Published Ahead of Print on May 18, 2017, as doi:10.3324/haematol.2017.166124. Copyright 2017 Ferrata Storti Foundation. Mutated ASXL1 and number of somatic mutations as possible indicators of progression to chronic myelomonocytic leukemia of myelodysplastic syndromes with single or multilineage dysplasia by Ana Valencia-Martinez, Alessandro Sanna, Erico Masala, Elisa Contini, Alice Brogi, Antonella Gozzini, and Valeria Santini Haematologica 2017 [Epub ahead of print] Citation: Valencia-Martinez A, Sanna A, Masala E, Contini E, Brogi A, Gozzini A, and Santini V. Mutated ASXL1 and number of somatic mutations as possible indicators of progression to chronic myelomonocytic leukemia of myelodysplastic syndromes with single or multilineage dysplasia Haematologica. 2017; 102:xxx doi:10.3324/haematol.2017.166124 Publisher's Disclaimer. E-publishing ahead of print is increasingly important for the rapid dissemination of science. Haematologica is, therefore, E-publishing PDF files of an early version of manuscripts that have completed a regular peer review and have been accepted for publication. E-publishing of this PDF file has been approved by the authors. After having E-published Ahead of Print, manuscripts will then undergo technical and English editing, typesetting, proof correction and be presented for the authors' final approval; the final version of the manuscript will then appear in print on a regular issue of the journal. All legal disclaimers that apply to the journal also pertain to this production process. Mutated ASXL1 and number of somatic mutations as possible indicators of progression to chronic myelomonocytic leukemia of myelodysplastic syndromes with single or multilineage dysplasia. Ana Valencia-Martinez1, Alessandro Sanna1, Erico Masala1, Elisa Contini2, Alice Brogi1,3, Antonella Gozzini1, and Valeria Santini1 1 Department of Hematology, Università degli Studi di Firenze, AOU Careggi, Florence, Italy. 2 SOD Diagnostica Genetica. AOU Careggi. Florence, Italy. 3 Department of Biotechnologies, University of Siena. Siena, Italy Address for correspondence: Valeria Santini, MD. Functional Unit of Haematology AOU Careggi. University of Florence. Largo Brambilla 3, 50134. Florence, Italy. Tel.: +390557947296; Fax: +390557947343 E-mail: [email protected] Running title: Role of mutations in the progression MDS-to-CMML Conflict of interest: The authors declare no conflict of interest 1 Myelodysplastic syndromes (MDS) are heterogeneous clonal disorders characterized by ineffective hematopoiesis and transformation in acute myeloid leukemia (AML).1However, disease progression is not always to overt AML: rarely MDS may develop myeloproliferative features, and move to overlap-diseases (MDS/MPN) like chronic myelomonocytic leukemia (CMML). Some authors reported unexpected transformation of de novo MDS to CMML, independently of the presence of relative monocytosis (>10%) at initial diagnosis of MDS.2,3 In these reports, apart from an evident increment of total white blood cells count (WBC) and monocytosis, alterations of other clinical parameters and/or cytogenetic and molecular abnormalities failed to be associated directly with progression.3 Deep sequencing demonstrated the high frequency of somatic mutations in MDS as well as the acquisition of additional mutations during disease history.4,5 Some somatic mutations are often shared by MDS and MDS/MPN and contribute differently to the prognosis of these disorders.6-8 Padron et al.4 identified similar pattern of mutations at diagnosis and in the myeloproliferative stage of MDS patients that transformed to CMML, with maintained variant allele frequency (VAF). The acquisition of new mutations was nevertheless evident at progression (ETV6, NRAS, CBL, and RUNX1). Differently, but in the same line of multi-step clonal evolution, it was observed that MDS progressing to AML acquired mutations of RUNX1, ETV6, PHF6, NRAS and KRAS.5 We molecularly describe here a cohort of lower risk MDS patients that evolved to CMML. All consecutive cases, diagnosed at Azienda Ospedaliero Universitaria Careggi (Firenze, Italy) as MDS in accordance with WHO 2008 criteria between April 2010 and September 2016, were revised. Out of 360 cases analysed, we identified 9 patients reclassified with revised WHO 20169 presenting diagnosis of MDS with single lineage dysplasia (MDS-SLD) or MDS with multilineage dysplasia (MDS-MLD) who progressed to overt CMML after variable follow-up periods (Table 1) (referred as Group 1). In all patients, absolute and relative monocytosis was absent during the entire duration of MDS and the median time to CMML transformation was 21 months (range, 10-41) (Table 1). Paired DNA samples of the MDS and CMML phases were isolated in all 9 cases. Bone marrow (BM) mononuclear cells were collected and cryopreserved at diagnosis (MDS phase) and at transformation (CMML phase). Informed consent was provided in accordance with the Declaration of Helsinki Principles and local Ethics Committee’s approval. Twenty-two candidate genes were selected for sequencing analysis (See Supplementary data for methods), referred in literature as most frequently mutated in MDS and CMML.10-12 ASXL1, EZH2, TP53, SF3B1, U2AF1, SRSF2, TET2, DNMT3A, ETV6, RUNX1, NPM1, FLT3, CBL, SETBP1, CSF3R, CEBPA, IDH1, IDH2, 2 JAK2, MPL, CARL, NRAS. Characteristics of the patients are presented in Supplementary Table 1. In brief, five were males, and the median age at diagnosis was 67 years (range, 56–76 years). At diagnosis, four patients had MDS-SLD and five patients had MDS-MLD. At transformation, three patients presented a CMML-0, four patients a CMML-1 and two patients a CMML-2 according the WHO classification 2016. WBC, absolute monocyte counts (AMC) and blast count in CMML phase were statistically higher than in MDS phase (WBC mean, 3.64 × 109/L vs. 13 × 109/L, P= 0.001; AMC, 0.21 × 109/L vs. 1,6 × 109/L, P= 0.004; blast count, 0% versus 6%; P= 0.0001). Mean hemoglobin level (10.85 g/dL versus 9.7 g/dL; P= 0.42) and platelet count (147× 109/L versus 86× 109/L; P= 0.11) were not significantly different between the MDS and CMML phases. After the initial diagnosis of MDS, all patients were treated exclusively with erythropoiesis-stimulating agents and all patients with and without stable disease were followed every three months. In both phases, five patients presented a normal karyotype, one patient a monosomy 7, one patient a trisomy 8 and one patient a trisomy 14. Only case #1 presented a new trisomy 8 at progression (Table 1). After sequencing, coverage across targeted regions was 2500X (minimum 316 and maximum 9877). In the MDS phase, somatic mutations were identified in 9 genes, resulting in 29 variants. All mutations were heterozygous, and comprised 10 missense, 10 nonsense and 9 frameshift mutations. Eight of the 9 CMML-progressing cases presented three mutations or more (median number of mutations: 3, range 2-5) (Supplementary Figure 1). The mutational analysis of the CMML phase confirmed the presence of all the 29 variants found at diagnosis (Figure 1). Generally, mutation VAF did not change significantly, while some mutated clones were marginally expanded during progression. An acquisition of two missense variants was presented in the CMML samples: case #3 with a new variant of the DNMT3A gene and case #7 with a new variant of the gene NRAS (Figure 1). In our cohort of patients, the acquisition of new somatic mutations was not closely correlated with progression, as in 7 of the 9 cases studied was absent. We then compared the mutational profile of Group 1 with a second cohort of lower risk MDS patients that did not present CMML transformation or progression to higher risk MDS or AML (referred as Group 2). Clinical data of Group 2 are summarized in Supplementary Table 1. Group 1 and 2 were matched by age, sex and IPSS risk; Group 2 had a longer OS than Group 1 (67 vs. 38 months) (Supplementary Figure 2). After sequencing of Group 2, coverage across the targeted regions of 3441X (minimum 410 and maximum 11401) was obtained. Thirteen cases (28%) did not present any mutation in the 22 genes analysed, and 33 cases (72%) presented at least one mutation (median number of mutations: 1, range 1-3). The first important observation is that Group 1 cases presented with a higher number of mutated genes: 88% cases of Group 1 showed ≥ 3 mutations compared with 2 cases (4%) of Group 2 (Figure 2 and Supplementary Figure 1). The second observation is that the most frequently 3 mutated genes in Group 1 were ASXL1 and TET2 that were mutated in all cases and in 6/9 cases, respectively (Figure 2A). Consistently to literature, TET2, SF3B1 and DNMT3A, were the most frequently mutated genes in Group 2 cases (19%, 24% and 28%, respectively),10,11 while ASXL1 was present in only three cases (7%): in two cases as an isolated mutation and in one case in combination with TET2 and SRSF2 (Figure 2B). The latter case has been censored because received an early hematopoietic stem cell transplant, and therefore was not possible to evaluate progression. Group 1 cases shared the constant presence of ASXL1 mutations. Based on average sequencing depth versus VAF, ASXL1 mutations in Group 1 appear both as clonal and subclonal.Moreover, VAF of ASXL1 in cases #3 and #8 did not vary significantly while other mutations presented in the same samples increased in size (Figure 1). It seems that together with the presence of ASXL1 mutations, the increase in size of other clones could be related with the disease progression. ASXL1 mutation is present in 45% of CMML cases and has adverse prognostic impact on OS.12,13 TET2 mutations, the second most frequent in Group 1, are widely prevalent in CMML (46%) and their prognostic relevance remains unclear14 ; in our series were not present in the totality of our MDSto-CMML progressing cases. Co-mutation of ASXL1 and TET2 is associated with very poor survival in CMML.14 In order to evaluate the weight of ASXL1 and TET2 mutation positive clones in this peculiar MDS-to-CMML progression, we compared VAF data of the MDS and CMML phases using the paired sign test. VAF of ASXL1 was significantly higher in CMML than in the corresponding MDS phase (42% versus 29%, respectively; P= 0.039) while VAF of TET2 was not significantly varied in both phases (55% versus 46%, respectively; P= 0.38) (Supplementary Figure 3A-B), suggesting a determinant and prominent role of early presence and increase in the burden of mutated ASXL1, during progression of the disease to myeloproliferative features. To be stressed that in matched lower risk MDS cases of Group 2 without any kind of progression, the presence of ASXL1 mutation was a rare event (7%). Although limited by the number of cases evaluated, no significant changes were observed in the mutation profile during progression to CMML. Admitting that the presence of acquired mutations in other genes not included in this study cannot be excluded, nevertheless a strong suggestion of the possibility to identify a “pre-CMML state” derives from our observations. All “pre-CMML” cases were characterized by worsening anemia that required treatment, in line with the role of ASXL1 in erythropoiesis.15 These peculiar “pre-CMML”-MDS cases seem to be well characterized by enhanced genetic instability, justifying multiple comutations, and by the constant feature of early ASXL1 mutation. To note, none of the patients with a “pre-CMML” MDS presented TP53 mutations, very rarely found in CMML. This suggests that the presence of ASXL1 mutations and TP53 wild type could be part of this definition of “pre-CMML” state. Although this kind of progression MDS-to-CMML is quite rare, it looks worth pursuing 4 studies with more such cases to confirm whether this kind of evolution is predictable and therefore justify inception of earlier therapy in lower risk MDS with ASXL1 mutations. CONFLICT OF INTEREST The authors declare no conflict of interest. ACKNOWLEDGMENTS FOR RESEARCH SUPPORT: This work was supported by Associazione Italiana Ricerca sul Cancro (AIRC: IG 2015 Id 16861). REFERENCES 1. Steensma DP, Bennett JM. The myelodysplastic syndromes: diagnosis and treatment. Mayo Clin Proc. 2006;81(1):104-130. 2. Rigolin GM, Cuneo A, Roberti MG, et al. Myelodysplastic syndromes with monocytic component: hematologic and cytogenetic characterization. Haematologica. 1997;82(1):25-30. 3. Wang SA, Galili N, Cerny J, et al. Chronic myelomonocytic leukemia evolving from preexisting myelodysplasia shares many features with de novo disease. Am J Clin Pathol. 2006;126(5):789797. 4. Padron E, Yoder S, Kunigal S, et al. ETV6 and signaling gene mutations are associated with secondary transformation of myelodysplastic syndromes to chronic myelomonocytic leukemia. Blood. 2014;123(23):3675-3677. 5. Pellagatti A, Roy S, Di Genua C, et al. Targeted resequencing analysis of 31 genes commonly mutated in myeloid disorders in serial samples from myelodysplastic syndrome patients showing disease progression. Leukemia. 2016;30(1):247-250. 6. Maxson JE, Gotlib J, Pollyea DA, et al. Oncogenic CSF3R mutations in chronic neutrophilic eukemia and atypical CML. N Engl J Med. 2013;368(19):1781-1790. 7. Meggendorfer M, Roller A, Haferlach T, et al. SRSF2 mutations in 275 cases with chronicmyelomonocytic leukemia (CMML). Blood. 20012;120(15):3080-3088. 8. Papaemmanuil E, Cazzola M, Boultwood J, et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011;365(15):1384-1395. 9. Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391-2405. 5 10. Papaemmanuil E, Gerstung M, Malcovati L, et al. Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood. 2013;122(22):3616-3627. 11. Haferlach T, Nagata Y, Grossmann V, et al. Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia. 2013;28(2):241-247. 12. Itzykson R, Kosmider O, Renneville A, et al. Prognostic score including gene mutations in chronic myelomonocytic leukemia. J Clin Oncol. 2013;31(19):2428–2436. 13. Patnaik MM, Itzykson R, Lasho TL, et al. ASXL1 and SETBP1 mutations and their prognostic contribution in chronic myelomonocytic leukemia: a two-center study of 466 patients. Leukemia. 2014;28(11):2206–2212. 14. Patnaik MM, Lasho TL, Vijayvargiya P, et al. Prognostic interaction between ASXL1 and TET2 mutations in chronic myelomonocytic leukemia. Blood Cancer J. 2016;6:e385. 15. Shi H, Yamamoto S, Sheng M, et al. ASXL1 plays an important role in erythropoiesis. Sci Rep. 2016;6:28789. 6 Table 1. Clinical and cytogenetic characteristics of MDS patients that progress to CMML Case# ** 4 5 6 7 8 9 70 76 63 67 71 72 64 Female Male Male Mal e Mal e Male Female Female 12,1 21, 2 39,2 10,5 17,0 20,6 41, 6 27,6 MDS- MDSMDS-SLD MDS-SLD MDS-SLD MDS-MLD MLD MLD Int-1 / Int Int-1 / Int 1 2 Age 63 56 Sex Female 20,8 3 Ti me to transformati on CMML (months) *WHO classification MDSMDS-MLD MDS-SLD MLD Low / Very Int-1 / Low / low Low Very low MDS 4,04 2,24 10, 3 2,79 5,7 3,64 1,74 4,54 2,40 CMML 13,2 12,1 59, 1 24,4 13 4,9 33,3 12, 1 4,5 MDS 2,2 1,7 6,8 2,01 3,4 2,1 1,2 2,66 1,9 CMML 9,4 8,2 56, 2 10,5 8,7 2,7 26,4 6,3 2,7 0,48 0,12 0,72 0,25 0,30 0,44 0,06 0,17 0,03 CMML 2,1 1,6 1,48 8,6 3,60 1,60 5,3 1,4 1,5 MDS 9,4 5,4 6,9 8,9 5,2 9,3 3,5 3,7 1,3 15,9 13,2 2,5 35,2 27,7 32,6 16 11, 5 33,3 0 0 0 4 4 0 4 0 0 12 4 6 9 19 5 9 4 0 11,2 12,4 8 5,6 14,7 10,8 10,4 10, 5 13,3 CMML 7,4 9,7 8,8 7,2 15 11,1 9,1 10, 1 12,3 MDS 145 78 173 208 86 145 37 354 149 80 82 94 110 45 142 30 86 104 Normal -7 Normal +14 +8 Normal Normal Normal Normal CMML +8 -7 Normal +14 +8 Normal Normal Normal Normal MDS No No No No No No No No No CMML Yes No Yes Yes Yes No No Yes No 8,8 NA NA NA 6,9 NA NA 3,1 NA IPSS/IPSS-R Low / Low / Int-1 / Int Very l ow Low / Low Very low WBC count 9 (x10 /L) ANC count 9 (x10 /L) MDS AMC count 9 (x10 /L) Monocytes (%) CMML MDS BM blasts (%) CMML MDS Hemoglobi n (g/dL) Platelets (x109/L) CMML MDS Cytogenetics Organomegal y Ti me AML evolution (months) * At initial diagnosis of MDS 7 ** To note that for case #3, criteria for diagnosis of CMML are not completely fulfilled. In fact in this case, the percentage of monocytes is < 10%, level required in WHO2016 definition of CMML. On the other hand, this patient cannot be diagnosed as atypical CML because the first condition according to WHO for such diagnosis namely “PB leukocytosis due to increased numbers of neutrophils and their precursors (promyelocytes, myelocytes, metamyelocytes) comprising ≥10% of leukocytes” is lacking. MDS/MPN-unclassifiable is also not applicable because AMC in the progression to MDS/MPN was > 1000/uL. Abbreviations: CMML, chronic myelomonocytic leukemia; WHO, world health organization; MDS-SLD, myelodysplastic syndrome with single lineage dysplasia; MDS-MLD, myelodysplastic syndrome with multilineage lineage dysplasia; IPSS, international prognostic score system; IPSS-R, revised international prognostic score system; Int-1, intermediate-1; Int, Intermediate; WBC, white blood cells; ANC, absolute neutrophils count; AMC, absolute monocyte count; BM, bone marrow; AML, acute myeloid leukemia; NA, not applicable. FIGURE LEGENDS Figure 1. Representation of mutations and VAF (%) in the paired DNA samples of the MDS and CMML phases in the Group 1 of patients. Every graph represents cases #1 to #9 of Group 1. Genes are colour coded and VAFs (axis y) and protein change (axis z) are represented for each variant. Our panel gene was as follows but only the first nine genes were mutated in the Group1 of patients at MDS diagnosis: ASXL1, EZH2, RUNX1, SETBP1, SF3B1, U2AF1, SRSF2, TET2, DNMT3A, TP53, ETV6, NPM1, FLT3, CBL, CSF3R, CEBPA, IDH1, IDH2, JAK2, MPL, CARL Figure 2. Mutated genes in patients included in Group 1 (A) and Group 2 (B). (A) All nine patients of Group 1 presented at least two mutations. (B) In Group 2, 13 cases (28%) did not present any mutation and are all represented in the last grey column. Genes are colour coded and every case is represented in a column 8 Supplementary data for methods The SureDesing of Agilent Technologies was used to design a custom enrichment of the candidate genes: ASXL1, EZH2, TP53, SF3B1, U2AF1, SRSF2, TET2, DNMT3A, ETV6, RUNX1, NPM1, FLT3, CBL, SETBP1, CSF3R, CEBPA, IDH1, IDH2, JAK2, MPL, CARL, NRAS. Genes were selected after a manually curated literature screening of the most commonly mutated genes in MDS and CMML. Library preparation was performed using the HaloPlex target enrichment protocol (Agilent technologies, Santa Clara, USA). The genomic DNA input for amplicon library preparation was 225 ng for each sample according to manufacturer’s instructions. All sample libraries were equimolarly pooled and sequenced on the Illumina MiSeq Sequencer (Illumina, San Diego, CA, USA) with a default 150 bp paired-end reads protocol, according to the manufacturer’s instructions. Data analysis and processing Reads quality was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and reads were aligned to the reference human genome hg19 with BWA mem [Li, Heng. "Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM." arXiv preprint arXiv:1303.3997 (2013)].Genome Analysis Toolkit (GATK) version 3.3 was used to recalibrate base qualities and realign aligned reads around indels. Coverage statistics was performed by DepthOfCoverage utility of GATK. BASH and R custom scripts were used to obtain the list of low coverage (≤100X) regions per sample. For the detection of low abundance variants: SNVs were identified using MuTect version 1.1.4 with standard parameters and GATK IndelGenotyperV2 was used to detect InDels. Genomic and functional annotation of detected variants was made by Annotate Variation Software (ANNOVAR, version 14 Dec, 2015). Detected variants were distilled on the basis of their exonic function, allele frequency, the presence in variants databases, such as the current release of dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), 1000 Genomes Project (http://ftp.ncbi.nih.gov/), Exome Sequencing Project (http://evs.gs.washington.edu/EVS/) and several prediction scores (SIFT, MutationTaster, PolyPhen2, Gerp and PhyloP). Allelic depths for the reference and altered alleles were used to calculate the variant allele frequency (VAF) of all variants. All variants showing a VAF >5% were extracted and annotated with ANNOVAR. Candidate somatic variants were filtered using the following criteria: 1. Removal of all synonymous variants and noncoding variants more than 6 bases from splice junctions were discarded; 2. Removal of missense SNVs which were positioned in coding regions and filtered as polymorphisms when corresponding to known SNPs in public and private databases, including dbSNP144, ESP6500 (version march 2015), the 1000 genomes project (version 1 000g2015aug), and our in-house database at a population frequency of 1% or more; 3. Removal of variants present within regions prone to sequence context specific artifacts, including regions enriched for reads of low mapping quality that harbor multiple mismatches; 4. Removal of variants generated by incorrect calling after a manually revision using The Integrative Genomics Viewer (IGV) 5. Retention of variants present in the COSMIC (v70), ClinVar (v 20150629) and in-house databases as known somatic variation in myeloid and other common malignancies. 6. Remaining variants were the somatic origin was confirmed after and accurate and extensive research of the PubMed database (www.pubmed.gov). Supplementary Table 1. Clinical and cytogenetic characteristics of patients of Group 2 Characteristics Age, years Sex Male Female WBC count (x109/L) ANC count (x109/L) AMC count (x109/L) Haemoglobin (g/dL) Platelets (x109/L) WHO Classification MDS-SLD MDS-RS-SLD MDS-MLD del(5q) Cytogenetics Normal Aberrant IPSS risk group Low Intermediate-1 IPSS-R risk group Very Low Low Intermediate Median (range) n = 46 % 26 20 56 44 17 2 24 3 37 4 52 7 32 14 69 31 28 18 61 39 17 20 9 36 42 19 65 (43-88) 4.15 (2.7-15.7) 2.3 (0.8-14.8) 0.4 (0.02-0.70) 10.25 (8.1-13.11) 140 (17-722) Abbreviations: AMC, absolute monocyte count; WHO, world health organization; MDS-SLD, myelodyplastic syndrome with single lineage dysplasia; MDS-RS-SLD, myelodyplastic syndromering syderoblasts with single lineage dysplasia; MDS-MLD, myelodyplastic syndrome with multilineage lineage dysplasia; IPSS, international prognostic score system; IPSS-R, revised international prognostic score system Supplementary Figure 2. Overall survival curves for Group 1 (dashed line) and 2 (solid line): median OS values, 38 months vs. 67 months, respectively; P=0.015. Supplementary Figure 3. (A) VAF value of ASXL1 and (B) TET2 mutations in case #1 to #9 of Group 1 of patients in the MDS phase (grey bars) and CMML phase (black bars). (A) The median VAF value of ASXL1 mutations was significantly higher in CMML than in the corresponding MDS phase (42% vs. 29%, respectively; P= 0.039) while the median VAF value of TET2 mutations (B) did not significantly varied in both phases (46% vs. 55%; P=0.38). A 70 ASXL1 VAF (%) 60 50 40 30 20 10 0 #1 #2 #3 #4 #5 #6 #7 #8 #9 B 90 80 TET2 VAF (%) 70 60 50 40 30 20 10 0 #1 #2 #3 #4 #5 #6 #7 #8 #9
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