Juvenile Myelomonocytic Leukemia Research Articles

The elevation of red blood cell distribution width is an independent prognostic factor for juvenile myelomonocytic leukemia.

Juvenile myelomonocytic leukemia (JMML) is a disorder characterized by the simultaneous presence of myeloproliferative and myelodysplastic features, primarily affecting infants and young children. Due to the heterogeneous genetic background among patients, the current clinical and laboratory prognostic features are insufficient for accurately predicting outcomes. Thus, there is a pressing need to identify novel prognostic indicators. Red cell distribution width (RDW) is a critical parameter reflecting the variability in erythrocyte size. Recent studies have emphasized that elevated RDW serves as a valuable predictive marker for unfavorable outcomes across various diseases. However, the prognostic role of RDW in JMML remains unclear. Patients with JMML from our single-center cohort between January 2008 and December 2019 were included. Overall, 77 patients were eligible. Multivariate Cox proportional hazard models showed that patients with red cell distribution width coefficient of variation (RDW-CV) >17.35% at diagnosis were susceptible to much worse overall survival rate (hazard ratio [HR] = 5.22, confidence interval [CI] = 1.50-18.21, P = .010). Besides, the combination of RDW elevation and protein phosphatase non-receptor type 11 (PTPN11) mutation was likely to predict a subgroup with the worst outcomes in our cohort. RDW is an independent prognostic variable in JMML subjects. RDW may be regarded as an inexpensive biomarker to predict the clinical outcome in patients with JMML.

Droplet digital PCR: An effective method for monitoring and prognostic evaluation of minimal residual disease in JMML.

Juvenile myelomonocytic leukaemia (JMML) is a rare myeloproliferative neoplasm requiring haematopoietic stem cell transplantation (HSCT) for potential cure. Relapse poses a significant obstacle to JMML HSCT treatment, as the lack of effective minimal residual disease (MRD)-monitoring methods leads to delayed interventions. This retrospective study utilized the droplet digital PCR (ddPCR) technique, a highly sensitive nucleic acid detection and quantification technique, to monitor MRD in 32 JMML patients. The results demonstrated that ddPCR detected relapse manifestations earlier than traditional methods and uncovered molecular insights into JMML MRD dynamics. The findings emphasized a critical 1- to 3-month window post-HSCT for detecting molecular relapse, with 66.7% (8/12) of relapses occurring within this period. Slow MRD clearance post-HSCT was observed, as 65% (13/20) of non-relapse patients took over 6 months to achieve ddPCR-MRD negativity. Furthermore, bone marrow ddPCR-MRD levels at 1-month post-HSCT proved to be prognostically significant. Relapsed patients exhibited significantly elevated ddPCR-MRD levels at this time point (p = 0.026), with a cut-off of 0.465% effectively stratifying overall survival (p = 0.007), event-free survival (p = 0.035) and cumulative incidence of relapse (p = 0.035). In conclusion, this study underscored ddPCR's superiority in JMML MRD monitoring post-HSCT. It provided valuable insights into JMML MRD dynamics, offering guidance for the effective management of JMML.

Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interface.

The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.

SH2B3 alterations in a novel genetic condition, juvenile myelomonocytic leukemia, and myeloproliferative neoplasia.

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Abstract 328: A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions

Abstract Introduction: Myeloid malignancies encompass diverse hematopoietic disorders, including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). We developed two assays to address the genetic complexity of myeloid malignancies, OncomineTM Myeloid Assay and OncomineTM Myeloid Assay GX v2, detecting mutations in 45 DNA genes and >30 fusion driver genes, including >700 fusion isoforms. Our panel includes genetic alterations such as FLT3-Internal Tandem Duplications (ITDs), IDH1/2, CEBPA, CALR, and TP53. Methods: Here we describe the genomic profiles of 8503 clinical research samples (including AML, MPN, MDS, CML, CMML, or JMML). A total of 4723 samples were run on the Ion GeneStudioTM S5 System and analyzed using the OncomineTM Myeloid Research workflow on Ion ReporterTM 5.18. A total of 3780 samples were run on the Ion TorrentTM Genexus Software 6.6 and analyzed using the OncomineTM Myeloid Assay GX v2. Results: On Genexus, the turnaround time (the time between starting the run and NGS data report) was 23-25 hours and the hands-on time was around 1 hour. The success rate of the samples was 100%. Frequency of relevant mutations and variant allele frequency by gene: Genes like TET2 (detected in 12.6% of samples), ASXL1 (9.3%), DNMT3A (7.8%), TP53 (7.5%) exhibited high mutation rates. 56.4% of samples had mutations, averaging 2.3 mutations per sample. Common co-occurring mutations included ASXL1-TET2 and SRSF2-TET2. Variant allele frequency varied greatly, e.g., ANKRD26 had a median VAF of 66%, while MYD88 had only 7%. Mutation spectrum of FLT3ITD variants: FLT3-ITD was observed in 3% of samples, with an average VAF of 0.32, featuring a multi-modal length with the highest peak at around 34 bp and maximum length at 151 bp. Mutation spectrums of fusions: 710 (8.4%) samples were fusion-positive with read counts ranging 21-113,000. ABL1 was the most common driver and BCR-ABL1 was the most common gene pair. Other common drivers included KMT2A, MYH11, RARA, and RUNX1. 17 distinct driver genes, 49 gene pairs, and 110 gene isoforms were observed, including rare fusions like ZMYM2-FGFR1 and KAT6A-CREBBP that are not detectable by traditional methods like qPCR (quantitative polymerase chain reaction) or FISH (fluorescence in-situ hybridization). Conclusions: The Oncomine Myeloid Assay is a fast, robust, and reproducible solution for comprehensive genomic profiling of myeloid malignancies. We describe the mutational spectrum of DNA variants and RNA fusions in a range of clinical research samples. (For research use only. Not for use in diagnostic procedures. © 2023 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.) Citation Format: Jiajie Huang, Haigang Gu, Janet Orton, Marina Sedova, Sophie Rozenzhak, Fiona Hyland, Guang Liu. A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 328.

Складність діагностики рефрактерної хвороби Кавасакі під «маскою» гемобластозу: клінічний випадок із досвіду гематолога

Kawasaki disease (KD) is an acute systemic vasculitis that is the most common cause of acquired heart disease in children under 5 years of age with hyperthermia. Diagnosis of KD is a clinical challenge, given the wide range of clinical manifestations and similarities with many viral and bacterial diseases. Purpose - to describe a clinical case of refractory КD in a three-month-old girl with an emphasis on the importance of echocardiography and coronary angiography for the final verification of the disease, urgent initiation of treatment with minimal suspicion of КD. Clinical case. The article reports on a three-month-old patient with a difficult diagnosis of refractory form of КD. The disease debuted with hyperthermia, enterocolitis, obstructive bronchitis, and hepatoliver syndrome. The manifestations of skin exanthema were initially considered as an allergic dermatitis to the use of a cephalosporin antibiotic. Multisystemic inflammatory syndrome associated with SARS-CoV-2 infection was suspected. After the use of immunosuppressive therapy with mega-doses of dexamethasone and intravenous human immunoglobulin 2 g/kg/day for 3 days, clinical improvement was achieved. Subsequently, the haemogram showed an increase in neutrophilic hyperleukocytosis to the appearance of blast cells, hyperthrombocytosis and severe anaemia. A differentiation was made between a leukemic reaction, the debut of myeloproliferative disease, juvenile myelomonocytic leukaemia. Against the background of a rapid decrease in the number of leukocytes, the girl developed hyperthermia, migratory intermittent maculopapular rash, and foots edema. Laboratory findings included thrombocytosis and an increase in acute-phase parameters. Echocardiography revealed left ventricular dilation, a small amount of excess fluid in the pericardium, dilatation of the left coronary artery evenly to the bifurcation. Computed tomography revealed giant coronary artery aneurysms, which gave grounds to diagnose KD. The study was performed in accordance with the principles of the Declaration of Helsinki. Informed consent of the parents of child was obtained for the study. No conflict of interests was declared by the authors.

A predictive classifier of poor prognosis in transplanted patients with juvenile myelomonocytic leukemia: a study on behalf of the Société Francophone de Greffe de Moelle et de Thérapie Cellulaire.

Juvenile myelomonocytic leukemia (JMML) is an aggressive pediatric myeloproliferative neoplasm requiring hematopoietic stem cell transplantation (HSCT) in most cases. We retrospectively analyzed 119 JMML patients who underwent first allogeneic HSCT between 2002 and 2021. The majority (97%) carried a RAS-pathway mutation, and 62% exhibited karyotypic alterations or additional mutations in SETBP1, ASXL1, JAK3 and/or the RAS pathway. Relapse was the primary cause of death, with a 5-year cumulative incidence of 24.6% (95%CI: 17.1-32.9). Toxic deaths occurred in 12 patients, resulting in treatmentrelated mortality (TRM) of 9.0% (95%CI: 4.6-15.3). The 5-year overall (OS) and event-free survival were 73.6% (95%CI: 65.7-82.4) and 66.4% (95%CI: 58.2-75.8), respectively. Four independent adverse prognostic factors for OS were identified: age at diagnosis >2 years, time from diagnosis to HSCT >6 months, monocyte count at diagnosis >7.2x109/L, and the presence of additional genetic alterations. Based on these factors, we proposed a predictive classifier. Patients with three or more predictors (21% of the cohort) had a 5-year OS of 34.2%, whereas those with none (7%) had a 5-year OS of 100%. Our study demonstrates improved transplant outcomes compared to prior published data, which can be attributed to the synergistic impacts of a low TRM and a reduced yet still substantial relapse incidence. By integrating genetic information with clinical and hematological features, we have devised a predictive classifier. This classifier effectively identifies a subgroup of patients who are at a heightened risk of unfavorable post-transplant outcomes who would benefit novel therapeutic agents and post-transplant strategies.

Juvenile Myelomonocytic Leukemia – Experience from a Tertiary Care Hospital in Eastern India

Background: Juvenile myelomonocytic leukemia (JMML), previously known as juvenile chronic myeloid leukaemia, is a rare, unique, and aggressive myeloproliferative neoplasm of early childhood. Making a diagnosis of JMML is challenging because of the overlapping clinical and haematological features with other myeloproliferative neoplasms (MPN). However, some unique features like monocytosis, the absence of BCR-ABL translocation, and the presence of specific mutations (PTPN-11, K-RAS, N-RAS, CBL, or NF1) clinch the correct diagnosis.Methods: A prospective analysis of six JMML patients with variable clinical features treated with injection azacytidine as frontline therapy during the study period of 2 years. Results: The median age was 4.5 years with male:female ratio 2:4. Pallor and splenomegaly were the most common presenting signs. Four patients (66.67%) achieved complete remission (CR), two patients (33.33%) had partial remission (PR), and one patient (16.67%) had progressive disease (PD). The overall survival rate was 66.67% (four out of six), and the mortality rate was 33.33%.Conclusion: Azacitidine is an effective treatment option as upfront therapy for JMML, especially in resource poor developing countries.

LNK/SH2B3 as a novel driver in juvenile myelomonocytic leukemia.

Mutations in five canonical Ras pathway genes (NF1, NRAS, KRAS, PTPN11 and CBL) are detected in nearly 90% of patients with juvenile myelomonocytic leukemia (JMML), a frequently fatal malignant neoplasm of early childhood. In this report, we describe seven patients diagnosed with SH2B3-mutated JMML, including five patients who were found to have initiating, loss of function mutations in the gene. SH2B3 encodes the adaptor protein LNK, a negative regulator of normal hematopoiesis upstream of the Ras pathway. These mutations were identified to be germline, somatic or a combination of both. Loss of function of LNK, which has been observed in other myeloid malignancies, results in abnormal proliferation of hematopoietic cells due to cytokine hypersensitivity and activation of the JAK/STAT signaling pathway. In vitro studies of induced pluripotent stem cell-derived JMML-like hematopoietic progenitor cells (HPCs) also demonstrated sensitivity of SH2B3- mutated HPCs to JAK inhibition. Lastly, we describe two patients with JMML and SH2B3 mutations who were treated with the JAK1/2 inhibitor ruxolitinib. This report expands the spectrum of initiating mutations in JMML and raises the possibility of targeting the JAK/STAT pathway in patients with SH2B3 mutations.

Too many white cells-TAM, JMML, or something else?

Leukocytosis is a common finding in pediatric patients, and the differential diagnosis can be broad, including benign reactive leukocytosis and malignant myeloproliferative disorders. Transient abnormal myelopoiesis is a myeloproliferative disorder that occurs in young infants with constitutional trisomy 21 and somatic GATA1 mutations. Most patients are observed, but outcomes span the spectrum from spontaneous resolution to life-threatening complications. Juvenile myelomonocytic leukemia is a highly aggressive myeloproliferative disorder associated with altered RAS-pathway signaling that occurs in infants and young children. Treatment typically involves hematopoietic stem cell transplantation, but certain patients can be observed. Early recognition of these and other myeloproliferative disorders is important and requires a clinician to be aware of these diagnoses and have a clear understanding of their presentations. This paper discusses the presentation and evaluation of leukocytosis when myeloproliferative disorders are part of the differential and reviews different concepts regarding treatment strategies.

P25 - The rare cases of co-occurrences of Down Syndrome Disease and Juvenile Myelomonocytic Leukemia

P25 - The rare cases of co-occurrences of Down Syndrome Disease and Juvenile Myelomonocytic Leukemia

Error-Corrected Next-Generation Sequencing Provides a Comprehensive Overview of the Subclonal Mutation Landscape and Its Prognostic Implications in Juvenile Myelomonocytic Leukemia

Introduction: Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm characterized by mutations in genes activating the RAS pathway ( PTPN11, NF1, NRAS, KRAS, and CBL). Approximately 20% of patients with JMML have secondary mutations in SETBP1 and/or JAK3, and recent droplet digital PCR (ddPCR) analyses revealed that mutations in these two genes, including very rare mutations (variant allele frequency [VAF] < 0.05) that are difficult to detect by conventional next-generation sequencing (NGS), are associated with poor prognoses. Meanwhile, the landscape of low VAF subclonal mutations of other genes in patients with JMML has not been adequately evaluated. Therefore, we utilized error-corrected NGS, which can reduce the systematic sequencing error rate of conventional NGS by incorporating molecular barcodes (MBCs). Methods: We performed error-corrected NGS in 93 patients with JMML and 11 patients with JMML-like myeloproliferative disorder with Noonan syndrome (NS/MPD) using a small panel associated with myeloid malignancies. Samples for error-corrected NGS were prepared using a SureSelect XT HS2 DNA Library Preparation Kit (Agilent Technologies), including unique dual index and duplex MBCs. A unique MBC is incorporated into each DNA fragment, and the incorporated MBC can differentiate true and false duplications, allowing for highly accurate sequencing that can detect mutations with VAF > 0.001. We used the HiSeq X platform (Illumina) and SureCall v.4.2 application (Agilent Technologies) for analysis. In addition, DNA methylation analysis was performed on the same cohort using the Infinium HumanMethylation 450K BeadChip and/or Digital Restriction Enzyme Analysis of Methylation as previously described (Murakami et al. 2018;131:1576-1586, Kitazawa et al. Blood Adv. 2021;5:5507-5518). This study was approved by the Ethics Committee of the Nagoya University Graduate School of Medicine. Results: In the cohort of 104 patients with JMML or NS/MPD, 160 mutations were identified, of which 30 (19%) had VAF < 0.05 (eight in JAK3, seven in NF1, five in ASXL1, three in NRAS, two each in PTPN11 and SOS1, and one each in SETBP1, SH2B3, and ZRSR2). Subclonal mutations in SETBP1 p.D868N and JAK3 p.R657Q identified by error-corrected NGS were confirmed using ddPCR, and consistent results were obtained for both assays (R 2 = 0.9977 and 0.9919 respectively). Of 93 patients with JMML, 30 (32%) had subclonal or clonal secondary mutations, whereas no such mutations were detected in patients with NS/MPD ( P = 0.031). Of 104 patients, 23 (22%) had secondary mutations with VAF ≥ 0.05 (Major group), 7 (7%) only had secondary mutations with VAF < 0.05 (Minor group), and the remaining 74 (71%) had no secondary mutations (Negative group). We assessed the associations of subclonal mutations detected by error-corrected NGS with the DNA methylation profile, the most important prognostic factor in JMML. Whereas 22 of 23 (96%) and 5 of 7 (71%) patients in the Major and Minor groups, respectively, had high methylation (HM) profiles, only 20 of 74 (27%) patients in the Negative group featured HM profiles ( P < 0.001). The 4-year overall survival (OS) rates were significantly lower in the Major (52.2% [95% confidence interval {CI} = 30.5%-70.0%], P = 0.01) and Minor groups (42.9% [95% CI = 9.8%-73.4%], P = 0.03) than in the Negative group (76.3% [95% CI = 64.6%-84.5%]). In a subgroup analysis of 30 patients with secondary mutations, patients with secondary mutations in RAS pathway genes (n = 18) had significantly lower 4-year OS rates than those with secondary mutations in other genes (n = 12; 32.4% [95% CI = 12.7%-54.0%] vs. 75.0% [95% CI: 40.8%-91.2%], P = 0.047). Conclusions: We successfully performed error-corrected NGS to assess comprehensive subclonal secondary mutational profiles, including very low VAF variants. The presence of subclonal mutations, particularly in RAS pathway genes, was associated with poor OS. These findings provide important information for appropriate risk stratification, which will contribute to the implementation of precision medicine for patients with JMML.

Risk Stratified Treatment for Patients with Newly Diagnosed Juvenile Myelomonocytic Leukemia: A Phase 1/2 Non-Randomized Study of Trametinib and Azacitidine with or without Chemotherapy

Background: Juvenile myelomonocytic leukemia (JMML) is an aggressive myeloproliferative disorder of childhood. The biochemical hallmark of JMML is aberrant signaling through the Ras pathway caused by initiating mutations in NF1, NRAS, KRAS, RRAS, RRAS2, SH2B3, PTPN11,or CBL. While hematopoietic stem cell transplantation (HSCT) can be curative, 5-year event-free survival of children with JMML after HSCT is only ~50%. Recently, several studies have identified mutational burden and DNA methylation as predictive of clinical outcomes in patients with JMML. In the T2020-004 phase 1/2 clinical trial, we will define lower-risk patients as those with one somatic alteration and low DNA methylation and high-risk patients as those with more than one somatic alteration or intermediate/high DNA methylation. Trametinib is an orally bioavailable, reversible, highly selective allosteric inhibitor of MEK1/2 in the Ras/MAPK signaling pathway. Trametinib is FDA-approved for the treatment of adults with advanced melanoma with BRAF V600E or V600K mutations and in children with Ras-mutant solid tumors in combination with dabrafenib. Clinical investigation of trametinib monotherapy via the Children's Oncology Group ADVL1521 phase 2 trial (NCT03190915) showed efficacy in children with relapsed/refractory JMML. Phase 2 clinical trial evaluation of azacitidine in children with newly-diagnosed JMML was also efficacious and led to its FDA approval. In this trial, trametinib will be tested in combination with azacitidine in lower-risk patients and in combination with azacitidine and chemotherapy for high-risk patients. Study Design and Methods: This is a non-randomized, risk stratified, Phase 1/2 study for patients with newly-diagnosed JMML (NCT05849662) conducted via the Therapeutic Advances in Childhood Leukemia and Lymphoma (TACL) Consortium with safety and efficacy phases for both lower-risk and high-risk cohorts. Lower-risk patients will receive trametinib once-daily for 28 days in combination with azacitidine administered daily for five days per cycle. Lower-risk patients can receive up to 12 cycles and will proceed to HSCT only if they experience progressive disease or relapse. High-risk patients will receive trametinib administered once-daily for 28 days in combination with azacitidine, fludarabine, and cytarabine (aza/FLA) administered daily for five days per cycle. High-risk patients will receive up to two cycles of therapy before proceeding to HSCT off protocol. Key Eligibility: Patients aged 1 month to 21 years who meet World Health Organization criteria for JMML will be eligible. Objectives: The primary safety objectives are to determine the safety of combining trametinib with azacitidine for lower-risk patients and combining trametinib with aza/FLA for high-risk patients. The secondary efficacy objectives are to determine the event-free survival for lower-risk patients in the absence of HSCT and the molecular response rates pre-HSCT for high-risk patients. Sample Size and Statistical Design: A rolling 6 trial design will be used during Phase 1 of the study to determine the recommended phase II dose (RP2D) of trametinib for lower-risk and high-risk patients in combination with their respective therapies. Starting trametinib dose is 0.032mg/kg daily if less than 6 years of age, or 0.025mg/kg daily if 6 years or older, with one dose level de-escalation if indicated. Phase II of the study involves lower-risk and high-risk cohort expansions at the RP2D of trametinib. Target accrual is 22 patients in the lower-risk arm and 42 patients in the high-risk arm. The study is open to accrual at all TACL consortium sites. We acknowledge the TACL Consortium's scientific contribution to and participation in this study, including participating member institutions, investigators, research teams, and the TACL Operations Center. Novartis Pharmaceuticals Corporation provided the investigative drug in support of this trial. This study is supported by the National Institute of Health, National Cancer Institute (R37CA266550), the Pediatric Cancer Research Foundation, and the Cannonball Kids Cancer Foundation.

Corelationship of Lymphocyte Subsets and Prognosis in Juvenile Myelomonocytic Leukemia

Objective: Juvenile Myelomonocytic Leukemia (JMML) is a rare hematopoietic stem cell malignant clonal disease in children and has the characteristics of MDS/MPN. Due to the poor response of JMML to chemotherapy, hematopoietic stem cell transplantation (HSCT) is currently the only cure method for JMML. Currently, there are some reports on the distribution of lymphocyte subsets in MDS. A significant lymphocytopenia was observed in MDS patients compared with similarly aged healthy people. Another study form Polish found patients with MDS have more CD3+T cells than healthy donors. But there are few related reports in JMML. The objective of this study is to analyze relationship between the distribution of lymphocyte subsets and prognosis in JMML patients, and explore new risk stratification indicatorsfor JMML personalized therapy. Method: This study retrospectively collected JMML patients clinical data from Institute of Hematology & Blood Diseases Hospital of CAMS during Jan 2008 and Nov 2022. All completed complete blood count and peripheral blood classification, fetal hemoglobin (HbF), granulocyte colony-stimulating factor (GM-CSF) high sensitivity, bone marrow morphology, immune typing, molecular biology, cytogenetics and other tests. We analyzed the relationship between distribution of lymphocyte and prognosis in these patients. Result: 96 newly diagnosed JMML patients were admitted to this study. The median age at diagnosis was 25 (2-82) months, and male to female was 3.8:1. 66 cases underwent lymphocyte subsets by flow cytometry. Median percentage of lymphocytes is 34.3%(1.8%-90.4%, normal range: 20%-40%), median percentage of CD3+T cells is 54.85%(10.3%-91%, normal range: 57%-88%), median percentage of CD3+CD4+ T cells is 30.95%(3.54%-53%, normal range: 27%-58%), median percentage of CD3+CD8+ T cells is 18.4%(2%-49.1%, normal range: 16%-45%), median percentage of NK cells is 13.95%(2.3%-50.3%, normal range: 3%-32%), and median percentage of B cells is 23.25%(4%-69.6%, normal range: 4%-18%). These cases were followed-up to Jan 2023, with a median follow-up time of 12 months (1-104 months). The overall survival (OS) rate was 52.67%, with a median OS time of 12 months (0-103 months). There were significant differences in the percentage of CD3+T cells (30.89% ± 9.46% vs 59.05% ± 10%, P<0.01) and CD3+CD4+T cells (14.87% ± 5.82% vs 35% ± 5.41%, P<0.01) between children with single NRAS mutation and compound mutations (≥2 classical five Ras pathway mutation ). In PTPN11 mutation patients, there is a significant positive correlation between OS and the percentage of lymphocytes (P=0.018). Conclusion: Our study shows differences in percentage of CD3+ T cells and CD3+CD4+ T cells between patients with NRAS mutation and compound mutations. Patients with PTPN11 mutation and higher percentage of lymphocytes will have better prognosis.

Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: A Report from the Children's Oncology Group

Background: Juvenile myelomonocytic leukemia (JMML) is an aggressive myeloproliferative neoplasm of infants and toddlers. Upfront therapies typically include high-dose cytarabine or azacitidine, but the only definitive treatment is hematopoietic stem cell transplantation (HSCT). While HSCT cures ~50% of patients, the prognosis is dismal for those who relapse. In the absence of a second HSCT, patients who relapse have a 2-year overall survival of ~10%. JMML is initiated by germline and somatic driver mutations in NF1, KRAS, NRAS, PTPN11, and CBL. These mutations converge on Ras signaling, leading to elevated levels of active Ras-GTP in specific cell lineages. Genetically engineered mouse (GEM) models accurately model key molecular, biologic, and biochemical features of JMML. Preclinical trials of the allosteric MEK inhibitors in Kras and Nf1 mutant mice demonstrated dramatic phenotypic responses with reduction in white blood cell counts, resolution of splenomegaly, and reversion to normal erythropoiesis. Based on the promising efficacy signal in GEM models, we evaluated trametinib, an orally bioavailable allosteric inhibitor of MEK1/2, in a prospective clinical trial in children with relapsed or refractory JMML to determine the overall response rate to trametinib. Results: Ten infants and children with JMML (median age 23.6 months) were enrolled and all were evaluable for safety and efficacy. Patients received age-adjusted dosing of trametinib for 28-day cycles and could remain on study for up to 12 cycles in the absence of disease progression or toxicity. A clonal Ras pathway mutation was confirmed in the blood and/or bone marrow of all patients. The objective response rate was 50% (two complete and three partial clinical responses). Four patients proceeded to HSCT after receiving protocol therapy and remain alive in complete remission with undetectable levels of the Ras pathway mutation identified at enrollment. Three additional patients completed 12 cycles of trametinib and continue to receive off-protocol therapy 6-24 months later with no change in the variant allele frequency of the underlying Ras pathway mutation. The remaining three patients had progressive disease with two demonstrating molecular evolution by the end of cycle 2. Paired pre- and post-trametinib RNASeq and proteomic analyses confirmed on-target biochemical effects of trametinib with down-regulation of both Ras/MAPK pathway related gene expression and MEK1/2 kinase activity, respectively. To gain deeper insight into how trametinib might affect distinct populations of hematopoietic cells, we generated single cell RNASeq data before and after treatment. The most prominent finding was a reduction in the proportions of classical and non-classical monocytes and broad downregulation of immune-related pathways in all cell populations. However, the downregulation of MAPK signaling genes was confined to specific cell types including, macrophages, classical monocytes, and granulocyte-monocyte progenitors, which uniquely displayed downregulated KRAS-related signatures following treatment. High DNA methylation and the presence of >1 mutation at enrollment correlated with lack of response to trametinib. Conclusions: We conducted an open label, phase 2 trial of trametinib in children with relapsed or refractory JMML. This is the first completed study of a MEK inhibitor in any hematologic malignancy in children. The trial met its primary objective and demonstrated a 50% objective response rate with 70% of patients bridging to a successful HSCT or completing the maximum 12 cycles permitted on study. The three patients who completed 12 cycles continue to receive trametinib off study for as long as 2 years. Although limited by a small number of patients, the long-term survival, and correlative molecular analyses from this trial raise provocative questions about whether certain patients with JMML might be spared the long-term adverse health risks of genotoxic HSCT conditioning regimens based on favorable molecular characteristics at diagnosis. This hypothesis will now be tested in a national, risk-stratified therapeutic trial (NCT05849662) of trametinib in combination with azacitidine in newly diagnosed patients. The authors would like to acknowledge funding and support from: NCTN Operations Center Grant (U10CA180886), NCTN Statistics & Data Center Grant (U10CA180899), and the St. Baldrick's Foundation.

Efficacy of Demethylated Drug Combine with Low Dose Chemotherapy in Juvenile Myelomonocytic Leukemia

Objection：Juvenile myelomonocytic leukemia (JMML) is a rare pediatric leukemia with a median survival time of less than 2 years. Currently, hematopoietic stem cell transplantation (HSCT) is the only possible cure of JMML. Most of the newly diagnosed pediatric patients with JMML have high tumor burden, and rapid disease progression, and may not tolerate HSCT. In the present study, we aimed to explore the effection of Demethylated drug in combination with low-dose chemotherapy on JMML patients before HSCT. Methods：A retrospective analysis of 16 JMML patients was performed from Jul 2017 to Nov 2021. All patients were given Demethylated drug in combination with low-dose chemotherapy, 10 patients decitabine at a dose of 20 mg/m2 for 5 days, supplemented with cytarabine (50-100 mg/m2×3~5 days), and /or etoposide (50 mg/m2×3~5 days), 6 patients Azacytidine at a dose of 75mg/m2 for 7 days combined with homoharringtonine 2mg/m2 for 5-7 days. Each treatment interval was 4 weeks, bridging to HSCT after three~four courses of treatment. Results：The median age of onset of the 16 JMML patients was 36 months (range 6-51 months), the male to female ratio was 14:2, and the median volume of the spleen at diagnosis was 357cm3 (range: 175-588) by Three-dimensional ultrasound of spleen. The median white blood cell (WBC) count was 39 (range 2-128) × 109/L, the median hemoglobin 84 (range 47-110) g/l, and the median platelet 36 (range 16-75) × 109/L，the median monocyte count was 8 (range 2-26) × 109/L at diagnosis, the median RDW-CV was 19 (15-30)%, the median RDW-SD 56 (45-77) fl, the median HbF 37(1-76)%. Chromosome was performed, of which 13 cases had normal karyotype. 2 cases had tirsomy 8, 1 case had structural abnormality in chrosome 9. Next-generation sequencing results showed that 11(68.8%) cases carried PTPN11 mutations, 6 (37.5%) cases NF1 mutation, 5 (31.3%) KRAS mutation, 4 (25%) NRAS mutation, 1 case without one of the Ras pathway genes. 8 cases (50%) had more than two types of canonical JMML mutations, among them 6 cases (75%) had PTPN11 and NF1 co-mutation. 10 cases had secondary gene mutations, 3 (3/10) cases JAK3 mutation, 2 (2/10) SETBP1 mutation, 2 (2/10) SH2B3 mutation, 2(2/10) ASXL1 mutation, 2 (2/10) ARID1A mutation, 1 (1/10) SRSF2 mutation. The median treatment course was three cycles (range: 1-6), and the response rate was 68.8% (11/16) after one cycle and 81.8% (9/11) after three cycles. One case achieved complete remission (CR) after four courses of therapy. The WBC and monocyte counts were significantly decreased after treatment (P<0.001), and the spleen volume showed a decreasing tendency. Eleven patients received HSCT, 9 cases were implanted successfully and 2 cases failed, of which 1 case was relieved by secondary transplantation and 2 patients died of grade IV graft-versus-host disease (GVHD) after transplantation. The median follow-up time was 31 months. The 2-year progression-free survival rate was 75.0±10.8%. Conclusions：Demethylated drug in combination with low-dose chemotherapy could reduce JMML patients' tumor burden, improve the general condition, and obtain a clinical response rate of 81.8% after 3 cycles therapy. Therefore, such a combination regimen could be used as a therapeutic option for JMML before HSCT.

Analysis of Methylation Level and Clinical Characteristics of Juvenile Myelomonocytic Leukemia

Objective: juvenile myelomonocytic leukemia (Juvenile myelomonocytic leukemia JMML) is a rare clonal disease of hematopoietic stem cells in young children. The response to chemotherapy is poor, the prognosis is poor, and a few patients can be relieved spontaneously. The level of methylation is closely related to the prognosis of JMML. In this study, the distribution characteristics and clinical indexes of JMML methylation were analyzed retrospectively. Methods: the newly diagnosed JMML from 2008.1 to 2022.11 in our center was selected as the research object. The samples were detected for DNA methylation and the clinical characteristics were analyzed. Results: methylation level was detected in 35 of 96 children with newly diagnosed JMML. The median age of onset was 27 months (3-82 months). There were 27 males and 8 females. The median platelet count was 70.6 × 109 × 10 ~ 9 × 10 ~ 9 × 10 ~ 9 / L, and the median absolute value of monocytes was 5.0 × 10 ~ 9 × 10 ~ 9 × 10 ~ 9 × 10 ~ 9 ml. All patients underwent JMML mutation and oral mucosal verification, including PTPN11 somatic mutation in 18 cases (51.4%), NRAS mutation in 10 cases (28.6%), KRAS mutation in 4 cases (11.4%), NF1 mutation in 7 cases (20%) and CBL mutation in 1 case (2.9%). Among them, 9 cases (25.7%) were compound mutations and 5 cases were recurrent mutations of PTPN11 and NF1. The DNA methylation level was divided into three subgroups: 4 cases (11.4%) hypomethylation (LM) group and 14 cases (40%) methylation group (IM) 17 cases (48.6%) hypermethylation (HM) group. Among the 17 patients in HM group, there were 7 cases of PTPN11 single mutation (41.2%) and 9 cases of compound mutation (52.9%), which were significantly higher than 3 cases of PTPN11 in IM group (21.4%). In IM group, simple NRAS or KRAS mutations accounted for 50%. The mutation distribution in LM group was 1 case of KRAS mutation, 2 cases of RANSBP2-ALK fusion gene and 1 case of no mutation. There were significant differences in age, platelet, fetal hemoglobin (HbF), PTPN11 mutation and ≥ 2 somatic mutation among different methylation subgroups (P < 0.05). The correlation analysis showed that methylation was positively correlated with 24 months of age, ≥ 33 × 10 9 mmol L, HbF, PTPN11 mutation and ≥ 2 somatic mutation (P < 0.05). Conclusion: high risk factors such as age at first diagnosis, PTPN11 mutation and compound mutation are significantly correlated with methylation in patients.

A Comprehensive Genomic Profiling of Myeloid Malignancies Demonstrates Mutational Spectrum of DNA Variants Including FLT3-ITDs, and Gene Fusions

Introduction Myeloid malignancies are a group of clonal hematopoietic disorders including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). These diseases are heterogenous and genetically complex and the number of genetic alterations associated with them continues to grow. To address the need for comprehensive genetics research we developed the Oncomine TM Myeloid Assay and the Oncomine TM Myeloid Assay GX v2, which both detect genomic alterations associated with myeloid malignancies including 45 DNA genes and >30 fusion driver genes with the ability to detect >700 fusion isoforms. Our panel includes genetic alterations in AML, MPN, and MDS such as FLT3-Internal Tandem Duplications (ITDs), IDH1/2, CEBPA, CALR, and TP53. Methods Here we describe the genomic profiles of 8503 clinical research samples (including AML, MPN, MDS, CML, CMML, or JMML). A total of 4723 samples were run on the Ion GeneStudio TM S5 System and analyzed using the Oncomine TM Myeloid Research workflow on Ion Reporter TM 5.18. A total of 3780 samples were run on the Ion Torrent TM Genexus Software 6.6 and analyzed using the Oncomine TM Myeloid Assay GX v2. Results The turnaround time (the time between starting the run and NGS data report) was 23-25 hours and the hands-on time was around 1 hour, which enabled fast and accurate profiling of myeloid malignancies, and facilitated the timely availability of results. The success rate of the samples was 100%. Frequency of relevant mutations by gene Some genes had a higher rate of genetic mutations. TET2 has the highest percentage of detection (12.6%, 1068 positive sample/8503 total number of samples). Other important genes with the highest percentage of detection included ASXL1 9.3% (787/8503), DNMT3A 7.8% (665/8503), TP53 7.5%, (640/8503), SRSF2 6.9% (587/8503), JAK2 6.6%, (562/8503), RUNX1 5.2% (446/8503), SF3B1 5.0% (423/8503), IDH2 4.0% (337/8503), NRAS 3.8% (318/8503), FLT3 3.4% (292/8503), ABL1 3.2% (273/8503), BCOR 2.7% (229/8503), NPM1 2.4% (201/8503), and IDH1 1.0% (170/8503). Overall, 4797 (56.4%) of samples had a mutation in at least one gene in the panels, and the average number of mutations per samples was 2.3 within these samples. The most co-occurring gene pairs include ASXL1 and TET2, as well as SRSF2 and TET2, both are detected in more than 2% co-occurring gene pairs. Variant allele frequency by gene We observed a substantial difference between the variant allele frequency (VAF) of relevant DNA mutations (SNP + Insertions + Deletions) in different genes. ANKRD26 has a median VAF of 66%, whereas MYD88 has a median VAF of only 7%. (Fig.1) Mutation spectrum of FLT3ITD variants We observed FLT3-ITD in 3% of samples. We observed the VAF of FLT3-ITD variants averaged around 0.32. Interestingly, the length of the FLT3-ITD duplication is multi-modal, with the highest peak at around 34 bp. The maximum duplication length detected is 151 bp. Mutation spectrums of fusions Of the 8480 samples with RNA fusion profiling, 710 were fusion positive (8.4%). ABL1 is the most common fusion driver (432 samples, 5.1%), with 88% of these being BCR- ABL1. Other common fusion drivers include KMT2A (171 samples, 2.0%; 29% are KMT2A-MLLT3 and 26% are KMT2A-MLLT1), MYH11 (126 samples, 1.5%; all are CBFB-MYH11), RARA (117 samples, 1.4%; all are PML-RARA), RUNX1 (95 samples, 1.1%; 56% are RUNX1-RUNX1T1). A total of 17 distinct driver genes, 49 distinct gene pairs and 110 distinct gene isoforms were observed, including rare fusions (for example, ZMYM2-FGFR1, KAT6A-CREBBP, etc) that are not detectable by traditional methods like qPCR (quantitative polymerase chain reaction) or FISH (fluorescence in-situ hybridization). The read count of the fusion positive samples ranges from 21 to 113,000. (Fig.2) Conclusions The Oncomine Myeloid Assay is a fast, accurate, robust, and reproducible solution for comprehensive genomic profiling of myeloid malignancies. We describe the mutational spectrum of DNA variants and RNA fusions in a range of clinical research samples, exploring the VAF, the abundance of mutations in different genes, and the properties of observed gene fusions. (For research use only. Not for use in diagnostic procedures.)

Impact of PTPN11 Mutations in De Novo, Secondary and Relapsed/Refractory Acute Myeloid Leukemia

Background Somatic mutations in the protein phosphatase non-receptor type 11 ( PTPN11) gene occur frequently in children with juvenile myelomonocytic leukemia and less commonly in adults with AML, being present in less than 5% of reported cases. Uncertainty exists regarding the prognostic impact of PTPN11 mutations in AML, largely owing to their observed rarity. Some retrospective studies have identified PTPN11 mutations as deleterious prognostic markers in AML, though others have noted that their negative impact is mitigated by concurrent NPM1 mutations, which frequently co-occur. We analyzed the outcomes of patients at our institution with AML and PTPN11 mutations in order to add to the literature regarding the relevance of this mutation. Methods We conducted a retrospective case series of patients at a single-center, tertiary-care institution who were diagnosed with AML between January 1 st, 2020 and June 1 st, 2023. Inclusion criteria included: 18 years of age or older, primary follow-up at the study institution, documented diagnosis of AML and identification of a PTPN11 mutation by NGS. Outcomes of interest included cytogenetic and molecular profiles, response to induction or salvage therapy, progression-free survival (PFS) and overall survival (OS). Results Twenty-two (12 men and 10 women) patients with PTPN11 mutant AML were identified. The median age at diagnosis was 60 years (range, 31-89 years). Nineteen patients had a PTPN11 mutation identified at diagnosis and 3 had a PTPN11 mutation appear at the time of relapse. Nine patients with de novo AML had PTPN11 mutations identified at diagnosis. Six were female and the average age at diagnosis was 60 years (range, 44-89 years). The most common co-occurring mutations were NPM1 (8 patients), DNMT3A (3 patients), TET2 (2 patients) and FLT3-TKD (2 patients). Cytogenetics were normal or non-adverse in 8 patients, and complex/adverse-risk in 1 patient. Seven patients received treatment - 4 with intensive chemotherapy and 3 with a hypomethylating agent (HMA) + venetoclax. Treatment response was CR/CRi in 6 patients (85.7%). At a median follow-up of 195 days, median PFS and OS were not reached. Two patients relapsed at 76 and 139 days after response. No patients received an allogeneic transplant in first remission. Ten patients with therapy-related or secondary-AML (t/s-AML) were identified, all with PTPN11 mutations noted at the time of AML diagnosis. Two patients had preceding MDS and 3 had preceding MDS/MPN. Median age was 63 years (range, 31-70 years). The most common co-occurring mutations were RUNX1 (5 patients), FLT3-ITD (2 patients) and NRAS/KRAS (3 patients). Chromosome 7 abnormalities were present in 4 of 5 patients with RUNX1 mutations. Cytogenetics were complex or adverse-risk in 9 patients. Eight patients received treatment - 6 with intensive chemotherapy and 2 with HMA + venetoclax. Treatment response was CR/CRi in 3 patients (37.5%). Median PFS was 183 days and median OS in treated patients was 307 days. The only patient with an ongoing response at the time of data cut-off received an allogeneic transplantation in CR1. Three patients with AML had emergence of a PTPN11 mutation at the time of relapse, at 245, 343 and 2262 days after initial diagnosis. PTPN11 was the only new mutation identified in 2 patients, and emerged in conjunction with an NRAS and KDM6A mutation in 1 patient. One patient received treatment, attaining a CRi after HMA + venetoclax, but relapsed 112 days later. The other 2 patients passed at 10 and 21 days after relapse. Conclusions PTPN11 mutations were relatively rare, occurring in only 22 patients with AML during a 3.5-year time span. Stark differences were noted in patients with de novo AML versus t/s-AML and PTPN11 mutations. De novo AML patients frequently demonstrated NPM1 mutations and a normal karyotype, while t/s-AML patients frequently had RUNX1 and FLT3 mutations, as well as adverse cytogenetics. Although the impact of PTPN11 mutations in AML may be influenced by concurrent NPM1 mutations or cytogenetic characteristics, the context of AML may ultimately have the largest impact.

Detection of KMT2A Partial Tandem Duplications ( KMT2A-PTDs) in Healthy Donors Using Next Generation Sequencing

Introduction KMT2A ( MLL) fusions are relevant biomarkers in myeloid malignancies. KMT2A-PTD (also called MLL-PTD, partial tandem duplication), a non-fusion gene rearrangement, also occurs and serves as an important biomarker for Menin-inhibitors. Traditionally, KMT2A-PTDs are detected by RT-qPCR (quantitative real-time PCR). Here we report the detection of KMT2A-PTDs in whole blood samples taken from healthy donors using the Oncomine TM Myeloid Assay GX v2, which is a next-generation sequencing (NGS) based assay that enables efficient detection of multiple genetic alterations in parallel. KMT2A-PTD positive clinical research samples were used as a control in this study. This study was initiated based on reports from various healthcare professionals who observed several healthy blood donors identified with KMT2A-PTD using the Oncomine TM Myeloid Assay GX v2. As a result, we conducted tests on healthy controls and compared them with clinical research samples known to have myeloid malignancies to explore this genomic alteration further. Methods We sequenced 20 whole blood samples (total 104 replicates) from healthy donors at 3 different sites of Thermo Fisher Scientific TM (South San Francisco, CA; Guilford, CT; Carlsbad, CA). These whole blood samples were received from Stanford Blood Center or purchased from Discovery Life Sciences. As a control, we also sequenced 20 clinical research samples (total 85 replicates) that are known to have myeloid malignancies in both Sonora Quest Laboratories and at Thermo Fisher Scientific TM South San Francisco site. These samples were run on the Ion Torrent TM Genexus TM Software 6.6 and analyzed using the Oncomine TM Myeloid Assay GX v2 with fusion profiling, where the assay design targets 6 different KMT2A-PTD variants. Results The data set has mean read length 90 - 120bp and total mapped fusion reads 20,000 - 30,000. We have found evidence of KMT2A-PTDs in confirmed positive samples from myeloid malignancies (including: AML, acute myeloid leukemia; MPN, myeloproliferative neoplasms; MDS, myelodysplastic syndromes; CML, chronic myeloid leukemia; CMML, chronic myelomonocytic leukemia; or JMML, juvenile myelomonocytic leukemia) and healthy donor samples. The read counts of PTDs detected in the healthy donor samples are on average about 1/3 of the read counts of PTDs detected in the myeloid positive samples, but the distributions overlap. Approximately 33% of myeloid positive samples have PTD read counts higher than the maximum read counts detected in any of the healthy donor samples. The sequences of KMT2A-PTDs found in both healthy donor samples and myeloid samples were further analyzed in BLAT (BLAST-Like Alignment Tool) to confirm that they match the specific exons on the KMT2A gene. Based on this data, only samples with myeloid malignancies have >2000 reads that support KMT2A-PTDs with this assay. Conclusions We describe the detection of KMT2A-PTDs in a range of clinical research samples, including healthy controls as well as samples with myeloid malignancies. KMT2A-PTDs were detected in healthy control samples at lower levels, however, one third of myeloid samples showed significantly higher KMT2A-PTD read counts compared to healthy controls. This intriguing finding warrants further investigation, as it opens up the possibility of conducting a prospective study to follow up on these individuals and observe if they develop myeloid malignancies. Moreover, this finding presents an opportunity for conducting retrospective studies to explore whether healthy controls previously identified with this alteration several years ago after blood donation were subsequently recorded in the health national system with myeloid malignancies. (For research use only. Not for use in diagnostic procedures.)