ALBERT

Description: Introduction Pediatric chronic myeloid leukemia (CML) accounts for 10 to 15% of children with myeloid leukemia and 2 to 9% of all pediatric leukemias. Prior to the discovery of tyrosine kinase inhibitors (TKI) such as imatinib, stem cell transplantation was the only curative treatment for both adults and children with CML. However, due to the small numbers of patients, standardized treatment approaches for pediatric CML have not been established. There are several unique characteristics of CML diagnosed in children and adolescents, and young adults (AYA; 16-29 years), compared to adults. Children and AYA with CML present with a higher white blood count and have larger spleens, higher peripheral blast counts, and lower hemoglobin levels, suggesting that the biology of pediatric CML is different than adult CML. In addition, potential side effects of TKIs unique to pediatric CML patients include impaired bone growth, fertility and immune function, however none have been extensively studied. We hypothesize that the differences in clinical presentation of pediatric CML patients are due to unique molecular characteristics that are absent in adult CML patients. To test this hypothesis, we studied the transcriptomic signature of pediatric CD34+ CML cells compared to adult CML and normal age-matched bone marrow CD34+ cells. Methods CD34+ cells were isolated from pediatric CML (n=7), adult CML (n=8), pediatric normal (n=2) and adult normal (n=3) bone marrow samples. Total RNA was isolated from cells, and then cDNA libraries were generated. Prepared libraries were sequenced on the Illumina HiSeq 4000 instrument. We aligned reads using the HISAT2 alignment software, and mapped to genes with HT-Seq. We removed genes that had zero reads across all the samples, resulting in a set of 4,696 genes that were detected in one or more samples. In case of technical replicates, we used mean of replicates. We performed three differential expression comparisons with edgeR: (1) Pediatric CML vs Adult CML, (2) Adult CML vs Adult Normal, and (3) Pediatric CML vs Pediatric Normal. We used a False Discovery Rate (FDR) of £ 20% and absolute log2 fold-change ³ 1 for selecting differentially expressed genes in each comparison. We used Fisher's exact test to identify significant KEGG pathways for the differentially expressed genes in each comparison. Results Pediatric CML vs Adult CML We found 24 differentially expressed genes (15 over- and 9 under-expressed). Though no pathway was found to be significant at the false discovery rate (FDR) £ 20%, we identified a number of sub-pathways that are relevant. For example, the Chemokine Signaling pathway shows at the top of the list (ordered by raw p-value) because of two genes, XCR1 and HCK, associated with VEGF and MAPK pathways involved in cell proliferation, angiogenesis, DNA repair, and cancer pathogenesis. Adult CML vs Adult Normal We found 60 genes (30 over- and 30 under-expressed) differentially expressed when comparing adult CML patients to normal adults. Ten genes overlapped with 24 genes we identified when comparing pediatric and adult CML patients. We found 11 pathways as significant at FDR £ 10%. Multiple pathways, including Cell adhesion, allograft rejection, Graft versus Host Disease, and Type I diabetes pathways, showed downregulation of MHC, with subsequent downstream reduction in expression of apoptosis-related genes. The IL-17 pathway makes sense, as MAPK, well-known to be associated with various cancers, is down-regulated. Lastly, in the NK pathway the gene DAP12 is up-regulated. This gene is known as a tyrosine kinase binding protein, and although tyrosine kinase inhibitors are the standard treatment for CML, the role of DAP12 in relation to leukemia has not yet been described. Pediatric CML vs Pediatric Normal We found 509 genes (350 over- and 159 under-expressed) differentially expressed in pediatric CML patients compared to normal. Interestingly, transcriptional regulators are differentially enriched in the hematopoietic stem cell differentiation function group including GATA1, GATA2, KLF1 and KLF2. RFC is down-regulated. RFC is a mismatch repair gene known to be involved in colorectal cancer. Many of the significant pathways are involved in glucose and fatty acid metabolism. Our pilot study identified novel molecular features of pediatric CML bone marrow stem cells, providing new insights into the novel biomarkers and pathogenesis of pediatric CML. Disclosures Gotlib: Blueprint Medicines: Consultancy, Honoraria, Research Funding; Promedior: Research Funding; Deciphera: Consultancy, Honoraria, Research Funding; Incyte: Consultancy, Honoraria, Research Funding; Kartos: Consultancy; Celgene: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Research Funding; Novartis: Consultancy, Honoraria, Research Funding.

Description: Abstract 315 Introduction: Dysregulated JAK-STAT signaling in chronic myeloproliferative neoplasms (MPNs) has primarily been attributed to activating mutations in tyrosine kinases. However, JAK-STAT activation can be demonstrated in some patients lacking JAK2 or MPL mutations, suggesting alteration of other regulatory elements in this pathway. One regulator of JAK-STAT signaling is LNK (SH2B3), an adapter protein that contains a proline-rich N-terminal dimerization domain (Pro/DD), a pleckstrin homology (PH) domain (plasma membrane localization), and an SH2 domain. LNK binds to cytokine receptors (e.g. MPL, EPOR) and JAK2 via its SH2 domain, inhibiting downstream STAT activation and providing critical negative feedback regulation. LNK-/- mice exhibit features consistent with an MPN phenotype. We recently reported the first human disease-related LNK mutations in two JAK2 V617F-negative MPN patients (Oh et al, Blood, Aug 12, 2010). One patient with primary myelofibrosis (PMF) exhibited a 5 base-pair (bp) deletion and missense mutation (DEL) leading to a premature stop codon and loss of the PH and SH2 domains. A second patient with essential thrombocythemia (ET) was found to have a missense mutation (E208Q) in the PH domain. Both mutations conferred aberrant JAK-STAT signaling in cell lines and primary patient samples, indicating that loss of LNK negative feedback regulation contributes to MPN pathogenesis. We now report the results of a comprehensive screen of a large cohort of MPN, overlap myelodysplastic syndrome (MDS)/MPN, and post-MDS/MPN acute myeloid leukemia (AML) patients for LNK mutations. Methods: A total of 341 samples were sequenced (Table 1; polycythemia vera (PV)=34, erythrocytosis=7, ET=61, PMF=75, post-PV/ET MF=25, MPN-U=7, chronic myelomonocytic leukemia (CMML)=71, juvenile myelomonocytic leukemia=20, MDS/MPN=8, MDS with fibrosis=2, refractory anemia with ring sideroblasts and thrombocytosis=4, idiopathic hypereosinophilic syndrome/chronic eosinophilic leukemia=4, systemic mastocytosis=4, and post MDS/MPN AML=19). A deep sequencing approach (Illumina multiplexing system) was used to evaluate 84 samples, in which all exons of LNK were sequenced. For the remainder of the samples, direct sequencing was performed on exon 2, the region containing the previously reported DEL and E208Q mutations. Results: After excluding variants previously reported in SNP databases, a total of 11/341 (3.2%) patients were found to have non-synonymous mutations, including 3/61 (4.9%) ET, 3/75 (4.0%) PMF, and 5/71 (7.0%) CMML patients (Table 1). Each of the mutations localized to exon 2 of LNK, implicating this region as a possible mutational hotspot. This included the aforementioned patients with the DEL and E208Q mutations, which were confirmed by deep sequencing. In two other patients, sequencing of DNA from cultured skin fibroblasts DNA indicated that the mutations were germline. For the remaining seven patients, germline analysis is currently ongoing. In one patient with CMML, a 1 bp deletion leading to a frameshift and premature stop codon was identified (Q72fs). This mutation localized to the Pro/DD, likely resulting in a complete loss of LNK function. Interestingly, this patient who is wild type for the JAK2 and RAS genes, also carries a heterozygous CBL mutation (C396Y), suggesting that LNK and CBL mutations may have cooperative effects. Four patients (one with PMF, three with CMML) were found to have a missense mutation (S186I) at a highly conserved residue in the Pro/DD. The previously reported E208Q mutation was also found in one patient with ET and one patient with CMML. None of the 81 patients known to be JAK2 V617F-positive exhibited somatic LNK mutations, suggesting that LNK mutations may provide an alternative basis for JAK-STAT activation in the absence of JAK2 V617F. Conclusion: Missense and deletion mutations of the LNK gene occur at a low frequency in MPNs and MDS/MPNs and segregate predominantly in exon 2. Further analysis of post-MPN AML samples (represented at a low frequency in the current cohort) and other subtypes of acute and chronic myeloid malignancies is warranted to better characterize the disease spectrum of LNK mutations and whether they are mutually exclusive of JAK2 V617F. We are currently investigating whether loss of negative feedback regulation of JAK-STAT signaling is related to haploinsufficiency of LNK or dominant negative effects of the mutant protein. Disclosures: No relevant conflicts of interest to declare.

Description: Abstract 3086 Background: Hereditary thrombocythemia (HT) is a rare autosomal dominant disorder related to mutations in either the gene encoding thrombopoietin (THPO), or its receptor MPL. In some cases of HT, mutational involvement of the THPO or MPL genes has been excluded. To date, five HT families with three distinct THPO mutations have been published, including Dutch, Japanese, and Polish pedigrees. In all cases, the mechanism of overproduction of platelets is related to alteration of the 5′ untranslated region (5′ UTR) of the THPO gene which results in enhanced translation of thrombopoietin (TPO) mRNA. We present our analysis of a Philippine family with a novel THPO gene mutation which segregates with the thrombocytosis phenotype. Methods: Informed consent was obtained from research participants. Peripheral blood was obtained from 6 family members, and serum was collected from 10 healthy adults. DNA was extracted with the Puregene DNA Isolation Kit (Qiagen). For the human TPO ELISA assay, the serum TPO concentrations of the family members as well as the healthy controls were measured with the human TPO Quantikine kit (R&D Systems). The exon 2 to intron 3 region of THPO gene covering the 3 previously reported mutations was amplified and purified PCR products were sequenced. To examine the functional effects of increased TPO levels on downstream JAK-STAT signaling, freshly obtained PB samples were incubated for 15 minutes at 37C, followed by fixation with paraformaldehyde and lysis of red blood cells. Fixed cells were permeabilized with methanol and stained with a combination of surface marker and intracellular phospho-specific antibodies, followed by analysis on a LSRII flow cytometer. Data analysis was performed with FlowJo (Tree Star). Results: The proband (see Figure 1a, pedigree subject II-1, arrow) is a 39 year-old Philippine woman who was informed at age 19 that she had an elevated platelet count. Although placed on hydroxyurea, anagrelide, and interferon-α in the distant past, she was currently maintained on only low-dose aspirin. At the time of her presentation at Stanford Cancer Center in March 2010, her complete blood count revealed a platelet count of 1,015,000/mm3 without other abnormalities. The peripheral blood smear revealed occasional large, hypogranular platelets. Reactive causes of thrombocytosis were excluded and her examination was normal. JAK2 V617F mutation analysis was negative. Routine CBC evaluation of her two children revealed thrombocytosis in her 11 year-old daughter (subject III-1; platelet count 550,000/mm3) and 9-year old son (subject III-2; platelet count 759,000/mm3). None of the three family members with thrombocytosis experienced a history arterial or venous thrombosis nor vasomotor symptoms. As shown in Figure 1b, DNA sequencing revealed a novel heterozygous mutation of T〉C at the splice donor site of intron 2 in the proband (II-1) and her two children (III-1, III-2), while the proband's parents (I-1, I-2) and husband (II-2)were wild type at this site. In Figure 1a, the pedigree of the six family members with serum TPO concentrations (pg/mL) (1st row) and platelet counts (/mm3)(2nd row) is shown. Figure 1c demonstrates that the serum TPO concentration of family members with the THPO mutation was significantly higher than those family members without the mutation (un-paired t-test, p=0.0378), or healthy controls (p=0.0003). The TPO level in non-affected family members showed no statistical difference with healthy controls (p=0.98). In Figure 1d, basal phosphorylated STAT5 (pSTAT5) levels in CD3−/CD66−/CD14− progenitors were evaluated, and the 95th percentile is presented in the mean with SEM format. An un-paired t-test revealed that pSTAT5 levels were significantly higher in the affected group (p = 0.024, denoted by *). Conclusion: In our Philippine family, we have identified a novel heterozygous mutation at the conserved T in the invariant donor splice site of intron 2 of the THPO gene. Mutations at this position result in splicing errors, leading to exon skipping, intron retention or exposure of cryptic splice sites. Loss of the inhibitory wild-type 5′UTR has been shown to result in enhanced THPO transcription. This autosomal dominant gain of function germline mutation is associated with thrombocytosis, increased TPO levels, and constitutive activation of JAK-STAT signaling. Disclosures: No relevant conflicts of interest to declare.

Description: Introduction: Cyclic thrombocytopenia (CT) is a rare disease characterized by periodic fluctuations in platelet counts. The etiology of this disease has not been fully elucidated. Here, we present molecular characterization of CT in a 53-year-old male patient who has platelet counts ranging between 1 x 109/L to 〉400 x 109/L during a cycle period of 40 days which has occurred over several years. Methods: Blood transcriptome profiles and plasma cytokine levels were investigated in 24 samples that were sequentially collected every 3-4 days to cover two complete cycles. Total RNA was extracted after lysing red blood cells. 3SEQ (3′-end RNA sequencing for expression quantification) was performed for transcriptome profiling. SAMSeq quantitative analyses were conducted to identify differentially expressed genes. Three screening criteria were applied to this data set to identify a panel of exclusive platelet-specific genes. Plasma TPO (thrombopoietin)/testosterone/ estradiol/CD41a/CD42b levels were detected by ELISA. A total of 62 cytokines were screened using a luminex immunoassay. MPL (TPO receptor) gene was Sanger-sequenced using blood DNA and mRNA templates. DNA was extracted from the patient's hair follicles to exam the presence of the identified MPL mutation, and in-silico predictions were conducted to evaluate the MPL mutation. The wild-type (WT) and c.1210G〉A mutant MPL expression constructs were generated and transfected into Ba/F3 cells for stable MPL expression. TPO-stimulated, IL-3 independent growth of MPL-expressing Ba/F3 cells were assessed to determine the function of MPL proteins. Results: Plasma TPO levels cycled between 6 to 2745 pg/mL during the sampling period; TPO levels inversely mirrored the fluctuation of platelet counts and preceded the latter by 3-4 days. Additional plasma cytokines demonstrated either an inverse correlation (e.g. FasL, GM-CSF, and TNF-β, etc.), or well synchronized correlation (e.g. BDNF, PDGF-BB, and RANTES etc.), with platelet counts. The patient was negative for platelet autoantibodies. Transcriptome analysis revealed 977 genes with expression that positively correlated with platelet count changes. Unsupervised clustering stratified these genes into subgroups, including: i) platelet-specific genes, which precede platelet count changes by 3-4 days; ii) platelet-modulated genes, which follow platelet count changes and are regulated by coagulation factors (e.g. F2) and platelet-contained growth factors (e.g. PDGF-BB and EGF); and iii) neutrophil-specific genes, which precede platelet count changes by 7-10 days. Among platelet-specific genes, 34 genes were identified to have 〉50-fold induction over a cycle, and are present in the platelet transcriptome [Rowley JW, 2011]. A heat map of these exclusive platelet genes is shown in Figure 1A. A novel MPL c.1210G〉A heterozygous mutation, which leads to a p.Gly404Arg substitution, was identified in both blood and hair follicle DNA samples of the patient. This substitution resides in a highly conserved site and is predicted to be deleterious. In addition, the mutation creates a novel splice site, which results in the insertion of a 36 bp intron fragment in approximately 15% of MPL transcripts. In vitro analysis confirmed that MPL c.1210G〉A is a loss-of-function (LOF) variant. Ba/F3 cells that express WT MPL exhibited IL-3 independent growth in the presence of TPO; however, the Gly404Arg mutant failed to support TPO-stimulated growth (Figure 1B). Conclusion: We describe a patient with CT who exhibits fluctuations of multiple cytokines including an inverse correlation between TPO and platelet counts, and profound gene expression changes in neutrophil- and platelet-specific gene expressions which precede platelet count fluctuations. These data suggest that the cyclic megakaryopoiesis and thrombopoiesis underlies pathogenesis of the disease. Moreover, the identified novel LOF MPL allele may contribute to the disease pathogenesis. The biologic and molecular annotation of this case presents a unique opportunity to examine the transcriptional regulation of platelet homeostasis. Figure 1 (A) Heat map of 34 genes that are exclusively expressed in platelet. (B) Growth of Ba/F3 cells expressing WT or c.1210G〉A MPL in IL-3 free medium containing TPO (50 ng/mL). Average viable cell numbers of duplicate experiments were plotted with SD as error bars. Figure 1. (A) Heat map of 34 genes that are exclusively expressed in platelet. (B) Growth of Ba/F3 cells expressing WT or c.1210G〉A MPL in IL-3 free medium containing TPO (50 ng/mL). Average viable cell numbers of duplicate experiments were plotted with SD as error bars. Disclosures No relevant conflicts of interest to declare.

Description: Introduction Pediatric chronic myeloid leukemia (CML) accounts for 10-15% of pediatric myeloid leukemias and 2-9% of all pediatric leukemias. There are several unique characteristics of CML diagnosed in children, adolescents, and young adults, compared to adults. They present with higher white blood counts and larger spleens, suggesting that the biology of pediatric CML is different from adult CML. We hypothesize that the differences in clinical presentation of pediatric CML patients are due to unique molecular characteristics that differ from adult CML patients. To test this hypothesis, we studied the transcriptomic signature of pediatric CD34+ CML cells compared to adult CML and normal age-matched bone marrow CD34+ cells. Methods CD34+ cells were isolated by FACS from pediatric CML (n=9), adult CML (n=10), pediatric normal (n=10) and adult normal (n=10) bone marrow samples. Total RNA was isolated from cells, and cDNA libraries were generated. Prepared libraries were sequenced on the Illumina HiSeq 4000 instrument. Raw sequences were trimmed and aligned to the hg38 reference genome with STAR/2.5.1b aligner. Gene level counts were determined with STAR -quantMode option using gene annotations from GENCODE (p5). Differential gene expression and pathway analysis were conducted with R/3.5.3. Counts were normalized with trimmed mean of M-values (TMM) from the EdgeR/ 3.24.3 package and further transformed with VOOM from the Limma/ 3.38.3 package. A linear model using the empirical Bayes analysis pipeline also from Limma was then used to obtain p-values, adjusted p-values and log-fold changes (LogFC). We performed three comparisons: (1) Pediatric CML vs Normal, (2) Adult CML vs Normal, and (3) Pediatric CML vs Adult CML. A False Discovery Rate (FDR) of £ .05 and absolute log2 fold-change 〉 1 was used to define differentially expressed genes in each comparison. Over-representation analysis was used to identify potentially unique pathways based on differentially expressed genes. Clinical and demographic features at diagnosis were extracted for pediatric and adult CML patients and compared using Fisher's exact test (categorical variables) or Wilcoxon rank sum test (continuous variables). Results Pediatric patients were diagnosed with CML at a median of 11 years (interquartile range (IQR): 10-14) compared to 54 years (IQR: 33-62) for adult patients. At diagnosis, pediatric patients had higher platelet counts (p=0.001) and larger spleen sizes (p=0.010) than adult patients, whereas the white blood cell count and phase at diagnosis did not differ. We found 606 genes (210 up- and 396 down-regulated) differentially expressed in pediatric CML CD34+ cells compared to pediatric normal controls. Interestingly, transcriptional regulators involved in blood cell differentiation including GATA1, TAL1, and KLF1 were differentially enriched in pediatric CML. In comparing adult CML patients to normal adult CD34+ cells, we found 920 genes (379 up- and 541 down-regulated) differentially expressed. Among all dysregulated genes we identified (1352 genes), 174 genes (54 up- and 120-down-regulated) overlapped when comparing pediatric and adult CML patients. Significantly enriched pathways in both adult and pediatric CML cells included PI3K/AKT signaling, MAPK signaling, and Notch/Wnt signaling, which have been previously reported. We found 437 unique genes that were dysregulated only in pediatric CML (270 up- and 167 down-regulated). Notch/Wnt signaling and Rho signaling pathways were significantly enriched. DLC1, a tumor suppressor gene that encodes a RhoGTPase-activating protein, has been known to be downregulated in solid tumors and hematologic malignancies. Interestingly, our data showed that DLC1 is significantly upregulated by 3-fold (p=0.0238) in pediatric CML, but not adult CML CD34+ cells. In addition, we observed that ABR, an inducer of C/EBPa that encodes an activator of RhoGEF and GTPase, was significantly downregulated by 2-fold (p=0.0119) in pediatric but not in adult CML CD34+ cells. Conclusion These results demonstrate unique molecular characteristics of pediatric CML that may contribute to the clinical differences at presentation between adult and pediatric disease. A better understanding of the particular biology of pediatric CML might impact the treatment of those patients in the future. Disclosures Gotlib: Deciphera: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: co-chair of the Study Steering Committee and Research Funding; Blueprint Medicines Corporation: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Chair of the Response Adjudication Committee and Research Funding, Research Funding.