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Transcriptomic analysis of breast cancer patients sensitive and resistant to chemotherapy: Looking for overall survival and drug resistance biomarkers

ABSTRACT: Transcriptomic analysis of breast cancer patients sensitive and resistant to chemotherapy: Looking for overall survival and drug resistance biomarkers

PROVIDER: PRJNA680808 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13147304_1.fastq.gz	Fastqsanger.gz
	SRR13147304_2.fastq.gz	Fastqsanger.gz
	SRR13147305_1.fastq.gz	Fastqsanger.gz
	SRR13147305_2.fastq.gz	Fastqsanger.gz
	SRR13147306_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of breast cancer patients sensitive and resistant to chemotherapy: Looking for overall survival and drug resistance biomarkers

Project description:Purpose: Neoadjuvant chemotherapy is one important therapeutic strategy for breast cancer with the drawback of resistance development. Chemotherapy has adverse effects that combined with resistance could contribute to lower overall survival. This work aimed to evaluate the molecular profile of patients who received neoadjuvant chemotherapy trying to discover differentially expressed genes (DEGs) that could be used as biomarkers of chemotherapy response and overall survival. Methods: Breast cancer patients who received neoadjuvant chemotherapy were enrolled in this study and according to their pathological response were assigned as sensitive or resistant. To evaluate DEGs, GO, KEGG and protein-protein interactions, RNAseq information from all patients was obtained by next generation sequencing. Results: A total of 1985 DEGs were found and KEGG analysis indicated a great number of DEGs in metabolic pathways, pathways in cancer, cytokine-cytokine receptor interactions, and neuroactive ligand-receptor interactions. A selection of 73 DEGs were used further for an analysis of overall survival using the METABRIC study. Seven of those DEGs were found to correlated with overall survival, of them the sub-expression of C1QTNF3, CTF1, OLFML3, PLA2R1, PODN and the over expression of TUBB and TCP1 were found in resistant patients and related to patients with lower overall survival. Conclusions: This work highlights differences at the level of gene expression in patients resistant and sensitive to neoadjuvant chemotherapy. Cellular components related to extracellular region and plasma membrane were mainly involved. Furthermore, 73 DEGs were able to discriminate patients resistant and sensitive to neoadjuvant chemotherapy, and 7 of them were able to predict overall survival.

2021-04-30 | GSE162187 | GEO

Transcriptomic Analysis of Breast Cancer Patients Sensitive and Resistant to Chemotherapy: Looking for Overall Survival and Drug Resistance Biomarkers.

Project description: Not available

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RNA-Seq of neuroblastoma Th-MYCN mouse model, samples sensitive to chemotherapy, and those with chemotherapy resistance

Project description:Some neuroblastoma patients relapse after chemotherapy. Here, a Th-MYCNCPM32 mouse model usually have spontaneously tumours which are sensitive to chemotherapy. By treating mice with consecutive cycles of sublethal cyclophosphamide (CPM) using a personal dose escalation protocol (PDE), resistant tumours may develop. This experiment aims to compare the expression profiles (RNA-Seq) of sensitive and resistant MYCN driven tumours in order to understand the mechanisms behind resistance. Samples also presented cross-resistance to vincristine and doxorubicin.

2018-09-30 | E-MTAB-5858 | biostudies-arrayexpress

HCL Overall Analysis

Project description:HCL Overall Analysis

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RNA-Seq of neuroblastoma Th-MYCN mouse model, samples sensitive to chemotherapy, and those with chemotherapy resistance

Project description:RNA-Seq of neuroblastoma Th-MYCN mouse model, samples sensitive to chemotherapy, and those with chemotherapy resistance

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Long noncoding RNA expression profile of chemotherapy-sensitive and resistant breast cancer tissues

Project description:To explore novel lncRNAs relative to chemo-resistance in breast cancer, we performed lncRNA microarray analysis using three anthracycline-resistant tissues and three anthracycline-sensitive tissues collected before neoadjuvant chemotherapy by Arraystar Human LncRNA Microarray V3.0.

2024-07-16 | GSE221060 | GEO

Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

Project description:PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared. Neoadjuvant validation cohort of 198 HER2-negative breast cancer cases treated with taxane-anthracycline chemotherapy pre-operatively and endocrine therapy if ER-positive. Response was assessed at the end of neoadjuvant treatment and distant-relapse-free survival was followed for at least 3 years post-surgery.

2011-05-11 | E-GEOD-25065 | biostudies-arrayexpress

Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

Project description:PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared. Neoadjuvant study of 310 HER2-negative breast cancer cases treated with taxane-anthracycline chemotherapy pre-operatively and endocrine therapy if ER-positive. Response was assessed at the end of neoadjuvant treatment and distant-relapse-free survival was followed for at least 3 years post-surgery.

2011-05-11 | E-GEOD-25055 | biostudies-arrayexpress

Haptoglobin and glutamine synthetase as potential biomarkers of chemotherapy-induced cachexia in skeletal muscle

Project description:Cancer cachexia is a multifactorial wasting syndrome affecting body and lean tissue mass that is often exacerbated by anticancer chemotherapy. In this study, we used a mouse model of acute myeloid leukemia chemotherapy induction regimen (CIR) comprising daunorubicin and cytarabine to investigate the molecular mechanisms underlying cachexia. Quantitative tandem mass tag (TMT) based proteomics was performed on skeletal muscle (quadriceps) to uncover biomarkers and pathways associated with chemotherapy induced muscle wasting. Our findings demonstrate that the AML CIR induced an acute cachexic phenotype characterized by approximately 10 percent body and lean mass loss and 20 percent muscle fibre atrophy. Through deep proteome profiling, two potential biomarkers—haptoglobin (Hp) and glutamine synthetase (Glul)—were identified. Haptoglobin in particular was responsive to cachexia severity, recovery, and exacerbation via exercise, indicating its potential as a conditionally sensitive biomarker of muscle wasting. Pathway analysis revealed upregulation of mitochondrial metabolism including branched chain amino acid catabolism and mitochondrial uncoupling proteins (Ucp1 and Ucp3), suggesting hypermetabolism as a key driver of the phenotype. These data support the use of skeletal muscle proteomics in characterizing chemotherapy induced cachexia and identifying sensitive muscle specific biomarkers for future translational and therapeutic studies.

2025-06-16 | PXD063910 | Pride

Multidrug Resistance-Linked Gene Signature Predicts Overall Survival of Patients with Primary Ovarian Serous Carcinoma

Project description:This study assesses the ability of multidrug resistance (MDR)-associated gene expression patterns to predict survival in patients with newly diagnosed carcinoma of the ovary. The scope of this research differs substantially from that of previous reports, as a very large set of genes was evaluated whose expression has been shown to affect response to chemotherapy. We applied a customized TaqMan Low-Density Array, a highly sensitive and specific assay, to study the expression profiles of 380 MDR-linked genes in 80 tumor specimens collected at initial surgery to debulk primary serous carcinoma of Mullerian origin. The RNA expression profiles of these drug resistance genes were correlated with clinical outcomes.

2012-04-19 | E-GEOD-30009 | biostudies-arrayexpress

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