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1. Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia

Author

E. Genescà, A. Lazarenkov, M. Morgades, G. Berbis, N. Ruíz-Xivillé, P. Gómez-Marzo, J. Ribera, J. Juncà, A. González-Pérez, S. Mercadal, R. Guardia, M. T. Artola, M. J. Moreno, J. Martínez-López, L. Zamora, P. Barba, C. Gil, M. Tormo, A. Cladera, A. Novo, M. Pratcorona, J. Nomdedeu, J. González-Campos, M. Almeida, J. Cervera, P. Montesinos, M. Batlle, S. Vives, J. Esteve, E. Feliu, F. Solé, A. Orfao, and J. M. Ribera

Subjects
T-ALL, CDKN2A/ARF, CDKN2B, Prognosis, MRD, Diseases of the blood and blood-forming organs, RC633-647.5, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Recurrent deletions of the CDKN2A/ARF/CDKN2B genes encoded at chromosome 9p21 have been described in both pediatric and adult acute lymphoblastic leukemia (ALL), but their prognostic value remains controversial, with limited data on adult T-ALL. Here, we investigated the presence of homozygous and heterozygous deletions of the CDKN2A/ARF and CDKN2B genes in 64 adult T-ALL patients enrolled in two consecutive trials from the Spanish PETHEMA group. Alterations in CDKN2A/ARF/CDKN2B were detected in 35/64 patients (55%). Most of them consisted of 9p21 losses involving homozygous deletions of the CDKNA/ARF gene (26/64), as confirmed by single nucleotide polymorphism (SNP) arrays and interphase fluorescence in situ hybridization (iFISH). Deletions involving the CDKN2A/ARF/CDKN2B locus correlated with a higher frequency of cortical T cell phenotype and a better clearance of minimal residual disease (MRD) after induction therapy. Moreover, the combination of an altered copy-number-value (CNV) involving the CDKN2A/ARF/CDKN2B gene locus and undetectable MRD (≤ 0.01%) values allowed the identification of a subset of T-ALL with better overall survival in the absence of hematopoietic stem cell transplantation.

Published
2018
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2. Additional file 1: of Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia

Author

E. Genescà, A. Lazarenkov, M. Morgades, G. Berbis, N. Ruíz-Xivillé, P. Gómez-Marzo, J. Ribera, J. Juncà, A. González-Pérez, S. Mercadal, R. Guardia, M. Artola, M. Moreno, J. Martínez-López, L. Zamora, P. Barba, C. Gil, M. Tormo, A. Cladera, A. Novo, M. Pratcorona, J. Nomdedeu, J. González-Campos, M. Almeida, J. Cervera, P. Montesinos, M. Batlle, S. Vives, J. Esteve, E. Feliu, F. Solé, and A. Orfao

Abstract

Table S1. Frequency and type of CDKN2A/ARF/CDKN2B gene deletions as detected by qPCR in adult T-ALL (n = 64). Table S2. Comparison between the CNA status of the CDKN2A/ARF and CDKN2B genes in adult T-ALL as assessed by qPCR, SNP-array and iFISH techniques. Table S3. Adult T-ALL: prognostic factors for overall survival. Table S4. Adult T-ALL patient characteristics at diagnosis and follow-up. Table S5. (A) RCN values obtained for the CDKN2A/ARF and CDKN2B genes in selected samples with a 100% blast cell content. (B). Most robust cut-off values to distinguish between normal, heterozygous and homozygous genotypes. The mean and standard deviation (SD) of the values obtained in panel A are indicated for each genotype. Figure S1. Prognostic impact of the CDKN2B gene CNA status on overall survival of adult T-ALL patients (n = 62). In panel A all CDKN2B gene deletions were analyzed together, while in panel B bi-allelic and mono-allelic CDKN2B gene deletions were separately considered. Figure S2. Flowchart summarizing the HR-20011 PETHEMA treatment protocol, including the time points at which MRD assessment was performed (highlighted in red). Figure S3. Calibration curves used to calculate RCN values according to the different percentage contamination of the sample by normal (i.e. non-blastic) cells. In panel A, a pure (100% blasts) homozygous sample was mixed with different amounts of normal (2 N) DNA, as shown on the x-axis. RCN values are shown on the y-axis. In panel B a pure (100%) heterozygous sample was mixed with different amounts of normal (2 N) DNA, as shown on the x-axis; RCN values are depicted on the y-axis. (PDF 274 kb)

Published
2018
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3. Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia.

Author

Genescà E, Lazarenkov A, Morgades M, Berbis G, Ruíz-Xivillé N, Gómez-Marzo P, Ribera J, Juncà J, González-Pérez A, Mercadal S, Guardia R, Artola MT, Moreno MJ, Martínez-López J, Zamora L, Barba P, Gil C, Tormo M, Cladera A, Novo A, Pratcorona M, Nomdedeu J, González-Campos J, Almeida M, Cervera J, Montesinos P, Batlle M, Vives S, Esteve J, Feliu E, Solé F, Orfao A, and Ribera JM

Subjects
Cyclin-Dependent Kinase Inhibitor p16 genetics, Humans, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma pathology, Prognosis, Cyclin-Dependent Kinase Inhibitor p15 genetics, Gene Deletion, Genes, p16, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma genetics, Tumor Suppressor Protein p14ARF genetics
Abstract

Recurrent deletions of the CDKN2A/ARF/CDKN2B genes encoded at chromosome 9p21 have been described in both pediatric and adult acute lymphoblastic leukemia (ALL), but their prognostic value remains controversial, with limited data on adult T-ALL. Here, we investigated the presence of homozygous and heterozygous deletions of the CDKN2A/ARF and CDKN2B genes in 64 adult T-ALL patients enrolled in two consecutive trials from the Spanish PETHEMA group. Alterations in CDKN2A/ARF/CDKN2B were detected in 35/64 patients (55%). Most of them consisted of 9p21 losses involving homozygous deletions of the CDKNA/ARF gene (26/64), as confirmed by single nucleotide polymorphism (SNP) arrays and interphase fluorescence in situ hybridization (iFISH). Deletions involving the CDKN2A/ARF/CDKN2B locus correlated with a higher frequency of cortical T cell phenotype and a better clearance of minimal residual disease (MRD) after induction therapy. Moreover, the combination of an altered copy-number-value (CNV) involving the CDKN2A/ARF/CDKN2B gene locus and undetectable MRD (≤ 0.01%) values allowed the identification of a subset of T-ALL with better overall survival in the absence of hematopoietic stem cell transplantation.

Published
2018
Full Text
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