Whole Genome Sequencing Identifies Recurring Somatic Mutations in the C-Terminal Domain of CXCR4, Including a Gain of Function Mutation in Waldenstrom's Macroglobinemia.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2715-2715
Author(s):  
Yang Cao ◽  
Lian Xu ◽  
Xia Liu ◽  
Yangsheng Zhou ◽  
Guang Yang ◽  
...  

Abstract Abstract 2715 Introduction: Waldenstrom's Macroglobulinemia (WM) is an indolent non-Hodgkin's lymphoma characterized by the accumulation of IgM secreting lymphoplasmacytic cells (LPC) in the bone marrow. Using paired normal/WM lymphoplasmacytic cell paired tissues and whole genome sequencing (WGS), we identified somatic mutations in the CXC chemokine receptor 4 (CXCR4) gene which were present in 16/55 (29%) WM patients. CXCR4 is a G-protein-coupled receptor, together with its ligand, the stromal cell- derived factor-1(CXCL12/SDF-1), play an important role in leukocyte and lymphocyte hematopoiesis and trafficking. Upon SDF-1 stimulation, CXCR4 is phosphorylated and interacts with b-arrestins, which then trigger extracellular signal-regulated kinase (ERK) MAPKs and chemotaxis. CXCR4 signaling is then terminated through receptor internalization which is mediated via phosphorylation of its C-terminal tail. Methods: Sanger sequencing was used to validate WGS results. To clarify the functional significance of one of the most common somatic mutation identified (C1013G), cloning by PCR was undertaken from CD19+ bone marrow cells from a WM patient with the C1013G CXCR4 (C1013G-CXCR4) mutation. Wild type (WT) and C1013G-CXCR4 cDNAs were subcloned into plenti-IRES-GFP vector, and transduced using an optimized lentiviral based strategy for WM cells into BCWM.1 WM cells. Five days after transduction, GFP positive cells were sorted and used for functional studies. Surface expression of CXCR4 was determined by FACS using PE-conjugated anti-CXCR4 monoclonal antibody 12G5. CXCR4 internalization was studied by comparing CXCR4 surface expression before and after SDF-1 stimulation. Chemotaxis studies were performed using a transwell assay. The expression of phosphorylated ERK1/2 and total ERK2 was determined by western blot. Results: Validated somatic mutations in CXCR4 were all present in the C-terminal domain and included premature stop codons (C1013A; C1013G), and frameshift mutations. Importantly, the identified mutations are similar to those reported in the germline of patients with WHIM (Warts, Hypogammaglobulinemia, Infections and Myelokathexis) Syndrome, a dominant autosomal genetic disorder caused by tonic CXCR4 activation by impairment of CXCR4 internalization, and stimulation of G-protein-dependent responses, and chemotaxis. Consistent with such a role, SDF-1a stimulation showed decreased internalization of CXCR4 in C1013G-CXCR4 versus WT CXCR4 transduced BCWM.1 WM cells. SDF-1a stimulated ERK1/2 phosphorylation was also more robust C1013G-CXCR4 versus WT CXCR4 expressing cells. Lastly, C1013G-CXCR4 transduced cells displayed stronger migratory response toward SDF-1a versus WT CXCR4 expressing BCWM.1 cells. Conclusions: C-terminal domain somatic mutations are common in WM and overlap with germline mutation identified in WHIM syndrome. Moreover, the most common of these mutations (C1013G) confers gain of function including decreased CXCR4 internalization, more robust ERK ½ phosphorylation, and chemotaxis. The findings provide new insights into the pathogenesis of WM, and a framework for the study of CXCR4 inhibitors for WM therapy. Disclosures: Treon: Onyx: Membership on an entity's Board of Directors or advisory committees; Millennium: Membership on an entity's Board of Directors or advisory committees.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 205-205
Author(s):  
Timothy James Ley ◽  
J. DiPersio ◽  
L. Ding ◽  
R. Ries ◽  
V. Magrini ◽  
...  

Abstract The genetic events responsible for the initiation and progression of AML are unknown for most patients. Although many important mutations for pathogenesis have been discovered, unbiased genomic approaches will be required to discover all relevant mutations. The development of “Next Generation” massively parallel sequencing approaches (454 and Solexa) have substantially reduced the cost of whole genome sequencing, and have allowed us to initiate a study designed to identify all potentially relevant mutations in a case of M1 AML. The first patient selected for study was a previously healthy 57-year-old Caucasian female who presented with a white blood count of 102,500 (91% blasts); the bone marrow biopsy revealed 100% blasts. Cytogenetics were normal. Tumor and skin (normal) samples were banked with informed consent, using our Washington University IRB-approved protocol that specifically permits whole genome sequencing. Resequencing of 14 genes frequently mutated in AML revealed somatic mutations in FLT3 (ITD) and NPM. Oligomer array-based comparative genomic hybridization using the 2.1 million-oligomer NimbleGen array revealed only one small (<10Kb) region of somatic amplification on chromosome 1p. 500K SNP array analysis of both tumor and skin DNA revealed no regions of “copy number neutral” LOH. Expression analysis of tumor RNA on the Affymetrix Hu133+2 platform revealed a signature that is typical for most patients with M1 AML. The patient’s bone marrow RNA was used to prepare a polyA-primed cDNA library that was enzymatically normalized (to bias towards less abundant mRNAs). Two runs of this material on the Solexa platform yielded approximately 1.5 billion bases of sequence (8x coverage). These reads were stringently aligned to micro-repeat masked versions of the human transcriptome and the human genome (Build 36) and then scored for single-nucleotide and small (1–3bp) indel variants. We further evaluated the coverage extent, depth, and gap size across the transcriptome, using custom scripts and the Synamatix Synamer™ algorithm. ∼4,500 sequence variants have been identified thusfar, which are currently being classified (e.g. known SNPs, non-synonymous variants, etc.) for further analysis. Non-amplified tumor and skin DNA samples were also prepared for sequencing. 25 Solexa runs have been completed on the tumor genome (∼19 billion bases; 6.3X coverage). ‘Actual’ coverage is being assessed by comparing the Solexa data to informative (i.e. heterozygous) SNPs detected in the patient’s tumor and/or skin samples on the 500K SNP array. At this time, 18% of the 135,167 informative SNPs have been detected in Solexa reads. Within a few months, we will complete ∼25x coverage of the patient’s tumor cDNA and genomic DNA. The patient’s skin DNA will then be sequenced to identify private SNPs. Potential somatic mutations will be verified with an established PCR-based resequencing pipeline, and the frequencies of validated somatic mutations will be further determined in 93 additional cases of AML. Using comprehensive array-based genomic platforms and Next Generation sequencing, we hope to define all of the inherited and acquired mutations that were relevant for AML pathogenesis in this patient.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3062-3062
Author(s):  
Oliver Lomas ◽  
Sarah Gooding ◽  
Karthik Ramasamy ◽  
Angela Hamblin ◽  
Maite Cabes ◽  
...  

Background Treatment decisions in Multiple Myeloma (MM) have been driven by a patient's age or ability to tolerate therapy, but as yet, not by their tumour genetics, even though understanding of the prognostic utility of genetic features continues to develop. The ability to identify genetic prognostic markers and potential therapeutic targets in a timely fashion within a health service is a vital step in delivering precision medicine to patients. The aims of this study were to assess the implementation of clinical grade whole genome sequencing (WGS) data at diagnosis to replicate, and ultimately replace, standard-of-care Fluorescence In Situ Hybridisation (FISH) cytogenetics; to provide markers for prognostication or MRD; and to identify actionable targets for clinical trials in precision therapy of MM. Methods Bone marrow aspirates from patients with newly-diagnosed myeloma were collected between June 2017 and April 2018 in a single tertiary hospital in the United Kingdom. The population comprised seven male and seven female patients with a mean age of 78 years. From the first-draw of bone marrow aspirate, standard-of-care FISH cytogenetic analyses were performed locally according to criteria from the International Myeloma Working Group (IMWG). From the remnant aspirate samples, CD138-positive plasma cells were enriched by magnetic bead-sorting and genomic DNA was extracted locally for WGS with a success rate of approximately 70%. Fourteen samples underwent successful plasma cell purification (78 - 99% morphological purity) with a yield of at least 0.5 μg DNA. To identify germline genomic variants, DNA was extracted from peripheral blood samples obtained simultaneously. WGS was performed at a centralised facility and mean coverage for germline samples was 35.1x and for plasma cell-enriched samples was 100.9x. Conventional cytogenetic FISH data were compared with genomic data for chromosome-level alterations. Identified somatic variants were automatically cross-referenced against publicly available databases that describe somatic mutations in cancer as well as a virtual panel of potentially actionable therapeutic targets including : NRAS, KRAS, BRAF, CDKN2C, FGFR3 and IDH2. Results In paired samples, WGS replicated all 13 translocation and chromosomal loss/gain events identified by FISH (Figure 1). Furthermore, three translocations involving the IGH locus suggested by FISH analysis were characterised by WGS. Using samples derived from surplus material, fast-track turnaround of 14 days was attainable. Five patients had no identifiable marker by FISH cytogenetics. In these patients, WGS found all five to possess somatic variants could be used as prognostic or potential Measurable Residual Disease (MRD) markers. Nine patients exhibited somatic variants in genes that may be subject to targetable therapy as determined by trials available on ClinicalTrials.gov: five NRAS, two KRAS, one BRAF and one FGFR3 mutation as of July 2019. Conclusion WGS assessment of newly diagnosed myeloma provides accurate, timely and actionable information beyond what is available from standard-of-care FISH. The application of WGS to myeloma diagnostics presents a number of advantages. Firstly, WGS can replicate and exceed existing myeloma FISH assessment of translocation and loss/gain events in a prompt turnaround time. Secondly, germline variants are deducted from tumour variants to provide a gold standard description of the somatic mutational landscape in the patient's disease. Thirdly, virtual panels of known somatic variants can be applied to the data as knowledge accumulates about the role of specific mutations on prognosis or therapeutic response. We demonstrate that centrally provided WGS and its analysis can be incorporated into routine local assessment of newly diagnosed myeloma. Therefore, these observations show that such technology has the potential to be rapidly scalable across existing hospital networks. Disclosures Gooding: Celgene Corporation: Research Funding. Ramasamy:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Grants; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Grants; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Grants; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Grants; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Oncopeptides: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3767-3767 ◽  
Author(s):  
Cody Ashby ◽  
Eileen M Boyle ◽  
Brian A Walker ◽  
Michael A Bauer ◽  
Katie Rose Ryan ◽  
...  

Background: Structural variants are key recurrent molecular features of myeloma (MM) with two types of complex rearrangement, chromoplexy and chromothripsis, having been described recently. The contribution of these to MM prognosis, rapid changes in clinical behavior and punctuated evolution is currently unknown as is the mechanism by which they deregulate gene function. Methods: We analyzed two sets of newly diagnosed MM data: 85 cases with phased whole genome sequencing; and 812 cases from CoMMpass where long-insert whole-genome sequencing was available. Patient derived xenografts from five MM cases were used to generate epigenetic maps for the histone marks, BRD4, MED1, H3K27Ac, H3K4me1, H3K4me3, H3K9me3, H3K36me3 and H3K27me3. Results: In the 10X data the median number of structural events per case was 25 (range 1 - 182); with a median of 14 intra-chromosomal events (range 1 - 179; P<0.001) and 7 inter-chromosomal events (range 0 - 29). Structural events were seen most frequently on chromosomes 14 (64%), 8 (53%), 1 (44%) and 6 (42%). Complex chromosomal rearrangements involving 3 or more chromosomal sites were seen in 46%, 4 or more sites in 20%, 5 or more in 10% and 6 or more in 5% of samples. There were significantly more structural events in the t(4;14) subgroup compared to the t(11;14) subgroup. Significantly more events were also seen in the bi-allelically inactivated TP53 cases. Using an elbow test defined cutoff, we identified cases with high structural variant load in 10% of cases. Chromoplexy called by "Chainfinder" was seen in 18% of cases. Chromothripsis called by "Shatterseek" was seen in 9% of cases. Cases with a high structural load alone were not associated with an adverse outcome whereas cases with chromoplexy or chromothripsis were associated with adverse PFS and OS, p=0.001. A new high-risk subgroup comprising approximately 5% of cases was identified with chromoplexy, chromothripsis and a high structural load. Gene set enrichment analysis of cases with chromoplexy and chromothripsis showed an excess of MYC, E2F and G2M targets, and a reduction in RAS signaling. Interferon a and g responses, an excess of TP53 and reduction in TRAF3 mutations was associated predominantly with chromothripsis. How chromoplexy and chromothripsis are tolerated by the cell is unknown and the association with the cGAS/STING response is further being explored. To determine how chromoplexy may deregulate multiple genes we identified the full spectrum of structural variants to the immunoglobulin (Ig) and non-Ig loci. A range of genes are deregulated by Ig loci including MAP3K14 at a frequency of 2% confirming the importance of non-canonical NFkB signaling. A novel intra-chromosomal rearrangement to ZFP36L1 was upregulated in 10% of cases but was not prognostic. Gene upregulation by non-Ig super enhancers is frequent and targets include PAX5, GLI3, CD40, NFKB1, MAP3K14, LRRC37A, LIPG, PHLDA3, ZNF267, CENPF, SLC44A2, MIER1, SOX30, TMEM258, PPIL1, and BUB3. The topologically associating domain (TADs) containing super enhancers bringing about gene deregulation include TXNDC5, FOXO3, FCHSD2, SP2, FAM46C, CACNA1C, TLCD2 and PIK3C2G. These super enhancers frequently contain important MM genes, the coding sequence of which are disrupted by the rearrangement and could contribute to the clinical phenotype. Accurately reconstructing the structure of the complex rearrangements will allow us to identify the mechanism of gene deregulation and to distinguish between either gene stacking, receptor stacking or both. Conclusions: Upregulation of gene expression by super enhancer rearrangement is a major mechanism of gene deregulation in MM and complex structural events contribute significantly to adverse prognosis by a range of mechanisms as well as simple gene overexpression. Disclosures Boyle: Amgen, Abbvie, Janssen, Takeda, Celgene Corporation: Honoraria; Amgen, Janssen, Takeda, Celgene Corporation: Other: Travel expenses. Walker:Celgene: Research Funding. Thakurta:Celgene: Employment, Equity Ownership. Flynt:Celgene Corporation: Employment, Equity Ownership. Davies:Amgen, Celgene, Janssen, Oncopeptides, Roche, Takeda: Membership on an entity's Board of Directors or advisory committees, Other: Consultant/Advisor; Janssen, Celgene: Other: Research Grant, Research Funding. Morgan:Amgen, Roche, Abbvie, Takeda, Celgene, Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Other: research grant, Research Funding.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Lydia Y. Liu ◽  
Vinayak Bhandari ◽  
Adriana Salcedo ◽  
Shadrielle M. G. Espiritu ◽  
Quaid D. Morris ◽  
...  

AbstractWhole-genome sequencing can be used to estimate subclonal populations in tumours and this intra-tumoural heterogeneity is linked to clinical outcomes. Many algorithms have been developed for subclonal reconstruction, but their variabilities and consistencies are largely unknown. We evaluate sixteen pipelines for reconstructing the evolutionary histories of 293 localized prostate cancers from single samples, and eighteen pipelines for the reconstruction of 10 tumours with multi-region sampling. We show that predictions of subclonal architecture and timing of somatic mutations vary extensively across pipelines. Pipelines show consistent types of biases, with those incorporating SomaticSniper and Battenberg preferentially predicting homogenous cancer cell populations and those using MuTect tending to predict multiple populations of cancer cells. Subclonal reconstructions using multi-region sampling confirm that single-sample reconstructions systematically underestimate intra-tumoural heterogeneity, predicting on average fewer than half of the cancer cell populations identified by multi-region sequencing. Overall, these biases suggest caution in interpreting specific architectures and subclonal variants.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3965-3965
Author(s):  
Lukas D. Wartman ◽  
Li Ding ◽  
David E. Larson ◽  
Michael D. McLellan ◽  
Heather Schmidt ◽  
...  

Abstract Abstract 3965 Poster Board III-901 We have recently established that whole genome sequencing is a valid, unbiased approach that can identify novel candidate mutations that may be important for AML pathogenesis (Ley et al Nature 2008, Mardis et al NEJM 2009). Acute promyelocytic leukemia (APL, FAB M3 AML) is a subtype of AML characterized by the t(15;17)(q22;q11.2) translocation that creates an oncogenic fusion gene, PML-RARA. Our laboratory has previously modeled APL in a mouse in an effort to understand the genetic events that lead to the disease. In our knockin mouse model, a human PML-RARA cDNA was targeted to the 5' untranslated region of the mouse cathepsin G gene on chromosome 14 (mCG-PR). The targeting vector was transfected into the RW-4 embryonic stem cell line, derived from a 129/SvJ mouse. The transfected RW-4 cells were injected into C57Bl/6 blastocysts, and chimeric offspring were bred to C57Bl/6 mice. F1 129/SvJ x C57Bl/6 mice were subsequently backcrossed onto the B6/Taconic background for 10 generations before establishing a tumor watch. About 60% of the mCG-PR mice in the Bl/6 background develop a disease that closely resembles APL only after a latent period of 7-18 months, suggesting that additional progression mutations are required for APL development. Array-based genomic techniques (expression array studies and high resolution CGH) have revealed some recurring genetic alterations that may be relevant for progression (i.e. an interstitial deletion of chromosome 2, trisomy 15, etc.), but gene-specific progression mutations have not yet been identified. To begin to identify these mutations in an unbiased fashion, we sequenced a cytogenetically normal, diploid mouse APL genome using massively parallel DNA sequencing via the Illumina platform. Since the tumor arose in a highly inbred mouse strain, we predicted that 15x coverage of the genome (approximately 40 billion base pairs of sequence) would be necessary to identify >90% of the heterozygous somatic mutations. We generated 2 Illumina paired-end libraries (insert sizes of 300-350 bp and 550-600 bp) and generated 59.64 billion base pairs of sequence with 3 full sequencing runs; the reads that successfully mapped generated 15.6x coverage. The sequence data predicted 87,778 heterozygous Single Nucleotide Variants (SNVs) compared to the mouse C57Bl6/J reference sequence, and 23,439 homozygous SNVs. Of the predicted heterozygous SNVs, 695 were non-synonymous (missense or nonsense, or altering a canonical splice site). Thus far, 80 of these putative non-synonymous SNVs have been further analyzed using Sanger sequencing of the original tumor DNA vs. pooled B6/Taconic spleen DNA and pooled129/SvJ spleen DNA as controls. 37/80 were shown to be false positive calls, and 37 were inherited SNPs from residual regions of the129/SvJ genome. 6/80 were present only in the tumor genome, and were candidate somatic mutations. These 6 were screened in 89 additional murine APL tumor samples derived from the same mouse model. Mutations in the Jarid2 (L915I) and Capns2 (N149S) genes occurred only in the proband, and are therefore of uncertain significance. 4/6 mutations were found in additional samples; 3 of these mutations were derived from a common ancestor of the proband and the other affected mice, and were therefore not relevant for pathogenesis. The other recurring mutation was in the pseudokinase domain of JAK1 (V657F), and was identified in one other mouse that was not closely related to the proband. This mutation is orthologous to the known activating mutation V617F in human JAK2, and is identical to a recently described JAK1 pseudokinase domain mutation (V658F) found in human APL and T-ALL samples (EG Jeong et al, Clin Can Res 14: 3716, 2008). We are currently testing the functional significance of this mutation by expressing it in bone marrow cells derived from young WT vs. mCG-PR mice. In summary, unbiased whole genome sequencing of a mouse APL genome has identified a recurring mutation of JAK1 found in both human and mouse APL samples. This approach may allow us to rapidly identify progression mutations that are common to human and murine AML, and provides an important proof-of-concept that this mouse model of AML is functionally related to its human counterpart. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 261-261 ◽  
Author(s):  
Lian Xu ◽  
Aliyah R. Sohani ◽  
Luca Arcaini ◽  
Zachary Hunter ◽  
Guang Yang ◽  
...  

Abstract Abstract 261 Lymphoplasmacytic (LPL) and marginal zone lymphoma (MZL) are distinct clinicopathological entities under the WHO classification system for B-cell lymphomas. Differentiation of LPL from MZL has been difficult due to overlapping clinical, morphological, histopathological, immunophenotypic, and cytogenetic features. We therefore sought to identify a molecular marker by which LPL could be differentiated from MZL. Using paired normal/tumor tissues from 10 LPL patients, whole genome sequencing was utilized to identify somatic variants. These studies identified a somatic variant at position 38182641 in chromosome 3p22.2 with a single nucleotide change from T→C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P) in 10 of 10 LPL patients. MYD88 L265P is an oncogenically active mutation in DLBCL ABC cell lines via activation of IRAK1/4/TRAF-6/NF-κβ signaling, and is present in tumors from 29% of patients with ABC subtype of DLBCL, and 6% of patients with MALT lymphomas (Ngo et al, Nature 2011, 470:115–119). Further to these efforts, we performed Sanger sequencing of MYD88 in malignant cells obtained from 51 patients with LPL, 49 of whom had an IgM monoclonal protein and were therefore classified as Waldenstrom's Macroglobulinemia (WM), and 2 with an IgG monoclonal protein, along with 46 patients with MZL, which included 21 Splenic (SMZL), 20 Extranodal (EMZL), and 5 Nodal (NMZL) Subtypes, as well as B-cells from 15 healthy donors. Among LPL patients, the MYD88 L265P variant was found in malignant cells from 46/51 (90.1%) cases, which included 44 patients with WM, and 2 patients with IgG LPL. Expression of the MYD88 L265P variant was heterozygous in 42, and homozygous in 4 LPL patients. By comparison, only 3/46 (6.5%) patients with MZL (1 SMZL; 1 EMZL; 1 NMZL) exhibited the MYD88 L265P variant which was heterozygous (p<0.0001), and included 2 patients (1 SMZL, 1 NMZL) with extensive bone marrow involvement, a monoclonal IgM protein, and whose clinicopathological characteristics overlapped with LPL. By comparison, the MYD88 L265P variant was absent in CD19+ cells from all 15 healthy donors. The results of this study demonstrate that the MYD88 L265P mutation is widely expressed in patients with LPL, and can be used to differentiate LPL from MZL. Disclosures: Treon: Millennium: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 404-404 ◽  
Author(s):  
John S. Welch ◽  
David Larson ◽  
Li Ding ◽  
Michael D. McLellan ◽  
Tamara Lamprecht ◽  
...  

Abstract Abstract 404 To characterize the genomic events associated with distinct subtypes of AML, we used whole genome sequencing to compare 24 tumor/normal sample pairs from patients with normal karyotype (NK) M1-AML (12 cases) and t(15;17)-positive M3-AML (12 cases). All single nucleotide variants (SNVs), small insertions and deletions (indels), and cryptic structural variants (SVs) identified by whole genome sequencing (average coverage 28x) were validated using sample-specific custom Nimblegen capture arrays, followed by Illumina sequencing; an average coverage of 972 reads per somatic variant yielded 10,597 validated somatic variants (average 421/genome). Of these somatic mutations, 308 occurred in 286 unique genes; on average, 9.4 somatic mutations per genome had translational consequences. Several important themes emerged: 1) AML genomes contain a diverse range of recurrent mutations. We assessed the 286 mutated genes for recurrency in an additional 34 NK M1-AML cases and 9 M3-AML cases. We identified 51 recurrently mutated genes, including 37 that had not previously been described in AML; on average, each genome had 3 recurrently mutated genes (M1 = 3.2; M3 = 2.8, p = 0.32). 2) Many recurring mutations cluster in mutually exclusive pathways, suggesting pathophysiologic importance. The most commonly mutated genes were: FLT3 (36%), NPM1 (25%), DNMT3A (21%), IDH1 (18%), IDH2 (10%), TET2 (10%), ASXL1 (6%), NRAS (6%), TTN (6%), and WT1 (6%). In total, 3 genes (excluding PML-RARA) were mutated exclusively in M3 cases. 22 genes were found only in M1 cases (suggestive of alternative initiating mutations which occurred in methylation, signal transduction, and cohesin complex genes). 25 genes were mutated in both M1 and M3 genomes (suggestive of common progression mutations relevant for both subtypes). A single mutation in a cell growth/signaling gene occurred in 38 of 67 cases (FLT3, NRAS, RUNX1, KIT, CACNA1E, CADM2, CSMD1); these mutations were mutually exclusive of one another, and many of them occurred in genomes with PML-RARA, suggesting that they are progression mutations. We also identified a new leukemic pathway: mutations were observed in all four genes that encode members of the cohesin complex (STAG2, SMC1A, SMC3, RAD21), which is involved in mitotic checkpoints and chromatid separation. The cohesin mutations were mutually exclusive of each other, and collectively occur in 10% of non-M3 AML patients. 3) AML genomes also contain hundreds of benign “passenger” mutations. On average 412 somatic mutations per genome were translationally silent or occurred outside of annotated genes. Both M1 and M3 cases had similar total numbers of mutations per genome, similar mutation types (which favored C>T/G>A transitions), and a similar random distribution of variants throughout the genome (which was affected neither by coding regions nor expression levels). This is consistent with our recent observations of random “passenger” mutations in hematopoietic stem cell (HSC) clones derived from normal patients (Ley et al manuscript in preparation), and suggests that most AML-associated mutations are not pathologic, but pre-existed in the HSC at the time of initial transformation. In both studies, the total number of SNVs per genome correlated positively with the age of the patient (R2 = 0.48, p = 0.001), providing a possible explanation for the increasing incidence of AML in elderly patients. 4) NK M1 and M3 AML samples are mono- or oligo-clonal. By comparing the frequency of all somatic mutations within each sample, we could identify clusters of mutations with similar frequencies (leukemic clones) and determined that the average number of clones per genome was 1.8 (M1 = 1.5; M3 = 2.2; p = 0.04). 5) t(15;17) is resolved by a non-homologous end-joining repair pathway, since nucleotide resolution of all 12 t(15;17) breakpoints revealed inconsistent micro-homologies (0 – 7 bp). Summary: These data provide a genome-wide overview of NK and t(15;17) AML and provide important new insights into AML pathogenesis. AML genomes typically contain hundreds of random, non-genic mutations, but only a handful of recurring mutated genes that are likely to be pathogenic because they cluster in mutually exclusive pathways; specific combinations of recurring mutations, as well as rare and private mutations, shape the leukemia phenotype in an individual patient, and help to explain the clinical heterogeneity of this disease. Disclosures: Westervelt: Novartis: Speakers Bureau.


2018 ◽  
Vol 72 (4) ◽  
pp. 280-294 ◽  
Author(s):  
Masaki Nishioka ◽  
Miki Bundo ◽  
Junko Ueda ◽  
Fumiki Katsuoka ◽  
Yukuto Sato ◽  
...  

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