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A new 3D culture system to identify disease-relevant genes in colorectal cancer [Microarray expression]

ABSTRACT: It is increasingly appreciated that properties of cultured epithelial cells differ dramatically in 2D compared to 3D, and the latter more faithfully recapitulates in vivo behavior. By studying a battery of human colorectal cancer (CRC) cell lines in type-1 collagen, we have found that HCA-7 cells form colonies with two distinctive and persistent morphological and functional properties. We observed predominantly single-layered polarized cysts (cystic colonies, CC) and a smaller fraction displaying disorganized solid masses (spiky colonies, SC) that were highly invasive in vivo. Despite overall genomic similarity, CC and SC exhibited distinct and dynamic patterns of gene expression in 3D.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76210 | GEO | 2017/08/30

SECONDARY ACCESSION(S): PRJNA306642

REPOSITORIES: GEO

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A new 3D culture system to identify disease-relevant genes in colorectal cancer [Exome-Seq]

Project description:It is increasingly appreciated that properties of cultured epithelial cells differ dramatically in 2D compared to 3D, and the latter more faithfully recapitulates in vivo behavior. By studying a battery of human colorectal cancer (CRC) cell lines in type-1 collagen, we have found that HCA-7 cells form colonies with two distinctive and persistent morphological and functional properties. We observed predominantly single-layered polarized cysts (cystic colonies, CC) and a smaller fraction displaying disorganized solid masses (spiky colonies, SC) that were highly invasive in vivo. Despite overall genomic similarity, CC and SC exhibited distinct and dynamic patterns of gene expression in 3D.

2017-08-30 | GSE76352 | GEO

Molecular characteristics of choledochal cysts in children: transcriptome sequencing

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Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture

Project description:We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p<0.01) between CC-CR and CC; there were 141 transcripts upregulated and 220 transcripts downregulated in CC-CR compared to CC. Small RNA-Seq detected 7 miRNAs upregulated and 24 miRNAs downregulated in CC-CR cells compared to CC cells (fold change>2, FDR<0.01). Differential expression analysis revealed several novel candidates that may contribute to cetuximab resistance. The whole-transcriptome profilings using cetuximab resistance model from 3D culture provide novel candidates for cetuximab resistance and further functional studies might open the door to a novel understanding of how non-mutational mechanisms mediate cetuximab resistance.

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Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry

Project description:Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Due to the sheer quantity of data generated, visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed for evaluation and comparison of algorithms. Findings We acquired high-quality 3D imaging MS datasets from different biological systems at several labs, supplied them with overview images and scripts demonstrating how to read them, and deposited them into MetaboLights, an open repository for metabolomics data. 3D imaging MS data was collected from five samples using two types of 3D imaging MS. 3D Matrix-Assisted Laser Desorption/Ionization (MALDI) imaging MS data was collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D Desorption Electrospray Ionization (DESI) imaging MS data was collected from a human colorectal adenocarcinoma. Conclusions With the aim to stimulate computational research in the field of computational 3D imaging MS, we provided selected high-quality 3D imaging MS datasets which can be used by algorithm developers as benchmark datasets.

2016-07-27 | MTBLS176 | MetaboLights

PKHD1-deficient human induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells (PKHD1-KO CCs) vs heterozygously mutated PKHD1 human iPS cell-derived cholangiocyte-like cells (PKHD1-Hetero CCs)

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Project description:Two biological replicates of Madin-Darby Canine Kidney Epithelial Cells grown as 3D cysts in Collagen Type I (7 days old) were exposed to six different concentrations of Hepatocyte Growth Factor (HGF) (0, 1.03, 2.07, 4.15, 8.33 and 16.67 ng/ml). Total RNA was isolated from the cysts after 12 hours of HGF induction. The data submitted here are the raw sequence files of the single read lengths of 50 bp for the 12 samples (2 replicates X 6 conditions) after RNA sequencing experiment using Illumina HiSeq 2000.15

2016-01-17 | E-MTAB-4959 | biostudies-arrayexpress

Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [CTCF ChIP-Seq]

Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.

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