Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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High throughput targeted RNA sequencing on RPTEC/TERT1 cell line exposed to multiple concentration levels of cyclosporine A at various different time points

ABSTRACT: This experiment was carried out to investigate the time dynamics of the proximal tubule cells upon the exposure of cyclosporine A in multiple severity scenario by varying the concentration. The RPTEC/TERT1 cells which are immortalized human proximal tubule cells were differentiated for 14 days to reach the optimal maturity where the cells express the proximal tubule markers and transporter similarly to human proximal tubule cells. The cells were then exposed to cyclosporine A at multiple concentration levels ranging from 0-40 uM for 4, 8,16, 24,48, and 72 hours. The cells were lysed and the lysates were collected for high throughput targeted RNA-seq with the human whole genome library. The gene expression profiles were analyzed to identify the modulated responses of the cells. This is part of the TransQST project.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Lukas Wijaya

PROVIDER: E-MTAB-11553 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Breast cancer is a heterogeneous disease classified into 3 major subtypes based on the presence or absence of molecular markers for oestrogen receptors (ER), progesterone receptors (PR) and human epidermal growth factor-2 (Her2) . Hormone receptor-positive BC (ER+, PR+ and Her-2-), accounts for approximately 70% of patients. Patients with ER- BC account for approximately 30 % of all cases and commonly have a worse prognosis than ER+ patients (9). However, a significant proportion of ER- cases have good outcomes and could potentially benefit from a less aggressive therapy. Triple negative breast cancer (TNBC, ER-, PR- and Her-2-) accounts for approximately 15% of breast cancers and has the poorest outcomes. An hypoxic microenvironment is an important intrinsic component of solid tumours that can result in rapid proliferation of cancer cells and is associated with the lack of oxgyen and abnormal tumour blood vessels. Hypoxia stimulates the hypoxia inducible factor-1α (HIF-1α) that transactivates genes associated with angiogenesis, tumour growth, metastasis, metabolic reprogramming, and treatment resistance. HIF-1α is recognised to induce the expression of carbonic anhydrase IX (CAIX), an enzyme that has been attributed a central role in pH regulation and cancer progression and is particularly pronounced in peri necrotic tumour areas, high-grade BCs. The adaption to hypoxia is governed by multiple transcriptional and post-transcriptional changes in gene expression. Up to 1.5 % of the human genome is estimated to be transcriptionally responsive to hypoxia. Genes and pathways which have been identified as being responsive to hypoxia may have the potential to be used as prognostic or predictive markers, and furthermore, can help identify novel therapeutic targets. The aim of the present study was to gain a better understanding of the transcriptomic and protein pathways associated with CAIX in ER- BC to identify potential therapeutic targets against this aggressive phenotype.

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High throughput targeted RNA sequencing on RPTEC/TERT1 cell line exposed to multiple concentration levels of cyclosporine A at various different time points

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