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Molecular biology and childhood leukemia: E2A-PBX1 and central nervous system relapse

How to cite this article: Núñez-Enríquez JC, Mejía Aranguré JM. Molecular biology and childhood leukemia: E2A-PBX1 and central nervous system relapse. Rev Med Inst Mex Seguro Soc. 2015;53 Suppl 3:S236-9.



Received: August 14th 2014

Accepted: September 1st 2015

Molecular biology and childhood leukemia: E2A-PBX1 and central nervous system relapse

Juan Carlos Núñez-Enríquez,a Juan Manuel Mejía Aranguréb

aUnidad de Investigación en Epidemiología Clínica, Hospital de Pediatría

bCoordinación de Investigación en Salud

Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Distrito Federal, México

Communication with: Juan Carlos Núñez-Enríquez

Telephone: (55) 5627 6900, extensión 22451


Acute lymphoblastic leukemia (ALL) is the most common cancer in children. The inclusion of molecular biology techniques in the diagnosis and prognostic stratification of these patients has allowed major treatment achievements in developed countries. One of the best studied gene rearrangements is E2A-PBX1, which predicts isolated central nervous system relapse in patients with ALL. However, further research on the search for new molecular markers related to prognosis of patients with childhood leukemia is required. Such studies need the integration of different disciplines, including epidemiology. Epidemiological studies are needed not only to accelerate the discovery of new molecular markers and new biological signals as to the etiology and pathophysiology of cancer, but also to evaluate the clinical impact of these findings in well-defined populations.

Keywords: Leukemia, Child, Gene rearrangement, Fusion oncogene proteins, Local neoplasm recurrence

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children.1 The last thirty years have seen significant advances in the treatment of ALL in developed countries with rates of event-free survival at five years of 80%.2 These developments have been mainly attributed to chemotherapy regimens based on the combination of multiple drugs, chemoprophylaxis in the central nervous system to prevent relapse at this site, intensification of conventional chemotherapy, and prognostic stratification of patients with ALL.3

Prognostic stratification and molecular markers in ALL

Prognostic stratification is an essential element for choosing the most appropriate treatment of children with ALL.4 This is done based on the risk of relapse assigned at diagnosis and accounting for variables such as age, initial leukocyte count, immunophenotype, specific genetic alterations, and initial response to chemotherapy (Table I).5 The aim of treatment based on prognostic stratification is to prevent relapse and increase event-free survival by reducing the intensity of chemotherapy in patients with ALL classified as standard risk, and increasing the intensity of chemotherapy for patients classified as high-risk.1

Table I Classification of risk used in St. Jude Total XV study for stratifying patients with leukemia treatment5
Criteria used Risk group (estimated % of patients per group)
Standard (40%) High (50%) Very high (10%)
Age 1 to 9.9 years Patients who do not
meet the criteria for standard risk or very high risk groups. Includes the majority of patients with T cell immunophenotype
< 1 year; > 10 years
Leukocyte count < 50,000 xmm3 > 100,000 xmm3
CNS infiltration (CNS-3)* No Yes
Testicular infiltration No Yes
Immunophenotype B lineage T lineage
Molecular markers TEL/AML1 positive,
BCR-ABL negative,
E2A-PBX1 negative,
BCR-ABL positive
Alteration in number of
chromosomes per cell
Hyperdiploidy (51 to 65 chromosomes) Hypodiploidy (< 45 chromosomes)
DNA index > 1.16 < 1:16
Early response to treatment Favorable Unfavorable
* > 5 leucocytes per field plus presence of blasts in cerebrospinal fluid or cranial nerve paralysis at moment of
< 5% of blasts at day 15 of induction to remission or < 0.01% of blasts at day 42
> 1% of blasts at day 42 of induction to remission or > 0.1% of blasts at four months for induction of remission

However, many of the features taken into account to stratify the risk of relapse in patients with ALL have been losing weight as prognostic factors due to the improvements that have been achieved in therapy for these children. Such is the case of patients with the T-cell immunophenotype, who showed very high relapse rates and morbidity. Currently the risk of relapse or death in developed countries is similar to that of patients with the pre-B immunophenotype.6-8

In addition, advances in genetics have discovered new factors associated with the prognosis of patients with ALL, such as gene rearrangements and abnormalities in number of chromosomes.9 

The most important genetic abnormalities in childhood ALL include the translocation t (12; 21) (p13; q22) that leads to the TEL-AML1 gene rearrangement; the BCR-ABL gene rearrangement arising from the translocation t (9; 22) (q34; q11), rearrangements of the MLL gene, and the E2A-PBX1 gene rearrangement. ALL patients who are positive for TEL-AML1 have a favorable prognosis, while those with the E2A-PBX1 fusion require more intensive treatment to get a good result. Moreover, patients positive for MLL-AF4 or BCR-ABL rearrangement are often candidates for allogeneic hematopoietic stem cell transplant in the first remission.10

Other genetic alterations associated with the prognosis of patients with ALL are numerical chromosome abnormalities such as hyperdiploidy, associated with a good prognosis, and hypodiploidy, associated with an extremely poor forecast.11

In this review we will focus on the impact of E2A-PBX1 gene rearrangement on prognosis of pediatric patients with ALL. The main role of E2A-PBX1 gene rearrangement involves the prediction for relapse isolated to the central nervous system (CNS). It has been reported that relapses occurring in the CNS was long a major obstacle to achieving better cure rates in children with ALL from developed countries, since 50% of patients who relapsed at this site had second relapses, disease progression, or death despite receiving heavy doses of intrathecal and systemic chemotherapy.12-14 CNS relapses are mostly asymptomatic and difficult to diagnose. The diagnosis of CNS relapse is confirmed by the presence of blasts in the cytospin of cerebrospinal fluid (CSF) or by specific CT findings.14 

An investigation by Pui et al. during the period from June 2000 to October 2007 studied 498 patients with ALL from 1 to 18 years of age.15 The authors reported a five-year cumulative risk of 2.7% (95% CI: 1.1-4.3) to present relapse in CNS. The main characteristics of the patients were: males represented 56% of cases with a median age of 5.3 years, 12% were Latino, and there was a median of 11,700 leukocytes x mm3. The T cell immunophenotype was found in 15.3% of patients and the frequency of E2A-PBX1 gene rearrangement was 5.8%. CNS relapse occurred in 3% of cases studied. The independent prognostic factors for relapse isolated to CNS were E2A-PBX1 gene rearrangement (hazard ratio [HR] of 15; 95% CI: 3.1-73.0; p = 0.001), leukemic infiltration into CNS at diagnosis (HR 6.4 95% CI: 1.7-23.0; p = 0.005), traumatic lumbar puncture (HR 2.6; 95% CI 1.2-5.2; p = 0.02), the T cell immunophenotype (HR 7.7, 95% CI: 1.4- 43.0; p = 0.02) and hyperleukocytosis higher than 100,000 x mm3.15

From these prognostic factors, treatment protocols began (the use of intrathecal chemotherapy plus "prophylactic" CNS radiation), which reduced the percentage of relapses to this site to less than 2%. The results of this study are considered today as one of the most significant advances in the treatment of children with ALL.15

E2A-PBX1 gene rearrangement

The E2A gene is located in chromosome band 19p13 and 3 in the so-called breakpoint of the translocation t (1; 19) (q23, p13). This is characteristic of patients with ALL of pre-B lineage, and can be found as a balanced translocation (1,19) or unbalanced der (19) t (1:19) (q23, p13) with 2 normal chromosomes. The most common form in pediatric patients with ALL corresponds to the unbalanced type.16-18 The prevalence of this gene rearrangement varies between 4 and 8% of patients with ALL.19

Translocation resulting from fusion of the E2A gene (also called TCF3) in the 19p13 site with the PBX1 gene on the 1q23 site results in the formation of a chimeric transcription factor which in turn causes an abnormal activation and dysfunction of the homeobox gene (PBX1), which leads to transactivation of various genes, and finally a malignant cell phenotype.16 Experimental studies have shown that E2A- PBX1 gene rearrangement initially causes a blockage of normal cell differentiation of myeloid progenitors and paradoxically induces apoptosis in the Pre-B cell lines. This in turn induces immortal proliferation of pro-thymocyte stem cell factor (SCF) by a mechanism dependent on transactivation and protective functions of deoxyribonucleic acid (DNA).17

It has been suggested by several authors that oncogenesis induced by this mechanism requires an aminoterminal activation domain called AD1, which is considered essential for the immortalization of bone marrow cells. However, these mechanisms have not been fully demonstrated.17,18

Methods used to detect E2A-PBX1  gene rearrangement

The methods that have so far proved adequate for detecting said genetic alteration are the FISH method (fluorescent in situ hybridization), real-time quantitative polymerase chain reaction (RQ-PCR), and reverse transcription polymerase chain reaction (RT-PCR).16 Another method used is multiple reverse transcription polymerase chain reaction (MRT-PCR), which is a recently validated cytogenetic method.20 However, the techniques used to detect this and other gene rearrangements take a long time to achieve the result, so recently techniques have been developed for detecting gene rearrangements based on flow cytometry which obtain results in a period not more than four hours.21


ALL is the most common cancer in children. The inclusion of molecular biology techniques in the diagnosis and prognostic stratification of these patients has made for major advances in treatment in developed countries. One of the most studied gene rearrangements is E2A-PBX1, which predicts isolated CNS relapse in patients with ALL. Today, thanks to the increased intensity of chemotherapy in the subgroup of patients positive for E2A-PBX1, these patients have achieved a survival similar to that of patients classified as standard risk.22

More research is needed on finding new molecular markers associated with prognosis of patients with childhood leukemia. Such studies require the integration of different disciplines in the field of research, including epidemiology. Epidemiological studies are needed not only to accelerate the discovery of new molecular markers and new biological signals for the etiology and pathophysiology of cancer, but also to evaluate the clinical impact of these findings in well-defined populations.


We appreciate the support from the Fondo de Investigación en Salud (FIS / IMSS / PROT / MD13 / 1254; FIS / IMSS / PROT / PRIO / 14/031) of the Instituto Mexicano del Seguro Social and from CONACyT (PDCPN2013-01-215726, FIS / IMSS / PROT / 1364).

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Conflict of interest statement: The authors have completed and submitted the form translated into Spanish for the declaration of potential conflicts of interest of the International Committee of Medical Journal Editors, and none were reported in relation to this article.

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