Mutations of Oncogenes Involved in Signal Transduction Pathways Are Common in AML.
Authors: Heinrich Michael C. , Haley Andrea , Harell Patina , Town Ajia , Bainbridge Troy , Schittenhelm Marcus , McGreevey Laura , Braziel Rita 
Published: October 2019

Abstract
AML is the most common type of acute leukemia in adults. Patients typically respond to initial treatment with anthracycline and cytosine arabanoside-based induction chemotherapy, but most patients ultimately relapse and die of refractory disease. Despite advances in supportive care and stem cell transplantation, the overall cure rate in adult AML has not improved significantly in the last decade. The recent success of imatinib mesylate in treating CML has fueled enthusiasm for the further development of AML therapeutic approaches that selectively target aberrant intracellular signaling. To date, inhibition of signaling pathways that are dysregulated by tumor associated somatic mutations have produced the best clinical results. The goal of our study was to more precisely define the frequency and spectrum of mutations affecting receptor tyrosine kinases (FLT3, KIT, PDGFRA, PDGFRB), MAPK pathway (NRAS, KRAS, BRAF), PI3K pathway (PIK3CA), or multiple pathways (PTPN11 tyrosine phosphatase) in adult AML. We analyzed 109 cases of adult AML for genomic DNA abnormalities involving these pathways using a combination of D-HPLC and direct sequencing. In the case of PDGFRA, we performed RT-PCR and FISH to detect FIP1L1-PDGFRA translocations. At least one gain-of-function mutation was found in 53/109 cases (48.6%) (see table) We found mutations of FLT3, KIT, NRAS, KRAS, PTPN11 or BRAF in one or more cases in our series. In contrast, none of the 109 cases had identifiable mutations of PIK3CA, PDGFRA, or PDGFRB. While mutations of NRAS or KRAS were relatively common (19 cases), mutation of BRAF was rare (1/109). In general, mutations of KIT, FLT3, NRAS and KRAS appeared to be mutually exclusive with only 1 AML case having more than one mutation of these genes (1 case with NRAS and KRAS mutations). However, mutations of PTPN11 did not appear to follow this general rule as 5 of the 9 cases with PTPN11 mutations had additional gain-of-function mutation of either FLT3 (3 cases), NRAS (1 case), or both NRAS and KRAS (1 case). We are currently in the process of correlating these mutations with other clinical parameters. We conclude that mutations involving genes directly involved in signal transduction pathways can be found in approximately 50% of cases of adult AML. These mutations represent potential therapeutic targets for treatment with an appropriate small molecular inhibitor. We hypothesize that a more comprehensive kinome wide screen of AML cases would identify an even larger percentage of cases with somatic mutations involving signal transduction pathways. Mutations of PTPN11 have been reported in non-syndromic JMML and rarely in pediatric leukemia. However, the association of PTPN11 mutations in adult AML with mutations of FLT3 or NRAS has not previously been noted. Further studies are required to fully understand the cellular consequences of dysregulated PTPN11 in myeloid leukemogenesis. Our results may also be relevant to ongoing trials of FLT3 or farnesyl transferase inhibitors in AML, as patients with a co-existent PTPN11 mutation may not respond as well to monotherapy with these agents.
Mutations of Signal Transduction Pathways in 109 Cases of Adult AML
Mutations Number (%) None (wild-type for all genes) 56 (51.4%) FLT3 only 18 (16.5%) FLT3+PTPN11 3 (2.8%) NRAS only 11 (10.1%) NRAS+PTPN11 2 (1.8%) NRAS+KRAS 1 (0.9%) NRAS+KRAS+PTPN11 1 (0.9%) KRAS only 5 (4.6%) KIT only 6 (5.5%) PTPN11 only 4 (3.7%) BRAF only 1 (0.9%)