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2 MOLECULAR DIAGNOSTICS
Leukemia Research 39 S1 (2015) S1–S166
Contents lists available at ScienceDirect
Leukemia Research j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / l e u k r e s
Abstracts of the 13th International Symposium on Myelodysplastic Syndromes (MDS) Washington, DC, USA, April 29–May 2, 2015
Invited Speaker Presentations 1 GENOMICS AND EPIGENOMICS M.E. Figueroa1 1 Pathology, University of Michigan, Ann Arbor, USA Epigenetic deregulation is a hallmark of MDS and the MDS/ MPN. Moreover, the DNA methyltransferase inhibitors (DMTi) Azacytidine and Decitabine (DAC) represent the only effective therapies for these disorders. However, little is understood about the precise nature and extent of epigenetic deregulation in the different forms of MDS or about how DMTis work in MDS and MDS/MPN. We have studied DNA methylation, gene expression and mutational profiles in patients with MDS and MDS/MPN. We first compared de novo and therapy-related MDS (t-MDS) and determined that these two forms of MDS are profoundly divergent, with marked hypermethylation in de novo MDS while t-MDS had widespread hypomethylation which affected the WNT and cadherin signaling pathways. Next we analyzed mechanisms of response to DMTi in a cohort of 40 CMML patients all of whom had been uniformly treated with DAC 20 mg/m2/day x 5 days. A comparison of profiles at diagnosis revealed no significant correlation between the presence of specific mutations and the likelihood of response to DAC. However, both DNA methylation and gene expression differences were identified that distinguished DAC-sensitive from DAC-resistant patients. Using a machine learning approach these DNA methylation differences could be harnessed into building an epigenetic classifier predictive of response, which when applied to an independent cohort of 28 patients was capable of predicting response to DAC with 87% accuracy. Finally, gene expression analysis demonstrated that DACresistant patients show high levels of CXCL4 and CXCL7. Treatment of normal CD34+ cells as well as primary CMML mononuclear cells with CXCL4 and CXCL7 completely abrogated the effects of DAC in vitro, indicating that upregulation of these chemokines may play a role in inducing primary resistance to DAC in CMML.
2 MOLECULAR DIAGNOSTICS R. Bejar1 1 Hematology/Oncology, University of California San Diego/Moores Cancer Center, San Diego, USA Establishing a diagnosis of MDS can be challenging as it requires quantification of morphologic bone marrow features like dysplasia and blast proportion. Many patients with unexplained cytopenias 0145-2126 – see front matter © 2015 Elsevier Ltd. All rights reserved.
fail to meet diagnostic criteria for MDS and are left without a clear diagnosis. The discovery of recurrent somatic mutations in patients with MDS has led to the speculation that these genetic lesions could have diagnostic utility in patients with idiopathic cytopenias of undetermined significance (ICUS) as they do with in myeloproliferative neoplasms and AML subtypes. However, using somatic mutations to establish a diagnosis of MDS is complicated by several issues: (1) no single gene is mutated in the majority of cases, (2) no genetic lesion is highly specific for MDS, (3) clonal hematopoiesis is strikingly common in older individuals, most of whom do not have clinical evidence of a hematologic disorder, (4) we lack data on outcomes for ICUS patients with clonal cytopenias (CCUS). Given these caveats, can genetic sequencing inform the diagnosis of MDS? Genetically, patients with CCUS more closely resemble patients with MDS than age matched controls with somatic mutations (i.e., clonal hematopoiesis of indeterminate potential or CHIP). Rates of clonality are higher in ICUS patients, particularly if they have at least equivocal evidence of dysplasia. Somatic variant allele fractions are also higher in CCUS. Genetic testing may identify alternative diagnoses in cytopenic patients. Finally, somatic mutations may identify diagnostic subgroups with comparable clinical features or risk. While we do not have the data needed to include somatic mutations in the diagnostic definition of MDS, it would be very useful to formally define CCUS so that these patients can be recognized and followed to determine their eventual outcomes.
3 MODELING SPLICING FACTOR MUTATIONS IN MDS M. Walter1 1 Department of Medicine, Washington University, St. Louis, USA Somatic mutations in spliceosome genes occur in up to ~50% of MDS patients. Mutations in SF3B1, SRSF2, U2AF1, and ZRSR2 are the most frequently mutated spliceosome genes in MDS. These genes encode factors that are involved in recognition of the 3’-intronic splice site and are mutually exclusive of one another in patient samples, implying that they may contribute similarly to MDS pathogenesis or, alternatively, may not be tolerated by a cell when they co-occur. It is unclear how these mutations contribute to disease. We examined the in vivo hematopoietic consequences of mutant U2AF1 expression using a doxycyclineinducible transgenic mouse model. Mice expressing mutant U2AF1(S34F) display altered hematopoiesis, including peripheral blood leukopenia, an increase in hematopoietic progenitor cells, bone marrow lineage perturbations, and a competitive disadvantage of stem cells compared to wild-type U2AF1
Contents lists available at ScienceDirect
Leukemia Research j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / l e u k r e s
Abstracts of the 13th International Symposium on Myelodysplastic Syndromes (MDS) Washington, DC, USA, April 29–May 2, 2015
Invited Speaker Presentations 1 GENOMICS AND EPIGENOMICS M.E. Figueroa1 1 Pathology, University of Michigan, Ann Arbor, USA Epigenetic deregulation is a hallmark of MDS and the MDS/ MPN. Moreover, the DNA methyltransferase inhibitors (DMTi) Azacytidine and Decitabine (DAC) represent the only effective therapies for these disorders. However, little is understood about the precise nature and extent of epigenetic deregulation in the different forms of MDS or about how DMTis work in MDS and MDS/MPN. We have studied DNA methylation, gene expression and mutational profiles in patients with MDS and MDS/MPN. We first compared de novo and therapy-related MDS (t-MDS) and determined that these two forms of MDS are profoundly divergent, with marked hypermethylation in de novo MDS while t-MDS had widespread hypomethylation which affected the WNT and cadherin signaling pathways. Next we analyzed mechanisms of response to DMTi in a cohort of 40 CMML patients all of whom had been uniformly treated with DAC 20 mg/m2/day x 5 days. A comparison of profiles at diagnosis revealed no significant correlation between the presence of specific mutations and the likelihood of response to DAC. However, both DNA methylation and gene expression differences were identified that distinguished DAC-sensitive from DAC-resistant patients. Using a machine learning approach these DNA methylation differences could be harnessed into building an epigenetic classifier predictive of response, which when applied to an independent cohort of 28 patients was capable of predicting response to DAC with 87% accuracy. Finally, gene expression analysis demonstrated that DACresistant patients show high levels of CXCL4 and CXCL7. Treatment of normal CD34+ cells as well as primary CMML mononuclear cells with CXCL4 and CXCL7 completely abrogated the effects of DAC in vitro, indicating that upregulation of these chemokines may play a role in inducing primary resistance to DAC in CMML.
2 MOLECULAR DIAGNOSTICS R. Bejar1 1 Hematology/Oncology, University of California San Diego/Moores Cancer Center, San Diego, USA Establishing a diagnosis of MDS can be challenging as it requires quantification of morphologic bone marrow features like dysplasia and blast proportion. Many patients with unexplained cytopenias 0145-2126 – see front matter © 2015 Elsevier Ltd. All rights reserved.
fail to meet diagnostic criteria for MDS and are left without a clear diagnosis. The discovery of recurrent somatic mutations in patients with MDS has led to the speculation that these genetic lesions could have diagnostic utility in patients with idiopathic cytopenias of undetermined significance (ICUS) as they do with in myeloproliferative neoplasms and AML subtypes. However, using somatic mutations to establish a diagnosis of MDS is complicated by several issues: (1) no single gene is mutated in the majority of cases, (2) no genetic lesion is highly specific for MDS, (3) clonal hematopoiesis is strikingly common in older individuals, most of whom do not have clinical evidence of a hematologic disorder, (4) we lack data on outcomes for ICUS patients with clonal cytopenias (CCUS). Given these caveats, can genetic sequencing inform the diagnosis of MDS? Genetically, patients with CCUS more closely resemble patients with MDS than age matched controls with somatic mutations (i.e., clonal hematopoiesis of indeterminate potential or CHIP). Rates of clonality are higher in ICUS patients, particularly if they have at least equivocal evidence of dysplasia. Somatic variant allele fractions are also higher in CCUS. Genetic testing may identify alternative diagnoses in cytopenic patients. Finally, somatic mutations may identify diagnostic subgroups with comparable clinical features or risk. While we do not have the data needed to include somatic mutations in the diagnostic definition of MDS, it would be very useful to formally define CCUS so that these patients can be recognized and followed to determine their eventual outcomes.
3 MODELING SPLICING FACTOR MUTATIONS IN MDS M. Walter1 1 Department of Medicine, Washington University, St. Louis, USA Somatic mutations in spliceosome genes occur in up to ~50% of MDS patients. Mutations in SF3B1, SRSF2, U2AF1, and ZRSR2 are the most frequently mutated spliceosome genes in MDS. These genes encode factors that are involved in recognition of the 3’-intronic splice site and are mutually exclusive of one another in patient samples, implying that they may contribute similarly to MDS pathogenesis or, alternatively, may not be tolerated by a cell when they co-occur. It is unclear how these mutations contribute to disease. We examined the in vivo hematopoietic consequences of mutant U2AF1 expression using a doxycyclineinducible transgenic mouse model. Mice expressing mutant U2AF1(S34F) display altered hematopoiesis, including peripheral blood leukopenia, an increase in hematopoietic progenitor cells, bone marrow lineage perturbations, and a competitive disadvantage of stem cells compared to wild-type U2AF1