Germline predisposition mutations and recurrent somatic mutations in Korean patients with ALL

The two most common malignancies in children are B-cell precursor and T-cell precursor acute lymphoblastic leukemia (B-ALL, T-ALL). Although genetic variations can be used to classify ALL, these are numerous and heterogenous. The 2016 revision to the World Health Organization (WHO) classification of ALL, added new provisional entities: BCR-ABL1-like (or Ph-like) ALL, iAMP21 (intrachromosomal amplification of chromosome 21), and early T-cell precursor ALL (ETP-ALL).¹ In addition to somatic mutations, the WHO classification also included genes that are associated with predisposition to myeloid neoplasms including CEBPA, DDX41, RUNX1, ANKRD26, ETV6, and GATA2. There are also several syndromes that increase susceptibility to ALL including Li Fraumeni (TP53), and Wiskott Aldrich syndrome (WAS). Some genes (PAX5, ETV6, TP53, and IKZF1) associated with ALL are found to have both germline and somatic mutations, thus increasing the susceptibility to ALL. The ALL Hub has previously published an article describing the different genes impacted by germline mutations.

In a recently published study by Shin et al., the association of genetic alterations and predisposition to ALL in both pediatric and adult patients was investigated.¹ The key findings are summarized below.

Methods

The study investigated genetic alterations in Korean patients with ALL using targeted gene panel sequencing.

Paired initial diagnosis and complete remission (CR) bone marrow samples from patients with ALL were selected.

Bone marrow slides of when the patients were in CR were used to detect germline mutations. Nearly a third of the patients had received allogeneic stem cell transplantation (allo-SCT), and in these patients, CR status bone marrow slides before transplantation were used to detect germline mutations. Slides with no apparent residual leukemic cells were used as control samples.

A gene panel consisting of 81 genes, known to be associated with 23 predisposition syndromes, was investigated. In addition to sequence variants, gene-level copy number variations (CNVs) were investigated.

Results

Baseline characteristics

In total, 65 pediatric (<20 years) and 28 adult patients with ALL were included. Patient characteristics are summarized in Table 1. The most common type of B-ALL in adults was BCR-ABL1, whereas in children was B-ALL not otherwise specified (NOS) and B-ALL with hyperdiploidy.

Table 1. Patient characteristics*

B-ALL, B-cell acute lymphoblastic leukemia; NOS, not otherwise specified; T-ALL, T-cell acute lymphoblastic leukemia. *Data from Shin et al.1
Characteristic	Children (n = 65)	Adults (n = 28)
Sex, n
Male	35	10
Female	30	18
Diagnosis, n
B-ALL, NOS	25	8
B-ALL with t(9;22)(q34.1;q11.2); BCR-ABL1	2	11
B-ALL with t(v;11q23.3); KMT2A rearranged	4	1
B-ALL with t(12;21)(p13.2; q22.1); ETV6-RUNX1	9	0
B-ALL with hyperdiploidy	16	1
B-ALL with t(1;19)(q23; p13.3); TCF3-PBX1	2	2
T-ALL	5	5
Early T-cell precursor acute leukemia	2	0
B-ALL cytogenic risk group, n
Good	26	2
Intermediate	26	9
High	6	12

Germline sequence variants

Only one pathogenic TP53 variant (Accession: NM_000546.5) was identified in an adult patient with B-ALL NOS. A known CNV, CASP10 (Accession: NM_032977.3), was identified in one pediatric patient with B-ALL NOS.

Five heterozygous autosomal recessive (AR) primary immunodeficiency disorder (PID)-associated gene variants were identified in five other patients (as shown in Table 2).

Table 2. Germline sequence variants*

AR, autosomal recessive; F, female; M, male. *Data from Shin et al.1
Patient ID	Age/Sex	Gene	% variant	Syndrome
ALL0009	51/F	TP53	40.3	Li-Fraumeni syndrome
ALL0067	18/M	CASP10	—	Autoimmune lymphoproliferative syndrome, Type II
ALL0077	10/M	TYK2	40.2	Immunodeficiency 35, AR
ALL0053	2/M	IL12RB1	50.7	Immunodeficiency 30, AR
ALL0060	40/M	LPIN2	44.0	Majeed syndrome, AR
ALL0071	2/F	CTC1	47.0	Dyskeratosis congenital, AR
ALL0021	2/M	LIG4	42.6	LIG4 syndrome, AR

Somatic sequence variants

A total of 197 somatic sequence variants and 223 somatic CNV were identified. The most common somatic sequence variants and CNVs in B-ALL and T-ALL patients are shown in Table 3. All NRAS and KRAS variants were previously reported variants. The majority of the FLT3 variants were known variants in hematological malignancies, and about 50% of the PAX5 variants were also recurrent variants.

Table 3. Somatic sequence variants*

B-ALL, B-cell acute lymphoblastic leukemia; CNV, copy number variations; T-ALL, T-cell acute lymphoblastic leukemia. *Data from Shin et al.1
Sequence variant	%
Somatic sequence variant in T-ALL
NOTCH1	50
FBXW7	25
IL7R	25
NRAS	25
DNMT3A	17
PHF6	17
GATA3	17
Somatic sequence variant in B-ALL
NRAS	17
FLT3	14
KRAS	9
SETD2	7
PAX5	6
CREBBP	6
CNV in T-ALL
CDKN2A/B	50
CRLF2	17
GATA3	8
CSF2RA	8
BCOR	8
CNV in B-ALL
CDKN2A/B	31
IKZF1	16
ETV6	12
ERG	12
RB1	11

IKZF1 alterations were present in 15 B-ALL patients:

• Seven patients had B-ALL with BCR-ABL1 and all had an IKZF1 deletion.
• Out of seven B-ALL patients with NOS, six had an IKZF1 deletion and one had a IKZF1 frameshift mutation.
• Only one patient with T-ALL had an IKZF1 alteration (missense mutation).
• Three B-ALL patients with BCR-ABL1 and two with B-ALL NOS with IKZF1 deletions also had deletion of PAX5.
• The frequency of IKZF1 deletion was higher in the adult high-risk cytogenic group (6/12, 50%) compared with the overall B-ALL group (13/81, 16%). This may be due to most adult cases (11/12) being ALL with BCR-ABL1.
• The study also found high concordance (83.7%) between fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS) for CDKN2A/B.
• Statistically significant differences were seen in the overall survival (OS) and relapse-free survival (RFS) (p < 0.5) in childhood ALL compared with adult ALL.
• The adverse effect of IKZF1 on OS and RFS was seen only in childhood ALL. No other genes had a consistent clinical effect in either childhood or adult ALL.

Conclusion

The study found recurrent somatic alterations in Korean T-ALL patients, consistent with previous studies. IKZF1 alteration was associated with an adverse effect on OS and RFS in childhood ALL. Six patients had variants in six genes associated with PID. Of the 81 genes associated with 23 predisposition syndromes, only one predisposition germline mutation (TP53) was identified. Taken together, the results indicate a low probability of germline mutation predisposition to ALL in Korean patients. However, the study was limited by the number of patients with early T-cell precursor ALL, and further studies should explore this patient group.