Pheno-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26737 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:3D-culture systems have advanced cancer modeling by reflecting physiological characteristics of in-vivo tissues, but our understanding of functional intratumor heterogeneity including visual phenotypes and underlying gene expression is still limited. Transcriptional heterogeneity can be dissected by single-cell RNA-sequencing, but these technologies suffer from low RNA-input and fail to directly correlate gene expression with contextual cellular phenotypes. Here we present pheno-seq for integrated high-throughput imaging and transcriptomic profiling of clonal tumor spheroids derived from 3D models of breast and colorectal cancer. Specifically, we identify characteristic expression signatures that are associated with heterogeneous invasive and proliferative behavior including a rare cell subtype. Furthermore, we identify functionally relevant transcriptional regulators missed by single-cell RNA-seq, link visual phenotypes defined by heterogenous expression to inhibitor response and infer single-cell regulatory states by deconvolution. We anticipate that directly linking molecular features with patho-phenotypes of cancer cells will improve the understanding of intratumor heterogeneity and consequently prove to be useful for translational research.
| EGAS00001002999 | EGA
Project description:Cancer spheroids are spherical, three-dimensional (3D), in vitro assemblies of cancer cells, which are gaining importance as a useful model in cancer behavior studies. Designed to simulate
key features of the in vivo tumor microenvironment, spheroids offer reliable insights for drug screening and testing applications. We observed contrasting phenotypes in 3D cervical cancer (CC)
cultures. Thus, in this study, we compared the proteomes of 3D and traditional two-dimensional (2D) cultures of CC cell lines, HeLa, SiHa, and C33A. When cultured in in-house poly-(2-hydroxy-ethyl methacrylate)-coated plates under conditions suitable for 3D spheroid formation, these CC cell lines yielded spheroids exhibiting different features. Proteomic analysis of cells cultured in 2D and 3D cultures revealed similar protein profiles but remarkable differences in the expression levels of some proteins. In SiHa and C33A cells, the upregulation of key proteins required for spheroid formation was insufficient for the formation of compact spheroids. In contrast, HeLa cells could form compact spheroids because they upregulated the proteins, including cadherin-binding, cytoskeleton, and adhesion proteins, necessary for spheroid formation during the remodeling process. Overall, this study unravels the mechanisms underlying the formation of spheroids in the commonly used CC cell lines
2024-12-04 | PXD056969 | JPOST Repository
Project description:Pheno-seq is a new approach that integrates high-throughput imaging and transcriptomic profiling of clonal spheroids/organoids to dissect functional tumor cell heterogeneity in 3D cell culture systems. The method is based on the iCELL8 technology (TakaraBio) that uses barcoded nanowells and a micro-solenoid valve dispenser. The CRC_spheroid dataset contains demultiplexed RNA-sequencing profiles (FASTQ file format, NextSeq 500) of 95 clonal tumor spheroids derived from a patient with colorectal cancer.
| EGAD00001004131 | EGA
Project description:Extracellular biophysical cues such as matrix stiffness are key stimuli tuning cell fate and affecting tumor progression in vivo. However, it remains unclear how spheroids in a 3D microenvironment perceive matrix mechanical stiffness stimuli and translate them into intracellular signals driving cancer. Mechanosensitive Piezo1 and TRPV4 ion channels, upregulated in many malignancies, are major transducers of such physical stimuli into biochemical responses. Most mechanotransduction studies probing the reception of changing stiffness cues by cells are, however, still limited to 2D culture systems or cell-extracellular matrix models which lack the major cell-cell interactions prevalent in 3D cancer tumors. Here, we engineered a 3D spheroid culture environment with varying mechanobiological properties to study the effect of static matrix stiffness stimuli on mechanosensitive and malignant phenotypes in oral squamous cell carcinoma spheroids. We find that spheroid growth is enhanced when cultured in stiff extracellular matrix. Using flow cytometry, we show that the expression of mechanoreceptor Piezo1 and stemness marker CD44 is upregulated in stiff matrix. We also report the upregulation of a selection of genes with associations to mechanoreception, ion channel transport, extracellular matrix organization, and tumorigenic phenotypes in stiff matrix spheroids. Together, our results indicate that cancer cells in 3D spheroids utilize mechanosensitive ion channels Piezo1 and TRPV4 to sense changes in static extracellular matrix stiffness and that stiffness drives pro-tumorigenic phenotypes in oral squamous cell carcinoma.
2024-03-28 | GSE262142 | GEO
Project description:Highly invasive integrin and protease-independent amoeboid migration is often employed by cancer cells at the invasive front, though little is known about the transcriptomic changes underlying the switch to an amoeboid migratory mode. Using a metastatic melanoma cell line expressing photoconvertible Dendra2 protein (WM983c-D2), tumour spheroids were cultured in 3D collagen matrices and imaged over time. Spheroids grown from WM983c-D2 cells generate cells of three distinct phenotypes: 1) compact, non-invading cells organised at the spheroid surface with no visual cell protrusions, hereafter termed ‘epithelial’; 2) cells still attached to the spheroid periphery that have commenced tumour escape, exhibiting cellular protrusions and an elongated phenotype, hereafter termed ‘escaping’; 3) singly migrating cells exhibiting a rounded phenotype and no lamellipodia consistent with amoeboid cell migration, hereafter termed 'amoeboid'. Individual amoeboid and escaping cells, as well as groups of epithelial cells at the spheroid edge were photoconverted and single cell sorted via FACS following enzymatic digestion of the collagen matrix. 10 Epithelial, 12 escaping and 13 amoeboid cells were subjected to scRNA-seq and differential expression analyses in order to identify changes in gene expression as melanoma cells convert from a non-invasive epithelial state to invasive amoeboid cells.
2022-05-21 | E-MTAB-11722 | biostudies-arrayexpress
Project description:To investigate epigenetic dynamics in a 3D liver spheroid model, liver spheroids were treated with sodium butyrate for 3 days and allowed to recover for 1 week. We then performed gene expression profiling analysis using data obtained from RNA-seq of spheroids at 4 time points
2022-09-26 | GSE213944 | GEO
Project description:Breast–mammary epithelial cells experience different local environments during tissue development and tumorigenesis. Microenvironmental heterogeneity gives rise to distinct cell-regulatory states whose identity and importance are just beginning to be appreciated. Cellular states diversify when clonal 3D spheroids are cultured in basement membrane, and prior transcriptomic analyses identified a state associated with stress tolerance and poor response to anticancer therapeutics. Here, we examined the regulation of this state and found that it is jointly coordinated by the NRF2 and p53 pathways, which are co-stabilized by spontaneous oxidative stress within the 3D cultures. To identify common adaptive programs downstream of NRF2 deficiency, we inducibly knocked down NRF2 and profiled 3D spheroids by RNA sequencing.
2020-02-04 | GSE141228 | GEO
Project description:2D culture as a model for drug testing often turns to be clinically futile. Therefore, 3D cultures (3Ds) show potential to better model responses to drugs observed in vivo. In preliminary studies, using melanoma (B16F10) and renal (RenCa) cancer, we confirmed that 3Ds better mimics the tumor microenvironment. Here, we evaluate how the proposed 3D mode of culture affects tumor cell susceptibility to anti-cancer drugs, which have distinct mechanisms of action (everolimus, doxorubicin, cisplatin). Melanoma spheroids show higher resistance to all used drugs, as compared to 2D. In RCC model, such modulation was only observed for doxorubicin treatment. As drug distribution was not affected by the 3D shape, we assessed the expression of MDR1 and mTor. Upregulation of MDR1 in RCC spheroids was observed, in contrast to melanoma. In both models mTor expression was not affected by the 3D cultures. By NGS, 10 genes related with metabolism of xenobiotics by cytochrome p450 were deregulated in renal cancer spheroids; 9 of them were later confirmed in melanoma model. The differences between 3D models and classical 2D cultures point to the potential to uncover new non canonical mechanisms to explain drug resistance set by the tumor in its microenvironment.
2022-01-20 | GSE190296 | GEO
Project description:Using pooled shRNA libraries we performed a focused screen of 115 genes in 3D ex vivo cultures of primary murine lung tumor cells and 2D cultures of murine LKR10 cells. These screens identify Uhrf1 as gene selectively important for the 3D growth of primary lung cancer spheroids.
2023-05-15 | GSE209923 | GEO
Project description:MicroRNAs regulate metabolic phenotypes during Multicellular Tumor Spheroids progression
| PRJEB41156 | ENA