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Dragomir M, Călugăru OT, Popescu B, Jardan C, Jardan D, Popescu M, Aposteanu S, Bădeliță S, Nedelcu G, Șerban C, Popa C, Vassu-Dimov T, Coriu D. DNA Sequencing of CD138 Cell Population Reveals TP53 and RAS-MAPK Mutations in Multiple Myeloma at Diagnosis. Cancers (Basel) 2024; 16:358. [PMID: 38254847 PMCID: PMC10813921 DOI: 10.3390/cancers16020358] [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: 12/12/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Multiple myeloma is a hematologic neoplasm caused by abnormal proliferation of plasma cells. Sequencing studies suggest that plasma cell disorders are caused by both cytogenetic abnormalities and oncogene mutations. Therefore, it is necessary to detect molecular abnormalities to improve the diagnosis and management of MM. The main purpose of this study is to determine whether NGS, in addition to cytogenetics, can influence risk stratification and management. Additionally, we aim to establish whether mutational analysis of the CD138 cell population is a suitable option for the characterization of MM compared to the bulk population. Following the separation of the plasma cells harvested from 35 patients newly diagnosed with MM, we performed a FISH analysis to detect the most common chromosomal abnormalities. Consecutively, we used NGS to evaluate NRAS, KRAS, BRAF, and TP53 mutations in plasma cell populations and in bone marrow samples. NGS data showed that sequencing CD138 cells provides a more sensitive approach. We identified several variants in BRAF, KRAS, and TP53 that were not previously associated with MM. Considering that the presence of somatic mutations could influence risk stratification and therapeutic approaches of patients with MM, sensitive detection of these mutations at diagnosis is essential for optimal management of MM.
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Affiliation(s)
- Mihaela Dragomir
- Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (M.D.); (T.V.-D.)
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Onda-Tabita Călugăru
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Bogdan Popescu
- Hematology Department, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Cerasela Jardan
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
- Hematology Department, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Dumitru Jardan
- Molecular Biology Laboratory, Medlife Bucharest, 010093 Bucharest, Romania;
| | - Monica Popescu
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Silvia Aposteanu
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Sorina Bădeliță
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Gabriela Nedelcu
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Cătălin Șerban
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
| | - Codruța Popa
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
- Hematology Department, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Tatiana Vassu-Dimov
- Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (M.D.); (T.V.-D.)
| | - Daniel Coriu
- Fundeni Clinical Institute, 022328 Bucharest, Romania; (C.J.); (M.P.); (S.A.); (S.B.); (G.N.); (C.Ș.); (C.P.); (D.C.)
- Hematology Department, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
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Melton CA, Freese P, Zhou Y, Shenoy A, Bagaria S, Chang C, Kuo CC, Scott E, Srinivasan S, Cann G, Roychowdhury-Saha M, Chang PY, Singh AH. A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. Cancers (Basel) 2023; 16:82. [PMID: 38201510 PMCID: PMC10777919 DOI: 10.3390/cancers16010082] [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: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.
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Kubicki T, Derman BA, Dytfeld D, Jakubowiak AJ. Measurable residual disease in peripheral blood in myeloma: dream or reality. Curr Opin Oncol 2023; 35:574-580. [PMID: 37621165 DOI: 10.1097/cco.0000000000000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
PURPOSE OF REVIEW Therapeutic advancements in multiple myeloma have led to increasingly deeper and more durable responses, creating a need for highly sensitive and applicable techniques for measurable residual disease (MRD) assessment. Bone marrow assays can deeply assess for MRD, but it is not conducive to performing frequent and dynamic evaluations, which may be needed for MRD-adapted treatment approaches. Recently, numerous techniques for MRD assessment in peripheral blood have come under investigation, and their integration into routine clinical practice is eagerly anticipated. RECENT FINDINGS The identification of circulating tumor cells (CTCs), evaluation of cell-free DNA, and measuring monoclonal protein concentration with mass spectrometry are promising research areas for assessing myeloma in peripheral blood. CTCs assessment and cell-free DNA may carry prognostic significance, but they lack the sensitivity of bone marrow-based techniques. Mass spectrometry has already been implemented in clinical practice in certain centers, but its full potential has yet to be fully realized. This review focuses on recent developments in these fields, emphasizing the potential future roles of these assessments. SUMMARY MRD assessment in peripheral blood is still in the development stage but holds promise for not only complementing bone marrow based evaluations but also potential for improving sensitivity.
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