A colorectal cancer 3D bioprinting workflow as a platform for disease modelling and chemotherapeutic screening
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA753099 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15376183_1.fastq.gz | Fastqsanger.gz | |||
| SRR15376183_2.fastq.gz | Fastqsanger.gz | |||
| SRR15376184_1.fastq.gz | Fastqsanger.gz | |||
| SRR15376184_2.fastq.gz | Fastqsanger.gz | |||
| SRR15376185_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:We have established an affordable, flexible and highly reproducible 3D bioprinted CRC model. Histological assessment of Caco-2 cells in 3D bioprints revealed the formation of glandular-like structures which show greater pathomorphological resemblance to tumours than monolayer cultures do. RNA expression profiles in 3D bioprinted cells were marked by upregulation of genes involved in cell adhesion, hypoxia, EGFR/KRAS signaling and downregulation of cell cycle programmes. Testing this 3D experimental platform with three of the most commonly used chemotherapeutics in CRC (5-fluoruracil, oxaliplatin and irinotecan), revealed overall increased resistance compared to 2D cell cultures. Lastly, we demonstrate that our workflow can be successfully extended to primary CRC samples. Thereby, we describe a novel accessible platform for disease modelling and drug testing, which may present an innovative approach in personalised therapeutic screening.
2021-11-05 | GSE181722 | GEO
Project description:Colorectal cancer (CRC) is the third most common malignancy and has recently moved up to the second leading cause of death among carcinomas. Prognosis, especially for advanced diseases or certain molecular subtypes of CRC, remains poor, which highlights the urgent need for better therapeutic strategies. However, currently, as little as 0.1% of all drugs make it from bench to bedside because of the inherently high false-positive and false-negative rates of current preclinical and clinical drug testing data. Therefore, the success of developing novel treatment agents lies in the introduction of improved preclinical disease models which resemble in vivo carcinomas closer, possess higher predictive properties, and offer opportunities for individualized therapies. Aiming to address these needs, we have established an affordable, flexible, and highly reproducible 3D bioprinted CRC model. The histological assessment of Caco-2 cells in 3D bioprints revealed the formation of glandular-like structures which show greater pathomorphological resemblance to tumors than monolayer cultures do. RNA expression profiles in 3D bioprinted cells were marked by upregulation of genes involved in cell adhesion, hypoxia, EGFR/KRAS signaling, and downregulation of cell cycle programs. Testing this 3D experimental platform with three of the most commonly used chemotherapeutics in CRC (5-fluoruracil, oxaliplatin, and irinotecan) revealed overall increased resistance compared to 2D cell cultures. Last, we demonstrate that our workflow can be successfully extended to primary CRC samples. Thereby, we describe a novel accessible platform for disease modeling and drug testing, which may present an innovative opportunity for personalized therapeutic screening.
| S-EPMC8638705 | biostudies-literature
Project description:A platform for generation of chamber specific cardiac tissues and disease modelling
| PRJNA505893 | ENA
Project description:Liver is dynamic, heterogeneous, and each cell type acts in concert to regulate its function. In vitro morphogenesis is limited, and self-assembled biliary and blood vessels system are absent from manufactured liver tissues. The combination of bioprinting and organoid technique offers spatial and cellular control over three-dimensional (3D) organ tissue manufacturing, allowing to build liver tissues with self-assembled structure in vitro. We developed a high-throughput PDMS microwell platform (PMP) generating uniform and functional hepatic organoid building blocks (HOBBs) which displayed cellular crosstalk and self-assembled structure. For bioprinting process, we developed three-level temperature control system and new quadratic material, i.e., alginate-gelatin-collagen-laminin (AGCL) biomaterial, realizing reproducible construction of liver tissues with requisite cellular density. Under long-term differentiation, bioprinted liver tissues exhibited enhanced hepatobiliary function, intrahepatic bile duct networks and angiogenic potential. To investigate the regulatory mechanisms of multicellular crosstalk and self-assembled of HOBBS, biliary branching morphogenesis, biomimetic liver tissue formation, and angiogenesis of HABs, transcriptome analysis was performed.
2024-07-24 | GSE230404 | GEO
Project description:Bioprinting is an emerging additive manufacturing approach to the fabrication of patient-specific, implantable three-dimensional (3D) constructs for regenerative medicine. However, developing cell-compatible bioinks with high printability, structural stability, biodegradability, and bioactive characteristics is still a primary challenge for translating 3D bioprinting technology to preclinical and clinal models. To overcome this challenge, we develop a nanoengineered ionic covalent entanglement (NICE) bioink formulation for 3D bone bioprinting. The NICE bioinks allow precise control over printability, mechanical properties, and degradation characteristics, enabling custom 3D fabrication of mechanically resilient, cellularized structures. We demonstrate cell- induced remodeling of 3D bioprinted scaffolds over 60 days, demonstrating deposition of nascent extracellular matrix proteins. Interestingly, the bioprinted constructs induce endochondral differentiation of encapsulated human mesenchymal stem cells (hMSCs) in absence of osteoinducing agents such as dexamethasone or bone morphogenic protein-2 (BMP-2). Using next-generation transcriptome sequencing (RNA-seq) technology, we establish the role of nanosilicates, a bioactive component of NICE bioink, to stimulate endochondral differentiation at the transcriptome level. Overall, the osteoinductive bioink has the ability to induce formation of osteo-related mineralized extracellular matrix by encapsulatedhMSCsingrowthfactor-freeconditions.Furthermore,wedemonstratedtheabilityofNICEbioinktofabricatepatient-specific, implantable 3D scaffolds for repair of craniomaxillofacial bone defects. We envision transformation of this NICE bioink technology toward a realistic clinical process for 3D bioprinting patient-specific bone tissue for regenerative medicine.
2020-03-04 | GSE146309 | GEO
Project description:Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements
| PRJNA450938 | ENA
Project description:Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements [HuGene2.0st]
| PRJNA451410 | ENA
Project description:Pterygium is an ocular surface disorder with high prevalence that can lead to vision impairment. As a pathological outgrowth of conjunctiva, pterygium involves neovascularization and chronic inflammation, but its pathogenesis remains largely unknown. Over the last decade, various types of disease models have been built to study pterygium. Here, we developed a 3D multicellular in vitro pterygium model using the digital light processing (DLP)-based 3D bioprinting of human conjunctival stem cells (hCjSCs). A novel feeder-free culture system was adopted and efficiently expanded the primary hCjSCs with homogeneity, stemness and differentiation potency. The DLP-based 3D bioprinting was able to fabricate hydrogel scaffolds that support the viability and biological integrity of the encapsulated hCjSCs. The bioprinted 3D pterygium model was fabricated with hCjSCs, immune cells and vascular cells to recapitulate the disease microenvironment. Transcriptomic analysis using RNA sequencing (RNA-seq) identified a distinct profile correlated to inflammation response, angiogenesis, and epithelial mesenchymal transition in the bioprinted 3D pterygium model. In addition, the pterygium signatures and disease relevance of the bioprinted model were validated with the public RNA-seq data from patient-derived pterygium tissues. By integrating the stem cell technology and 3D bioprinting, this is the first reported 3D in vitro disease model for pterygium that can be utilized by future studies towards the personalized medicine and the drug screening.
2022-06-01 | GSE180343 | GEO
Project description:We empirically assess the measurement precision and sensitivity of a suite of gene expression technologies via a consensus modelling method called the row-linear model.
2018-09-01 | GSE113506 | GEO
Project description:Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. To investigate the cellular reprogramming underlying the initial cell divisions prior to microcallus formation, we collected RNA from isolated differentiated root cells immediately, 1, and 3 days after bioprinting. We showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli and of which the timing coincides with the induction of core cell cycle genes and regeneration-related genes. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.
2022-08-15 | GSE208176 | GEO