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PROGNOSTIC IMPACT OF ADDITIONAL MOLECULAR LESIONS IN PH+ ACUTE LYMPHOBLASTIC LEUKEMIA (ALL)
Author(s):
Anna Lucia Fedullo
,
Anna Lucia Fedullo
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Monica Messina
,
Monica Messina
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Antonella Vitale
,
Antonella Vitale
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Loredana Elia
,
Loredana Elia
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Alfonso Piciocchi
,
Alfonso Piciocchi
Affiliations:
GIMEMA Data Center,Rome,Italy
Valentina Gianfelici
,
Valentina Gianfelici
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Alessia Lauretti
,
Alessia Lauretti
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Anna Guarini
,
Anna Guarini
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Sabina Chiaretti
,
Sabina Chiaretti
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
Robin Foà
Robin Foà
Affiliations:
Hematology, Department of Cellular Biotechnology and Hematology,Sapienza University,Rome,Italy
(Abstract release date: 05/18/17) EHA Library. Fedullo A. 06/25/17; 182087; S800
Anna Lucia Fedullo
Anna Lucia Fedullo
Contributions
PDF Abstract
Abstract

Abstract: S800

Type: Oral Presentation

Presentation during EHA22: On Sunday, June 25, 2017 from 08:15 - 08:30

Location: Room N103

Background
The outcome of Ph+ acute lymphoblastic leukemia (Ph+ ALL) has drastically improved since the introduction of tyrosine kinase inhibitors (TKI). At present however, well-defined prognostic markers, beyond the monitoring of minimal residual disease (MRD) during follow-up and to a lesser extent IKZF1 deletions, are lacking.

Aims
To identify genomic lesions of prognostic value, we evaluated copy number aberrations (CNA) by SNP arrays, confirmed them by multiplex ligation-dependent probe amplification (MLPA) and we set up a droplet digital PCR (ddPCR) assays for additional lesions. Furthermore, we correlated the lesions identified with MRD monitoring, outcome and biological features, such as the type of fusion protein (p190 or p210). Finally, in a subset of patients gene expression profiling (GEP) was carried out.

Methods

Genomic DNA of 116 newly diagnosed adult Ph+ ALL patients enrolled in 4 consecutive GIMEMA trials, namely 0201B, 0904, 1205 and 1509, was evaluated. All the trials were based on an induction with steroids and TKI, the first 2 with imatinib and the remainders with dasatinib. For CNA, the Cytoscan HD Arrays (Affymetrix, Santa Clara, CA) were used. The lesions were confirmed by MLPA on all samples using the Salsa MLPA P335-A3 ALL-IKZF1 kit (MRC-Holland, Amsterdam, The Netherlands). ddPCR was used to validate lesions targeting MEF2C. In 42 cases, GEP experiments were performed using the HGU133 Plus 2.0 gene chips (Affymetrix, Santa Clara, CA). 

Results

We found a similar load and type of lesions across the 4 trials, one of which included elderly. The majority of lesions targeted IKZF1 (84%), PAX5 (36%) and CDKN2A/B (32%). In our cohort, IKZF1 deletions alone did not affect complete molecular response (CMR) achievement or disease-free survival (DFS), while patients harboring CDKN2A/B and PAX5 deletions had a significant inferior outcome (p=0.004, p=0.003 respectively). In line with this, a worse DFS was observed for the so-called “IKZF1 plus” cases, i.e. concomitant deletions of IKZF1 and CDKN2A/B and/or PAX5 (46% vs 24% at 36 months, p=0.005). MLPA confirmed the incidence of these deletions and allowed the study of IKZF1 isoforms. Among IKZF1 deleted cases, patients carrying the ∆4-7 isoform (25%) had a worse DFS (p=0.02) than patients harboring other IKZF1 isoforms.
Importantly, SNP arrays highlighted novel genomic lesions targeting MEF2C in 13% of cases, which were associated to the achievement of a CMR (p=0.05) and had a significant impact on DFS (62% vs 32% at 36 months, p=0.02). The association with CMR was not affected by the trial (p=0.76) or the TKI used (p=0.57). This result was confirmed by ddPCR.
Unsupervised hierarchical clustering of GEP experiments identified 3 subgroups: the first comprised mainly patients who reached a CMR, the second one patients who had IKZF1 alone, and the last one comprised “IKZF1 plus” patients. ANOVA analysis showed an overexpression of genes involved in cell communication and protein modification process in PAX5 deleted cases, suggesting that these genes could be contributing factors in BCR/ABL1-driven leukemogenesis. 

Conclusion
In adult Ph+ ALL, IKZF1 deletions have a prognostic impact only if associated with other lesions. Among IKZF1 deletions, only the ∆4-7 deletion has a deleterious effect. MEF2C lesions carry prognostic implications, being significantly associated with a better prognosis. This study paves the way to design a prognostic model for adult Ph+ ALL that includes these findings and more conventional features, in order to better stratify patients at diagnosis and to further optimize treatment.

Session topic: 1. Acute lymphoblastic leukemia - Biology

Keyword(s): SNP, Prognostic factor, Ph+ ALL, Gene expression profile

Abstract: S800

Type: Oral Presentation

Presentation during EHA22: On Sunday, June 25, 2017 from 08:15 - 08:30

Location: Room N103

Background
The outcome of Ph+ acute lymphoblastic leukemia (Ph+ ALL) has drastically improved since the introduction of tyrosine kinase inhibitors (TKI). At present however, well-defined prognostic markers, beyond the monitoring of minimal residual disease (MRD) during follow-up and to a lesser extent IKZF1 deletions, are lacking.

Aims
To identify genomic lesions of prognostic value, we evaluated copy number aberrations (CNA) by SNP arrays, confirmed them by multiplex ligation-dependent probe amplification (MLPA) and we set up a droplet digital PCR (ddPCR) assays for additional lesions. Furthermore, we correlated the lesions identified with MRD monitoring, outcome and biological features, such as the type of fusion protein (p190 or p210). Finally, in a subset of patients gene expression profiling (GEP) was carried out.

Methods

Genomic DNA of 116 newly diagnosed adult Ph+ ALL patients enrolled in 4 consecutive GIMEMA trials, namely 0201B, 0904, 1205 and 1509, was evaluated. All the trials were based on an induction with steroids and TKI, the first 2 with imatinib and the remainders with dasatinib. For CNA, the Cytoscan HD Arrays (Affymetrix, Santa Clara, CA) were used. The lesions were confirmed by MLPA on all samples using the Salsa MLPA P335-A3 ALL-IKZF1 kit (MRC-Holland, Amsterdam, The Netherlands). ddPCR was used to validate lesions targeting MEF2C. In 42 cases, GEP experiments were performed using the HGU133 Plus 2.0 gene chips (Affymetrix, Santa Clara, CA). 

Results

We found a similar load and type of lesions across the 4 trials, one of which included elderly. The majority of lesions targeted IKZF1 (84%), PAX5 (36%) and CDKN2A/B (32%). In our cohort, IKZF1 deletions alone did not affect complete molecular response (CMR) achievement or disease-free survival (DFS), while patients harboring CDKN2A/B and PAX5 deletions had a significant inferior outcome (p=0.004, p=0.003 respectively). In line with this, a worse DFS was observed for the so-called “IKZF1 plus” cases, i.e. concomitant deletions of IKZF1 and CDKN2A/B and/or PAX5 (46% vs 24% at 36 months, p=0.005). MLPA confirmed the incidence of these deletions and allowed the study of IKZF1 isoforms. Among IKZF1 deleted cases, patients carrying the ∆4-7 isoform (25%) had a worse DFS (p=0.02) than patients harboring other IKZF1 isoforms.
Importantly, SNP arrays highlighted novel genomic lesions targeting MEF2C in 13% of cases, which were associated to the achievement of a CMR (p=0.05) and had a significant impact on DFS (62% vs 32% at 36 months, p=0.02). The association with CMR was not affected by the trial (p=0.76) or the TKI used (p=0.57). This result was confirmed by ddPCR.
Unsupervised hierarchical clustering of GEP experiments identified 3 subgroups: the first comprised mainly patients who reached a CMR, the second one patients who had IKZF1 alone, and the last one comprised “IKZF1 plus” patients. ANOVA analysis showed an overexpression of genes involved in cell communication and protein modification process in PAX5 deleted cases, suggesting that these genes could be contributing factors in BCR/ABL1-driven leukemogenesis. 

Conclusion
In adult Ph+ ALL, IKZF1 deletions have a prognostic impact only if associated with other lesions. Among IKZF1 deletions, only the ∆4-7 deletion has a deleterious effect. MEF2C lesions carry prognostic implications, being significantly associated with a better prognosis. This study paves the way to design a prognostic model for adult Ph+ ALL that includes these findings and more conventional features, in order to better stratify patients at diagnosis and to further optimize treatment.

Session topic: 1. Acute lymphoblastic leukemia - Biology

Keyword(s): SNP, Prognostic factor, Ph+ ALL, Gene expression profile

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