Laboratory of Hematology, route 475
Contributions
Type: Oral Presentation + travel grant
Presentation during EHA20: From 12.06.2015 11:30 to 12.06.2015 11:45
Location: Room Lehar 3 + 4
Background
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic neoplasms characterized by bone marrow dysplasia and one or more peripheral blood cytopenias. Underlying this heterogeneity is a variety of genetic abnormalities. Within the bone marrow and blood of an individual patient, several clones of cells with their own set of mutations may be present simultaneously. During the course of the disease, the clonal composition may change and additional genetic defects can be acquired. Patient-specific (sub)clonal architectures may contribute to the heterogeneity of MDS, both in terms of clinical manifestations and response to treatment.
Aims
We studied the clonal composition of MDS on the basis of somatic mutation profiles, the long-term diachronous changes in clonal architecture throughout the course of the disease, and the correlations between clonal architecture/evolution and clinical parameters and treatment response.
Methods
Bone marrow and blood samples from 12 patients with low- to intermediate-risk MDS with long follow-up times (2.5-11 years) were collected at regular intervals (5-19 sampling moments/patient). Whole-exome sequencing was applied on the first and last and several intermediate time points for each patient. In total, 64 samples were used for whole-exome sequencing, to an average depth of 110x. Cultured T-cell DNA was used as reference. In addition, the same samples were analyzed using high resolution SNP-arrays. From this, in total 348 different acquired somatic mutations were identified in 300 different genes. In order to be able to quantify the presence of these mutations with high accuracy, for all mutations specific assays were developed for amplicon-based deep sequencing (IonTorrent, with a coverage of ≈ 10,000 x). This was used to measure the mutational burden at the different sampling time points.
Results
The median number of validated cancer-associated gene mutations per patient was 14 (range 10-26) and 3 (range 0-5) for well-known, recurrently mutated driver mutations in MDS. Integrated analysis revealed the clonal architecture and its evolution over time. Both linear and branched evolution were present in different patients. Diverse patterns of clonal evolution, ranging from a single clone remaining stably dominant for many years, to cases with highly dynamic shifts in the subclonal composition were observed. Five patients were treated with lenalidomide, four of which achieved complete remission. In one of these patients, clinical complete remission was accompanied by molecular remission (mutations < 1%), followed by a relapse after acquisition of a TP53 and RELN mutation in the original clone, containing six other mutations. One doubly-TET2-mutated patient, treated with EPO and G-CSF displayed a branched evolutionary process with two competitive subclones: an initially major NRAS-mutated subclone and a minor RRAS-mutated subclone. Over the course of two years, the RRAS-mutated subclone became dominant with subsequent transformation to AML.
Summary
Our study demonstrates that great diversity in clonal composition and evolution underlies the clinical heterogeneity of MDS. In some patients, clonal composition was very stable over time, whereas in others, a highly dynamic pattern was observed. Our findings emphasize the importance of genetically unbiased disease monitoring and the development of therapeutic strategies aiming to eradicate multiple different clones.
Keyword(s): Clonality, MDS, Mutation analysis
Session topic: Biology in MDS
Type: Oral Presentation + travel grant
Presentation during EHA20: From 12.06.2015 11:30 to 12.06.2015 11:45
Location: Room Lehar 3 + 4
Background
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic neoplasms characterized by bone marrow dysplasia and one or more peripheral blood cytopenias. Underlying this heterogeneity is a variety of genetic abnormalities. Within the bone marrow and blood of an individual patient, several clones of cells with their own set of mutations may be present simultaneously. During the course of the disease, the clonal composition may change and additional genetic defects can be acquired. Patient-specific (sub)clonal architectures may contribute to the heterogeneity of MDS, both in terms of clinical manifestations and response to treatment.
Aims
We studied the clonal composition of MDS on the basis of somatic mutation profiles, the long-term diachronous changes in clonal architecture throughout the course of the disease, and the correlations between clonal architecture/evolution and clinical parameters and treatment response.
Methods
Bone marrow and blood samples from 12 patients with low- to intermediate-risk MDS with long follow-up times (2.5-11 years) were collected at regular intervals (5-19 sampling moments/patient). Whole-exome sequencing was applied on the first and last and several intermediate time points for each patient. In total, 64 samples were used for whole-exome sequencing, to an average depth of 110x. Cultured T-cell DNA was used as reference. In addition, the same samples were analyzed using high resolution SNP-arrays. From this, in total 348 different acquired somatic mutations were identified in 300 different genes. In order to be able to quantify the presence of these mutations with high accuracy, for all mutations specific assays were developed for amplicon-based deep sequencing (IonTorrent, with a coverage of ≈ 10,000 x). This was used to measure the mutational burden at the different sampling time points.
Results
The median number of validated cancer-associated gene mutations per patient was 14 (range 10-26) and 3 (range 0-5) for well-known, recurrently mutated driver mutations in MDS. Integrated analysis revealed the clonal architecture and its evolution over time. Both linear and branched evolution were present in different patients. Diverse patterns of clonal evolution, ranging from a single clone remaining stably dominant for many years, to cases with highly dynamic shifts in the subclonal composition were observed. Five patients were treated with lenalidomide, four of which achieved complete remission. In one of these patients, clinical complete remission was accompanied by molecular remission (mutations < 1%), followed by a relapse after acquisition of a TP53 and RELN mutation in the original clone, containing six other mutations. One doubly-TET2-mutated patient, treated with EPO and G-CSF displayed a branched evolutionary process with two competitive subclones: an initially major NRAS-mutated subclone and a minor RRAS-mutated subclone. Over the course of two years, the RRAS-mutated subclone became dominant with subsequent transformation to AML.
Summary
Our study demonstrates that great diversity in clonal composition and evolution underlies the clinical heterogeneity of MDS. In some patients, clonal composition was very stable over time, whereas in others, a highly dynamic pattern was observed. Our findings emphasize the importance of genetically unbiased disease monitoring and the development of therapeutic strategies aiming to eradicate multiple different clones.
Keyword(s): Clonality, MDS, Mutation analysis
Session topic: Biology in MDS