allows for precise selection and amplification of living and rare cells. SaGA was used on collectively invading 3-D cancer cell packs to create purified leader and follower cell lines. The leader cell cultures are phenotypically stable and highly invasive in contrast to follower cultures, which show phenotypic plasticity over time and minimally invade in a sheet-like pattern. Genomic and molecular interrogation reveals an atypical VEGF-based vasculogenesis signaling that facilitates recruitment of follower cells but not for leader cell motility itself, which instead utilizes focal adhesion kinase-fibronectin signaling. While leader cells provide an escape mechanism for followers, follower cells in turn provide leaders with increased growth and survival. These data support a symbiotic model of collective invasion where phenotypically distinct cell types cooperate to promote their escape. A single tumor can harbor distinct genetic and epigenetic cellular sub-populations that drive tumor initiation and progression. This intratumor heterogeneity is proposed to be one of the major confounding factors of treatment causing relapse and poor clinical outcome1. Genomic instability and epigenetic modifications generate intratumor heterogeneity creating distinct genetic and epigenetic sub-populations or clones. A branched tumor evolutionary architecture can emerge containing the plasticity to progress under harsh environmental conditions and thwart therapeutic attempts to eradicate the tumor. It can be argued that until we discover how intratumor heterogeneity can be circumvented, precision oncology initiatives may fall short of expectations. Single cell sequencing methodologies have improved the genomic, transcriptomic, and epigenomic resolution of clonal tumor populations; however, the phenotypic implications of these alterations remain unclear. This is partly due to experimental challenges and is compounded by phenotypic plasticity that allows cancer cells to adapt to local changes in the microenvironment, without changes to the genome itself (e.g., epithelial to mesenchymal transition). Despite repeated observations that a small number of rare cancer cells or clones, hidden within a larger tumor population can drive tumor growth and spread, studies linking single cell or clonal phenotypes with genomic data have been limited. To probe the biology of a rare and phenotypically heterogeneous cell populations, single cells or subclones need to be isolated based upon user-defined criteria, instead of a random isolation approach; therefore, we developed a technique to image live cells within a biologically relevant 3-D environment, select a cell or cellular group based upon user-defined criteria, extract the cell(s), and subject the cell(s) to genomic and molecular analyses. In this way, we can purify, amplify, and systematically dissect the biologies of rare cells. This new technique, termed spatiotemporal genomic and cellular analysis (SaGA), was used to dissect the phenotypic heterogeneity of collective cancer cell invasion in a 3-D lung cancer model. These data incorporate the first SaGA-derived leader and follower cell lines to reveal that leader cells utilize atypical vasculogenesis signaling machinery by secreting VEGF to attract follower cells in invasive cell chains. In contrast, follower cells support leader cell growth by increasing their mitotic efficiency. This relationship argues for a cellular symbiosis within the collective invasion pack. Furthermore, these data provide proof of concept that SaGA is a powerful technology for dissecting phenotypic heterogeneity within cancer cell populations.
2017-02-10 | GSE93865 | GEO
Project description:The vascular endothelium contains morphologically similar cells throughout, but individual cells along the length of a single vascular tree or in different regional circulations function quite dissimilarly. When observations made in large arteries are extrapolated to explain the function of endothelial cells (EC) in the resistance vasculature/microcirculation, only a fraction of these observations are consistent between artery sizes. To what extent endothelial (EC) and vascular smooth muscle (VSMC) cells from different arteriolar segments of the same tissue differ phenotypically at the single-cell level remains unknown. Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system.
2023-03-09 | GSE202244 | GEO
Project description:Breast tumors often exhibit intratumoral heterogeneity. We hypothesized that phenotypically distinct clonal subpopulations in heterogeneous tumors may affect overall tumor morphology and cancer cell invasion. In order to study heterogeneous tumors, we isolated individual cells from a parental 4T1 murine mammary carcinoma cell line and generated four clonal subpopulations (E1, E2, A, and M). To characterize these subpopulations, we examined gene expression by performing bulk RNA-sequencing.
2024-01-31 | GSE252177 | GEO
Project description:To confirm the role of the collective dissemination in the mechanisms of tumoral invasion of colorectal cancers
| 2279691 | ecrin-mdr-crc
Project description:Tumor heterogeneity drives disease progression, treatment resistance, and patient relapse, yet remains largely under-explored in invasion and metastasis. Here, we investigated heterogeneity within collective cancer invasion by integrating DNA methylation and gene expression analysis in rare purified lung cancer leader and follower cells. Our results showed global DNA methylation rewiring in leader cells and revealed the filopodial motor MYO10 as a critical gene at the intersection of epigenetic heterogeneity and 3D collective invasion. We further identified JAG1 signaling as a novel upstream activator of MYO10 expression in leader cells. Using live cell imaging, we discovered that MYO10 drives filopodial persistence necessary for micropatterning extracellular fibronectin into linear tracks at the edge of 3D collective invasion exclusively in leaders. Our data fit a model where epigenetic heterogeneity and JAG1/Notch signaling jointly drive collective cancer invasion through MYO10 upregulation in epigenetically permissive leader cells, which induces filopodia dynamics necessary for linearized fibronectin micropatterning.
2020-07-31 | GSE147153 | GEO
Project description:Triple negative breast tumors contain heterogeneous cancer cells expressing distinct KRAS-dependent collective and disseminative invasion programs
| PRJNA888356 | ENA
Project description:Characterizing phenotypically distinct T cell populations
| PRJNA648405 | ENA
Project description:Collective behaviours are key in development. In a cell population, cells must coordinate to take on the right identity at the right place and time. In an embryo, cell populations must coordinate to undergo robust patterning and morphogenesis. The mechanisms underlying these coordinated behaviours remain poorly understood, in part because answering these questions requires the extensive bridging across biological scales—from molecules to whole embryos. In this thesis, I address these questions across two projects both using the chick embryo as a model system. Chapters 3-5 (“collective cell invasion project”; PhD years 1-3) investigates the first question, “How do cells coordinate to take on the right identity at the right place and time?” through examining how morphogen signalling, cell fate specification, and epithelial-to-mesenchymal transition (EMT) are coordinated during two contexts of collective cell invasion. First, the ingression and subsequent migration of nascent mesoderm through the morphogenetic structure called the primitive streak during gastrulation. Second, the delamination and subsequent migration of neural crest cells from the dorsal neural tube during neurulation. By comparing across developmental contexts and utilising a mixture of classical and modern techniques (experimental embryology, gain-of-function and loss-of-function assays, transcriptomics), I show that EMT and bone morphogenetic protein (BMP) signalling are reciprocally coupled to drive collective cell invasion. This coupling provides a molecular mechanism for synchronising cell fate specification with invasion progression, repositioning EMT as not just a process that guides changes in cell behaviour but as an active regulatory process that modulates morphogen signalling activity to coordinate tissue-level behaviours during collective cell invasion. Chapters 6-7 (“developmental checkpoint project”; PhD year 4 onwards) investigates the second question, “How do embryonic cell populations coordinate to undergo robust patterning and morphogenesis?” through the identification of a novel developmental bottleneck that gates the transition between primary gastrulation and axis elongation. Convergent evidence from several orthogonal approaches (tracking of normal developmental progression, resilience to temperature-induced diapause, regulative capacity following node ablation, and sensitivity to toxins) all point to the existence of a global embryonic bottleneck at Hamburger and Hamilton (HH) stage 4+. Further analysis reveals that this HH4 to HH5 transition seems to be dependent on the level of translation, providing a mechanistic basis for understanding coordinated developmental progression. Bulk RNA sequencing experiments further shed light on potential mechanisms that may be regulating the HH4 to HH5 transition, including surveilling translation activity. Future work will test whether the mechanisms underlying this novel bottleneck satisfies the four criteria of a checkpoint: dependency, active enforcement, separability, and dispensability. Together, these two projects demonstrate that collective behaviours in the embryo are achieved in part by distinct mechanisms—molecular coupling between morphogen signalling and EMT at the level of invading cell populations and translational regulation gating a global transition at the level of the whole embryo—thus advancing our understanding of how development is coordinated across different biological scales.
2026-09-28 | GSE348387 | GEO
Project description:Collective behaviours are key in development. In a cell population, cells must coordinate to take on the right identity at the right place and time. In an embryo, cell populations must coordinate to undergo robust patterning and morphogenesis. The mechanisms underlying these coordinated behaviours remain poorly understood, in part because answering these questions requires the extensive bridging across biological scales—from molecules to whole embryos. In this thesis, I address these questions across two projects both using the chick embryo as a model system. Chapters 3-5 (“collective cell invasion project”; PhD years 1-3) investigates the first question, “How do cells coordinate to take on the right identity at the right place and time?” through examining how morphogen signalling, cell fate specification, and epithelial-to-mesenchymal transition (EMT) are coordinated during two contexts of collective cell invasion. First, the ingression and subsequent migration of nascent mesoderm through the morphogenetic structure called the primitive streak during gastrulation. Second, the delamination and subsequent migration of neural crest cells from the dorsal neural tube during neurulation. By comparing across developmental contexts and utilising a mixture of classical and modern techniques (experimental embryology, gain-of-function and loss-of-function assays, transcriptomics), I show that EMT and bone morphogenetic protein (BMP) signalling are reciprocally coupled to drive collective cell invasion. This coupling provides a molecular mechanism for synchronising cell fate specification with invasion progression, repositioning EMT as not just a process that guides changes in cell behaviour but as an active regulatory process that modulates morphogen signalling activity to coordinate tissue-level behaviours during collective cell invasion. Chapters 6-7 (“developmental checkpoint project”; PhD year 4 onwards) investigates the second question, “How do embryonic cell populations coordinate to undergo robust patterning and morphogenesis?” through the identification of a novel developmental bottleneck that gates the transition between primary gastrulation and axis elongation. Convergent evidence from several orthogonal approaches (tracking of normal developmental progression, resilience to temperature-induced diapause, regulative capacity following node ablation, and sensitivity to toxins) all point to the existence of a global embryonic bottleneck at Hamburger and Hamilton (HH) stage 4+. Further analysis reveals that this HH4 to HH5 transition seems to be dependent on the level of translation, providing a mechanistic basis for understanding coordinated developmental progression. Bulk RNA sequencing experiments further shed light on potential mechanisms that may be regulating the HH4 to HH5 transition, including surveilling translation activity. Future work will test whether the mechanisms underlying this novel bottleneck satisfies the four criteria of a checkpoint: dependency, active enforcement, separability, and dispensability. Together, these two projects demonstrate that collective behaviours in the embryo are achieved in part by distinct mechanisms—molecular coupling between morphogen signalling and EMT at the level of invading cell populations and translational regulation gating a global transition at the level of the whole embryo—thus advancing our understanding of how development is coordinated across different biological scales.
2026-09-02 | GSE345511 | GEO
Project description:Collective behaviours are key in development. In a cell population, cells must coordinate to take on the right identity at the right place and time. In an embryo, cell populations must coordinate to undergo robust patterning and morphogenesis. The mechanisms underlying these coordinated behaviours remain poorly understood, in part because answering these questions requires the extensive bridging across biological scales—from molecules to whole embryos. In this thesis, I address these questions across two projects both using the chick embryo as a model system. Chapters 3-5 (“collective cell invasion project”; PhD years 1-3) investigates the first question, “How do cells coordinate to take on the right identity at the right place and time?” through examining how morphogen signalling, cell fate specification, and epithelial-to-mesenchymal transition (EMT) are coordinated during two contexts of collective cell invasion. First, the ingression and subsequent migration of nascent mesoderm through the morphogenetic structure called the primitive streak during gastrulation. Second, the delamination and subsequent migration of neural crest cells from the dorsal neural tube during neurulation. By comparing across developmental contexts and utilising a mixture of classical and modern techniques (experimental embryology, gain-of-function and loss-of-function assays, transcriptomics), I show that EMT and bone morphogenetic protein (BMP) signalling are reciprocally coupled to drive collective cell invasion. This coupling provides a molecular mechanism for synchronising cell fate specification with invasion progression, repositioning EMT as not just a process that guides changes in cell behaviour but as an active regulatory process that modulates morphogen signalling activity to coordinate tissue-level behaviours during collective cell invasion. Chapters 6-7 (“developmental checkpoint project”; PhD year 4 onwards) investigates the second question, “How do embryonic cell populations coordinate to undergo robust patterning and morphogenesis?” through the identification of a novel developmental bottleneck that gates the transition between primary gastrulation and axis elongation. Convergent evidence from several orthogonal approaches (tracking of normal developmental progression, resilience to temperature-induced diapause, regulative capacity following node ablation, and sensitivity to toxins) all point to the existence of a global embryonic bottleneck at Hamburger and Hamilton (HH) stage 4+. Further analysis reveals that this HH4 to HH5 transition seems to be dependent on the level of translation, providing a mechanistic basis for understanding coordinated developmental progression. Bulk RNA sequencing experiments further shed light on potential mechanisms that may be regulating the HH4 to HH5 transition, including surveilling translation activity. Future work will test whether the mechanisms underlying this novel bottleneck satisfies the four criteria of a checkpoint: dependency, active enforcement, separability, and dispensability. Together, these two projects demonstrate that collective behaviours in the embryo are achieved in part by distinct mechanisms—molecular coupling between morphogen signalling and EMT at the level of invading cell populations and translational regulation gating a global transition at the level of the whole embryo—thus advancing our understanding of how development is coordinated across different biological scales.
2026-09-02 | GSE345510 | GEO