Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptomic profiling of HT1080 fibrosarcoma cells of mesenchymal or amoeboid migratory phenotype

ABSTRACT: Amoeboid and mesenchymal migration of cancer cells both contribute to metastatic spreading of tumors. To characterize gene expression profiles underlying the different migratory modes, we performed RNA sequencing of HT1080 fibrosarcoma cells undergoing mesenchymal-amoeboid transition induced by either doxycycline-inducible constitutively active RhoA or dasatinib treatment. Cells were kept in three-dimensional collagen gels with or without induction for 48 hours. RNA was isolated with a modified Chomczynski protocol. RNA-seq libraries were constructed from DNase I treated, rRNA depleted total RNA and sequenced with Illumina 2000/2500 sequencers.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Vladimír Čermák

PROVIDER: E-MTAB-6823 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-throughput transcriptomic and proteomic profiling of mesenchymal-amoeboid transition in 3D collagen.

Čermák Vladimír V Gandalovičová Aneta A Merta Ladislav L Harant Karel K Rösel Daniel D Brábek Jan J

Scientific data 20200527 1

The plasticity of cancer cell invasion represents substantial hindrance for effective anti-metastatic therapy. To better understand the cancer cells' plasticity, we performed complex transcriptomic and proteomic profiling of HT1080 fibrosarcoma cells undergoing mesenchymal-amoeboid transition (MAT). As amoeboid migratory phenotype can fully manifest only in 3D conditions, all experiments were performed with 3D collagen-based cultures. Two previously described approaches to induce MAT were used: ...[more]

PMID: 32461585

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Project description:Microglia, the resident immune cells of the central nervous system (CNS), have two distinct phenotypes in the developing brain: amoeboid form, known to be amoeboid microglial cells (AMC) and ramified form, known to be ramified microglial cells (RMC) alongside several intermediate forms. The AMC are characterized by being proliferative, phagocytic and migratory whereas the RMC are quiescent and exhibit a slow turnover rate. The AMC transform into RMC with advancing age, and this transformation is indicative of the gradual shift in the microglial functions. Both AMC and RMC respond to CNS inflammation, and they become hypertrophic when they are activated by trauma, infection or neurodegenerative stimuli. The molecular mechanisms and functional significance of morphological transformation of microglia during normal development and in disease conditions is not clear. It is hypothesized that AMC and RMC are functionally regulated by a specific set of genes encoding various signaling molecules and transcription factors. To address this, we carried out cDNA microarray analysis using lectin-labeled AMC and RMC isolated from frozen tissue sections of the corpus callosum of 5-day and 4-week old rat brain respectively, by laser capture microdissection (LCM). The global gene expression profiles of both microglial phenotypes were compared and the differentially expressed genes in AMC and RMC were clustered based on their functional annotations. This genome wide comparative analysis helps in identifying genes that are specific to AMC and RMC. The novel and specific molecules identified in both microglial phenotypes can be targeted for therapeutic purposes in developing and adult brain diseases. We used microarrays to identify the genes specific to amoeboid and ramified microglia. RNA was isolated from the laser-captured amoeboid and ramified microglia from the corpus callosum of 5-day and 4-week old rat brain. The RNA was hybridised onto Affymetrix Rat 230 2.0 array.

Dataset Information

Transcriptomic profiling of HT1080 fibrosarcoma cells of mesenchymal or amoeboid migratory phenotype

Publications

High-throughput transcriptomic and proteomic profiling of mesenchymal-amoeboid transition in 3D collagen.

Similar Datasets

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