Classification of Acute Myeloid Leukemia and Myelodysplastic Syndrome Based on Molecular Profiling

Acute myeloid leukemia (AML) is currently distinguished from myelodysplastic syndrome (MDS) based on the presence of 20% blasts in bone marrow, an arbitrary cut-off adopted by the WHO classification and replacing the 30% cut-off required by the older FAB (French, American and British) classification.   Patients with t(15;17), t(8;21), or inversion 16 cytogenetic abnormalities are classified as having AML irrespective of the percentage of blasts.   We explored the possibility that currently defined molecular abnormalities can distinguish AML from MDS without relying on an arbitrary percentage of blasts in the bone marrow.  We compared the molecular profiles obtained by next generation sequencing (NGS) from consecutive patients with a clinical diagnosis of AML or MDS by WHO criteria.

Methods:  NGS data from 251 patients with the diagnosis of AML and 294 patients with the diagnosis of MDS was studied.  All samples were analyzed using a panel of 25 genes including FLT3, NPM1 SF3B1, CBL, DNMT3A, ASXL1, BRAF, CEBPA, CSFR3, ETV6, EZH2, IDH1, IDH2, JAK2, c-KIT, KRAS, NRAS, PHF6, PTPN11, RUNX1, SETBP1, TET2, TP53, WT1, and ZRSR2. We compared the frequency of mutations in each gene between AML and MDS patients.  

Results:   Mutations in FLT3 and NPM1 were uniquely and commonly detected in AML (27% and 22%, respectively).   In contrast, mutations in SF3B1 gene were uniquely dominant (22%) in MDS and FLT3 and NPM1 mutations were rare (2% and 3%, respectively).  SF3B1 mutations were extremely rare in AML (1%).  Overall, 102 (41%) of all AML patients had mutations in either FLT3 or NPM1 and 8% of AML patients had mutations in both FLT3 and NPM1.  In addition, WT1 gene was mutated in 8% of AML cases, but none of the MDS cases showed WT1 mutation.  TET2 gene was commonly mutated in both AML and MDS (25% and 36%, respectively), but the frequency was significantly higher in MDS (P=0.003).   IDH1, IDH2, NRAS, and PTPN11 were mutated slightly more often in AML than in MDS, while ASXL1, EZH2, and ZRSR2 were more frequently mutated in MDS than in AML.  There was no statistically significant difference in mutation frequency between AML and MDS for the other genes analyzed. 

Conclusion:   Mutations in FLT3, NPM1 and WT1 are molecular abnormalities characteristically detected in patients with AML and can be used as objective criteria for the classification of AML rather than blast count in bone marrow.  These mutations are detected in 49% of AML patients.  This suggests that approximately half of AML patients can be diagnosed based on the detection of molecular abnormalities, irrespective of bone marrow morphology.   The presence of mutation in SF3B1 gene is also a characteristic molecular finding for MDS.  

  

	AML (No=251)		MDS (No=294)		P-Value
	No	%	No	%
FLT3	68	27	5	2	0.00001
NPM1	55	22	8	3	0.0001
SF3B1	3	1	66	22	0.00006
CBL	4	2	10	3	NS
DNMT3A	51	20	51	17	0.07
ASXL1	44	18	75	26	0.01
BRAF	3	1	1	0	NS
CEBPA	38	15	51	17	NS
CSFR3	11	4	11	4	NS
ETV6	3	1	6	2	NS
EZH2	8	3	25	9	0.03
IDH1	20	8	7	2	0.03
IDH2	17	7	7	2	0.04
JAK2	4	2	10	3	NS
KIT	2	1	0	0	NS
KRAS	11	4	6	2	NS
NRAS	34	14	18	6	0.01
PHF6	5	2	2	1	NS
PTPN11	26	10	6	2	0.01
RUNX1	31	12	33	11	NS
SETBP1	5	2	9	3	NS
TET2	64	25	105	36	0.003
TP53	61	24	75	26	NS
WT1	19	8	0	0	0.01
ZRSR2	7	3	30	10	0.02