Exome sequencing reveals <i>DNMT3A</i> and <i>ASXL1</i> variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy

Kim, TaeHyung,Tyndel, Marc S.,Zhang, Zhaolei,Ahn, Jaesook,Choi, Seunghyun,Szardenings, Michael,Lipton, Jeffrey H.,Kim, Hyeoung-Joon,Kim Dong Hwan, Dennis Elsevier 2017 Leukemia research Vol.59 No.-

<P><B>Abstract</B></P> <P><B>Objective</B></P> <P>The development of tyrosine kinase inhibitors (TKIs) has significantly improved the treatment of chronic myeloid leukemia (CML). However, approximately one third of patients are resistant to TKI and/or progress to advanced disease stages. TKI therapy failure has a well-known association with <I>ABL1</I> kinase domain (KD) mutations, but only around half of TKI non-responders have detectable <I>ABL1</I> KD mutations.</P> <P><B>Method</B></P> <P>We attempt to identify genetic markers associated with TKI therapy failure in 13 patients (5 resistant, 8 progressed) without <I>ABL1</I> KD mutations using whole-exome sequencing.</P> <P><B>Results</B></P> <P>In 6 patients, we detected mutations in 6 genes commonly mutated in other myeloid neoplasms: <I>ABL1</I>, <I>ASXL1</I>, <I>DNMT3A</I>, <I>IDH1</I>, <I>SETBP1</I>, and <I>TP63</I>. We then used targeted deep sequencing to validate our finding in an independent cohort consisting of 100 CML patients with varying drug responses (74 responsive, 18 resistant, and 8 progressed patients). Mutations in genes associated with epigenetic regulations such as <I>DNMT3A</I> and <I>ASXL1</I> seem to play an important role in the pathogenesis of CML progression and TKI-resistance independent of <I>ABL1</I> KD mutations.</P> <P><B>Conclusion</B></P> <P>This study suggests the involvement of other somatic mutations in the development of TKI resistant progression to advanced disease stages in CML, particularly in patients lacking <I>ABL1</I> KD mutations.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Acquisition of somatic mutation is associated with TKI therapy failure and progression in CML patients. </LI> <LI> Exome sequencing revealed mutations in 6 genes: <I>ABL1, ASXL1, DNMT3A, IDH1, SETBP1,</I> and <I>TP63.</I> </LI> <LI> Somatic mutations is responsible for TKI resistance esp. lacking <I>ABL1</I> KD mutations. </LI> </UL> </P>

The clonal origins of leukemic progression of myelodysplasia

Kim, T,Tyndel, M S,Kim, H J,Ahn, J-S,Choi, S H,Park, H J,Kim, Y-k,Yang, D-H,Lee, J-J,Jung, S-H,Kim, S Y,Min, Y H,Cheong, J-W,Sohn, S K,Moon, J H,Choi, M,Lee, M,Zhang, Z,Kim, D(D H) Nature Publishing Group 2017 Leukemia Vol.31 No.9

<P>The genetics behind the progression of myelodysplasia to secondary acute myeloid leukemia (sAML) is poorly understood. In this study, we profiled somatic mutations and their dynamics using next generation sequencing on serial samples from a total of 124 patients, consisting of a 31 patient discovery cohort and 93 patients from two validation cohorts. Whole-exome analysis on the discovery cohort revealed that 29 of 31 patients carry mutations related to at least one of eight commonly mutated pathways in AML. Mutations in genes related to DNA methylation and splicing machinery were found in T-cell samples, which expand at the initial diagnosis of the myelodysplasia, suggesting their importance as early disease events. On the other hand, somatic variants associated with signaling pathways arise or their allelic burdens expand significantly during progression. Our results indicate a strong association between mutations in activated signaling pathways and sAML progression. Overall, we demonstrate that distinct categories of genetic lesions play roles at different stages of sAML in a generally fixed order.</P>

Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy

Kim, TaeHyung,Tyndel, Marc S.,Kim, Hyeoung Joon,Ahn, Jae-Sook,Choi, Seung Hyun,Park, Hee Jeong,Kim, Yeo-kyeoung,Kim, Soo Young,Lipton, Jeffrey H.,Zhang, Zhaolei,Kim, Dennis (Dong Hwan) American Society of Hematology 2017 Blood Vol. No.

<P>Somatic mutations commonly detected in a variety of myeloid neoplasms have not been systematically investigated in chronic myeloid leukemia (CML). We performed targeted deep sequencing on a total of 300 serial samples from 100 CML patients; 37 patients carried mutations. Sixteen of these had evidence of mutations originating from preleukemic clones. Using unsupervised hierarchical clustering, we identified 5 distinct patterns of mutation dynamics arising following tyrosine kinase inhibitor (TKI) therapy. This study demonstrates that patterns of mutation acquisition, persistence, and clearance vary but have a number of interesting correlations with clinical outcomes. Mutation burden often persisted despite successful TKI response (pattern 1), providing indirect evidence that these mutations also originated from preleukemic mutations, whereas patients exhibiting mutation clearance (pattern 3) showed mixed clinical outcomes. Unsurprisingly, patients acquiring new mutations during treatment failed TKI therapy (pattern 2). These patterns show that CML mutation dynamics following TKI therapy are markedly distinct from other myeloid neoplasms. In summary, clinical implications of mutation profiles and dynamics in CML should be interpreted with caution.</P>

Clonal dynamics in a single AML case tracked for 9 years reveals the complexity of leukemia progression

Kim, T,Yoshida, K,Kim, Y K,Tyndel, M S,Park, H J,Choi, S H,Ahn, J-S,Jung, S-H,Yang, D-H,Lee, J-J,Kim, H J,Kong, G,Ogawa, S,Zhang, Z,Kim, H J,Kim, D D Macmillan Publishers Limited 2016 Leukemia Vol.30 No.2

<P>Most types of cancers are made up of heterogeneous mixtures of genetically distinct subclones. In particular, acute myeloid leukemia (AML) has been shown to undergo substantial clonal evolution over the course of the disease. AML tends to harbor fewer mutations than solid tumors, making it challenging to infer clonal structure. Here, we present a 9-year, whole-exome sequencing study of a single case at 12 time points, from the initial diagnosis until a fourth relapse, including 6 remission samples in between. To the best of our knowledge, it covers the longest time span of any data set of its kind. We used these time series data to track the hierarchy and order of variant acquisition, and subsequently analyzed the evolution of somatic variants to infer clonal structure. From this, we postulate the development and extinction of subclones, as well as their anticorrelated expansion via varying drug responses. In particular, we show that new subclones started appearing after the first complete remission. The presence and absence of different subclones during remission and relapses implies differing drug responses among subclones. Our study shows that time series analysis contrasting remission and relapse periods provides a much more comprehensive view of clonal structure and evolution.</P>

Next-generation sequencing–based posttransplant monitoring of acute myeloid leukemia identifies patients at high risk of relapse

Kim, TaeHyung,Moon, Joon Ho,Ahn, Jae-Sook,Kim, Yeo-Kyeoung,Lee, Seung-Shin,Ahn, Seo-Yeon,Jung, Sung-Hoon,Yang, Deok-Hwan,Lee, Je-Jung,Choi, Seung Hyun,Lee, Ja-yeon,Tyndel, Marc S.,Shin, Myung-Geun,Lee American Society of Hematology 2018 Blood Vol.132 No.15

<P>Next-generation sequencing (NGS) has been applied to define clinically relevant somatic mutations and classify subtypes in acute myeloid leukemia (AML). Persistent allelic burden after chemotherapy is associated with higher relapse incidence, but presence of allelic burden in AML patients after receiving allogeneic hematopoietic cell transplantation (HCT) has not been examined longitudinally. As such, we aimed to assess the feasibility of NGS in monitoring AML patients receiving HCT. Using a targeted gene panel, we performed NGS in 104 AML patients receiving HCT using samples collected at diagnosis, pre-HCT, and post-HCT at day 21 (post-HCTD21). NGS detected 256 mutations in 90 of 104 patients at diagnosis, which showed stepwise clearances after chemotherapy and HCT. In a subset of patients, mutations were still detectable pre-HCT and post-HCT. Most post-HCT mutations originate from mutations initially detected at diagnosis. Post-HCTD21 allelic burdens in relapsed patients were higher than in nonrelapsed patients. Post-HCTD21 mutations in relapsed patients all expanded at relapse. Assessment of variant allele frequency (VAF) revealed that overall VAF post-HCTD21 (VAF(0.2%)-post-HCTD21) is associated with an increased risk of relapse (56.2% vs 16.0% at 3 years; P < .001) and worse overall survival (OS; 36.5% vs 67.0% at 3 years; P = .006). Multivariate analyses confirmed that VAF(0.2%)-post-HCTD21 is an adverse prognostic factor for OS (hazard ratio [HR], 3.07; P =.003) and relapse incidence (HR, 4.75; P < .001), independent of the revised European LeukemiaNet risk groups. Overall, current study demonstrates that NGS-based posttransplant monitoring in AML patients is feasible and can distinguish high-risk patients for relapse.</P>