Gene mutation and expression profiles in acute lymphoblastic leukemia based on the next-generation sequencing and their relationship with prognosis / 白血病·淋巴瘤

ABSTRACT

Objective:To investigate the gene mutation and expression profiles in patients with acute lymphoblastic leukemia (ALL) and the effect of gene mutations on the prognosis of patients.Methods:DNA samples from 128 newly diagnosed ALL patients in the First Affiliated Hospital of Soochow University from June 2016 to June 2017 were collected. The targeted specific next-generation sequencing technology was used to analyze 51 gene mutations related to hematological malignancies, and the occurrence spectrum was described. Because the gene mutation spectrum varied with the subtype of disease, the gene mutations involved 8 types of pathways including DNA methylation, chromosomal modification, transcriptional regulation, tumor suppression, signal transduction, RNA splicing, adhesive complexes and other pathways. The effects of clinical factors and gene mutations on overall survival (OS) and relapse-free survival (RFS) were analyzed by Kaplan-Meier method and Cox regression model.Results:Of the 128 patients, the results of next-generation sequencing showed that 86 patients (67.2%) harbored at least one mutation, and 27 patients (21.1%) harbored ≥3 mutations based on the next-generation sequencing. In all ALL patients, the genes with high mutation rates were JAK (10.9%, 14/128), NOTCH1 (10.1%, 13/128), KRAS (8.6%, 11/128), SETD2 (7.0%, 9/128), CSMD1 (7.0%, 9/128), ETV6 (7.0%, 9/128), and RUNX1 (7.0%, 9/128). In B-cell acute lymphoblastic leukemia (B-ALL) patients, the genes with high mutation rates were KRAS (9.4%, 10/106), CSMD1 (7.5%, 8/106), JAK (7.5%, 8/106), PTPN11 (6.6%, 7/106), SETD2 (5.7%, 6/106), TET2 (5.7%, 6/106), TP53 (5.7%, 6/106), and PAX5 (5.7%, 6/106). While in T-cell acute lymphoblastic leukemia (T-ALL) patients, the genes with high mutation rates were NOTCH1 (54.5%, 12/22), PHF6 (27.3%, 6/22), JAK (27.3%, 6/22), RUNX1 (22.7%, 5/22), and ETV6 (18.2%, 4/22). In 128 ALL patients, the total frequency of gene mutations was 181 times. Among them, signal transduction, transcriptional regulation, tumor suppression and chromosomal modification-related gene mutations occurred more frequently, and similar phenomena were found in T-ALL and B-ALL. In terms of clinical features, male patients were more likely to present gene co-mutations( P=0.002), and mutations involved in tumor suppressor pathways were also more common in male patients ( P=0.054). The older the patient, the greater the possibility of mutations involved in transcriptional regulation and DNA methylation regulatory pathway-related genes ( P=0.067, P=0.009). T-ALL was more susceptible to have gene mutations than B-ALL ( P=0.002), and easily had gene co-mutations ( P < 0.01), and mutations mainly involved in signal transduction, transcriptional regulation, tumor suppression and chromosome modification were dominant (all P < 0.05). Cox regression univariate analysis showed that younger age of onset and allogeneic hematopoietic stem cell transplantation could significantly prolong the OS time of ALL patients ( P=0.005, P=0.003), but the difference was not statistically significant on RFS (both P > 0.05). However, 8 types of regulatory pathways were irrelevant to OS and RFS in ALL patients (all P > 0.05). The ALL patients with JAK gene mutation had short OS time ( P=0.024). Conclusions:Gene mutations are prevalent in ALL patients, the frequency spectrum varies with the subtype of disease and involves a variety of signaling pathways. Among them, signal transduction, transcriptional regulation, tumor suppression and chromosomal modification pathway-related genes have high mutation rates. The co-occurrence of gene mutations is a frequently phenomenon in ALL patients and it indicates genetic complexity and instability of ALL patients. JAK family gene mutations usually indicate poor prognosis, but the effects of other gene mutations on the prognosis of ALL need to be further explored.