Bulk RNA-seq analysis of prostate tissues treated with neoadjuvant ADT plus enzalutamide
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PROVIDER: PRJNA759198 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goals of this study is to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant miRNome profiling to Androgen Deprivation Therapy (ADT) sensitive miRNome profile in African American prostate cancer cells and validate by reverse transcription polymerase chain reaction (qRT–PCR) methods. Method: Mirco-RNA were isolated from different CaP cells who were sensitive and resistant to Androgen Deprivation Therapy (ADT). Total micro-RNA were subjected to miRNA-Seq. Results: We performed whole miRNA-Seq analysis through paired-end deep sequencing to systematically investigate the molecular features of different CaP cell models- RC-77-N, RC-77T/E, RCC7T/E-ADT, RCC7T/E-CD133-plus, E006AA-hT and E006AA-hT-ADT. Conclusions: Our study represents the first detailed analysis of African American ADT resistant miRNome, with biologic replicates, generated by miRNA-seq technology.
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Project description:This phase II study examined the pathological complete response (pCR) rate and safety of two gemcitabine-based combinations administered sequentially in breast cancer. We also examined gene expression profiles from tumor biopsies to identify biomarkers predictive of response. Methods: Indian women with large or locally advanced breast cancer received 4 cycles of gemcitabine 1200 mg/m2 plus doxorubicin 60 mg/m2 (Gem+Dox), then 4 cycles of gemcitabine 1000 mg/m2 plus cisplatin 70 mg/m2 (Gem+Cis), and surgery. To examine dynamic changes in molecular profiles after one dose of therapy, we used three alternate sequences during cycle 1 (Gem d1, 8; Dox d2; Gem d1, 8; Dox d1; or Gem d2, 8; Dox d1). Results: Of 65 women (median age 46) treated, 13 (24.5% of 53 patients with surgery) had a pCR and 22 (33.8%) had a complete clinical response. Patients who received Gem d1, 8 and Dox d2 in cycle 1 (20/65) reported more toxicities, with G3/4 neutropenic infection/febrile neutropenia (7/20) and vomiting (5/20) as the most common cycle 1 events. Four drug-related deaths occurred. 46/65 patients yielded successful pretreatment gene expression profiles. Ten-fold cross-validated supervised analyses identified gene expression patterns that predicted with >73% accuracy (1) clinical complete response after eight cycles, (2) overall clinical complete response, and (3) pCR. Conclusions: This neoadjuvant regimen showed strong activity. A subset of patients receiving Gem d1, 8 and Dox d2 experienced unacceptable toxicity, whereas patients on other sequences had more manageable safety profiles. The predictive gene expression patterns may provide a method for selecting patients most likely to benefit from gemcitabine-containing neoadjuvant therapy. Key words: breast cancer, chemotherapy, gemcitabine, , gene expression, microarrays, neoadjuvant therapy Keywords: Dose response
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Project description:Prostate cancer C4-2B cells were cultured in enzalutamide in a dose-escalation manner. After sixty passages cells were resistant to enzalutamide, with a specific sets of genes been deregulated. We performed global gene expression analysis by cDNA microarrays to identify genes responsible for enzalutamide resistance in C4-2B-MDVR cells. Enzalutamide resistant C4-2B-MDVR cells were selected from C4-2B cells during long time enzalutamide treatment. Genes responsible for enzalutamide resistance were identified using C4-2B vs. C4-2B-MDVR RNA extraction and hybridization on Affymetrix microarrays.
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