Gene Aberrations in Adult Patients with Ph-Negative ALL in the Czech Republic
Authors: Vrzalova Zuzana , Jelinkova Hana , Hrabovsky Stepan , Folber Frantisek , Salek Cyril , Horacek Jan , Zaliova Marketa , Stika Jiri , Slavikova Martina , Pospisilova Sarka , Doubek Michael 
Published: October 2019

Abstract
Introduction
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is an identified high-risk B-lineage ALL subtype, accounting for approximately 20% of adult patients with B-ALL. Ph-like ALL is characterized by poor outcome, very high risk of disease relapse and poor overall survival (OS). The leukemic cell gene expression profile of Ph-like ALL is similar to that of Ph-positive ALL. However, instead of BCR-ABL1, such patients harbor a highly diverse range of genetic alterations. The gene aberrations detected in Ph-like ALL patients are associated with JAK/STAT, Ras, Ikaros and ABL signaling pathways. These aberrations can be subdivided into five distinct subgroups based on the type of cytokine receptor or kinase fusion present: 1) rearrangements of CRLF2; 2) ABL-class gene rearrangements; 3) JAK2 and EPOR rearrangements; 4) sequence mutations or deletions activating JAK-STAT or MAPK signaling pathways and 5) other rare kinase alterations. The study aimed to define the frequency of high-risk genetic aberrations associated with Ph-like subtype in adults with Ph-negative ALL from the Czech Republic. The genetic basis in adult patients with Ph-like ALL has not been studied to date.
Patients and Methods
The molecular genetic analysis was performed in 74 Ph-negative ALL adult patients from routine hematologic practice. DNA and RNA were isolated from patient´s peripheral blood or bone marrow. The mutational analysis was focused on the detection of the P2RY8-CRLF2 fusion gene (real-time PCR) and the "hot spot" region of the JAK2 gene (PCR/Sanger sequencing) in patient´s cohort. Minimal residual disease (MRD) value was also assessed in all patients prior to the first consolidation cycle (week 11) by real-time PCR. The detection of copy number variations (MLPA method) and targeted sequencing (NGS) was performed in a selected set of patients.
Results
The patient cohort of Ph-negative ALL consisted of 46.6% young adults (age 15 to 39 years), 35.6% adults (age 40 to 59 years), and 17.8% older adults (age 60 to 75 years). Among all patients, increasing age was associated with an inferior outcome of the disease. The difference in OS was significant for young adults compared with adults and older adults (median: 126.7, 23.5 and 22.6, respectively; P=0.0087). The above-mentioned gene aberrations were identified in 36.5% of patients with Ph-negative ALL. The 3-year OS for patients with and without gene aberrations was 36% and 49%. Copy number alterations were detected in almost a third of patient cohort in several genes (IKZF1, PAX5, BTG, ETV6, EBF1, CDKN2A/2B, and SHOX). Deletions in IKZF1 were the most frequent aberration (17.8%). Within the patient cohort, the presence of IKZF1 deletions did not influence the OS significantly. The presence of P2RY8-CRLF2 fusion gene was identified in 16.4% patients with markedly inferior OS in comparison to a patient group without detected P2RY8-CRLF2 (median: 33.2 and 126.7). Sequence mutations of TP53, IL7R, and JAK2 genes occurred in 14.3%, 2.9%, and 1.6% patients, respectively. All patients with the detected sequence variant were carriers of at least one other gene aberration. Achieving MRD negativity in patients with Ph-like aberrations tended to more favorable OS in comparison to those MRD positive, but this trend was not statistically significant enough.
Conclusions
Our findings demonstrate the representation of selected gene aberrations in Ph-negative ALL adults patients. Also they have led to the introduction of molecular genetic diagnostics of Ph-like ALL to routine hematological practice in the Czech Republic. MRD negativity and younger age are the most important prognostic factors in this subgroup of patients according to our analysis.
This study was supported by TA CR (TE02000058), MH CZ - DRO (FNBr, 65269705) and CEITEC 2020 (LQ1601), and MEDGENET 2020 (692298).

Disclosures
Folber: Affimed: Research Funding. Doubek:Roche: Consultancy, Honoraria; Affimed: Research Funding; AbbVie: Consultancy, Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Novartis: Consultancy.