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Whether quantum state transitions occur by instantaneous jumps (a la Bohr) or deterministic dynamics (Schrödinger's preference) has been intensely debated. Recent experimental measurements of shelved electrons have reignited the debate. We examine aspects of the time-dependent numerical solutions of the Schrödinger equation in quantum systems with two and three levels perturbed by a sinusoidal field. A geometrical construction involving quantum state phase differences illuminates the role of interstate phase differences in a deterministic, rather than random, process of multiphoton absorption. Alternate halves of the Rabi cycle exhibit phase reversals much like the classical beats of coupled oscillators. For non-zero detuning, population inversion does not occur because the exciting field drifts out of the proper phase before inversion is complete. A close correspondence with classical, coupled oscillator beats offers insights for interpretation of deterministic quantum dynamics and suggests an experimental test for the correctness of this picture depending on the long-time phase stability of exciting fields.

Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression.Significance:Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML.See related article by Guess et al., p. 316 (33).See related commentary by Romine and van Galen, p. 270.This article is highlighted in the In This Issue feature, p. 265

Supplementary Figure from Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression

Supplementary Table from Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression

Supplementary Data from Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression

Acute myeloid leukemia (AML) with RARG rearrangement has clinical, morphologic, and immunophenotypic features similar to classic acute promyelocytic leukemia. However, AML with RARG rearrangement is insensitive to all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) and carries a poor prognosis. We initiated a global cooperative study to define the clinicopathological features, genomic and transcriptomic landscape, and outcomes of AML with RARG rearrangements collected from 29 study groups/institutions worldwide. Thirty-four AML with RARG rearrangements were identified. Bleeding or ecchymosis was present at 18 (54.5%) patients. Morphology diagnosed as M3 and M3v accounted for 73.5% and 26.5% of cases, respectively. Immunophenotyping showed following characteristics: positive for CD33, CD13, and MPO but negative for CD38, CD11b, CD34, and HLA-DR. Cytogenetics showed normal karyotype in 38% and t(11;12) in 26% of patients. The partner genes of RARG were diverse and included CPSF6 (n=14), NUP98 (n=11), HNRNPc (n=6), HNRNPm (n=1), PML (n=1), and NPM1 (n=1). WT1- and NRAS/KRAS-mutations were common co-mutations. None of the 34 patients responded to ATRA and/or ATO. Death within 45 days from diagnosis occurred in 10 patients (~29%). At the last follow-up, 23 patients had died, and the estimated 2-year cumulative incidence of relapse, event-free survival, and overall survival were 68.7%, 26.7%, and 33.5%, respectively. Unsupervised hierarchical clustering using RNA-seq data from 201 AML patients showed that 81.8% of the RARG fusion samples clustered together, suggesting a new molecular subtype. RARG rearrangement is a novel entity of AML that confers a poor prognosis.

Hematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain hematopoietic fitness throughout life. In steady-state conditions, HSC exhaustion is prevented by the maintenance of most HSCs in a quiescent state, with cells entering the cell cycle only occasionally. HSC quiescence is regulated by retinoid and fatty-acid ligands of transcriptional factors of the nuclear retinoid X receptor (RXR) family. Here, we show that dual deficiency for hematopoietic RXRa and RXRb induces HSC exhaustion, myeloid cell/megakaryocyte differentiation, and myeloproliferative-like disease. RXRa and RXRb maintain HSC quiescence, survival, and chromatin compaction; moreover, transcriptome changes in RXRa;RXRb-deficient HSCs include premature acquisition of an aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Fitness loss and associated RNA transcriptome and splicing alterations in RXRa;RXRb-deficient HSCs are prevented by Myc haploinsufficiency. Our study reveals the critical importance of RXRs for the maintenance of HSC fitness and their protection from premature aging. We thank the members of the J.A.C. and M.R. laboratories for extensive discussions and critiques of the manuscript. We thank Daniel Metzger (Université de Strasbourg, France) for Rxrbf/f 418 mice, Juan Carlos Zúñiga-Pflücker (Sunnybrook Health Sciences Centre, Canada) for OP9-NL1 cells, Daniel Jiménez-Carretero (CNIC) for t-SNE analysis, the CRG (Barcelona, Spain) Genomics Unit for ATACseq sequencing, and S. Bartlett (CNIC) for editorial assistance. We also thank the staff of the CNIC Cellomics and Animal facilities for technical support. This study was supported by grants from the Spanish Ministerio de Ciencia e Innovación (MICIN) (SAF2017-90604-REDT-NurCaMein, RTI2018- 095928-B100, and PID2021-122552OB-I00), La Marató de TV3 Foundation (201605-32), and the Comunidad de Madrid (MOIR-B2017/BMD-3684) to M.R and from the Formación de Profesorado Universitario (FPU17/01731) program (MICIN) to J.P. The project also received funding from the US National Institutes of Health (R01 DK124115, P01 HL158688, R01 HL147536, R01 CA237016 and U54 DK126108 to J.A.C). The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN), and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MICIN/AEI/10.13039/501100011033). Sí

Head and neck squamous cell cancers (HNSCCs) represent a diverse group of tumors emerging within different mucosal surfaces of the oral cavity, nasopharynx, oropharynx, larynx, and hypopharynx. HNSCCs share common clinical risk factors and genomic features, including smoking, alcohol, age, male sex, aneuploidy, and TP53 mutations. Viral initiating and contributing events are increasingly recognized in HNSCCs. While both Epstein–Barr Virus (EBV) and human papilloma virus (HPV) are observed, EBV is more frequently associated with nasopharyngeal cancers whereas HPV is associated with oropharyngeal cancers. HNSCCs are associated with high tumor mutational burden and loss of tumor suppressor gene function, especially in TP53 and X-linked genes. Multiple lines of evidence suggest that HNSCCs are subject to immunologic surveillance and immune-induced evolutionary pressure that correlate with negative clinical outcomes. This review will discuss genomic mechanisms related to immune-mediated pressures and propose prognostic and therapeutic implications of detectable immune escape mechanisms that drive tumorigenesis and disease progression.

Patients with multiple myeloma (MM) who are treated with lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients with MM treated with lenalidomide, who subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, and immunoglobulin heavy chain (IgH) clonality assessment. Samples were assessed for shared mutations and recurrently mutated genes. Through whole exome sequencing and cytogenetics/FISH analysis of 7 paired samples (MM vs matched B-ALL), no mutational overlap between samples was observed. Unique dominant IgH clonotypes between the tumors were observed in 5 paired MM/B-ALL samples. Across all 17 B-ALL samples, 14 (83%) had a TP53 variant detected. Three MM samples with sufficient sequencing depth (>500×) revealed rare cells (average of 0.6% variant allele frequency, or 1.2% of cells) with the same TP53 variant identified in the subsequent B-ALL sample. A lack of mutational overlap between MM and B-ALL samples shows that B-ALL developed as a second malignancy arising from a founding population of cells that likely represented unrelated clonal hematopoiesis caused by a TP53 mutation. The recurrent variants in TP53 in the B-ALL samples suggest a common path for malignant transformation that may be similar to that of TP53-mutant, treatment-related acute myeloid leukemia. The presence of rare cells containing TP53 variants in bone marrow at the initiation of lenalidomide treatment suggests that cellular populations containing TP53 variants expand in the presence of lenalidomide to increase the likelihood of B-ALL development.

Introduction: Offering the optimal frontline treatment to a patient with acute myeloid leukemia (AML) requires trading off expected benefit and risk. Typical standard of care intensive induction chemotherapy (e.g., cytarabine plus idarubicin (7+3)) results in high clinical response rates. However, many patients receive a less intensive regimen (e.g., venetoclax plus decitabine (VenDec)) because their individual toxicity risk is high based on lack of medical fitness. Predicting an individual patient’s clinical response prior to treatment has the potential to increase the benefit/risk ratio (therapeutic index) for some patients and optimize their treatment selection. Here, we demonstrate the ability of an automated high-throughput, multi-color flow cytometry predictive precision medicine platform (PPMP) to predict response to 7+3 or VenDec. Methods: To assess correlation between PPMP-predicted and actual clinical response to 7+3 or VenDec in clinical trial NCT04263181, pre-induction blood samples were collected from 31 patients of which 18 received 7+3 (all newly diagnosed (ND) AML) and 13 VenDec (7 ND AML, 5 secondary AML, 1 MDS). We measured drug effects on leukemic blasts by applying a cutoff at the total blast count that optimizes separation between predicted responders and non-responders (“conventional approach”) or by a machine learning (ML) approach considering multiple cell populations. For the former approach, training sets represented 13 patients for 7+3 and 8 for VenDec. Both 7+3 and VenDec models were validated with 5 patients. For the ML approach, the model was trained on all 13 VenDec patients and monitored using leave-one-out cross-validation. Results: For the conventional approach, predicted and true clinical responses were highly correlated for 7+3 (AUC = 0.91) and VenDec (AUC = 0.81), with 100% precision (positive predictive values (PPV)) for both, i.e., all predicted responders were true clinical responders. Some true clinical responders were not identified (negative predictive value (NPV) = 67% for 7+3 and 57% for VenDec), resulting in an accuracy of 94% (7+3) and 77% (VenDec). To maximize NPV and accuracy for predicting VenDec clinical outcomes, we applied a novel ML-based algorithm to integrate the behavior of malignant and non-malignant cell populations, yielding a model with 100% accuracy (100% PPV and NPV). Additional outcome data, including overall survival, are under evaluation. Summary: Total blast-based predictions yielded accuracies of 94% for 7+3 and 77% for VenDec. An ML algorithm for VenDec considering additional cell populations increased the accuracy to 100%. Further studies will expand patient numbers. We plan to use this platform to inform our frontline decision making with the goal to maximize the therapeutic benefit/risk ratio and ensure that the most appropriate frontline therapy is used for each individual patient. Citation Format: Meagan A. Jacoby, John S. Welch, Peter Westervelt, Matthew Christopher, Geoffrey L. Uy, Ravi Vij, Keith E. Stockerl-Goldstein, Brad S. Kahl, Iskra Pusic, John F. DiPersio, Mark A. Schroeder, Miriam Y. Kim, Todd A. Fehniger, Armin Ghobadi, Christine J. Gu, Wade Anderson, Kathryn Vanderlaag, Kamran Ali, Camille Pataki, Markus D. Lacher. Predictive precision medicine platform accurately predicts individual patient response to AML treatments to maximize outcomes. [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 4342.

The molecular events responsible for decitabine responses in myelodysplastic syndrome and acute myeloid leukemia patients are poorly understood. Decitabine has a short serum half-life and limited stability in tissue culture. Therefore, theoretical pharmacologic differences may exist between patient molecular changes in vitro and the consequences of in vivo treatment. To systematically identify the global genomic and transcriptomic alterations induced by decitabine in vivo, we evaluated primary bone marrow samples that were collected during patient treatment and applied whole-genome bisulfite sequencing, RNA-sequencing, and single-cell RNA sequencing. Decitabine induced global, reversible hypomethylation after 10 days of therapy in all patients, which was associated with induction of interferon-induced pathways, the expression of endogenous retroviral elements, and inhibition of erythroid-related transcripts, recapitulating many effects seen previously in in vitro studies. However, at relapse after decitabine treatment, interferon-induced transcripts remained elevated relative to day 0, but erythroid-related transcripts now were more highly expressed than at day 0. Clinical responses were not correlated with epigenetic or transcriptional signatures, although sample size and interpatient variance restricted the statistical power required for capturing smaller effects. Collectively, these data define global hypomethylation by decitabine and find that erythroid-related pathways may be relevant because they are inhibited by therapy and reverse at relapse.

RARA and RXRA contribute to myeloid maturation in both mice and humans, and deletion of Rxra and Rxrb augments leukemic growth in mice. While defining the domains of RXRA that are required for anti-leukemic effects in murine KMT2A-MLLT3 leukemia cells, we unexpectedly identified RXRA DT448/9PP as a constitutively active variant capable of inducing maturation and loss of their proliferative phenotype. RXRA DT448/9PP was associated with ligand-independent activity in reporter assays, with enhanced co-activator interactions, reduced engraftment in vivo, and activation of myeloid maturation transcriptional signatures that overlapped with those of cells treated with the potent RXRA agonist bexarotene, suggestive of constitutive activity that leads to leukemic maturation. Phenotypes of RXRA DT448/9PP appear to differ from those of two other RXRA mutations with forms of constitutive activity (F318A and S427F), in that DT448/9PP activity was resistant to mutations at critical ligand-interacting amino acids (R316A/L326A) and was resistant to pharmacological antagonists, suggesting it may be ligand-independent. These data provide further evidence that activated retinoid X receptors can regulate myeloid maturation and provide a novel constitutively active variant that may be germane for broader studies of retinoid X receptors in other settings. This work was supported by National Institutes of Health grant R01 HL128447 (JSW), by the Siteman Investment Program (JSW), the Washington University SPORE DRP (JSW and MAF), the Children’s Discovery Institute (JSW), the Alex’s Lemonade Stand Foundation Young Investigator Award (MAF), the National Institutes of Health 5K12HD07622408 (MAF), and grants from the Spanish Ministerio de Ciencia e Innovación (MCI) (SAF2017- 90604-REDT-NurCaMeIn, RTI2018-095928-BI00) (MR). Sí

Significance Current acute myeloid leukemia (AML) risk assessment relies on cytogenetics and gene-sequencing studies but is imperfect, especially for patients with normal karyotypes and intermediate risk. To understand factors associated with excellent responses in these patients, we compared genetic and transcriptional data from patients with first remissions lasting more than 5 y after chemotherapy, to matched controls with first remissions lasting fewer than 2 y. AML cells from patients with early relapse displayed an immunosuppressive phenotype that blocked CD4 T cell activation via the T cell receptor; the long first-remission AML cells did not display this phenotype. Inhibiting LAG3 reversed this immunosuppression in most tested cases. This immunosuppressive phenotype may help to stratify risk of relapse at presentation, and outcomes., Acute myeloid leukemia (AML) patients rarely have long first remissions (LFRs; >5 y) after standard-of-care chemotherapy, unless classified as favorable risk at presentation. Identification of the mechanisms responsible for long vs. more typical, standard remissions may help to define prognostic determinants for chemotherapy responses. Using exome sequencing, RNA-sequencing, and functional immunologic studies, we characterized 28 normal karyotype (NK)-AML patients with >5 y first remissions after chemotherapy (LFRs) and compared them to a well-matched group of 31 NK-AML patients who relapsed within 2 y (standard first remissions [SFRs]). Our combined analyses indicated that genetic-risk profiling at presentation (as defined by European LeukemiaNet [ELN] 2017 criteria) was not sufficient to explain the outcomes of many SFR cases. Single-cell RNA-sequencing studies of 15 AML samples showed that SFR AML cells differentially expressed many genes associated with immune suppression. The bone marrow of SFR cases had significantly fewer CD4+ Th1 cells; these T cells expressed an exhaustion signature and were resistant to activation by T cell receptor stimulation in the presence of autologous AML cells. T cell activation could be restored by removing the AML cells or blocking the inhibitory major histocompatibility complex class II receptor, LAG3. Most LFR cases did not display these features, suggesting that their AML cells were not as immunosuppressive. These findings were confirmed and extended in an independent set of 50 AML cases representing all ELN 2017 risk groups. AML cell–mediated suppression of CD4+ T cell activation at presentation is strongly associated with unfavorable outcomes in AML patients treated with standard chemotherapy.

Acute myeloid leukemia (AML) patients rarely have long first remissions (> 5 years) after standard-of-care chemotherapy, unless classified as favorable risk at presentation. Identification of the mechanisms responsible for long vs. more typical, short remissions may help to define prognostic determinants for chemotherapy responses. Using exome sequencing, RNA sequencing and functional immunologic studies, we characterized 28 Normal Karyotype (NK)-AML patients with >5 year first remissions after chemotherapy (Long First Remissions, LFR) and compared them to a well-matched group of 31 NK-AML patients who relapsed within 2 years (Standard First Remissions, SFR). Our combined analyses indicated that genetic risk profiling at presentation (as defined by ELN 2017 Criteria) was not sufficient to explain the outcomes of many SFR cases. Single cell RNA-sequencing studies of 15 AML samples showed that SFR AML cells differentially expressed many genes associated with immune suppression. The bone marrow of SFR cases had significantly fewer CD4+ Th1 cells; these T cells expressed an exhaustion signature and were resistant to activation by T-cell receptor stimulation in the presence of autologous AML cells. T cell activation could be restored by removing the AML cells, or blocking the inhibitory MHC Class II receptor, LAG3. Most LFR cases did not display these features, suggesting that their AML cells were not as immunosuppressive. These findings were confirmed and extended in an independent set of 50 AML cases representing all ELN 2017 risk groups. AML cell-mediated suppression of CD4+ Tcell activation at presentation is strongly associated with unfavorable outcomes in AML patients treated with standard chemotherapy.

Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression.Significance:Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML.See related article by Guess et al., p. 316 (33).See related commentary by Romine and van Galen, p. 270.This article is highlighted in the In This Issue feature, p. 265

The orphan nuclear receptor Nur77 is an immediate-early response gene that based on tissue and cell context is implicated in a plethora of cellular processes, including proliferation, differentiation, apoptosis, metabolism, and inflammation. Nur77 has a ligand-binding pocket that is obstructed by hydrophobic side groups. Naturally occurring, cell-endogenous ligands have not been identified, and Nur77 transcriptional activity is thought to be regulated through posttranslational modification and modulation of protein levels. To determine whether Nur77 is transcriptionally active in hematopoietic cells in vivo, we used an upstream activating sequence (UAS)-GFP transgenic reporter. We found that Nur77 is transcriptionally inactive in vivo in hematopoietic cells under basal conditions, but that activation occurs following cytokine exposure by G-CSF or IL-3. We also identified a series of serine residues required for cytokine-dependent transactivation of Nur77. Moreover, a kinase inhibitor library screen and proximity labeling-based mass spectrometry identified overlapping kinase pathways that physically interacted with Nur77 and whose inhibition abrogated cytokine-induced activation of Nur77. We determined that transcriptional activation of Nur77 by G-CSF or IL-3 requires functional JAK and mTor signaling since their inhibition leads to Nur77 transcriptional inactivation. Thus, intracellular cytokine signaling networks appear to regulate Nur77 transcriptional activity in mouse hematopoietic cells.

The retinoids all-trans retinoic acid (ATRA) and bexarotene are active in acute myeloid leukemia (AML), but responses beyond acute promyelocytic leukemia (APL) have been more modest than APL responses. To determine whether chemical modification of bexarotene might augment retinoid responses in AML, we screened a series of 38 bexarotene derivatives for activity in a mouse MLL-AF9 leukemia cell line, which exhibits strong synergistic sensitivity to the combination of ATRA and bexarotene. We found that RXRA potency correlated with anti-leukemic activity and that only one compound (103-4) with dual RARA/RXRA activity was capable of ATRA-independent anti-leukemic activity. We evaluated bioisostere and cyclohexane modifications for potential resistance to P450 metabolism and found that bioisosteres reduced potency and that bezopyran, cyclopentane, and cyclohexene modifications only modestly reduced susceptibility to metabolism. Collectively, these studies provide a map of the structure-activity relationships of bexarotene with outcomes related to RXRA and RARA activity, corepressor binding, compound stability, and anti-leukemic potential.

BACKGROUND: As consolidation therapy for acute myeloid leukemia (AML), allogeneic hematopoietic stem-cell transplantation provides a benefit in part by means of an immune-mediated graft-versus-leukemia effect. We hypothesized that the immune-mediated selective pressure imposed by allogeneic transplantation may cause distinct patterns of tumor evolution in relapsed disease. METHODS: We performed enhanced exome sequencing on paired samples obtained at initial presentation with AML and at relapse from 15 patients who had a relapse after hematopoietic stem-cell transplantation (with transplants from an HLA-matched sibling, HLA-matched unrelated donor, or HLA-mismatched unrelated donor) and from 20 patients who had a relapse after chemotherapy. We performed RNA sequencing and flow cytometry on a subgroup of these samples and on additional samples for validation. RESULTS: On exome sequencing, the spectrum of gained and lost mutations observed with relapse after transplantation was similar to the spectrum observed with relapse after chemotherapy. Specifically, relapse after transplantation was not associated with the acquisition of previously unknown AML-specific mutations or structural variations in immune-related genes. In contrast, RNA sequencing of samples obtained at relapse after transplantation revealed dysregulation of pathways involved in adaptive and innate immunity, including down-regulation of major histocompatibility complex (MHC) class II genes (HLA-DPA1, HLA-DPB1, HLA-DQB1, and HLA-DRB1) to levels that were 3 to 12 times lower than the levels seen in paired samples obtained at presentation. Flow cytometry and immunohistochemical analysis confirmed decreased expression of MHC class II at relapse in 17 of 34 patients who had a relapse after transplantation. Evidence suggested that interferon-γ treatment could rapidly reverse this phenotype in AML blasts in vitro. CONCLUSIONS: AML relapse after transplantation was not associated with the acquisition of relapse-specific mutations in immune-related genes. However, it was associated with dysregulation of pathways that may influence immune function, including down-regulation of MHC class II genes, which are involved in antigen presentation. These epigenetic changes may be reversible with appropriate therapy. (Funded by the National Cancer Institute and others.)

TP53 mutated acute myeloid leukemia (AML) responds poorly to chemotherapy and has a short overall survival rate with a median of 5–9 months. Poor outcomes in TP53 mutated AML following chemotherapy have been observed and treatment options remain limited, although the presence of TP53 mutations alone should not be a barrier to therapy. Decitabine is emerging as an alternative treatment option for patients with TP53 mutated AML, although the agent has not been associated with deep molecular remissions and requires additional consolidation. The clinical and genomic characteristics of TP53 mutated AML are reviewed in this paper.

Altered DNA methylation is a common feature of acute myeloid leukemia (AML) and is thought to play a significant role in disease pathogenesis. Gain of function mutations in IDH1 or IDH2 result in widespread but highly focal regions of hypermethylation across the genome that occurs due to the production of 2-hydroxyglutarate that inhibits TET-mediated demethylation. We used whole-genome bisulfite sequencing to identify canonical regions of DNA hypermethylation that are associated specifically with IDH1 and IDH2 mutations in primary AML samples. Consistent with previous reports, IDH mutant (IDHmut) AMLs were the most hypermethylated among all mutationally-defined AML categories analyzed. We observed notable differences in the degree of hypermethylation associated with IDH mutation type, with IDH1mut AMLs having more profound hypermethylation at specific regions than IDH2mut samples. AMLs with biallelic inactivating mutations in TET2 displayed more modest DNA methylation changes compared to normal hematopoietic stem/progenitor cells, but methylation in these samples was increased in the IDHmut-specific regions, providing further support that these mutations act on the same TET-mediated demethylation pathway. Focal hypermethylated regions in IDHmut AML samples tended to occur in regions with low steady state methylation levels in normal stem/progenitor cells, which implies that both DNA methylation and demethylation pathways are active at these loci. Indeed, analysis of AML samples containing mutations in both IDH1 or IDH2 and DNMT3AR882 were less hypermethylated, providing evidence that focal IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific regions of hypermethylation were largely distinct from CpG island hypermethylation, and showed a significant enrichment for putative enhancers. Analysis of three-dimensional genome interactions from primary hematopoietic cells showed that differentially methylated enhancers formed direct interactions with highly expressed genes, including MYC and ETV6. Taken together, these results suggest that focal hypermethylation in IDH-mutant AML cells occurs by disrupting the balance of DNA methylation and demethylation, which is highly active in genomic regions involved in gene regulation.

Retinoid therapy transformed response and survival outcomes in acute promyelocytic leukemia (APL), but has demonstrated only modest activity in non-APL forms of acute myeloid leukemia (AML). The presence of natural retinoids in vivo could influence the efficacy of pharmacologic agonists and antagonists. We found that natural RXRA ligands, but not RARA ligands, were present in murine MLL-AF9-derived myelomonocytic leukemias in vivo and that the concurrent presence of receptors and ligands acted as tumor suppressors. Pharmacologic retinoid responses could be optimized by concurrent targeting RXR ligands (e.g. bexarotene) and RARA ligands (e.g. all-trans retinoic acid, ATRA), which induced either leukemic maturation or apoptosis depending on cell culture conditions. Co-repressor release from the RARA:RXRA heterodimer occurred with RARA activation, but not RXRA activation, providing an explanation for the combination synergy. Combination synergy could be replicated in additional, but not all, AML cell lines and primary samples, and was associated with improved survival in vivo, although tolerability of bexarotene administration in mice remained an issue. These data provide insight into the basal presence of natural retinoids in leukemias in vivo and a potential strategy for clinical retinoid combination regimens in leukemias beyond acute promyelocytic leukemia. This work was supported by NIH R01 HL128447 (to JSW), NIH P50 CA171963 (Project 1, to JSW and DRP) by the Siteman Investment Program (to JSW), and grants from the Spanish Ministerio de Ciencia e Innovacion (MCI) (SAF201571878-REDT-NurCaMeIn, RTI2018-095928-B100) (to MR). The CNIC is supported by the MCI and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (SEV2015-0505). Sí

PURPOSE Physicians treating hematologic malignancies increasingly order targeted sequencing panels to interrogate recurrently mutated genes. The precise impact of these panels on clinical decision making is not well understood. METHODS Here, we report our institutional experience with a targeted 40-gene panel (MyeloSeq) that is used to generate a report for both genetic variants and variant allele frequencies for the treating physician (the limit of mutation detection is approximately one AML cell in 50). RESULTS In total, 346 sequencing reports were generated for 325 patients with suspected hematologic malignancies over an 8-month period (August 2018 to April 2019). To determine the influence of genomic data on clinical care for patients with acute myeloid leukemia (AML), we analyzed 122 consecutive reports from 109 patients diagnosed with AML and surveyed the treating physicians with a standardized questionnaire. The panel was ordered most commonly at diagnosis (61.5%), but was also used to assess response to therapy (22.9%) and to detect suspected relapse (15.6%). The panel was ordered at multiple timepoints during the disease course for 11% of patients. Physicians self-reported that 50 of 114 sequencing reports (44%) influenced clinical care decisions in 44 individual patients. Influences were often nuanced and extended beyond identifying actionable genetic variants with US Food and Drug Administration–approved drugs. CONCLUSION This study provides insights into how physicians are currently using multigene panels capable of detecting relatively rare AML cells. The most influential way to integrate these tools into clinical practice will be to perform prospective clinical trials that assess patient outcomes in response to genomically driven interventions.

Summary Background Venetoclax combined with hypomethylating agents is a new standard of care for newly diagnosed patients with acute myeloid leukaemia (AML) who are 75 years or older, or unfit for intensive chemotherapy. Pharmacodynamic studies have suggested superiority of the longer 10-day regimen of decitabine that has shown promising results in patients with high-risk AML in phase 2 trials. We hypothesised that venetoclax with 10-day decitabine could have improved activity in patients with newly diagnosed AML and those with relapsed or refractory AML, particularly in high-risk subgroups. Methods This single centre, phase 2 trial was done at the University of Texas MD Anderson Cancer Center (Houston, TX, USA). The study enrolled older patients (aged >60 years) with newly diagnosed AML, not eligible for intensive chemotherapy; secondary AML (progressed after myelodysplastic syndrome or chronic myelomonocytic leukaemia); and relapsed or refractory AML. Patients were required to have an Eastern Cooperative Oncology Group (ECOG) performance status of 3 or less, white blood cell count less than 10 × 109 per L, and adequate end-organ function. Patients with favourable-risk cytogenetics (eg, t[15;17] or core-binding factor AML) or who had received previous BCL2-inhibitor therapy were excluded. Patients received decitabine 20 mg/m2 intravenously for 10 days with oral venetoclax 400 mg daily for induction, followed by decitabine for 5 days with daily venetoclax for consolidation. The primary endpoint was overall response rate. The secondary endpoints analysed within this report include safety, overall survival, and duration of response, in keeping with recommendations of European LeukemiaNet 2017 guidelines. All patients who received at least one dose of treatment were eligible for safety and response assessments. The trial was registered on ClinicalTrials.gov ( NCT03404193 ) and continues to accrue patients. Findings Between Jan 19, 2018, and Dec 16, 2019, we enrolled 168 patients; 70 (42%) had newly diagnosed AML, 15 (9%) had untreated secondary AML, 28 (17%) had treated secondary AML, and 55 (33%) had relapsed or refractory AML. The median age was 71 years (IQR 65–76) and 30% of patients had ECOG performance status of 2 or higher. The median follow-up for all patients was 16 months (95% CI 12–18; actual follow-up 6·5 months; IQR 3·4–12·4). The overall response rate was 74% (125 of 168 patients; 95% CI 67–80) and in disease subgroups were: 89% in newly diagnosed AML (62 of 70 patients; 79–94), 80% in untreated secondary AML (12 of 15 patients; 55–93), 61% in treated secondary AML (17 of 28 patients; 42–76), and 62% in relapsed or refractory AML (34 of 55 patients; 49–74). The most common treatment-emergent adverse events included infections with grades 3 or 4 neutropenia (n=79, 47%) and febrile neutropenia (n=49, 29%). 139 (83%) of 168 patients had serious adverse events, most frequently neutropenic fever (n=63, 38%), followed by pneumonia (n=17, 10%) and sepsis (n=16, 10%). The 30-day mortality for all patients was 3·6% (n=6, 95% CI 1·7–7·8). The median overall survival was 18·1 months (95% CI 10·0–not reached) in newly diagnosed AML, 7·8 months (2·9–10·7) in untreated secondary AML, 6·0 months (3·4–13·7) in treated secondary AML, and 7·8 months (5·4–13·3) relapsed or refractory AML. The median duration of response was not reached (95% CI 9·0–not reached) in newly diagnosed AML, 5·1 months (95% CI 0·9–not reached) in untreated secondary AML, not reached (95% CI 2·5–not reached) in previously treated secondary AML, and 16·8 months (95% CI 6·6–not reached) in relapsed or refractory AML. Interpretation Venetoclax with 10-day decitabine has a manageable safety profile and showed high activity in newly diagnosed AML and molecularly defined subsets of relapsed or refractory AML. Future larger and randomised studies are needed to clarify activity in high-risk subsets. Funding US National Institutes of Health and National Cancer Institute.

This essay explores historical interpretation or categorizations of Hampton Institute as a vocational project in order to reassert liberal arts as an underlying philosophical tenet of the founding and early history of this now venerated historically Black university. Today, Hampton’s educational mission and its museum are understood to be within the liberal arts tradition. This essay argues Hampton’s nineteenth-century founding ethos also situates the university and museum within the spirit of liberal arts education, even where vocational or manual labor components of its early curriculum may have been defining in early twentieth century historical interpretations of the institution’s mission and purpose. Contributions of the Hampton University Museum throughout its history give readers insight into the Hampton tradition of educating hand, heart, and mind and speak to the university’s 150-year engagement with liberal arts.

Key Points Novel RARG-CPSF6 fusion in an AML case with promyelocytic features and no evidence of PML-RARA or X-RARA fusion. Gene fusions involving RARG can initiate AML with promyelocytic morphological features.

Acute myeloid leukemia (AML) was initially subdivided according to morphology (the French-American-British system), which proved helpful in pathologic categorization. Subsequently, clinical and genomic factors were found to correlate with response to chemotherapy and with overall survival. These included a history of antecedent hematologic disease, a history of chemotherapy or radiation therapy, the presence of various recurrent cytogenetic abnormalities, and, more recently, the presence of specific point mutations. This article reviews the biology and responses of one AML subgroup with consistent response and good outcomes following chemotherapy (core-binding factor leukemia), and two subgroups with persistently bad, and even ugly, outcomes (secondary AML and TP53-mutated AML).

Mechanisms of in vivo AML response and resistance to chemotherapy remain poorly characterized. To determine whether response to lenalidomide might share features with response to other forms of chemotherapy, we applied immunohistochemistry and gene panel sequencing to serial samples from a patient

Background: DEC10-VEN is an effective regimen and offers better outcomes compared to intensive chemotherapy in older pts with newly diagnosed (ND) or relapsed/refractory (R/R) AML (Maiti. Am J Hematol 2021; Maiti. Cancer 2021). We report long term outcomes in major genomic subgroups. Methods: Pts received decitabine 20 mg/m 2 on D1-10 until CR/CRi, followed by 5-day cycles. VEN dose was 400 mg daily but held on C1D21 if D21 bone marrow (BM) had ≤5% blasts. VEN could be reduced to Concomitant TKIs included gilteritinib (18), sorafenib (13), midostaurin (5), enasidenib (3) and ponatinib (1). Eligible pts could proceed to stem cell transplantation (SCT) after response. Endpoints were defined per ELN2017. NGS targeting entire coding regions of 81 myeloid genes was performed on screening BM sample with an analytical sensitivity of 5%. Measurable residual disease (MRD) was tested by multiparametric flow cytometry (sensitivity 0.1%). Results: Between January 2018 and April 2021 we enrolled 199 pts with ND AML (n=83), untreated sAML (n=20), treated sAML (n=25), and R/R AML (n=71). Median age of treatment-naïve pts was 72 yrs (range 61-72) and of previously treated pts was 67 yrs (range 18-85, Table 1). No pts had favorable risk cytogenetics. Median no. of prior therapies in previously treated pts was 2 (range 1-8) and 24% pts (23/96) had prior SCT. 21 treatment-naïve and 20 previously treated pts underwent SCT after response. Median follow-up for all pts was 25.4 mo. Among treatment-naïve pts, CR/CRi rates were high in all mutations subgroups ranging from 70-88% in pts with NPM1mut, FLT3mut, IDH1/2mut, TP53mut, RUNX1mut, K/NRASmut. Pts with ASXL1mut had modest CR/CRi rate of 56% (Table 2). FLT3 TKI was used in 71% FLT3mut pts (n=15/21). MRD negative rate among responding pts were high across all mutational subgroups ranging from 62-91%, except 55% in pts with ASXL1mut and 50% in pts with TP53mut. Median overall survival (OS) for treatment-naïve pts with NPM1mut was not reached (NR), IDH1/2mut was 29.6 mo, FLT3mut was 24.5 mo, RUNX1mut was 16.2 mo, ASXL1mut was 15.2 mo, K/NRASmut was 12.1 mo and TP53mut was 5.4 mo (Fig 1a-b). The median relapse-free survival (RFS) among treatment-naïve pts with NPM1mut was NR, IDH1/2mut was NR, FLT3mut was 20.0 mo, RUNX1mut was 9.7 mo, ASXL1mut was 8.5 mo, K/NRASmut was 6.5 mo and TP53mut was 3.1 mo (Fig 1c-d). Among NPM1+FLT3 co-mutated pts, outcomes in treatment-naïve pts (n=26) included ORR of 96%, CR/CRi in 88%, MRD negative in 92% (22/24), median OS NR and median RFS NR. Among previously treated NPM1+FLT3 pts (n=9), ORR was 78%, CR/CRi in 56%, MRD negative in 86% (6/7), median OS 12.4 mo and median RFS 6.6 mo. Among NPM1+DNMT3A co-mutated pts, outcomes in treatment-naïve pts (n=28) included ORR of 93%, CR/CRi in 89%, MRD negative in 79% (19/24), median OS 15.2 mo and median RFS 9.0 mo. Among previously treated NPM1+DNMT3A pts (n=6), ORR was 75%, CR/CRi in 50%, MRD negative in 75% (3/4), median OS was 4.7 mo and median RFS was 5.2 mo. Among previously treated pts CR/CRi rates in pts with NPM1mut was 68%, IDH1/2mut 50%, FLT3mut 42%, RUNX1mut 45%, ASXL1mut 38%, TP53mut 30%, and K/NRASmut was 26% (Table 2). FLT3 TKI used in 95% of FLT3mut pts (n=18/19). MRD negative rate among responding pts were high for pts with NPM1mut, FLT3mut, IDH1/2mut, RUNX1mut and ASXL1mut ranging from 60-87%, but were low for pts with K/NRASmut at 56% and TP53mut at 37%. The median OS among previously treated pts with IDH1/2mut was 16.9 mo, RUNX1mut was 13.7 mo, NPM1mut was 12.4 mo, ASXL1mut was 9.0 mo, FLT3mut was 6.4 mo, K/NRASmut was 6.0 mo, and for TP53mut was 4.5 mo (Fig 1e-f). The median RFS among treatment-naïve pts with K/NRASmut was 18.9 mo, NPM1mut was 15.6 mo, IDH1/2mut was 15.3, RUNX1mut was 12.9 mo, ASXL1mut was 10.7 mo, TP53mut was 9.4 mo, and for FLT3mut was 6.6 mo (Fig 1g-h). Conclusions: DEC10-VEN offered high rates of CR/CRi, negative MRD, favorable OS and RFS across several genomic subgroups of treatment-naïve AML including NPM1, FLT3, IDH1/2 and modest outcomes in pts with these mutations in salvage setting. Outcomes in pts with TP53, RUNX1, ASXL1 and K/NRAS were suboptimal. Outcomes with FLT3 VEN HMA triplet was encouraging, particularly for frontline FLT3mut pts. Figure 1 Figure 1. Disclosures DiNardo: Novartis: Honoraria; Takeda: Honoraria; ImmuneOnc: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria, Research Funding; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Agios/Servier: Consultancy, Honoraria, Research Funding; Foghorn: Honoraria, Research Funding; AbbVie: Consultancy, Research Funding; Forma: Honoraria, Research Funding; Celgene, a Bristol Myers Squibb company: Honoraria, Research Funding. Pemmaraju: Affymetrix: Consultancy, Research Funding; Cellectis S.A. ADR: Other, Research Funding; Samus: Other, Research Funding; Blueprint Medicines: Consultancy; Celgene Corporation: Consultancy; Clearview Healthcare Partners: Consultancy; Dan's House of Hope: Membership on an entity's Board of Directors or advisory committees; Protagonist Therapeutics, Inc.: Consultancy; Aptitude Health: Consultancy; Incyte: Consultancy; Novartis Pharmaceuticals: Consultancy, Other: Research Support, Research Funding; LFB Biotechnologies: Consultancy; Stemline Therapeutics, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other, Research Funding; ASH Communications Committee: Membership on an entity's Board of Directors or advisory committees; ASCO Leukemia Advisory Panel: Membership on an entity's Board of Directors or advisory committees; HemOnc Times/Oncology Times: Membership on an entity's Board of Directors or advisory committees; Sager Strong Foundation: Other; Plexxicon: Other, Research Funding; CareDx, Inc.: Consultancy; Daiichi Sankyo, Inc.: Other, Research Funding; Springer Science + Business Media: Other; DAVA Oncology: Consultancy; Roche Diagnostics: Consultancy; MustangBio: Consultancy, Other; Abbvie Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other, Research Funding; Bristol-Myers Squibb Co.: Consultancy; ImmunoGen, Inc: Consultancy; Pacylex Pharmaceuticals: Consultancy. Daver: Amgen: Consultancy, Research Funding; Trovagene: Consultancy, Research Funding; FATE Therapeutics: Research Funding; Sevier: Consultancy, Research Funding; Astellas: Consultancy, Research Funding; Hanmi: Research Funding; Genentech: Consultancy, Research Funding; Abbvie: Consultancy, Research Funding; Gilead Sciences, Inc.: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Daiichi Sankyo: Consultancy, Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; Novimmune: Research Funding; Glycomimetics: Research Funding; Trillium: Consultancy, Research Funding; ImmunoGen: Consultancy, Research Funding; Novartis: Consultancy; Jazz Pharmaceuticals: Consultancy, Other: Data Monitoring Committee member; Dava Oncology (Arog): Consultancy; Celgene: Consultancy; Syndax: Consultancy; Shattuck Labs: Consultancy; Agios: Consultancy; Kite Pharmaceuticals: Consultancy; SOBI: Consultancy; STAR Therapeutics: Consultancy; Karyopharm: Research Funding; Newave: Research Funding. Issa: Syndax Pharmaceuticals: Research Funding; Novartis: Consultancy, Research Funding; Kura Oncology: Consultancy, Research Funding. Borthakur: Astex: Research Funding; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; University of Texas MD Anderson Cancer Center: Current Employment; Ryvu: Research Funding; Protagonist: Consultancy; Takeda: Membership on an entity's Board of Directors or advisory committees; ArgenX: Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy. Ravandi: Taiho: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Agios: Honoraria, Research Funding; Xencor: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Astex: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Prelude: Research Funding; AbbVie: Honoraria, Research Funding; AstraZeneca: Honoraria; Novartis: Honoraria; Syros Pharmaceuticals: Consultancy, Honoraria, Research Funding. Alvarado: BerGenBio: Research Funding; Jazz Pharmaceuticals: Research Funding; Sun Pharma: Consultancy, Research Funding; MEI Pharma: Research Funding; FibroGen: Research Funding; CytomX Therapeutics: Consultancy; Daiichi-Sankyo: Research Funding; Astex Pharmaceuticals: Research Funding. Kadia: BMS: Other: Grant/research support; Dalichi Sankyo: Consultancy; Cure: Speakers Bureau; Jazz: Consultancy; Liberum: Consultancy; Aglos: Consultancy; Amgen: Other: Grant/research support; Novartis: Consultancy; AbbVie: Consultancy, Other: Grant/research support; Genentech: Consultancy, Other: Grant/research support; Pfizer: Consultancy, Other; Pulmotech: Other; Sanofi-Aventis: Consultancy; Cellonkos: Other; Ascentage: Other; Genfleet: Other; Astellas: Other; AstraZeneca: Other. Jabbour: Amgen, AbbVie, Spectrum, BMS, Takeda, Pfizer, Adaptive, Genentech: Research Funding. Short: Novartis: Honoraria; Jazz Pharmaceuticals: Consultancy; NGMBio: Consultancy; Astellas: Research Funding; AstraZeneca: Consultancy; Takeda Oncology: Consultancy, Research Funding; Amgen: Consultancy, Honoraria. Jain: Adaptive Biotechnologies: Honoraria, Research Funding; Janssen: Honoraria; Aprea Therapeutics: Research Funding; Genentech: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria, Research Funding; Precision Biosciences: Honoraria, Research Funding; Fate Therapeutics: Research Funding; Servier: Honoraria, Research Funding; ADC Therapeutics: Honoraria, Research Funding; TG Therapeutics: Honoraria; Beigene: Honoraria; Incyte: Research Funding; Cellectis: Honoraria, Research Funding; Pfizer: Research Funding; AstraZeneca: Honoraria, Research Funding; Pharmacyclics: Research Funding; AbbVie: Honoraria, Research Funding. Wierda: Juno Therapeutics: Research Funding; KITE Pharma: Research Funding; Pharmacyclics LLC, an AbbVie Company: Research Funding; Cyclacel: Research Funding; Loxo Oncology, Inc.: Research Funding; Acerta Pharma Inc.: Research Funding; Genzyme Corporation: Consultancy; Miragen: Research Funding; Oncternal Therapeutics, Inc.: Research Funding; Sunesis: Research Funding; GSK/Novartis: Research Funding; Genentech: Research Funding; Gilead Sciences: Research Funding; Xencor: Research Funding; Janssen: Research Funding; Karyopharm: Research Funding; AbbVie: Research Funding; AstraZeneca: Research Funding. Sasaki: Daiichi-Sankyo: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Research Funding; Pfizer: Membership on an entity's Board of Directors or advisory committees. Takahashi: GSK: Consultancy; Celgene/BMS: Consultancy; Symbio Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy. Yilmaz: Daiichi-Sankyo: Research Funding; Pfizer: Research Funding. Burger: Beigene: Research Funding, Speakers Bureau; Pharmacyclics LLC: Consultancy, Other: Travel/Accommodations/Expenses, Research Funding, Speakers Bureau; Gilead: Consultancy, Other: Travel/Accommodations/Expenses, Research Funding, Speakers Bureau; TG Therapeutics: Other: Travel/Accommodations/Expenses, Research Funding, Speakers Bureau; AstraZeneca: Consultancy; Novartis: Other: Travel/Accommodations/Expenses, Speakers Bureau; Janssen: Consultancy, Other: Travel/Accommodations/Expenses, Speakers Bureau. Verstovsek: Incyte Corporation: Consultancy, Research Funding; PharmaEssentia: Research Funding; Promedior: Research Funding; AstraZeneca: Research Funding; NS Pharma: Research Funding; Ital Pharma: Research Funding; Celgene: Consultancy, Research Funding; Protagonist Therapeutics: Research Funding; Roche: Research Funding; Sierra Oncology: Consultancy, Research Funding; Gilead: Research Funding; Genentech: Research Funding; CTI BioPharma: Research Funding; Blueprint Medicines Corp: Research Funding; Novartis: Consultancy, Research Funding; Constellation: Consultancy; Pragmatist: Consultancy. Andreeff: Karyopharm: Research Funding; Syndax: Consultancy; Medicxi: Consultancy; Oxford Biomedica UK: Research Funding; Amgen: Research Funding; ONO Pharmaceuticals: Research Funding; Glycomimetics: Consultancy; Novartis, Cancer UK; Leukemia & Lymphoma Society (LLS), German Research Council; NCI-RDCRN (Rare Disease Clin Network), CLL Foundation; Novartis: Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Consultancy, Research Funding; Breast Cancer Research Foundation: Research Funding; Aptose: Consultancy; Senti-Bio: Consultancy; AstraZeneca: Research Funding; Reata, Aptose, Eutropics, SentiBio; Chimerix, Oncolyze: Current holder of individual stocks in a privately-held company. Bose: CTI BioPharma: Honoraria, Research Funding; Incyte Corporation: Honoraria, Research Funding; Astellas: Research Funding; Kartos Therapeutics: Honoraria, Research Funding; Sierra Oncology: Honoraria; NS Pharma: Research Funding; Celgene Corporation: Honoraria, Research Funding; BMS: Honoraria, Research Funding; Blueprint Medicines: Honoraria, Research Funding; Novartis: Honoraria; Constellation Pharmaceuticals: Research Funding; Pfizer: Research Funding; Promedior: Research Funding. Ferrajoli: BeiGene: Other: Advisory Board, Research Funding; Janssen: Other: Advisory Board ; AstraZeneca: Other: Advisory Board, Research Funding. Thompson: Gilead: Other: Institution: Advisory/Consultancy, Honoraria; Janssen: Consultancy, Honoraria; AbbVie: Other: Institution: Advisory/Consultancy, Honoraria, Research Grant/Funding; Pharmacyclics: Other: Institution: Advisory/Consultancy, Honoraria, Research Grant/Funding; Adaptive Biotechnologies: Other: Institution: Advisory/Consultancy, Honoraria, Research Grant/Funding, Expert Testimony; Genentech: Other: Institution: Advisory/Consultancy, Honoraria, Research Grant/Funding; Amgen: Other: Institution: Honoraria, Research Grant/Funding. Welch: Janssen: Research Funding; Notable Labs: Research Funding. Kantarjian: Ipsen Pharmaceuticals: Honoraria; Immunogen: Research Funding; Pfizer: Honoraria, Research Funding; Aptitude Health: Honoraria; Jazz: Research Funding; NOVA Research: Honoraria; KAHR Medical Ltd: Honoraria; Astellas Health: Honoraria; Daiichi-Sankyo: Research Funding; BMS: Research Funding; AbbVie: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Astra Zeneca: Honoraria; Amgen: Honoraria, Research Funding; Ascentage: Research Funding; Precision Biosciences: Honoraria; Taiho Pharmaceutical Canada: Honoraria. Konopleva: Ablynx: Other: grant support, Research Funding; Agios: Other: grant support, Research Funding; Rafael Pharmaceuticals: Other: grant support, Research Funding; AbbVie: Consultancy, Honoraria, Other: Grant Support, Research Funding; AstraZeneca: Other: grant support, Research Funding; Reata Pharmaceuticals: Current holder of stock options in a privately-held company, Patents & Royalties: intellectual property rights; Ascentage: Other: grant support, Research Funding; Calithera: Other: grant support, Research Funding; Forty Seven: Other: grant support, Research Funding; F. Hoffmann-La Roche: Consultancy, Honoraria, Other: grant support; Cellectis: Other: grant support; KisoJi: Research Funding; Genentech: Consultancy, Honoraria, Other: grant support, Research Funding; Novartis: Other: research funding pending, Patents & Royalties: intellectual property rights; Eli Lilly: Patents & Royalties: intellectual property rights, Research Funding; Sanofi: Other: grant support, Research Funding; Stemline Therapeutics: Research Funding. OffLabel Disclosure: Off-label use - venetoclax in relapsed/refractory AML

Background: A normal karyotype is the most common cytogenetic finding in acute myeloid leukemia cells ("NK-AML") and has highly variable and difficult to predict outcomes at presentation. Refinements introduced with the ELN 2017 Criteria (presence or absence of mutations in NPM1, FLT3-ITD, and/or biallelic CEBPA mutations) have improved--but not completely solved--up-front risk classification. NK-AML patients with very long first remissions after chemotherapy only are rare, and their genetic and epigenetic characteristics have not yet been definitively evaluated, but could potentially provide clues regarding determinants that affect chemotherapy responses. Results: Using exome sequencing, RNA-sequencing, and functional studies, we performed an in-depth characterization of 28 de novo adult NK-AML patients with >5 year, Long First Remissions (LFR) after chemotherapy only (7+3 with HiDAC consolidation). As comparators, we studied a well-matched group of 31 NK-AML patients who relapsed within 2 years (Standard First Remissions, SFR). None of the patients in either group received an allogeneic transplant in first remission. Bulk RNA sequencing and targeted investigation of cell type proportions and pathways expected to be relevant for chemotherapy sensitivity (i.e. cell cycle, DNA repair, or AraC responsiveness) revealed no significant differences between LFR and SFR AML samples. However, single cell RNA sequencing (sc-RNAseq) analyses of genetically-defined AML cells from 8 LFR and 7 SFR cases showed that SFR AML cells expressed significantly higher levels of stem cell markers, and of several immunomodulatory genes (MHC class II, CD200, MRC1). Combined sc-RNAseq and flow cytometry analyses of the AML bone marrow samples from LFR patients revealed well-preserved CD4 and CD8 populations that responded robustly to TCR-mediated activation, achieved through CD3/28 bead stimulation. In contrast, SFR AML marrows had reduced numbers of immune cells (particularly of CD4 Th1 cells) and their residual T cells expressed an exhaustion signature. TCR-mediated T cell activation was blocked in the SFR samples by the presence of the AML cells in the bone marrow samples: removing the AML cells released this blockade. Evaluation of T cell immune checkpoints and their putative ligands revealed LAG3 to be a leading candidate for immune suppression, because of its high expression in SFR T cells, and because the genes encoding its major ligands (MHC Class II) were highly expressed in SFR AML cells. Indeed, blocking the inhibitory receptor LAG-3 was able to reverse the AML cell-mediated T cell suppression of most SFR cases. To validate and extend these findings, we performed the T cell activation assay in an independent cohort of 50 AML cases representing all ELN risk groups. The ability of marrow derived CD4+ T cells to activate correlated strongly with ELN groups. Importantly, for the ELN intermediate patients, the immune activation assay stratified these patients in 2 groups with very different relapse free survival (RFS): the T cell "activators" had an RFS of 1200 days, while the "non-activators" had RFS of 146 days (Mantel-Cox Log-rank = 0.02). A multivariate analysis of covariates at diagnosis, including sex, age, ELN risk category, WBC count, bone marrow blast count at presentation, and mutation status (for DNMT3A, NPM1, FLT3, NRAS, WT1, TET2, CEBPA, PTPN11, IDH1, IDH2, RUNX1, RAD21, SMC1A, and SRSF2) identified none that were predictive of CD4 T cell activation status at presentation. Conclusions: These data strongly suggest that most AML cases have an immunosuppressive phenotype at presentation, mediated by inhibitory T cell receptors (e.g. LAG3) via ligands that are expressed by AML cells (e.g. MHC Class II proteins). The absence of this immunosuppressive phenotype was strongly correlated with favorable clinical outcomes with standard chemotherapy. The ability of CD4 T cells to be activated via the TCR in the presence of AML cells at presentation (which indirectly measures AML cell-mediated immunosuppression) is a novel biomarker for risk assessment that is currently not captured by any other well-recognized covariate (especially for ELN intermediate risk cases), and should be further evaluated for its predictive potential in prospective clinical trials. Disclosures Eisfeld: Karyopharm (spouse): Current Employment. Retting: BioLineRx Ltd.: Research Funding. Uy: GlaxoSmithKline: Consultancy; Agios: Consultancy; Novartis: Consultancy; Genentech: Consultancy; AbbVie: Consultancy; Macrogenics: Research Funding; Astellas: Honoraria, Speakers Bureau; Jazz: Consultancy. Spencer: Wugen, Inc.: Consultancy, Other: Stock options.