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Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach. iScience 2023; 26:105799. [PMID: 36619972 PMCID: PMC9813793 DOI: 10.1016/j.isci.2022.105799] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/20/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Although systemic chemotherapy remains the standard of care for TNBC, even combination chemotherapy is often ineffective. The identification of biomarkers for differential chemotherapy response would allow for the selection of responsive patients, thus maximizing efficacy and minimizing toxicities. Here, we leverage TNBC PDXs to identify biomarkers of response. To demonstrate their ability to function as a preclinical cohort, PDXs were characterized using DNA sequencing, transcriptomics, and proteomics to show consistency with clinical samples. We then developed a network-based approach (CTD/WGCNA) to identify biomarkers of response to carboplatin (MSI1, TMSB15A, ARHGDIB, GGT1, SV2A, SEC14L2, SERPINI1, ADAMTS20, DGKQ) and docetaxel (c, MAGED4, CERS1, ST8SIA2, KIF24, PARPBP). CTD/WGCNA multigene biomarkers are predictive in PDX datasets (RNAseq and Affymetrix) for both taxane- (docetaxel or paclitaxel) and platinum-based (carboplatin or cisplatin) response, thereby demonstrating cross-expression platform and cross-drug class robustness. These biomarkers were also predictive in clinical datasets, thus demonstrating translational potential.
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Zhang Y, Fan H, Zou C, Wei F, Sun J, Shang Y, Chen L, Wang X, Hu B. Screening seven hub genes associated with prognosis and immune infiltration in glioblastoma. Front Genet 2022; 13:924802. [PMID: 36035134 PMCID: PMC9412194 DOI: 10.3389/fgene.2022.924802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Glioblastoma (GBM) is the most common and deadly primary brain tumor in adults. Diagnostic and therapeutic challenges have been raised because of poor prognosis. Gene expression profiles of GBM and normal brain tissue samples from GSE68848, GSE16011, GSE7696, and The Cancer Genome Atlas (TCGA) were downloaded. We identified differentially expressed genes (DEGs) by differential expression analysis and obtained 3,800 intersected DEGs from all datasets. Enrichment analysis revealed that the intersected DEGs were involved in the MAPK and cAMP signaling pathways. We identified seven different modules and 2,856 module genes based on the co-expression analysis. Module genes were used to perform Cox and Kaplan-Meier analysis in TCGA to obtain 91 prognosis-related genes. Subsequently, we constructed a random survival forest model and a multivariate Cox model to identify seven hub genes (KDELR2, DLEU1, PTPRN, SRBD1, CRNDE, HPCAL1, and POLR1E). The seven hub genes were subjected to the risk score and survival analyses. Among these, CRNDE may be a key gene in GBM. A network of prognosis-related genes and the top three differentially expressed microRNAs with the largest fold-change was constructed. Moreover, we found a high infiltration of plasmacytoid dendritic cells and T helper 17 cells in GBM. In conclusion, the seven hub genes were speculated to be potential prognostic biomarkers for guiding immunotherapy and may have significant implications for the diagnosis and treatment of GBM.
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Affiliation(s)
- Yesen Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, GD, China
- Department of Neurosurgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Huasheng Fan
- Department of Neurosurgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Chun Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Feng Wei
- Department of Neurosurgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Jiwei Sun
- Department of Neurosurgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yuchun Shang
- Department of Neurosurgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Liechun Chen
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Xiangyu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, GD, China
- *Correspondence: Xiangyu Wang, ; Beiquan Hu,
| | - Beiquan Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
- *Correspondence: Xiangyu Wang, ; Beiquan Hu,
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