Dissecting Genomic Aberrations In CML and Bcr-Abl Negative Myeloproliferative Neoplasms By The Use Of Multiplex-PCR and Parallel Resequencing
Authors: Kirschner Martin M. , Schemionek Mirle , Schubert Claudia , Chatain Nicolas , Sontag Stephanie , Isfort Susanne , Ortiz-Brüchle Nadina , Bennemann Karla , Zerres Klaus , Zenke Martin , Bruemmendorf Tim H. , Koschmieder Steffen 
Published: October 2019

Abstract

Introduction
Next-Generation Sequencing holds the promise of comprehensive analysis of molecular aberrations in human malignancies and therapeutic approaches individually tailored to each patient.

Methods
We investigated the use of a multiplex-PCR (TruseqAmplicon Cancer Panel, Illumina) of 212 amplicons covering genomic mutational hotspots in 48 cancer-related genes to identify mutations in a cohort of patients with myeloproliferativeneoplasms (MPN). After signed informed consent, samples from 59 patients with MPN (19 MF [8 PMF, 11 post-PV/ET-MF], 14 PV, 10 ET, 10 CML, 4 HES, and 2 SM), two patients with reactive erythrocytosis, and two anonymized healthy controls as well as six myeloid cell lines (K562, HEL, HMC1, SUPB15, HL60, U937) were analyzed on a Miseq sequencer (Illumina), using 250 ng of genomic DNA from peripheral blood -derived cells.

Results
Altogether, the quality of the sequencing runs was very good, with Q30 values above 90%. 151 bidirectional cycles were performed, yielding between 2 and 6 Gigabases of sequencing data.Healthy donor and reactive erythrocytosis samples showed several SNPs but no known pathogenic mutation. Sequencing of the cell lines confirmed the presence of a TP53 frameshift mutation (c.405_406insC; in 98% of transcripts) in K562, JAK2 V617F (100%) and TP53 M133K (99%) mutations in HEL, two heterozygous KIT mutations (V560G in 51% and D816V in 52%) and a TP53 C277F (16%) mutation in HMC1, while SUP-B15, HL60, and U937 showed no abnormality in the tested gene set.JAK2 V617F was present in all PV, 4 of 10 ET, and 14 of 19 MF patients.The JAK2 V617F allele burden was significantly higher in MF than ET (p=0.026) but not PV (71+/-27% vs. 33+/-22% vs. 55+/-29%, respectively). Further analysis detected a previously described G12V NRAS mutation (13% of transcripts) in a patient with JAK2 V617F negative PMF and an additional IDH1 R132H mutation (24%) in a JAK2 V617F positive (46%) MF patient with 20% basophils and hyperhistaminemia. Another JAK2 V617F positive (31%) MF sample showed an E255G ABL mutation (10%). One patient with JAK2 V617F negative ET showed an ERBB2 A847D sequence variant (50%). Moreover, an S935N CSF1R mutation (17%) and a V125G IDH1 mutation (9%) were each detected in one case of PV, but the biological relevance remains unclear so far.
Four patients with CML-CP (n=3) or –AP (n=1) showed subclones with sequence variants in the HNF1A gene, with two S304P changes (9 and 10% of transcripts) and two 872delC mutations (6 and 5%), the latter of which have already been implicated in colon cancer. Two patients with CML-CP showed KIT mutations (a V532I mutation and a known oncogenic mutation V530I). This latter patient also harbored the known E255K ABL mutation – leading to imatinib resistance. Interestingly, this patient showed a good response to dasatinib (which is also active against KIT) but not to bosutinib (which has no activity against KIT). These data suggest that HNF1A and KIT may play a role in CML pathogenesis. One patient with lymphoid BC/Ph+ ALL who had a T315I ABL mutation and was treated with ponatinib, was found to harbor a newly acquired V216M TP53 mutation (12% of transcripts) when becoming resistant to ponatinib. Ponatinib had led to a decrease of ABL T315I positive transcripts from 47% before ponatinib treatment to 16% at the time of ponatinib resistance in this patient, suggesting that both TP53 and ABL mutations were present in the same clone and that the newly acquired TP53 mutation may have caused ponatinib resistance in this patient. Additionally, other not yet defined aberrations may have been responsible for the observed resistance. Finally, while both SM patients were negative for KIT D816V, one of them harbored a KRAS 436G>A(146A>T) mutation (34%) which is a known oncogene in colorectal cancer and may thus also play a role in SM pathogenesis. We are currently generating induced pluripotent stem cells from patients harboring selected mutations described above in order to better be able to study the functional properties of genetically unstable malignant stem cell populations.

Conclusion
Amplicon-based next-generation sequencing may uncover additional oncogenic mutations in patients with MPN, potentially explaining therapy resistance and opening new therapeutic options for individual patients.

Disclosures:
Off Label Use: Two individual patients mentioned that were treated with ponatinib or bosutinib within compassionate use trials before these drugs were approved for the indication. Bruemmendorf:Bristol-Myers Squibb: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees; Pfizer: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees, Speakers Bureau; Novartis: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding; Ariad: Consultancy, Honoraria. Koschmieder:Bristol-Myers Squibb: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding; Pfizer: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees; Novartis: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding.