An early thymic precursor phenotype predicts outcome exclusively in HOXA-overexpressing adult T-cell acute lymphoblastic leukemia: a Group for Research in Adult Acute Lymphoblastic Leukemia study

Abstract

Gene expression studies have consistently identified a HOXA-overexpressing cluster of T-cell acute lymphoblastic leukemias, but it is unclear whether these constitute a homogeneous clinical entity, and the biological consequences of HOXA overexpression have not been systematically examined. We characterized the biology and outcome of 55 HOXA-positive cases among 209 patients with adult T-cell acute lymphoblastic leukemia uniformly treated during the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003 and -2005 studies. HOXA-positive patients had markedly higher rates of an early thymic precursor-like immunophenotype (40.8% versus 14.5%, P=0.0004), chemoresistance (59.3% versus 40.8%, P=0.026) and positivity for minimal residual disease (48.5% versus 23.5%, P=0.01) than the HOXA-negative group. These differences were due to particularly high frequencies of chemoresistant early thymic precursor-like acute lymphoblastic leukemia in HOXA-positive cases harboring fusion oncoproteins that transactivate HOXA Strikingly, the presence of an early thymic precursor-like immunophenotype was associated with marked outcome differences within the HOXA-positive group (5-year overall survival 31.2% in HOXA-positive early thymic precursor versus 66.7% in HOXA-positive non-early thymic precursor, P=0.03), but not in HOXA-negative cases (5-year overall survival 74.2% in HOXA-negative early thymic precursor versus 57.2% in HOXA-negative non-early thymic precursor, P=0.44). Multivariate analysis further revealed that HOXA positivity independently affected event-free survival (P=0.053) and relapse risk (P=0.039) of chemoresistant T-cell acute lymphoblastic leukemia. These results show that the underlying mechanism of HOXA deregulation dictates the clinico-biological phenotype, and that the negative prognosis of early thymic precursor acute lymphoblastic leukemia is exclusive to HOXA-positive patients, suggesting that early treatment intensification is currently suboptimal for therapeutic rescue of HOXA-positive chemoresistant adult early thymic precursor acute lymphoblastic leukemia.

Trial registration: The GRAALL-2003 and -2005 studies were registered at http://www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively.

Copyright© Ferrata Storti Foundation.

Figures

Figure 1.

Definition of HOXAPos adult T-ALL. (A) HOXA ratios (HOXA9/ABL) were calculated for 209 T-ALL patients treated as part of the GRAALL-2003 and -2005 studies. Each point represents an individual measurement. The threshold of HOXA positivity (0.66) was defined by the lowest HOXA ratio associated with a known HOXA-deregulating abnormality (PICALM-MLLT10). For HOXAPos cases for which the etiology of HOXA locus activation remained undefined, the measurement point is indicated by a diamond. Cases with an ETP-like phenotype are shown in red. (B) Taqman low density array (TLDA) analysis of HOX gene expression in HOXANeg (n = 8) and HOXAPos (n = 13) patients, compared with normal thymus (Thy) (n = 3) controls. HOXAPos cases exhibit specific activation of the HOXA locus, while HOXANeg samples have uniformly low expression of all HOX genes.

Figure 2.

Molecular mechanism of HOXA deregulation in adult T-ALL. (A) Flowchart of investigation of the etiology of HOXA positivity. Numbers of patients in each diagnostic subgroup are shown.*One patient had co-existing diagnoses of both TCRβ-HOXA and PICALM-MLLT10. RNA-seq = RNA-sequencing. FISH = Fluorescence in situ hybridization. Representative results are depicted in panels (B) – (E). (B) Positive FISH for TCRβ-HOXA. (C) Direct (Sanger) sequencing confirms the presence of the NAP1L1-MLLT10 translocation. Exon numbers are indicated. (D) Reverse transcriptase polymerase chain reaction amplification of NUP98-RAP1GDS1 using fusion-specific primers. Patients 2 and 3 are positive for NUP98-RAP1GDS1, while patients 1 and 4 are negative. NTC = no template control. (E) Diagnosis of DDX3X-MLLT10 by RNA-sequencing. A schematic representation of paired-end and fusion-spanning reads is shown. Plain lines indicate split reads spanning two exons, and dotted lines indicate two reads of the same fragment. Exon numbers are indicated.

Figure 3.

HOXAPos and HOXANeg adult T-ALL patients have similar survival outcomes. (A) Overall survival (OS) and (B) event-free survival (EFS) of HOXAPos and HOXANeg patients are shown. Five-year OS was estimated to be 55% (95% CI, 38.46% – 68.79%) in the HOXAPos group, as compared with 58.1% (95% CI, 48.50% – 66.49%) in HOXANeg cases. The corresponding figures for 5-year EFS were 45.9% (95% CI, 30.58% – 59.91%) for HOXAPos and 48.9% (95% CI, 39.73% – 57.53%) for HOXANeg.

Figure 4.

An ETP-like immunophenotype is associated with an inferior prognosis in HOXAPos, but not HOXANeg adult T-ALL. The results of survival analyses after separation of the HOXAPos and HOXANeg groups according to the presence or absence of an ETP-like immunophenotype are shown. The 5-year survival figures were as follows: (A) overall survival (OS) for HOXAPos ETP 31.3% (95% CI, 11.4% – 53.7%), HOXAPos non-ETP 66.7% (95% CI, 42.5% – 82.5%), HOXANeg ETP 74.2% (95% CI, 45% – 89.4%), HOXANeg non-ETP 57.2% (95% CI, 46.1% – 66.9%). (B) Event-free survival (EFS) for HOXAPos ETP 25% (95% CI, 10.2% – 43.1%), HOXAPos non-ETP 52.7% (95% CI, 35.5% – 67.4%), HOXANeg ETP 60.8% (95% CI, 39.4% – 76.6%), HOXANeg non-ETP 50.7% (95% CI, 41.1% – 59.5%). (C) Disease-free survival (DFS) for HOXAPos ETP 28.6% (95% CI, 11.7% – 48.2%), HOXAPos non-ETP 53.6% (95% CI, 35.9% – 68.5%), HOXANeg ETP 64.7% (95% CI, 43.1% – 79.8%), HOXANeg non-ETP 52.2% (95%CI, 42.1% – 61.3%). (D) Cumulative incidence of relapse (CIR) for HOXAPos ETP 53.7% (95% CI, 34.3% – 75.6%), HOXAPos non-ETP 25.4% (95% CI, 13.6% – 44.4%), HOXANeg ETP 29.2% (95% CI, 15.1% – 51.6%), HOXANeg non-ETP 39.2% (95% CI, 30.6% – 49.3%).