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Risinskaya N, Kozhevnikova Y, Gavrilina O, Chabaeva J, Kotova E, Yushkova A, Isinova G, Zarubina K, Obukhova T, Kulikov S, Julhakyan H, Sudarikov A, Parovichnikova E. Loss of Heterozygosity in the Tumor DNA of De Novo Diagnosed Patients Is Associated with Poor Outcome for B-ALL but Not for T-ALL. Genes (Basel) 2022; 13:genes13030398. [PMID: 35327952 PMCID: PMC8952291 DOI: 10.3390/genes13030398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/29/2022] Open
Abstract
Despite the introduction of new technologies in molecular diagnostics, one should not underestimate the traditional routine methods for studying tumor DNA. Here we present the evidence that short tandem repeat (STR) profiling of tumor DNA relative to DNA from healthy cells might identify chromosomal aberrations affecting therapy outcome. Tumor STR profiles of 87 adult patients with de novo Ph-negative ALL (40 B-ALL, 43 T-ALL, 4 mixed phenotype acute leukemia (MPAL)) treated according to the “RALL-2016” regimen were analyzed. DNA of tumor cells was isolated from patient bone marrow samples taken at diagnosis. Control DNA samples were taken from the buccal swab or the blood of patients in complete remission. Overall survival (OS) analysis was used to assess the independent impact of the LOH as a risk factor. Of the 87 patients, 21 were found with LOH in various STR loci (24%). For B-ALL patients, LOH (except 12p LOH) was an independent risk factor (OS hazard ratio 3.89, log-rank p-value 0.0395). In contrast, for T-ALL patients, the OS hazard ratio was 0.59 (log-rank p-value 0.62). LOH in particular STR loci measured at the onset of the disease could be used as a prognostic factor for poor outcome in B-ALL, but not in T-ALL.
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Affiliation(s)
- Natalya Risinskaya
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Yana Kozhevnikova
- School of Medicine, Lomonosov Moscow State University, 27-1, Lomonosovsky Prospect, 119991 Moscow, Russia;
| | - Olga Gavrilina
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Julia Chabaeva
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Ekaterina Kotova
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Anna Yushkova
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Galina Isinova
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Ksenija Zarubina
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Tatiana Obukhova
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Sergey Kulikov
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Hunan Julhakyan
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
| | - Andrey Sudarikov
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
- Correspondence:
| | - Elena Parovichnikova
- National Research Center for Hematology, Novy Zykovski Lane, 4a, 125167 Moscow, Russia; (N.R.); (O.G.); (J.C.); (E.K.); (A.Y.); (G.I.); (K.Z.); (T.O.); (S.K.); (H.J.); (E.P.)
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Ampatzidou M, Florentin L, Papadakis V, Paterakis G, Tzanoudaki M, Bouzarelou D, Papadhimitriou SI, Polychronopoulou S. Copy Number Alteration Profile Provides Additional Prognostic Value for Acute Lymphoblastic Leukemia Patients Treated on BFM Protocols. Cancers (Basel) 2021; 13:cancers13133289. [PMID: 34209196 PMCID: PMC8268490 DOI: 10.3390/cancers13133289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Recent advances in genomic analyses of acute lymphoblastic leukemia (ALL) have identified novel prognostic markers associated with patient outcome. In this frame, copy number alterations (CNAs) are constantly gaining relevance as potential risk stratification markers. Herein, we present our data of a proposed CNA-profile risk-index applied on a Greek ALLIC-BFM cohort. The results of our study demonstrate that EFS for GR(good-risk)-CNA-profile patients was 96.0% versus 57.6% of PR(poor-risk)-CNA-profile ones (p < 0.001) in the whole cohort. EFS within the IR-group for the GR-CNA vs. PR-CNA subgroups was 100.0% vs. 60.0% (p < 0.001), and within the HR-group, 88.2% vs. 55.6% (p = 0.047), respectively. The above results indicate that the application of the proposed CNA-profile classifier is feasible in BFM-based protocols, adding prognostic value to the existing prognostic markers and successfully stratifying patients within prognostic subgroups. This novel genomic risk index can be incorporated in future risk-stratification algorithms, further refining MRD-based stratification and possibly reassigning optimal treatment strategies. Abstract We present our data of a novel proposed CNA-profile risk-index, applied on a Greek ALLIC-BFM-treated cohort, aiming at further refining genomic risk-stratification. Eighty-five of 227 consecutively treated ALL patients were analyzed for the copy-number-status of eight genes (IKZF1/CDKN2A/2B/PAR1/BTG1/EBF1/PAX5/ETV6/RB1). Using the MLPA-assay, patients were stratified as: (1) Good-risk(GR)-CNA-profile (n = 51), with no deletion of IKZF1/CDKN2A/B/PAR1/BTG1/EBF1/PAX5/ETV6/RB1 or isolated deletions of ETV6/PAX5/BTG1 or ETV6 deletions with a single additional deletion of BTG1/PAX5/CDKN2A/B. (2) Poor-risk(PR)-CNA-profile (n = 34), with any deletion of ΙΚΖF1/PAR1/EBF1/RB1 or any other CNA. With a median follow-up time of 49.9 months, EFS for GR-CNA-profile and PR-CNA-profile patients was 96.0% vs. 57.6% (p < 0.001). For IR-group and HR-group patients, EFS for the GR-CNA/PR-CNA subgroups was 100.0% vs. 60.0% (p < 0.001) and 88.2% vs. 55.6% (p = 0.047), respectively. Among FC-MRDd15 + patients (MRDd15 ≥ 10−4), EFS rates were 95.3% vs. 51.7% for GR-CNA/PR-CNA subjects (p < 0.001). Similarly, among FC-MRDd33 + patients (MRDd33 ≥ 10−4), EFS was 92.9% vs. 27.3% (p < 0.001) and for patients FC-MRDd33 − (MRDd33 < 10−4), EFS was 97.2% vs. 72.7% (p = 0.004), for GR-CNA/PR-CNA patients, respectively. In a multivariate analysis, the CNA-profile was the most important outcome predictor. In conclusion, the CNA-profile can establish a new genomic risk-index, identifying a distinct subgroup with increased relapse risk among the IR-group, as well as a subgroup of patients with superior prognosis among HR-patients. The CNA-profile is feasible in BFM-based protocols, further refining MRD-based risk-stratification.
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Affiliation(s)
- Mirella Ampatzidou
- Department of Pediatric Hematology-Oncology, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece; (V.P.); (S.P.)
- Correspondence:
| | - Lina Florentin
- Alfa Laboratory Diagnostic Center, YGEIA Hospital, 11524 Athens, Greece; (L.F.); (D.B.)
| | - Vassilios Papadakis
- Department of Pediatric Hematology-Oncology, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece; (V.P.); (S.P.)
| | - Georgios Paterakis
- Laboratory of Flow Cytometry, Department of Immunology, “G.Gennimatas” General Hospital, 11527 Athens, Greece;
| | - Marianna Tzanoudaki
- Department of Immunology, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece;
| | - Dimitra Bouzarelou
- Alfa Laboratory Diagnostic Center, YGEIA Hospital, 11524 Athens, Greece; (L.F.); (D.B.)
| | - Stefanos I. Papadhimitriou
- Laboratory of Hematology, Department of Molecular Cytogenetics, “G.Gennimatas” General Hospital, 11527 Athens, Greece;
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece; (V.P.); (S.P.)
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