Patient listing of prior myelofibrosis treatment and time since discontinuation if known

Individual patient data for AUC, Cmax and Tmax for dose levels 1 and 2 (lot A). Summary measures for DL 1 and DL2 are shown in red.

PK data for Cycle 1 (first 24 hours only) for A) 180 mg/m2 dose level and B) 550 mg/m2 dose level during dose escalation phase I.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, presenting with heterogeneous clinical and molecular subtypes. While gene fusions are predominantly associated with alveolar RMS, spindle cell RMS, especially congenital and intraosseous variants, are also linked to specific gene fusions. Furthermore, recently, FGFR1 kinase-driven RMSs were published. Here, we describe a case of RMS harboring an EWSR1::NF2 gene fusion, a deletion-driven genetic alteration that has not been previously documented in RMS or other soft tissue tumors. The patient was a 29-year-old female who presented with a lobulated ankle mass. Histologic examination revealed a malignant round cell tumor extensively infiltrating large nerve bundles. Immunohistochemical analysis demonstrated rhabdomyoblastic differentiation, consistent with rhabdomyosarcoma. While some areas showed features resembling the sclerosing and others the embryonal subtypes, the overall findings were considered unclassifiable. Targeted RNA sequencing revealed EWSR1(exon 9):: NF2(exon 7) gene fusion, which was confirmed on whole genome and targeted DNA sequencing. The latter did not yield specific diagnostic insights but revealed mutations in TSC2 (p.T1330M), ZFHX3 (p.A301T), and a NOTCH3 rearrangement, all of unknown oncogenic significance. MYC gene amplification was detected, but there was no evidence of chromosome 8 amplification or chromosome 11p15 loss of heterozygosity. Whole genome sequencing revealed a low tumor mutation burden (2.69/Mb) and showed no other significant potentially oncogenic events. DNA methylation studies using dimensionality reduction and unsupervised clustering placed the case within the embryonal RMS subtype. Although the absence of other oncogenic driver alterations suggests that the fusion may have played a pivotal role in pathogenesis, we cannot exclude the possibility that it represents a passenger alteration rather than a true driver mutation. If the former is true, further studies will be required to determine whether this fusion represents a novel RMS subtype or a rare driver in existing subtypes of RMS.

Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical presentation and outcomes. Integrating single-cell genotyping and transcriptomics, we demonstrate a stem-like and inflammatory phenotype of IDH-mutant AML and identify clone-specific programs associated with NPM1, NRAS, and SRSF2 co-mutations. Furthermore, these clones had distinct responses to treatment with combination IDH inhibitors and chemotherapy, including elimination, reconstitution of myeloid differentiation, or retention within progenitor populations. At relapse after IDH inhibitor monotherapy, we identify upregulated stemness, inflammation, mitochondrial metabolism, and anti-apoptotic factors, as well as downregulated major histocompatibility complex (MHC) class II antigen presentation. At the pre-leukemic stage, we observe upregulation of IDH2-associated pathways, including inflammation. We deliver a detailed phenotyping of IDH-mutant AML and a framework for dissecting contributions of recurrently mutated genes in AML at diagnosis and following therapy, with implications for precision medicine.

Representativeness of Study Participants.

Introduction Follicular lymphoma (FL) is the most common type of indolent non-Hodgkin's lymphoma with BCL6 rearrangements (BCL6-R) observed in 5-15% of cases. BCL6-R FL frequently exhibit concurrent canonical BCL2 rearrangements (BCL2-R). However, a subset presents with BCL6-R exclusively and shares biological features with the recently described genomic subgroup of diffuse large B-cell lymphoma, BN2, characterized by BCL6-R and a mutational profile suggestive of marginal zone lymphoma (MZL) (Schmitz 2018). In this study, we analyzed 14 BCL6-R FL samples to study the mechanisms generating the BCL6 and BCL2 rearrangements. Methods WGS was performed in 14 FL tumors determined to be BCL6 rearranged by clinical cytogenetics (median coverage 71x) and matched germline controls (median coverage 41x). Bioinformatics analysis was performed to align sequencing reads, call somatic variants - mutations, indels, rearrangements, and detect mutational signatures and clonal structures as described (Shukla, Levine, Gundem 2022). Kataegis was detected using {katdetectR} (Hazelaar 2023) and Ig loci were characterized by IgCaller (Nadeu 2020). The LymphGen classification algorithm was run on the NCI website (Wright 2020). Results and Discussion Genome-wide mutation calling identified a median of 16.7k SNVs, 10.7k Indels and 0.2k SVs per sample. Driver events were detected in all 14 samples with 93% of samples having at least 5 events. Mutations in epigenetic modifier genes like KMT2D, CREBBP, ARID1A and deletions in the CDKN2A/CDKN2B/MTAP locus were the most frequent. Non-canonical (SBS9) and canonical (SBS84) AID mutational signatures were detected in all samples. Recurrent driver rearrangements were identified in BCL6 (n = 14) and BCL2 (n = 10). BCL2-R (n = 8) were found to be predominantly created by RAG mediated aberrant VDJ recombination, whereas most BCL6-R (n = 11) were found to be generated through AID mediated aberrant class switch recombination or somatic hypermutation. These results suggest that in cases with concurrent BCL2-R and BCL6-R, BCL2-R occurred early in the B-cell ontogeny within the bone marrow whereas BCL6-R occurred later within the germinal center. Most BCL6-R associated with a BCL2-R involved non-Ig partners (n = 8), whereas exclusive BCL6-R were partnered with IgH. The LymphGen algorithm classified samples into EZB (n = 11, 78.57%), BN2 (n = 2, 14.28%), EZB/A53 (n = 1, 7.14%). Two cases with exclusive BCL6-R showed mutational profiles similar to MZL, including mutations in the NOTCH pathway, and were classified as BN2. Conclusions WGS-based comprehensive genomic profiling of BCL6-R FL revealed that BCL6-R are generated by AID mediated CSR or somatic hypermutation, regardless of whether they were the primary driver (BCL6-R only) or secondary to existing BCL2-R. Exclusive BCL6-R were associated IgH gene region enhancers and are likely to be pathogenic drivers associated with overexpression of the BCL6 protein, whereas BCL6-R with concurrent BCL2-R revealed different partners and might represent passenger events rather than true oncogenic drivers. Cases with BCL6-R only exhibit MZL like mutations and may represent a unique subset of B-cell lymphomas biologically closer to MZL than to FL.

Background: Growth of multiple myeloma (MM) beyond the bone marrow (BM) represents clinically aggressive disease and is associated with inferior therapy response. We hypothesize that genomic changes underlie the increasing BM independence seen from focal intra-medullary lesions (IMD) to para-medullary (PMD) and extra-medullary disease (EMD). To address this hypothesis, we have analyzed the largest sequencing cohort of IMD/PMD/EMD to date, comparing with paired BM samples where available. Methods: Genomic assessment of all available IMD/PMD/EMD from Memorial Sloan Kettering Cancer Center (MSK) and the University of Heidelberg (DKFZ) were included. IMD was defined by MRI appearance, PMD by local extension through bone and EMD as non-contiguous with bone. Comprehensive genomic characterization combined SNP-array, extended targeted sequencing (MSK-IMPACT-Heme), whole exome (WES) and whole genome sequencing (WGS). New data was combined with our published pre-therapy BM WGS (Maura Nat Can 2023), PMD/EMD WGS from autopsy (Landau Nat Comm 2020) and spatially distinct WES (Rasche Nat Comm 2022). In total, 84 IMD, 105 PMD and 55 EMD samples were assessed; 128 pre-therapy and 126 post-therapy. 134 patients had paired BM samples (113 coincident and 26 distant in time), with 12 patients having > 1 PMD/EMD biopsy. Including our previously published data, the cohort comprised 444 samples from 271 patients; 125 WGS, 66 WES, 145 MSK-IMPACT-Heme and 25 SNP-array. Analyses included GISTIC for significant copy number aberrations (CNA), dndscv for positively selected mutational drivers and mmsig for mutational signatures. Results: Compared to paired BM and the independent control set of BM samples, PMD and EMD had considerably more CNA, while IMD was more similar to BM. Significant CNAs in PMD/EMD included gains affecting 1q, 8q (MYC), 20p and 20q, with focal gains at 1q21, 6p25 and 18q21. Deletions frequently affected 4p, 8p and 17p (TP53), and numerous focal deletions were detailed. While there was only a trend to difference in 1p/1q between BM and IMD, gain/amp1q was observed in 38% BM, 56% PMD, 78% of EMD overall, and in 83% of post-therapy EMD samples. Prevalent mutations in PMD/EMD involved KRAS, NRAS and TP53, with KRAS being enriched in PMD (38%), while EMD was enriched for NRAS (40%) and TP53 (33%). PMD/EMD were also enriched for loss-of-function mutations (p=0.007). In contrast, there was no significant difference in any of KRAS/NRAS/BRAF or TP53 between BM and IMD. Dndscv analysis revealed multiple genes positively selected as driver events in PMD/EMD, including epigenetic modifiers (KMT2A, KMT2C, TET2, SMARCA4), immune response (PRMD1, LTB), proliferation (STAT3, NF1, BTG1), adhesion (FAT1), and DNA-damage response (TP53, ATM, BRCA2). Paired BM-PMD/EMD showed 2 patterns; some had increased mutational burden in PMD/EMD, while others had retained mutations but increased CNA. Within those with > 1 PMD/EMD sample, diverging clones were defined by a variety of mutations (including KRAS, TP53, STAT3, IGF1R, DNMT3A), CNA affecting multiple chromosomes (including 8q; MYC, 17p; TP53), noncanonical translocations, and CNA consistent with chromothripsis. In the WGS data, we note spatial divergence in mutational signature contribution and emergence of complex structural variants. Several patients with prior melphalan exposure have SBS99 evident in several biopsies, consistent with single cell expansion from MM cells surviving transplant and subsequently seeding in multiple sites. Conclusions: PMD and EMD demonstrate multiple features of genomic complexity when compared with BM-based myeloma, which include emerging copy number aberrations, mutational burden and complex structural variants. EMD are more complex in general than PMD, while IMD shows only trends to increased genomic aberration compared with BM. Ongoing analyses include an expansion in WGS samples, and correlation of genomic features with clinical response to therapy.

Myelodysplastic syndromes/neoplasms (MDS) are clonal hematologic disorders characterized by morphologic abnormalities of myeloid cells and peripheral cytopenias. While genetic abnormalities underlie the pathogenesis of these disorders and their heterogeneity, current classifications of MDS rely predominantly on morphology. We performed genomic profiling of 3,233 patients with MDS or related disorders to delineate molecular subtypes and define their clinical implications. Gene mutations, copy-number alterations (CNAs), and copy-neutral loss of heterozygosity (cnLOH) were derived from targeted sequencing of a 152-gene panel, with abnormalities identified in 91, 43, and 11% of patients, respectively. We characterized 16 molecular groups, encompassing 86% of patients, using information from 21 genes, 6 cytogenetic events, and LOH at the TP53 and TET2 loci. Two residual groups defined by negative findings (molecularly not-otherwise specified, absence of recurrent drivers) comprised 14% of patients. The groups varied in size from 0.5% to 14% of patients and were associated with distinct clinical phenotypes and outcomes. The median bone marrow blast percentage across groups ranged from 1.5 to 10%, and the median overall survival from 0.9 to 8.2 years. We validated 5 well-characterized entities, added further evidence to support 3 previously reported subsets, and described 8 novel groups. The prognostic influence of bone marrow blasts depended on the genetic subtypes. Within genetic subgroups, therapy-related MDS and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) had comparable clinical and outcome profiles to primary MDS. In conclusion, genetically-derived subgroups of MDS are clinically relevant and may inform future classification schemas and translational therapeutic research.

Mutations in UBA1, which are disease-defining for VEXAS syndrome, have been reported in patients diagnosed with myelodysplastic syndromes (MDS). Here, we define the prevalence and clinical associations of UBA1 mutations in a representative cohort of patients with MDS. Digital droplet PCR profiling of a selected cohort of 375 male patients lacking MDS disease-defining mutations or established WHO disease classification identified 28 patients (7%) with UBA1 p.M41T/V/L mutations. Using targeted sequencing of UBA1 in a representative MDS cohort (n=2,027), we identified an additional 27 variants in 26 patients (1%), which we classified as likely/pathogenic (n=12) and unknown significance (n=15). Among the total 40 patients with likely/pathogenic variants (2%), all were male and 63% were classified by WHO2016 as MDS-MLD/SLD. Patients had a median of one additional myeloid gene mutation, often in TET2 (n=12), DNMT3A (n=10), ASXL1 (n=3), or SF3B1 (n=3). Retrospective clinical review where possible showed that 83% (28/34) UBA1-mutant cases had VEXAS-associated diagnoses or inflammatory clinical presentation. The prevalence of UBA1-mutations in MDS patients argues for systematic screening for UBA1 in the management of MDS.

Background Mutations in UBA1 are associated with VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome, an adult-onset inflammatory disorder (Beck DB et al. NEJM 2020). Approximately 40% of VEXAS patients are also diagnosed with myelodysplastic syndromes (MDS). We previously profiled UBA1 p.M41 mutations in a select subset of the International Working Group for MDS (IWG-PM) cohort (Bernard E et al. NEJM Evid 2022) including 375 male patients lacking disease-defining mutations or established disease classification by WHO guidelines, and identified 28 patients (7%) with UBA1 p.M41T/V/L mutations (Cohort A, Sirenko M et al. Blood 2022). However, the prevalence and characteristics of UBA1 mutations in MDS have not been systematically evaluated in a representative MDS population. Methods We used targeted next-generation sequencing of the full UBA1 locus to profile 2027 diagnostic and treatment-naive MDS samples (Cohort B, 61% male) ascertained through the IWG-PM (Figure 1). Clinical associations of UBA1 mutations were evaluated and clinical history was reviewed for inflammatory conditions when available. Results In Cohort B, 35 UBA1 mutations in 34 (1.7%) patients were identified, of which 20 (0.97%) had likely pathogenic variants and 14 had variants of unknown significance (VUS). Likely pathogenic variants included 13 p.M41T/V/L mutation (variant allele fraction [VAF] range 0.013-0.94), and 7 non-p.M41 mutations where 6/7 had VAF>0.35: 2 with p.S56F (VAF 0.87 and 0.93), 2 p.A478S (VAF 0.72 and 0.80), 2 p.S621C (VAF 0.80 and 0.82) and 1 p.Y55H (VAF 0.025). Three VUS were in female patients. 204 cases were profiled by both assays and of those, all 8 ddPCR positive cases were identified by NGS with concordant VAF (R2=0.999 p<0.0001). Integration of Cohort A and B (n=2,198) yielded 40 patients (all male, median age 72; range 44-89 years) with pathogenic UBA1 variants. The WHO 2016 classification (available for n=38 of 40) was MDS-SLD/MLD (25), MDS-EB1 (4), MDS-U (3), CMML (2), MDS-RS-MLD (1), aCML (1), MDS/MPN-RS-T (1), MDS/MPN-U (1). Patients had a median of 1 myeloid gene mutation in addition to UBA1 (range: 0-4) with most frequent co-occurring events in TET2 (n=12), DNMT3A (n = 10), ASXL1 (n=3), SF3B1 (n=3) and loss of the Y chromosome (n=5). In 8 patients with pathogenic UBA1 > 2% VAF and co-occurring DNMT3A mutations, DNMT3A and UBA1 VAF were correlated (slope = 0.88, r = 0.87, p = 0.0005), suggesting that co-mutation may lead to clonal expansion. Conversely, TET2 co-mutations were either subclonal (n=4) or clonal (n=8) to UBA1. Among patients with pathogenic UBA1 variants, the majority had IPSS-M Very-Low/Low risk (73% 27/37). In contrast, patients with VUS were more likely to have Moderate or High risk (64% 7/11). Partial clinical history was available for 33 cases with pathogenic UBA1 variants. 50% (9/18) had inflammatory-rheumatic disease (IRD) including psoriatic arthritis, relapsing polychondritis, Sweet syndrome, bronchiolitis obliterans with organizing pneumonia, ear chondritis, and rosacea. 3 patients had more than one IRD. 8 were treated for IRD with steroids (n=6) or methotrexate (n=2). 4 patients had MGUS. Other manifestations included vacuoles (4/8), thromboembolic disease (5/16), non-infection fever (5/14), weight loss (4/14), ocular symptoms (5/15), arthralgia (3/16), chondritis (5/15), and other inflammation (6/14). IRD diagnosis usually preceded MDS (average time 0.28 years; range 16.5 years prior to 1.4 years after). Three patients transformed to acute myeloid leukemia (AML). One patient had a low VAF UBA1 p.M41V (0.0002 by ddPCR) and TET2, SF3B1, FLT3, and ASXL2 co-mutations at baseline. The second had UBA1 p.S56F (VAF 0.868) and a Chr 7q deletion. The third had VUS UBA1 p.R869L (VAF 0.222) and IRF1, NFE2 and RRAS co-mutations. Among the other UBA1-mutant patients that died or were censored after 1 year (n=37), none transformed to AML. Conclusion Within the large, representative, diagnostic and well-characterized IWG-PM MDS cohort, we find likely pathogenic UBA1 mutations in 1% of patients, with enrichment in male patients with few or no mutations in myeloid driver genes (7%). UBA1-mutant patients were predominantly IPSS-M low risk with a median of 1 additional mutation, usually in DNMT3A or TET2. UBA1 mutations may define a distinct subset of MDS and its recognition in future guidelines will improve the management of patients with MDS/VEXAS overlap.

AbstractPurpose: Myelofibrosis (MF) is a clonal myeloproliferative neoplasm characterized by systemic symptoms, cytopenias, organomegaly, and bone marrow fibrosis. JAK2 inhibitors afford symptom and spleen burden reduction but do not alter the disease course and frequently lead to thrombocytopenia. TGFβ, a pleiotropic cytokine elaborated by the MF clone, negatively regulates normal hematopoiesis, downregulates antitumor immunity, and promotes bone marrow fibrosis. Our group previously showed that AVID200, a potent and selective TGFβ 1/3 trap, reduced TGFβ1-induced proliferation of human mesenchymal stromal cells, phosphorylation of SMAD2, and collagen expression. Moreover, treatment of MF mononuclear cells with AVID200 led to increased numbers of progenitor cells (PC) with wild-type JAK2 rather than JAK2V617F. Patients and Methods: We conducted an investigator-initiated, multicenter, phase Ib trial of AVID200 monotherapy in 21 patients with advanced MF. Results: No dose-limiting toxicity was identified at the three dose levels tested, and grade 3/4 anemia and thrombocytopenia occurred in 28.6% and 19.0% of treated patients, respectively. After six cycles of therapy, two patients attained a clinical benefit by IWG-MRT criteria. Spleen and symptom benefits were observed across treatment cycles. Unlike other MF-directed therapies, increases in platelet counts were noted in 81% of treated patients with three patients achieving normalization. Treatment with AVID200 resulted in potent suppression of plasma TGFβ1 levels and pSMAD2 in MF cells. Conclusions: AVID200 is a well-tolerated, rational, therapeutic agent for the treatment of patients with MF and should be evaluated further in patients with thrombocytopenic MF in combination with agents that target aberrant MF intracellular signaling pathways.

Introduction Adult B-cell acute lymphoblastic leukemia (B-ALL) comprises 75% of adult ALL cases. The classification and risk stratification of patients have conventionally relied on cytogenetics analysis. However, cytogenetics has limitations due to its reliance on metaphase cells, which can mitigate classification accuracy. In recent years, transcriptome sequencing (RNA-seq) of large pediatrics ALL cohorts has expanded the number of recurrent gene fusions recognized as disease defining events and informed risk stratification [Brady et al. 2022, Mullighan et al. 2017]. This study aims to evaluate the diagnostic utility of RNA-seq for clinical subtype classification in adult B-ALL in a large representative cohort. Methods The study cohort comprised 338 adult patients (25-65 years) with newly diagnosed ALL (UKALL14, ISRCTN66541317, NCT01085617). Paired-end RNA-seq data at 60 Million reads per sample were generated. Analysis focused on the detection of disease-defining gene fusions and gene expression signatures. Three RNA fusion callers (FusionCatcher, FuSeq, and STAR-Fusion) and three expression-based classifiers (ALLSorts, ALLspice, and ALLCatchR) were used for consensus fusion calling and expression-based classification, respectively [Nicorici et al. 2014, Vu et al. 2018, Haas et al. 2019, Schmidt et al., Mäkinen et al., Bader et al. 2022]. Integration of classification results from expression-based classifiers and the consensus gene fusions provides 4 levels of RNA-derived subtype information, denoted as “RNA evidence” in this study. These RNA-seq based classification results were compared with clinical cytogenetics findings. Results Out of 338 samples in this cohort, cytogenetics unequivocally classified 73% (246/338) of the samples. By integrating RNA expression-based classification with fusion subtypes, we confidently classified 87% (295/338) of the cohort with at least 2 levels of RNA evidence. In total, consensus gene fusions were identified in 74% (249/338), while expression-based classifiers assigned a confident subtype to 82% (319/338). Subsequently, we compared cytogenetics with RNA-seq derived classification and found a high concordance of 98% (240/246) between the two approaches. Only 6 (<2%) samples with cytogenetics subtypes were not classified by RNA-seq, attributed to specific subtype characteristics (near-haploid) or lower RNA purity/quality. 27% (92/338) of subjects were not classified by cytogenetics (31 missing/failed and 61 indeterminate cytogenetics). Of the 31 samples with failed/missing cytogenetics, RNA-seq confidently assigned a class in 74% (23/31). For the remaining 61 cases with indeterminate cytogenetic (complex/other), RNA-seq resolved classification in 74% (45/61). Taken together, this improved the classification for 20% (68/338) of the entire cohort that was previously unclassified through cytogenetics. Notably, RNA-seq-exclusive findings were enriched in subtypes like DUX4, PAX5alt, and ZNF384, which are challenging for cytogenetics to discern. Importantly, integration of RNA-seq with cytogenetics led to a confident subtype classification for 93% of the cohort (314/338), a significant improvement over the initial 73% based on cytogenetics alone. Conclusions In conclusion, our study highlights the relevance of integrated RNA-seq analysis for reliable and comprehensive subtype classification in adult B-ALL. The high concordance between cytogenetics and RNA-derived subtypes underscores their complementary roles, providing valuable insights into disease mechanisms and guiding personalized treatment strategies.

Despite a detailed understanding of the genes mutated in myelodysplastic syndromes (MDS), diagnostic and treatment decisions for patients with MDS rely primarily on clinical and cytogenetic variables as considered by the Revised International Prognostic Scoring System (IPSS-R). Here we describe the recently developed Molecular IPSS (IPSS-M), a clinico-genomic risk stratification system that considers clinical, cytogenetic and genetic parameters; the implementation of a web portal to facilitate its adoption, a strategy to handle missing variables, and the worldwide utilization of the web calculator as a clinical support tool. The IPSS-M was trained on 2,957 clinically annotated diagnostic MDS samples profiled for mutations in 156 driver genes. To maximize the clinical applicability of the IPSS-M and account for missing genetic data (i.e genes missing from a sequencing panel), we implemented a strategy to calculate a risk score under three scenarios: best, worst and average. Last, we developed an online calculator as a standalone single-page web application using VueJs, and D3Js for the interactive visualizations, deployed through a CI/CD pipeline on AWS, where collection of anonymous usage analytics allows to track adoption and usability of the new proposed model. The model incorporates clinical, morphological, genetic variables informed by cytogenetics and constructed from the presence of oncogenic mutations in 31 genes. It delivers a unique risk score for each individual patient, as well as an assignment to one of six IPSS-M risk strata. Compared to the IPSS-R the IPSS-M re-stratified 46% of MDS patients. The model was validated in an external dataset of 754 MDS patients. We released an open-access IPSS-M web calculator available at https://mds-risk-model.com. By specifying the patient clinical and molecular profiles, the tool returns the patient-specific IPSS-M risk score and category, and the probability estimates over time for three clinical endpoints, i.e. leukemia free survival (LFS), overall survival, and incidence of leukemic transformation. Since its launch in June 2022, the calculator has been used by >6000 users in >75 countries, reaching a daily average of 100 users per day. Risks have been calculated for >45,000 patient profiles. 99.28% of the sessions initiated reach an IPSS-M score, suggesting that the calculator is intuitive and easy to use. We trained and validated the IPSS-M on 3,711 patients, a patient tailored risk stratification tool for patients with MDS that considers clinical, morphological and genetic variables inclusive of cytogenetics and mutations in one of 31 genes. The development of a web based tool was instrumental to the global dissemination of the model, enabling non-expert users to leverage the power of molecular biomarkers in risk stratification for patients with MDS. Citation Format: Elsa Bernard, Juan E. Arango Ossa, Heinz Tuechler, Peter L. Greenberg, Robert P. Hasserjian, Yasuhito Nannya, Sean M. Devlin, Maria Creignou, Philippe Pinel, Lily Monier, Juan S. Medina-Martinez, Dylan Domenico, Martin Jädersten, Ulrich Germing, Guillermo Sanz, Arjan A. van de Loosdrecht, Olivier Kosmider, Matilde Y. Follo, Felicitas Thol, Lurdes Zamora, Ronald F. Pinheiro, Andrea Pellagatti, Detlef Haase, Pierre Fenaux, Monika Belickova, Michael R. Savona, Virginia M. Klimek, Fabio P. Santos, Jacqueline Boultwood, Ioannis Kotsianidis, Valeria Santini, Francesc Solé, Uwe Platzbecker, Michael Heuser, Peter Valent, Kazuma Ohyashiki, Carlo Finelli, Maria Teresa Voso, Lee-Yung Shih, Michaela Fontenay, Joop H. Jansen, José Cervera, Norbert Gattermann, Benjamin L. Ebert, Rafael Bejar, Luca Malcovati, Mario Cazzola, Seishi Ogawa, Eva Hellström-Lindberg, Elli Papaemmanuil. Implementation and adoption of a web tool to support precision diagnostic and treatment decisions for patient with myelodysplastic syndromes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6168.

Objective: The osteosarcoma genome is characterized by high levels of genomic instability, however whether there is pervasive ongoing genomic instability, or instability introduced by an early catastrophic event, is still unsettled. Methods: We performed 30-80x whole genome sequencing (WGS) of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and one sample from a metastatic or relapse site. A set of high confidence single nucleotide variants (SNV), copy number alterations (CNA), structural variations (SV) were called for each sample using our pediatric expanded genomics pipeline and an analysis focused on markers of genomic instability was performed using a custom pipeline of computational tools. Results: Of the 8 patients in our cohort, 4 had localized disease at diagnosis (OSCE4, OSCE5, OSCE6, OSCE9) and 4 had metastatic disease at diagnosis (OSCE1, OSCE2, OSCE3, OSCE10). There were 17 samples from primary sites, 7 pretreatment biopsies, 10 on therapy primary resections, 20 metastatic sites, 15 of which were from lung metastases. We have previously reported on the clonal evolution regarding SNVs and CNAs within this cohort. TP53 structural variants involving intron 1/2 were seen in 6/8 patients (OSCE2, OSCE3, OSCE4, OSCE6, OSCE9, OSCE10). No new structural variants in consensus driver genes emerged in metastatic or relapse samples. Comparing the earliest sample to most recent sample in each patient, only OSCE1, OSCE9, and OSCE10 demonstrated an increase of ≥100 structural variants at the final timepoint. In OSCE2, OSCE5, and OSCE6, there were less structural variants identified at the final timepoint when compared to the earliest timepoint. Homologous recombination deficiency (HRD) scores were calculated for each sample. Only 4/8 patients (OSCE3, OSCE4, OSCE9, OSCE10) had an HRD score in the most recently acquired sample higher than the score from the primary site. Regions of hypermutation consistent with kataegis were identified for each sample, with the number of kataegis events remaining unchanged or decreasing in some instances. Kataegis events co-localized with rearrangement events a majority of the time (range 50-100%, Avg= 72.6%). Complex rearrangements such as chromothripsis and chromoplexy were assesed. In 6 patients there were > 9 chromosomal arms involved in complex rearrangements that were shared between primary sites and metastatic/recurrent sites, while ≤ 4 chromosomal arms were involved with new complex rearrangements unique to the metastatic sites. Conclusion: The patterns observed in our cohort reveal that osteosarcoma is relatively stable from diagnosis through subsequent relapses, supporting the model that an early catastrophic event accounts for the genomic instability observed in osteosarcoma. Citation Format: Michael David Kinnaman, Simone Zaccaria, Alvin Makohon-Moore, Gunes Gundem, Juan E. Arango Ossa, Filemon S. Dela Cruz, Paul A. Meyers, Meera Hameed, William D. Tap, Julia Lynne Glade Bender, Elli Papaemmanuil, Andrew Kung, Christine Iacobuzio Donahue. Assessing patterns of genomic instability in recurrent osteosarcoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3556.

The mortality rate of diabetic patients on dialysis is higher than that of non-diabetic patients. Asymmetric dimethylarginine and inflammation are strong predictors of death in hemodialysis. This study aimed to evaluate asymmetric dimethylarginine and C-reactive protein interaction in predicting mortality in hemodialysis according to the presence or absence of diabetes.Asymmetric dimethylarginine and C-reactive protein were measured in 202 patients in maintenance hemodialysis assembled from 2011 to 2012 and followed for four years. Effect modification of C-reactive protein on the relationship between asymmetric dimethylarginine and all-cause mortality was investigated dividing the population into four categories according to the median of asymmetric dimethylarginine and C-reactive protein.Asymmetric dimethylarginine and C-reactive protein levels were similar between diabetics and non-diabetics. Asymmetric dimethylarginine – median IQR μM – (1.95 1.75–2.54 versus 1.03 0.81–1.55 P = 0.000) differed in non-diabetics with or without evolution to death (HR 2379 CI 1.36–3.68 P = 0.000) and was similar in diabetics without or with evolution to death. Among non-diabetics, the category with higher asymmetric dimethylarginine and C-reactive protein levels exhibited the highest mortality (69.0% P = 0.000). No differences in mortality were seen in diabetics. A joint effect was found between asymmetric dimethylarginine and C-reactive protein, explaining all-cause mortality (HR 15.21 CI 3.50–66.12 P = 0.000).Asymmetric dimethylarginine is an independent predictor of all-cause mortality in non-diabetic patients in hemodialysis. Other risk factors may overlap asymmetric dimethylarginine in people with diabetes. Inflammation dramatically increases the risk of death associated with high plasma asymmetric dimethylarginine in hemodialysis.La tasa de mortalidad de los pacientes diabéticos em diálisis se ha referido que es superior a la de los no diabéticos. La dimetilarginina asimétrica y la inflamación son potentes predictores de muerte en hemodiálisis. Este estudio tuvo como objetivo evaluar la interacción de dimetilarginina asimétrica y proteína C reactiva en la predicción de mortalidad en hemodiálisis según la presencia o ausencia de diabetes.Se midieron dimetilarginina asimétrica y proteína C reactiva en 202 pacientes en hemodiálisis de mantenimiento reclutados entre 2011 a 2012 y seguidos durante cuatro años. Se investigó la modificación del efecto de la proteína C reactiva en la relación entre dimetilarginina asimétrica y la mortalidad por todas las causas dividiendo la población en cuatro categorías según la mediana de dimetilarginina asimétrica y proteína C reactiva.Los niveles de dimetilarginina asimética y proteína C reactiva fueron similares entre diabéticos y no diabéticos. Dimetilarginina asimétrica - mediana IQR μM - (1,95 1,75 - 2,54 versus 1,03 0,81 - 1,55 P = 0,000) difirió en los no diabéticos con o sin evolución a la muerte (OR 2379 IC 1,36 - 3,68 P = 0,000) y fue similar en los diabéticos sin o con evolución a muerte. Entre los no diabéticos, la categoría con niveles más altos de dimetilarginina asimétrica y proteína C reactiva presentó la mayor mortalidad (69,0% P = 0,000). No se observaron diferencias en la mortalidad en los diabéticos. Se encontró un efecto conjunto entre la dimetilarginina asimétrica y la proteína C reactiva, lo que explica la mortalidad por todas las causas (OR 15,21 IC 3,50-66,12 P = 0,000).La dimetilarginina asimétrica es un predictor independiente de mortalidad por todas las causas en pacientes no diabéticos en hemodiálisis. Otros factores de riesgo pueden superponerse a la dimetilarginina asimétrica en personas con diabetes. La inflamación aumenta drásticamente el riesgo de muerte asociado con niveles plasmáticos elevados de dimetilarginina asimétrica en pacientes en hemodiálisis.

Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression remain limited. Here, using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease-defining loci ( MYCN , TERT , MDM2-CDK4 ) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.