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Kakati RT, Kim H, Whitman A, Spanheimer PM. High expression of the RET receptor tyrosine kinase and its ligand GDNF identifies a high-risk subset of estrogen receptor positive breast cancer. Breast Cancer Res Treat 2023; 199:589-601. [PMID: 37061618 PMCID: PMC10182256 DOI: 10.1007/s10549-023-06937-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
Abstract
PURPOSE Resistance to endocrine therapy is the primary cause of treatment failure and death in patients with ER-positive (ER +)/luminal breast cancer. Expression and activation of the RET receptor tyrosine kinase may be driving poor outcomes. We aim to identify high-risk patients and druggable pathways for biomarker-based clinical trials. METHODS We obtained batch-normalized mRNA expression data from Breast Invasive Carcinoma-The Cancer Genome Atlas, PanCancer Atlas (BRCA-TCGA). To determine clinically significant cutoffs for RET expression, patients were grouped at different thresholds for Kaplan-Meier plotting. Differential gene expression (DGE) analysis and enrichment for gene sets was performed. transcriptomic dataset of antiestrogen-treated ER + tumors stratified by clinical response was then analyzed. RESULTS High RET expression was associated with worse outcomes in patients with ER + tumors, and stratification was enhanced by incorporating GDNF expression. High RET/GDNF patients had significantly lower overall survival (HR = 2.04, p = 0.012), progression-free survival (HR = 2.87, p < 0.001), disease-free survival (HR = 2.67, p < 0.001), and disease-specific survival (HR = 3.53, p < 0.001) than all other ER + patients. High RET/GDNF tumors were enriched for estrogen-independent signaling and targetable pathways including NTRK, PI3K, and KRAS. Tumors with adaptive resistance to endocrine therapy were enriched for gene expression signatures of high RET/GDNF primary tumors. CONCLUSION Expression and activation of the RET receptor tyrosine kinase may be driving poor outcomes in some patients with ER + breast cancer. ER + patients above the 75th percentile may benefit from clinical trials with tyrosine kinase inhibitors.
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Affiliation(s)
- Rasha T Kakati
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Austin Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Philip M Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA.
- Department of Surgery, University of North Carolina, Chapel Hill, NC, USA.
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Prexler C, Knape MS, Erlewein-Schweizer J, Roll W, Specht K, Woertler K, Weichert W, von Luettichau I, Rossig C, Hauer J, Richter GHS, Weber W, Burdach S. Correlation of Transcriptomics and FDG-PET SUVmax Indicates Reciprocal Expression of Stemness-Related Transcription Factor and Neuropeptide Signaling Pathways in Glucose Metabolism of Ewing Sarcoma. Cancers (Basel) 2022; 14:cancers14235999. [PMID: 36497479 PMCID: PMC9735504 DOI: 10.3390/cancers14235999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In Ewing sarcoma (EwS), long-term treatment effects and poor survival rates for relapsed or metastatic cases require individualization of therapy and the discovery of new treatment methods. Tumor glucose metabolic activity varies significantly between patients, and FDG-PET signals have been proposed as prognostic factors. However, the biological basis for the generally elevated but variable glucose metabolism in EwS is not well understood. METHODS We retrospectively included 19 EwS samples (17 patients). Affymetrix gene expression was correlated with maximal standardized uptake value (SUVmax) using machine learning, linear regression modelling, and gene set enrichment analyses for functional annotation. RESULTS Expression of five genes correlated (MYBL2, ELOVL2, NETO2) or anticorrelated (FAXDC2, PLSCR4) significantly with SUVmax (adjusted p-value ≤ 0.05). Additionally, we identified 23 genes with large SUVmax effect size, which were significantly enriched for "neuropeptide Y receptor activity (GO:0004983)" (adjusted p-value = 0.0007). The expression of the members of this signaling pathway (NPY, NPY1R, NPY5R) anticorrelated with SUVmax. In contrast, three transcription factors associated with maintaining stemness displayed enrichment of their target genes with higher SUVmax: RNF2, E2F family, and TCF3. CONCLUSION Our large-scale analysis examined comprehensively the correlations between transcriptomics and tumor glucose utilization. Based on our findings, we hypothesize that stemness may be associated with increased glucose uptake, whereas neuroectodermal differentiation may anticorrelate with glucose uptake.
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Affiliation(s)
- Carolin Prexler
- Department of Pediatrics and Children’s Cancer Research Center, Kinderklinik München Schwabing, Klinikum Rechts der Isar, Fakultät für Medizin, Technische Universität München, 80804 Munich, Germany
| | - Marie Sophie Knape
- Department of Pediatrics and Children’s Cancer Research Center, Kinderklinik München Schwabing, Klinikum Rechts der Isar, Fakultät für Medizin, Technische Universität München, 80804 Munich, Germany
| | | | - Wolfgang Roll
- Department of Nuclear Medicine, University Hospital Münster, Albert-Schweitzer-Campus 1 A1, 48149 Munster, Germany
| | - Katja Specht
- Institute of Pathology, Technische Universität München, 81675 Munich, Germany
| | - Klaus Woertler
- Musculoskeletal Radiology Section, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 81675 Munich, Germany
| | - Irene von Luettichau
- Department of Pediatrics and Children’s Cancer Research Center, Kinderklinik München Schwabing, Klinikum Rechts der Isar, Fakultät für Medizin, Technische Universität München, 80804 Munich, Germany
- ERN PaedCan, 1090 Vienna, Austria
| | - Claudia Rossig
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Muenster, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Muenster, 48149 Muenster, Germany
| | - Julia Hauer
- Department of Pediatrics and Children’s Cancer Research Center, Kinderklinik München Schwabing, Klinikum Rechts der Isar, Fakultät für Medizin, Technische Universität München, 80804 Munich, Germany
| | - Guenther H. S. Richter
- Department of Pediatrics, Division of Oncology and Hematology, Charite–Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, 13353 Berlin, Germany
| | - Wolfgang Weber
- German Cancer Consortium (DKTK), Partner Site Munich, 81675 Munich, Germany
- Department of Nuclear Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Stefan Burdach
- Department of Pediatrics and Children’s Cancer Research Center, Kinderklinik München Schwabing, Klinikum Rechts der Isar, Fakultät für Medizin, Technische Universität München, 80804 Munich, Germany
- Institute of Pathology, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 81675 Munich, Germany
- Academy of Translational Medicine and Department of Molecular Oncology–British Columbia Cancer Research Centre, University of British Columbia, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
- Correspondence:
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Chandra S, Sarkar S, Mandal P. Identification of novel genetic and epigenetic regulators of different tissue types of cervical cancer. J Obstet Gynaecol Res 2022; 48:3179-3190. [PMID: 36184073 DOI: 10.1111/jog.15454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES The study aimed to find differential gene mutations, DNA methylation, and expression profiles among different categories of cervical cancer samples. METHODS The study was based on freely available gene mutations, promoter methylation, and gene expression status of The Cancer Genome Atlas (TCGA) cervical cancer samples and adjacent normal tissues in the Genomic Data Commons (GDC) portal. The association of CpG island methylation with gene expression was determined through negative correlation analysis. RESULTS We identified that the ErbB signaling pathway and proteoglycans pathway was significantly associated with adenocarcinoma cervical cancers patients. In these pathways, missense mutation especially S310F in the ERBB2 gene as well as G12D and A146T in the KRAS gene were significantly associated with adenocarcinoma cases. Furthermore, a comparison of SCC cases with adjacent control tissues revealed differential hypermethylation of two CpG positions of the KAAG1 gene and differential downregulation of NPY1R and NPY5R genes in cervical squamous cell carcinoma compared to cervical adenocarcinoma cases and adjacent normal tissues. Specifically, the hypermethylation of the promoter region of the KAAG1 gene might be responsible for the carcinogenesis of cervical squamous cells exclusively and methylation marks can be reversible by the widely used drug, azacytidine. In contrast, adenocarcinoma cervical cancer cases may be treated with floxuridine which is successfully utilized for other tissue-specific adenocarcinoma cases. CONCLUSIONS These results provide valuable insight into the differential molecular markers among the categories of cervical cancer, which helps our ability to classify these cancers and for targeted therapy.
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Affiliation(s)
- Sanchita Chandra
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, West Bengal, India
| | - Subham Sarkar
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, West Bengal, India
| | - Paramita Mandal
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, West Bengal, India
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