Eisfeld, Ann‐Kathrin

Abstract Introduction Ph-like B-ALL is a poor-risk B-ALL subtype defined by gene expression signatures that resemble the BCR::ABL1-associated transcriptional program in the absence of the BCR-ABL1 oncoprotein. Recent studies have demonstrated that up to 80% of Ph-like B-ALLs have recurrent gene fusions involving cytokine receptors or tyrosine kinases that can be identified via cytogenetics, fluorescence in situ hybridization (FISH) or RNA sequencing. However, the inability to rapidly and accurately identify these alterations in the clinical setting is a major impediment to developing therapeutic strategies that may have efficacy in this B-ALL subtype. Here we used 88 patient (pt) samples to validate a rapid, streamlined clinical WGS assay (ChromoSeq) for B-ALL and assessed the diagnostic yield for Ph-like-associated SVs in 136 pts enrolled in the Alliance A041501 clinical trial. Methods ChromoSeq is a clinical WGS assay for hematologic malignancies that uses rapid laboratory workflows and focused analysis methods to identify clinically relevant SVs, copy number alterations and gene-level mutations. We updated the ChromoSeq pipeline for use in B-ALL pts and validated it using 88 retrospective B-ALL samples (80 adult/young adult and 8 pediatric from Washington University School of Medicine and St. Louis Children's Hospital), 54 of which were analyzed via RNAseq for gene fusions and a 6-gene Ph-like B-ALL signature (CA6, SPATS2L, MUC4, JCHAIN, BMPR1B, ADGRF1, NRXN3 and CRLF2). The “ChromoSeqV2” assay was then used to analyze 136 pretreatment blood or bone marrow samples from the Alliance A041501 (trial NCT03150693). These results were compared to data from RNAseq obtained for research purposes (N=35), clinical cytogenetics (N=69) and Ph-like classification via low-density microarray (LDA) card analysis (all pts). Results ChromoSeqV2 was validated in a CLIA-licensed setting using cohort of 88 retrospective B-ALL samples, 45 of which had ICC and WHO class-defining SVs based on G-banded karyotyping, FISH or RNAseq. ChromoSeqV2 detected 100% of the non-Ph-like SVs (37/37), including BCR::ABL1 (N=20), KMT2Ar (N=9), ETV6::RUNX1 (N=3), TCF3::PBX1 (N=1), and rearrangements involving MYC (N=2) or MEF2D (N=2). Fifteen patients met criteria for Ph-like B-ALL via cytogenetics or RNAseq either due to rearrangements of CRLF2 (N=5), JAK2 (N=2) or ABL2 (N=1) or high expression of a 6-gene Ph-like signature (N=7). ChromoSeqV2 detected a Ph-like SV in 93% of these cases (14/15) with 100% specificity in samples negative by RNAseq (N=23). ChromoSeqV2 was then used to profile 136 samples from the Alliance A041501 trial, where it identified ICC and WHO class-defining SVs in 87 pts (64%; 95% CI: 55-72%), including Ph-like SVs (56/136, 41%), KMT2A rearrangements (N=5), TCF3::PBX1 (N=3) and SVs involving MYC (N=3), MEF2D (N=2), DUX4 (N=2), and ZNF384 (N=1). Ph-like SVs were dominated by CRLF2 rearrangements (N=45) and included SVs involving EPOR (N=4), JAK2 (N=3), ABL1/ABL2 (N=2) and PDGFRB (N=1). IGH was the most common CRLF2 partner (N=32), followed by P2RY8::CRLF2 (N=7) and other genes (N=5). Multiple CRLF2 SVs were detected in 4 pts, and 33% (15/45) of pts with a CRLF2 rearrangement had a co-occurring CRLF2 gene mutation. The yield of ChromoSeqV2 for SVs in pts with the Ph-like expression signature via LDA card analysis was 66% (54/82; 95% CI 55%-76%) compared to 24% (11/45; 95% CI 13%-40%) by cytogenetics when these studies were successful and 70% (12/17; 95% CI 44%-90%) vs RNAseq in pts with available data. The sensitivity of ChromoSeqV2 for Ph-like SVs identified by either cytogenetics, FISH or RNAseq was 100% (21/21; 95% CI 84%-100%) and the positive predictive value of Ph-like SVs for the Ph-like expression signature by the LDA card assay was 96% (54/56; 95% CI 88%-99%). Conclusions Genomic assessment of 136 B-ALL pts from the Alliance A041501 trial using the ChromoSeqV2 rapid clinical WGS assay was 100% sensitive for Ph-like SVs identified by other molecular methods and had a 96% PPV for the Ph-like expression signature via LDA card analysis. The diagnostic yield of SV pts with the Ph-like signature was 66% using ChromoSeqV2, which was similar to RNAseq and superior to cytogenetics. These results demonstrate that ChromoSeqV2 is an effective approach for identifying potentially targetable rearrangements in B-ALL pts suspected of having the Ph-like phenotype. Support: U10CA180821, U10CA180882; . Servier; Pfizer.

PURPOSE: Clinical trials are important for managing older patients with AML. We investigated differences in outcomes of older patients with AML on the basis of whether patients participated in intensive chemotherapy trials at community versus academic cancer centers. METHODS: We used data from the Alliance for Clinical Trials in Oncology phase III trials that enrolled patients age ≥ 60 years with newly diagnosed AML between 1998 and 2002 in the Cancer and Leukemia Group B (CALGB) 9720 trial and between 2004 and 2006 in the CALGB 10201 trial. Centers funded by the NCI Community Oncology Research Program were identified as community cancer centers; others were designated as academic cancer centers. Logistic regression models and Cox proportional hazards models were used to compare 1-month mortality and overall survival (OS) by center type. RESULTS: Seventeen percent of the 1,170 patients were enrolled in clinical trials in community cancer centers. The study results demonstrated comparable rates of grade ≥3 adverse events (97% v 93%), 1-month mortality (19.1% v 16.1%), and OS (43.9% v 35.7% at 1 year) between community versus academic cancer centers, respectively. After adjusting for covariates, 1-month mortality (odds ratio, 1.40; 95% CI, 0.92 to 2.12; P = .11) and OS (hazard ratio, 1.04; 95% CI, 0.88 to 1.22; P = .67) were not statistically different among patients treated in community versus academic cancer centers. CONCLUSION: An older patient population, who have complex health care needs, can be successfully treated on intensive chemotherapy trials in select community cancer centers with outcomes comparable with that achieved at academic cancer centers.

PURPOSE Representativeness in acute leukemia clinical research is essential for achieving health equity. The National Cancer Institute's mandate for Comprehensive Cancer Centers (CCCs) to define and assume responsibility for cancer control and treatment across a geographic catchment area provides an enforceable mechanism to target and potentially remediate participatory inequities. METHODS We examined enrollee characteristics across 15 Cancer and Leukemia Group B/Alliance cooperative group adult acute leukemia clinical trials (N = 3,734) from 1998 to 2013, including participation in optional companion biobanks. We determined enrollment odds by race-ethnicity for all participants adjusted for national incidence, and for those enrolled at CCCs adjusted for catchment area incidence. We modeled biobank participation by sociodemographics using logistic regression. RESULTS Non-Hispanic (NH)-White patients were more likely to be enrolled than NH-Black, NH-Asian, or Hispanic patients (odds ratio [OR], 0.75, 0.48, and 0.44, respectively; all P < .001), but less likely than NH-Native American patients (OR, 1.91; P < .001), adjusted for national incidence. Enrollment odds were lower for NH-Black, NH-Asian, and Hispanic patients at CCCs adjusted for catchment area incidence (OR, 0.57, 0.26, and 0.32, respectively; P < .001); differences were driven by overenrollment of NH-White patients from outside self-defined catchment areas (18.1% v 12.3%; χ2 P = .01) and by CCCs with less absolute enrollee diversity (rank sum P = .03). Among all enrollees, NH-White race-ethnicity and lower neighborhood deprivation correlated with biobank participation (OR, 1.81 and 1.45, respectively; P = .01 and .03). For CCC enrollees, the correlation of race-ethnicity with biobank participation was attenuated by a measure accounting for their site's degree of enrollment disparity but not neighborhood deprivation. CONCLUSION Acute leukemia clinical research disparities are substantial and driven by structural trial enrollment barriers at CCCs. Real-time CCC access and enrollment monitoring is needed to better align research participation with local populations.

Abstract Introduction Race-ethnic disparities in clinical trial enrollment have the potential to bias findings, limit generalizability, misdirect drug development, and reduce equitable access to novel therapy. The degree to which such disparities exist within acute myeloid leukemia (AML) North American cooperative group trials, biobanks, and correlative studies remain unclear, as are the factors that influence biobank and correlative study participation among trial enrollees. In addition, the National Cancer Institute's (NCI) mandate for Comprehensive Cancer Centers (CCC) to designate catchment areas has not been explored as a mechanism through which AML enrollment disparities can be addressed. Methods We analyzed enrollment data from the 9 Alliance/CALGB AML treatment trials, 2 biobank protocols, and 2 correlative studies active from 1998-2013 and with published results. Trial enrollees could consent to biobank and/or correlative study participation. We compared participation rates of United States (US) enrollees for the mutually exclusive racial-ethnic groups of non-Hispanic (NH)-white, NH-Black, NH-Asian, NH-Native American, and Hispanic using X 2 testing, with NH-white as the comparator and reporting odds ratios (OR) and 95% confidence intervals (CI). Rates were adjusted by national incidence according to the Surveillance, Epidemiology, and End Results program and the US Census. Testing was repeated for the 55% of participants enrolled at 15 NCI CCCs recruiting ≥10 patients, where incidence was adjusted for catchment area size and demographics. Logistic regression models, clustered by trial, were performed to assess the following predictors for biobank and correlative study participation among trial enrollees: race-ethnicity (NH-white vs non-white), site type (CCC status), age (10-year increments), sex, neighborhood urbanity (urban vs rural) and poverty (&lt;20% vs ≥20% below poverty line) by zip code, and distance from site (10-mile increments). Results There were 3041 trial enrollees at US sites; participant characteristics and demographics by race-ethnicity are shown in Table 1. 93.9% of patients participated in a biobanking study and 60.0% in a correlative study. National incidence adjusted enrollment odds by race-ethnicity are shown in the Figure (top); NH-Black, NH-Asian, and Hispanic persons were enrolled at significantly lower rates than NH-whites; NH-Native American enrollment was significantly higher. Enrollment odds were even lower for NH-Black, NH-Asian, and Hispanic enrollees at CCC sites when adjusted by catchment area incidence (Figure; bottom). Among trial enrollees, there were no univariable predictors of biobank participation, however, male sex (OR 1.12; 95% CI 1.01, 1.37; p=0.04) and NH-white race-ethnicity (OR 1.33; 95% CI 1.12,1.57; p&lt;0.001) were associated with correlative study participation. Multivariable models of correlative study participation, with predictors selected based on univariable significance, are shown in Table 2 for all trial enrollees and when restricted to biobank enrollees; in both cases, NH-white race predicted participation. Conclusions Across 15 years of AML cooperative group studies, there were several enrollment disparities by race-ethnicity, which were more pronounced at CCC sites. Over 90% of trial enrollees participated in biobanking, with no race-ethnic differences seen. However, correlative study participation among trial enrollees was higher for NH-whites. Taken together, these data suggest that efforts should focus on increasing trial and correlative study participant diversity-but not biobanking-within NCI-designated CCC catchment areas. Reasonable next steps include identifying key structural, provider, and patient-based barriers to trial and correlative study participation at CCC sites and developing inclusive, multilevel interventions to address them. Figure 1 Figure 1. Disclosures Eisfeld: Karyopharm (spouse): Current Employment. Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. Stone: AbbVie Inc, Actinium Pharmaceuticals Inc, Aprea Therapeutics, BerGenBio ASA, ElevateBio, Foghorn Therapeutics, GEMoaB, GlaxoSmithKline, Innate Pharma, Syndax Pharmaceuticals Inc, Syros Pharmaceuticals Inc, Takeda Oncology: Other: Advisory Committee; Agios Pharmaceuticals Inc, Novartis;: Research Funding; ACI Clinical, Syntrix Pharmaceuticals, Takeda Oncology: Other: Data Safety & Monitoring. DeAngelo: Abbvie: Research Funding; Blueprint: Research Funding; Takeda: Consultancy; Autolus: Consultancy; Forty-Seven: Consultancy; Incyte: Consultancy; Jazz: Consultancy; Novartis: Consultancy, Research Funding; Pfizer: Consultancy; Servier: Consultancy; Amgen: Consultancy; Agios: Consultancy; Glycomimetrics: Research Funding. Byrd: Newave: Membership on an entity's Board of Directors or advisory committees; Vincerx Pharmaceuticals: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Novartis, Trillium, Astellas, AstraZeneca, Pharmacyclics, Syndax: Consultancy, Honoraria.

Abstract Overexpression of B-cell leukemia/lymphoma 2 (BCL2) renders acute myeloid leukemia (AML) cells resistant to chemotherapy and has been associated with unfavorable outcomes. Oblimersen (G3139) is a phosphorothioate 18-mer antisense oligonucleotide directed against the first 6 BCL2 codons. In a phase 1 study of AML patients treated with G3139, cytarabine, and daunorubicin induction with cytarabine consolidation, no antisense-related toxicity was reported, and BCL2 downregulation occurred in patients achieving complete remission. In this phase 3 trial, untreated older AML patients were randomized to cytarabine (100 mg/m2 per day on days 4-10) and daunorubicin (60 mg/m2 per day on days 4-6) followed by cytarabine consolidation (2000 mg/m2 per day on days 4-8) with (arm A) or without (arm B) G3139 (7 mg/m2 per day on days 1-10 [induction] or days 1-8 [consolidation]). A total of 506 patients were enrolled. No differences in toxicity were observed between arms. Estimated overall survival (OS) at 1 year was 43% for arm A and 40% for arm B (1-sided log rank P = .13), with no differences in disease-free (DFS; P = .26) or event-free survival (P = .80). Subgroup analyses showed patients age &lt;70 years in arm A had improved OS by 1 month vs those in arm B (P = .04), and patients with secondary AML in arm A had better DFS vs those in arm B (P = .04). We conclude that addition of G3139 to chemotherapy failed to improve outcomes of older AML patients. However, more effective means of inhibiting BCL2 are showing promising results in combination with chemotherapy in AML. This trial was registered at www.clinicaltrials.gov as #NCT00085124.

Abstract In CN-AML, mutations of specific genes have prognostic significance and are used for treatment guidance. However, these mutations are in general not mutually exclusive and CN-AML patients (pts) frequently harbor mutational combinations with unclear prognostic significance because of the concurrent presence of mutations with favorable (CEBPA, NPM1) and unfavorable (ASXL1, DNMT3A, IDH1, IDH2, FLT3-ITD, MLL-PTD, RUNX1, TET2, WT1) impact on outcome. Here, we report the frequency and clinical significance of isolated mutations and their combinations in 364 CN-AML pts. Younger [<60 years (y); n=163] and older (≥60 y; n=201) pts were intensively treated on frontline CALGB/Alliance protocols and, per protocol, did not undergo allogeneic stem cell transplantation in first complete remission (CR). Median follow-up for pts alive was 8.7 y. Pts were analyzed centrally for mutations in the ASXL1, CEBPA, DNMT3A, IDH1, IDH2, NPM1, RUNX1, TET2, and WT1 genes and the presence of FLT3-ITD, FLT3-TKD and MLL-PTD. We found that 99% of pts had ≥1 and 88% ≥2 of the 12 mutations. Specifically, 11% of pts had 1 gene mutated (n1), 40% had 2 (n2), 31% 3 (n3), and 18% harbored ≥4 mutated genes (n4). The distribution of the different n groups in younger and older pts was similar (Fig 1). The expected frequency of each mutated gene in every numerical (n) group was calculated as follows: [no. of pts with the mutated gene] x [total no. of mutations in the n group] / [total no. of mutations in all pts], and compared with the observed frequency. CEBPA, IDH2, NPM1, and RUNX1 mutations were overrepresented in the n1 and n2 groups (P<.001, P<.001, P=.002, P=.02, respectively) and thus likely represent “early” events in leukemogenesis. In contrast, DNMT3A, FLT3-ITD, and TET2 mutations were more frequent in the n3 and n4 groups (P=.008, P<.001, P=.02, respectively) suggesting that they are likely “late” events. The distribution among age groups and clinical impact of the “early” mutations (i.e., CEBPA, NPM1, IDH2) presenting as isolated mutations or in combination with other mutations were then investigated. Isolated RUNX1 mutations could not be evaluated due to small sample size. Younger pts were more likely to harbor an isolated “early” mutated gene than older pts (21% v 12%, P=.03). Specifically, isolated CEBPA and NPM1 mutations were more frequent in younger pts compared with the older (7% v 2%, P=.007; 7% v 3%, P=.07, respectively). In pts with isolated CEBPA mutations, these were always bi-allelic. Single “early” mutated genes varied in their impact on CR achievement (CEBPA: 100%, NPM1: 94%, IDH2: 67%), and overall survival (OS; 3-y OS: CEBPA: 87%, NPM1: 69%, IDH2: 22%). Acquisition of additional mutations adversely modified the prognostic significance of favorable “early” mutations in the CEBPA (Fig 2A) and NPM1 (Fig 2B) genes, but left unchanged the unfavorable effect of IDH2 mutations (Fig 2C). Two mutational combinations were exceptions to this: younger pts with both NPM1 and DNMT3A mutations (8 pts) had an excellent prognosis with 3-y OS of 100%; and older pts with concurrent NPM1 and IDH2 mutations (9 pts; all IDH2 mutations were in codon R140) had a high 3-y OS rate of 67%. We conclude that CEBPA and NPM1 mutations mainly define pts with favorable prognosis when they present as single markers, whereas mutated IDH2 predominantly associates with adverse outcome. The NPM1+DNMT3A and NPM1+IDH2 mutational patterns may define novel favorable molecular subtypes in younger and older CN-AML pts, respectively, but these results require corroboration in larger pt cohorts. Disclosures: Mrózek: AMERICAN SOCIETY OF HEMATOLOGY: I will review abstracls submitted for presentation at the 55th ASH Annual Meeting in the 611 category Other. Eisfeld:AMERICAN SOCIETY OF HEMATOLOGY: I will review abstracls submitted for presentation at the 55th ASH Annual Meeting in the 608 category Other.

Abstract Monosomy of chromosome 7 is the most frequent autosomal monosomy in acute myeloid leukemia (AML), where it associates with poor clinical outcomes. However, molecular features associated with this sole monosomy subtype (-7 AML), which may give insights into the basis for its poor prognosis, have not been characterized. In this study, we analyzed 36 cases of -7 AML for mutations in 81 leukemia/cancer-associated genes using a customized targeted next-generation sequencing panel (Miseq). Global gene and miRNA expression profiles were also determined using paired RNA and small RNA sequencing data. Notably, gene mutations were detected in all the major AML-associated functional groups, which include activated signaling, chromatin remodeling, cohesin complex, methylation, NPM1, spliceosome, transcription factors, and tumor suppressors. Gene mutations in the chromatin remodeling groups were relatively more frequent in patients &lt;60 years of age, who also had less mutations in the methylation and spliceosome groups compared with patients ≥60 years of age. Novel recurrent mutational events in AML were identified in the SMARCA2 gene. In patients ≥60 years of age, the presence of spliceosome mutations associated with a lower complete remission rate (P = 0.03). RNA sequencing revealed distinct gene and miRNA expression patterns between the sole -7 and non -7 AML cases, with reduced expression, as expected, of many genes and miRNAs mapped to chromosome 7, and overexpression of ID1, MECOM, and PTPRM, among others. Overall, our findings illuminate a number of molecular features of the underlying aggressive pathobiology in -7 AML patients. Cancer Res; 77(1); 207–18. ©2016 AACR.

SummarySomatic mutation of the DNMT3A gene at the arginine R882 site is common in acute myeloid leukaemia (AML). The prognostic significance of DNMT3A R882 mutation clearance, using traditional diagnostic next generation sequencing (NGS) methods, during complete remission (CR) in AML patients is controversial. We examined the impact of clearing DNMT3A R882 mutations at diagnosis to the detectable threshold of ˂3% during CR on outcome in 56 adult AML patients. Mutational remission, defined as clearance of pre‐treatment DNMT3A R882 and all other AML‐associated mutations to a variant allele frequency ˂3%, occurred in 14 patients whereas persistent DNMT3A R882 mutations were observed in 42 patients. There were no significant differences in disease‐free or overall survival between patients with and without DNMT3A R882 mutation clearance. Patients with persistent DNMT3A R882 who cleared all other AML mutations and did not acquire new mutations (n = 30), trended towards longer disease‐free survival (1·6 vs. 0·6 years, P = 0·06) than patients with persistence of DNMT3A R882, in addition to other mutations or acquisition of new AML‐associated mutations, such as those in TET2, JAK2, ASXL1 and TP53 (n = 12). These data demonstrate that DNMT3A R882 mutations, as assessed by traditional NGS methods, persist in the majority of AML patients in CR.

Significance Long noncoding RNAs (lncRNAs) are involved in numerous biological roles including epigenetic regulation, apoptosis, and cell cycle. Whereas lncRNAs contribute to epigenetic gene regulation, metastasis, and prognosis in solid tumors, their role in acute myeloid leukemia (AML) has not been hitherto reported. Here, we show that lncRNA expression profiles are associated with recurrent mutations, clinical features, and outcome in AML. A fraction of these lncRNAs may have a functional role in leukemogenesis. Furthermore, lncRNAs could be used as biomarkers for outcome in AML. The identification of patients likely to achieve complete remission with standard therapy alone, based on lncRNA expression, is a significant advance potentially sparing such patients from other toxicities and focusing investigational approaches on postremission studies.

Purpose To evaluate the impact of miR-155 on the outcome of adults with cytogenetically normal (CN) acute myeloid leukemia (AML) in the context of other clinical and molecular prognosticators and to gain insight into the leukemogenic role of this microRNA. Patients and Methods We evaluated 363 patients with primary CN-AML. miR-155 levels were measured in pretreatment marrow and blood by NanoString nCounter assays that quantified the expression of the encoding gene MIR155HG. All molecular prognosticators were assessed centrally. miR-155–associated gene and microRNA expression profiles were derived using microarrays. Results Considering all patients, high miR-155 expression was associated with a lower complete remission (CR) rate (P < .001) and shorter disease-free survival (P = .001) and overall survival (OS; P < .001) after adjusting for age. In multivariable analyses, high miR-155 expression remained an independent predictor for a lower CR rate (P = .007) and shorter OS (P < .001). High miR-155 expressers had approximately 50% reduction in the odds of achieving CR and 60% increase in the risk of death compared with low miR-155 expressers. Although high miR-155 expression was not associated with a distinct microRNA expression profile, it was associated with a gene expression profile enriched for genes involved in cellular mechanisms deregulated in AML (eg, apoptosis, nuclear factor-κB activation, and inflammation), thereby supporting a pivotal and unique role of this microRNA in myeloid leukemogenesis. Conclusion miR-155 expression levels are associated with clinical outcome independently of other strong clinical and molecular predictors. The availability of emerging compounds with antagonistic activity to microRNAs in the clinic provides the opportunity for future therapeutic targeting of miR-155 in AML.