Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Melanoma B16 transcriptome sequencing in C57BL16 mice under dacarbazine treatment

ABSTRACT: On day 7 after B16 melanoma cells transplantation, C57Bl6 mice with subcutaneous palpable tumors were randomly divided into 2 groups for experimental treatment with Dacarbazine. Group 1 «Control (PBS) », n=5, animals in this group were intraperitoneally injected with phosphate buffered saline in a volume of 250 µl. Group 2 «DTIC», n=5, animals in this group were intraperitoneally injected with a solution of Dacarbazine (DTIC) (Sigma-Aldrich, USA) in phosphate buffer at a concentration of 50 mg/kg of animal weight. Injections with PBS or DTIC were carried out three times on days 8, 10 and 12 after melanoma cell transplantation, on day 14, mice were sacrificed for further analysis of primary tumors and organs.

INSTRUMENT(S): DNBSEQ-G400, RNeasy Mini Kit

ORGANISM(S): Mus musculus

SUBMITTER: Ivan Zinchenko

PROVIDER: E-MTAB-13737 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Technological advances in transcriptional profiling and in the availability of the single-cell sampling from rare and specialised cell types have come together to allow us to explore molecular processes in the development of tumours and in solid tumour biology. None of the existing gene expression profiling platforms has the sensitivity to directly deal with the small mRNA population from single-cells. Therefore, it is essential to amplify the mRNA from a single cell without distorting the relative transcript abundance and studying the products of this amplification with the available transcriptome profiling techniques. We used such an exponential amplification approach to study the transcriptional heterogeneity and the representation of cancer-associated pathways in single cells isolated from the clonal progenies of a murine colon cancer cell line (CT26). With the methods developed and single-cell microarray analysis (Affymetrix GeneChipM-. Mouse Genome 430 2.0 3M-^R arrays), we were able to demonstrate considerable, intra- as well as inter-clonal, transcriptional heterogeneity. Detailed ontological classification indicated that most of the transcriptional variations existed towards the genes involved in DNA replication, nucleic acid synthesis and cellular machinery biogenesis. Finally, with the help of the IngenuityTM pathway elucidation software, 51 genes commonly expressed between single-cells and previously shown to be associated with cancers of different histological origins were used to create a pathway of genes acting potentially of direct or indirect importance in promoting such cancers of this specific histological origin. This study demonstrated the utility of single-cell micro-genomic studies to understand the molecular mechanisms at the single cancer cell level and thereby to understand the early transcriptional reprogramming in tumorigenesis. It also provided further evidence of the transcriptomic variations between each cell of a tumour and the rapid diversity of cloned (single) cells, thereby reinforcing the major task faced by researchers to define potent treatments to eradicate cancer.

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Melanoma B16 transcriptome sequencing in C57BL16 mice under dacarbazine treatment

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