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Muralidharan K, Yekula A, Small JL, Rosh ZS, Kang KM, Wang L, Lau S, Zhang H, Lee H, Bettegowda C, Chicoine MR, Kalkanis SN, Shankar GM, Nahed BV, Curry WT, Jones PS, Cahill DP, Balaj L, Carter BS. TERT Promoter Mutation Analysis for Blood-Based Diagnosis and Monitoring of Gliomas. Clin Cancer Res 2020; 27:169-178. [PMID: 33051308 DOI: 10.1158/1078-0432.ccr-20-3083] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/15/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Liquid biopsy offers a minimally invasive tool to diagnose and monitor the heterogeneous molecular landscape of tumors over time and therapy. Detection of TERT promoter mutations (C228T, C250T) in cfDNA has been successful for some systemic cancers but has yet to be demonstrated in gliomas, despite the high prevalence of these mutations in glioma tissue (>60% of all tumors). EXPERIMENTAL DESIGN Here, we developed a novel digital droplet PCR (ddPCR) assay that incorporates features to improve sensitivity and allows for the simultaneous detection and longitudinal monitoring of two TERT promoter mutations (C228T and C250T) in cfDNA from the plasma of patients with glioma. RESULTS In baseline performance in tumor tissue, the assay had perfect concordance with an independently performed clinical pathology laboratory assessment of TERT promoter mutations in the same tumor samples [95% confidence interval (CI), 94%-100%]. Extending to matched plasma samples, we detected TERT mutations in both discovery and blinded multi-institution validation cohorts with an overall sensitivity of 62.5% (95% CI, 52%-73%) and a specificity of 90% (95% CI, 80%-96%) compared with the gold-standard tumor tissue-based detection of TERT mutations. Upon longitudinal monitoring in 5 patients, we report that peripheral TERT-mutant allele frequency reflects the clinical course of the disease, with levels decreasing after surgical intervention and therapy and increasing with tumor progression. CONCLUSIONS Our results demonstrate the feasibility of detecting circulating cfDNA TERT promoter mutations in patients with glioma with clinically relevant sensitivity and specificity.
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Affiliation(s)
- Koushik Muralidharan
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Julia L Small
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Zachary S Rosh
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keiko M Kang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,School of Medicine, University of California, San Diego, La Jolla, California
| | - Lan Wang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Spencer Lau
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hui Zhang
- Biostatistics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael R Chicoine
- Department of Neurosurgery, Washington University Medicine in St. Louis, St. Louis, Missouri
| | - Steven N Kalkanis
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan
| | - Ganesh M Shankar
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brian V Nahed
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - William T Curry
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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Wang L, Yekula A, Muralidharan K, Small JL, Rosh ZS, Kang KM, Carter BS, Balaj L. Novel Gene Fusions in Glioblastoma Tumor Tissue and Matched Patient Plasma. Cancers (Basel) 2020; 12:cancers12051219. [PMID: 32414213 PMCID: PMC7281415 DOI: 10.3390/cancers12051219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/27/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
Sequencing studies have provided novel insights into the heterogeneous molecular landscape of glioblastoma (GBM), unveiling a subset of patients with gene fusions. Tissue biopsy is highly invasive, limited by sampling frequency and incompletely representative of intra-tumor heterogeneity. Extracellular vesicle-based liquid biopsy provides a minimally invasive alternative to diagnose and monitor tumor-specific molecular aberrations in patient biofluids. Here, we used targeted RNA sequencing to screen GBM tissue and the matched plasma of patients (n = 9) for RNA fusion transcripts. We identified two novel fusion transcripts in GBM tissue and five novel fusions in the matched plasma of GBM patients. The fusion transcripts FGFR3-TACC3 and VTI1A-TCF7L2 were detected in both tissue and matched plasma. A longitudinal follow-up of a GBM patient with a FGFR3-TACC3 positive glioma revealed the potential of monitoring RNA fusions in plasma. In summary, we report a sensitive RNA-seq-based liquid biopsy strategy to detect RNA level fusion status in the plasma of GBM patients.
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Affiliation(s)
- Lan Wang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
| | - Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
| | - Koushik Muralidharan
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
| | - Julia L. Small
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
| | - Zachary S. Rosh
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
| | - Keiko M. Kang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
- School of Medicine, University of California San Diego, San Diego, CA 92092, USA
| | - Bob S. Carter
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
- Correspondence: (B.S.C.); (L.B.)
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; (L.W.); (A.Y.); (K.M.); (J.L.S.); (Z.S.R.); (K.M.K.)
- Correspondence: (B.S.C.); (L.B.)
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