Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of human ex vivo ovarian cancer models - part IV

ABSTRACT: Ascites or solid tumour samples from patients with ovarian cancer were collected and grown in culture as ex vivo models of purified tumour cells. RNA-seq was performed on these models to establish gene expression profiles, which allows identification of genes that are differentially expressed between models with differing tumour intrinsic properties. These samples have been interrogated (1) for their mRNA levels of the ATP-binding cassette (ABC) transporter protein ABCB1 and (2) for differentially expressed genes associated with sensitivity/resistance to the SAE inhibitor ML-792. These samples are processed in the same manner as previous studies: E-MTAB-7223, E-MTAB-10801 and E-MTAB-11000 with no stromal counterparts included in this current sequencing batch.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

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PROVIDER: E-MTAB-14568 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-10801

REPOSITORIES: biostudies-arrayexpress

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Project description:Despite the high prevalence and poor outcome of patients with metastatic lung cancer, the mechanisms of tumour progression and metastasis remain largely uncharacterized. We modelled human lung adenocarcinoma, which frequently harbours activating point mutations in KRAS1 and inactivation of the p53-pathway2, using conditional alleles in mice3-5. Lentiviral-mediated somatic activation of oncogenic Kras and deletion of p53 in the lung epithelial cells of KrasLSL-G12D/+;p53flox/flox mice initiates lung adenocarcinoma development4. Although tumours are initiated synchronously by defined genetic alterations, only a subset become malignant, suggesting that disease progression requires additional alterations. Identification of the lentiviral integration sites allowed us to distinguish metastatic from non-metastatic tumours and determine the gene expression alterations that distinguish these tumour types. Cross-species analysis identified the NK-2 related homeobox transcription factor Nkx2-1 (Ttf-1/Titf1) as a candidate suppressor of malignant progression. In this mouse model, Nkx2-1-negativity is pathognomonic of high-grade poorly differentiated tumours. Gain- and loss-of-function experiments in cells derived from metastatic and non-metastatic tumours demonstrated that Nkx2-1 controls tumour differentiation and limits metastatic potential in vivo. Interrogation of Nkx2-1 regulated genes, analysis of tumours at defined developmental stages, and functional complementation experiments indicate that Nkx2-1 constrains tumours in part by repressing the embryonically-restricted chromatin regulator Hmga2. While focal amplification of NKX2-1 in a fraction of human lung adenocarcinomas has focused attention on its oncogenic function6-9, our data specifically link Nkx2-1 downregulation to loss of differentiation, enhanced tumour seeding ability, and increased metastatic proclivity. Thus, the oncogenic and suppressive functions of Nkx2-1 in the same tumour type substantiate its role as a dual function lineage factor. 23 cell lines derived from primary tumor or metastasis. 6 samples analyzed to determine the effect of Nkx2-1 knockdown on gene expression

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RNA-seq of human ex vivo ovarian cancer models - part IV

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