Diagnostic Utility of IGF2BP1 and Its Targets as Potential Biomarkers in ETV6-RUNX1 Positive B-Cell Acute Lymphoblastic Leukemia

Around 85% of childhood Acute Lymphoblastic Leukemia (ALL) are of B-cell origin and characterized by the presence of different translocations including BCR-ABL1, ETV6-RUNX1, E2A-PBX1, and MLL fusion proteins. The current clinical investigations used to identify ETV6-RUNX1 translocation include FISH and fusion transcript specific PCR. In the current study we assessed the utility of IGF2BP1, an oncofetal RNA binding protein, that is over expressed specifically in ETV6-RUNX1 translocation positive B-ALL to be used as a diagnostic marker in the clinic. Further, public transcriptomic and Crosslinked Immunoprecipitation (CLIP) datasets were analyzed to identify the putative targets of IGF2BP1. We also studied the utility of using the mRNA expression of two such targets, MYC and EGFL7 as potential diagnostic markers separately or in conjunction with IGF2BP1. We observed that the expression of IGF2BP1 alone measured by RT-qPCR is highly sensitive and specific to be used as a potential biomarker for the presence of ETV6-RUNX1 translocation in future.

Screening for pre-leukemia TEL-AML1 chromosomal translocation in banked cord blood units: cord blood bank perspective

Acute lymphocytic leukemia is the most common leukemia in children. Many studies suggest the existence of two subsequent hits in order for the disease to occur. TEL-AML1 (ETV6-RUNX1) is considered an initial genetic hit that occurs prenatally and generates a pre-leukemia clone. In cord blood (CB) stem cell transplantation, donor cell leukemia (DCL) is one of the complications associated with the presence of the pre-leukemic clone. The aim of this study was to identify the prevalence of ETV6-RUNX1 translocation in CB units and the feasibility in implementing such a screening test, to ensure the safety of the CB units. A total of 424 CB samples were tested from the CB units banked at KAIMRC-CBB. RNA was extracted and cDNA synthesis was performed on 1 ug input RNA using Reverse Transcriptase RT-PCR methodology. Chromosomal translocation ETV6-RUNX1 was tested using real time quantitative PCR methodology. Our study showed undetectable levels of ETV6-RUNX1 in all tested CB samples. The samples were analyzed for the chromosomal translocation ETV6-RUNX1 under controlled conditions, using control and fusion genes with known concentrations. The result of this study does not rule out the importance of this screening test in predicting and/or preventing DCL. Moreover, the outcome strengthens the adopted system in our CBB for mother medical history screening prior to donation. We propose adding this test during the verification testing stage, prior to the release of CB units selected for transplantation rather than at the banking stage.

Analysis of common cytogenetic abnormalities in New Zealand pediatric ALL shows ethnically diverse carriage of ETV6-RUNX1, without a corresponding difference in survival

BACKGROUND

The frequency of common cytogenetic abnormalities in pediatric acute lymphoblastic leukemia (ALL) is known to vary by geographic location and ethnic origin. This study aimed to determine the frequency of hypodiploidy, ETV6-RUNX1, BCR-ABL1, and MLL rearrangement within New Zealand's pediatric ALL population and to assess whether the frequency of these ALL prognostic markers varies according to ethnicity.

PROCEDURE

The New Zealand Children's Cancer Registry provided information for all registered pediatric ALL patients that were diagnosed between 2000 and 2009, with medical records available for 246 patients. Each patient's medical record was reviewed to determine the frequency of hypodiploidy, ETV6-RUNX1, BCR-ABL1, MLL rearrangement, and cell lineage. Chi-square tests for independence were undertaken to compare the frequencies of cytogenetic abnormalities according to prioritized ethnicity.

RESULTS

The frequency of cytogenetic ALL abnormalities in the New Zealand pediatric population were consistent with international reference values. A low frequency of ETV6-RUNX1 was evident for Maori pediatric ALL patients (5.4%, P = 0.018), when compared to Pacific peoples (21.1%) and non-Maori/non-Pacific peoples (27.4%). This has not impacted on outcome, however, with equivalent 5-year overall survival being observed in Maori (89.4%) compared to Pacific peoples (92.0%) and non-Maori/non-Pacific peoples (90.2%).

CONCLUSIONS

A lower frequency of the favorable prognostic marker ETV6-RUNX1 was observed in Maori pediatric ALL patients. This did not translate into poorer survival. Future research into biological and nonbiological prognostic factors in this patient population may assist in explaining this finding.

Whole-Exome Sequencing of ETV6/RUNX1 in Four Childhood Acute Lymphoblastic Leukaemia Cases

Background:

ETV6/RUNX1 gene fusion is the most frequently seen chromosomal abnormality in childhood acute lymphobastic leukamia (ALL). However, additional genetic changes are known to be required for the development of this type of leukaemia. Therefore, we here aimed to assess the somatic mutational profile of four ALL cases carrying the ETV6/RUNX1 fusion gene using whole-exome sequencing.

Methods:

DNA was isolated from bone marrow samples using a QIAmp DNA Blood Mini kit and subsequently sequenced using the Illumina MiSeq system.

Results:

We identified 12,960 to17,601 mutations in each sample, with a total of 16,466 somatic mutations in total. Some 15,533 variants were single nucleotide polymorphisms (SNPs), 129 were substitutions, 415 were insertions and 389 were deletions. When taking into account the coding region and protein impact, 1,875 variants were synonymous and 1,956 were non-synonymous SNPs. Among non-synonymous SNPs, 1,862 were missense, 13 nonsense, 35 frameshifts, 11 nonstop, 3 misstart, 15 splices disrupt and 17 in-frame indels. A total of 86 variants were located in leukaemia-related genes of which 32 variants were located in the coding regions of GLI2, SP140, GATA2, SMAD5, KMT2C, CDH17, CDX2, FLT3, PML and MOV10L1.

Conclusions:

Detection and identification of secondary genetic alterations are important in identifying new therapeutic targets and developing rationally designed treatment regimens with less toxicity in ALL patients.