Establishment of EGFR-inhibitor resistant triple negative breast cancer models from patient derived xenografts
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ABSTRACT:
PROVIDER: PRJNA782552 | ENA |
REPOSITORIES: ENA
Dataset's files
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| SRR16992317_1.fastq.gz | Fastqsanger.gz | |||
| SRR16992317_2.fastq.gz | Fastqsanger.gz | |||
| SRR16992318_1.fastq.gz | Fastqsanger.gz | |||
| SRR16992318_2.fastq.gz | Fastqsanger.gz | |||
| SRR16992319_1.fastq.gz | Fastqsanger.gz |
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Project description:Establishment of EGFR-inhibitor resistant triple negative breast cancer models from patient derived xenografts [scRNA-seq]
| PRJNA782558 | ENA
Project description:Establishment of EGFR-inhibitor resistant triple negative breast cancer models from patient derived xenografts [Bulk RNA-seq]
| PRJNA782262 | ENA
Project description:Aim: The goals of this study were to identify transcriptomic changes that arise in basal-like breast cancer cells during the development of resistance to epidermal growth factor receptor inhibitors (EGFRi) and to identify drugs that are cytotoxic once EGFRi resistance occurs. Methods: Human patient-derived xenografts (PDXs) were grown in immunodeficient mice and were treated with a set of EGFRi; the EGFRi erlotinib was selected for more expansive in vivo studies. Single-cell RNA sequencing was performed on mammary tumors from the basal-like PDX WHIM2 that was treated with vehicle or erlotinib for nine weeks. The PDX was then subjected to long-term erlotinib treatment in vivo and through serialserially passaging, an erlotinib-resistant subline of WHIM2 was generated. Bulk RNA-sequencing was performed on parental and erlotinib-resistant tumors. In vitro high-throughput drug screening with >500 clinically used compounds was performed on parental and erlotinib-resistant cells. Previously published bulk gene expression microarray data from MMTV-Wnt1 tumors were contrasted with the WHIM2 PDX data. Results: Erlotinib effectively inhibited WHIM2 tumor growth for ~four weeks. Compared to untreated cells, single-cell RNA sequencing revealed that a greater proportion of erlotinib-treated cells were in the G1 phase of the cell cycle. Comparison of WHIM2 and MMTV-Wnt1 RNA level data revealed a set of 37 overlapping genes that were differentially expressed in the erlotinib-resistant subsets of WHIM2 and MMTV-Wnt1 tumors. Comparison of all three data types revealed five genes that were upregulated across all erlotinib-resistant samples: IL19, KLK7, LCN2, SAA1, and SAA2. Despite transcriptomic differences, parental and erlotinib-resistant WHIM2 displayed similar responses to the majority of drugs assessed for cytotoxicity in vitro. Conclusion: This study identified transcriptomic changes arising in erlotinib-resistant basal-like breast cancer. Interestingly, four of the five genes that were found to be upregulated in the basal-like erlotinib-resistant samples were also upregulated in erlotinib-resistant non-small cell lung cancer samples. These gene signatures could be used to identify basal-like breast cancer patients that would best respond to EGFRi. Future studies should explore the predictive capacity of these gene signatures as well as how these differentially expressed genes contribute to the development of EGFRi resistance.
2022-12-07 | GSE189324 | GEO
Project description:Aim: The goals of this study were to identify transcriptomic changes that arise in basal-like breast cancer cells during the development of resistance to epidermal growth factor receptor inhibitors (EGFRi) and to identify drugs that are cytotoxic once EGFRi resistance occurs. Methods: Human patient-derived xenografts (PDXs) were grown in immunodeficient mice and were treated with a set of EGFRi; the EGFRi erlotinib was selected for more expansive in vivo studies. Single-cell RNA sequencing was performed on mammary tumors from the basal-like PDX WHIM2 that was treated with vehicle or erlotinib for nine weeks. The PDX was then subjected to long-term erlotinib treatment in vivo and through serialserially passaging, an erlotinib-resistant subline of WHIM2 was generated. Bulk RNA-sequencing was performed on parental and erlotinib-resistant tumors. In vitro high-throughput drug screening with >500 clinically used compounds was performed on parental and erlotinib-resistant cells. Previously published bulk gene expression microarray data from MMTV-Wnt1 tumors were contrasted with the WHIM2 PDX data. Results: Erlotinib effectively inhibited WHIM2 tumor growth for ~four weeks. Compared to untreated cells, single-cell RNA sequencing revealed that a greater proportion of erlotinib-treated cells were in the G1 phase of the cell cycle. Comparison of WHIM2 and MMTV-Wnt1 RNA level data revealed a set of 37 overlapping genes that were differentially expressed in the erlotinib-resistant subsets of WHIM2 and MMTV-Wnt1 tumors. Comparison of all three data types revealed five genes that were upregulated across all erlotinib-resistant samples: IL19, KLK7, LCN2, SAA1, and SAA2. Despite transcriptomic differences, parental and erlotinib-resistant WHIM2 displayed similar responses to the majority of drugs assessed for cytotoxicity in vitro. Conclusion: This study identified transcriptomic changes arising in erlotinib-resistant basal-like breast cancer. Interestingly, four of the five genes that were found to be upregulated in the basal-like erlotinib-resistant samples were also upregulated in erlotinib-resistant non-small cell lung cancer samples. These gene signatures could be used to identify basal-like breast cancer patients that would best respond to EGFRi. Future studies should explore the predictive capacity of these gene signatures as well as how these differentially expressed genes contribute to the development of EGFRi resistance.
2022-12-07 | GSE189257 | GEO
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2022-12-07 | GSE189325 | GEO
Project description:Inhibitor of apoptosis (IAP) proteins constitute a conserved family of molecules which regulate both apoptosis and receptor signaling. They are often deregulated in cancer cells and represent potential targets for therapy. In our work, we investigated the effect of IAP inhibition in vivo to identify novel downstream genes expressed in an IAP-dependent manner that could contribute to cancer aggressiveness. To this end, immunocompromised mice engrafted subcutaneously with the triple negative breast cancer MDA-MB231 cell line were treated with SM83, a pan-IAP inhibitor developed by us, and tumor nodules were profiled for gene expression. Our work suggests that IAP-targeted therapy could contribute to EGFR inhibition and the reduction of its downstream mediators. This approach could be particularly effective in cells characterized by high levels of EGFR and Snai2, such as triple negative breast cancer.
2018-12-06 | GSE98691 | GEO
Project description:Patient derived xenografts (PDX) were created from two triple-negative breast cancers (PDX-110 and PDX-332) taken at the time of surgery from drug-naive patients. Freshly sorted epithelial cells were profiled by single-cell RNA-seq (scRNA-seq) using a 10X Genomics Chromium System.
2019-02-26 | GSE123926 | GEO
Project description:The mechanisms by which tumors develop resistance to angiogenesis inhibitors, and the relative contributions of tumor cells and stroma to resistance, are not completely understood. We developed three human lung adenocarcinoma murine models of resistance to the VEGF inhibitor bevacizumab and, using species-specific profiling, separately investigated tumor cell and stromal molecules associated with resistance. Gene expression changes associated with acquired resistance occurred predominantly in stromal (mouse) and not tumor (human) cells. Components of the EGFR and FGFR2 pathways were significantly upregulated in stroma, but not in tumor cells. Increased activated EGFR was detected on pericytes of xenografts that acquired resistance and on endothelium of tumors with relative primary resistance. Acquired resistance was associated with a pattern of pericyte-covered, normalized revascularization, whereas tortuous, uncovered vessels were observed in relative primary resistance. Dual targeting of VEGF and EGFR pathways with bevacizumab and erlotinib, or the VEGFR/EGFR inhibitor vandetanib, reduced pericyte coverage and increased progression-free survival. These findings demonstrate that alterations in tumor stromal pathways, including EGFR and FGFR2, are associated with, and may contribute to VEGF inhibitor resistance and that targeting these pathways may improve therapeutic efficacy. Understanding stromal signaling may be critical for developing biomarkers for angiogenesis inhibitors and improving combination regimens.
2011-04-22 | GSE26644 | GEO
Project description:Dimerization is believed necessary for receptor tyrosine kinases (RTKs) activation. Here we report that monomeric epidermal growth factor receptor (EGFR) directly phosphorylates the signal transducer and activator of transcription-3 (STAT3) in the absence of transmembrane protein TMEM25 (hereafter referred to as TAMER (Transmembrane protein Antagonizing Monomeric EGF Receptor signaling) to reflect its molecular function). We identified TAMER as a checkpoint for the monomeric-EGFR/STAT3 signaling, and downregulation of TAMER in triple-negative breast cancer (TNBC) results in a persistent activation of STAT3 that is required for TNBC progression, which gives a good explanation why targeting EGFR dimerization by antibodies showed no significant benefit to TNBC patients in clinical trials. Remarkably, supply of TAMER strongly suppressed TNBC progression, presenting a promising targeted therapy for TNBC. Hence, our study demonstrated the first RTK monomer-mediated signaling pathway, introducing an unprecedented pattern of RTK signaling that may play key roles in certain physiological or pathological contexts, which might need to be inspected for therapeutically targeting RTKs in the future.In this paper, RNA-seq were used to identify different gene expression in WT and TMEM25 knockout MDA-MB-231 cells.
2024-07-28 | GSE180989 | GEO
Project description:DNA methylation of two triple-negative patient-derived breast cancer xenografts
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