As described previously, mutations involved in the
Ras signaling pathway (
NRAS,
KRAS,
FLT3,
PTPN11, and
NF1) occurred in more than half of B-ALL patients [
14,
15] . Also, a higher incidence of mutations was detected in
NRAS rather than
KRAS. This finding was contradictory to the previous studies in the Chinese cohort [
15] but was in agreement to that from the USA, Sweden, and Korea [
14‐
19]. These discrepancies might be related to the population distribution and environmental factors, which highlighted the genetic heterogeneity of pediatric ALL. Compared to
CBL,
TET2,
CDKM2A, and
BCORL1 genes with a higher median VAF, Ras signaling pathway-related genes, such as
FLT3,
NRAS,
KRAS, and
PTPN11, displayed a lower median VAF of 5–20%. The lower VAF indicated that Ras mutations were more likely subclones rather than a major clone [
20], suggesting that B-ALL is driven by other fusion genes. Reportedly,
Ras pathway functioned as a molecular switch for signaling pathways that regulated cell proliferation, survival, growth, migration, and differentiation [
21]. Thus, we speculated that
Ras pathway mutations occurred during B-ALL progression rather than tumorigenesis. Based on genetic testing of a large number of ALL patients, Shu et al. and Perentesis et al. demonstrated that
RAS mutations did not present any unique clinical manifestation nor predicted clinical outcomes [
18,
19]. Moreover, some recent studies showed that ALL patients with
Ras pathway mutations, especially
KRAS/
NRAS mutations, present high-risk features, including early relapse and CNS involvement [
22‐
24]. In our cohort, no correlation was established between the presence of Ras mutation and clinical characteristics, risk stratification, and MRD level. This phenomenon could be attributed to the neutralization effect of other genomic variations, such as low-risk hyperdiploidy and high-risk hypodiploidy on prognosis [
25‐
28]. To determine whether Ras pathway status influences the clinical characteristics and risk stratification, additional studies are warranted on various cytogenetic subgroups of B-ALL. Notch pathway mutations, especially
NOTCH1 and
FBXW7, were enriched in T-ALL patients, as previously reported [
29‐
32].
NOTCH1 was the most common mutated gene in about 60.9% of all T-ALL cases, followed by
PTEN (21.7%) and
FBXW7 (21.7%). Notch signaling pathway, especially
NOTCH1, plays a crucial role in all stages of T lymphocyte development and can promote the differentiation of lymphoid precursor cells into T lymphocytes and inhibit their differentiation into B lymphocytes [
33,
34]. Except for the excessive activation of the Notch pathway, impaired
CDKN2A/2B cell cycle regulators also played a prominent role in T-ALL pathogenesis. Strikingly,
CDKN2A/
2B deletions were detected in > 50% of T-ALL cases [
10,
35]. However, the copy number variations were not detected and analyzed in the present study, and only a few
CDKN2A gene point mutations were identified in T-ALL. Recent sequencing studies demonstrated that T-ALL was an aggressive malignancy caused by the accumulation of genomic lesions. On average, 10–20 mutations were detected in T-ALL cells [
10,
36‐
38]. Although our study showed that T-ALL had a significantly higher mutation level than B-ALL, the average number of mutations was still lower than the expected value. This deviation could be attributed to the scope of sequencing, the evaluated variation types, the sensitivity of the test, and the filter criteria of mutation calling. We also found that the accumulation of mutations in T-ALL did not occur randomly [
39]. Interestingly, the coexistence of
NOTCH1-PTEN-FBXW7 and
DNM2-USP7-PHF6 mutations was observed in our T-ALL cohort. The coexistence phenomenon suggested that those Notch pathway and non-Notch pathway genes interconnect physiologically and cooperate during the development and progression of the T-ALL, respectively.
MLL translocations and
PIK3R1 mutations were common in infant ALL, a group characterized as immature cytologically, resistant to conventional therapies, and showing poor prognosis. Moreover, a significant coexistence between
MLL gene arrangement and
PIK3R1 mutations was detected in our cohort. This observation indicated that
PI3K/AKT is a secondary hit for partial
MLL-positive ALL.
In summary, our study depicted the specific genomic landscape and revealed the relevance between mutational spectrum and clinical features of Chinese pediatric ALL in a single cohort, including patient characteristics, cytogenetics, genetic subtypes, risk stratification and treatment outcomes. The discovery of this mutational spectrum highlights the need for molecular classification, risk stratification, and prognosis evaluation and also provide the basis for the development and application of new targeted therapy for pediatric ALL.