Precision Medicine In Acute Myeloid Leukemia Research Articles

Immune-based subgroups uncover diverse tumor immunogenicity and implications for prognosis and precision therapy in acute myeloid leukemia

BackgroundAlthough a considerable proportion of acute myeloid leukemia (AML) patients achieve remission through chemotherapy, relapse remains a recurring and significant event leading to treatment failure. This study aims to investigate the immune landscape in AML and its potential implications for prognosis and chemo-/immune-therapy.MethodsIntegrated analyses based on multiple sequencing datasets of AML were performed. Various algorithms estimated immune infiltration in AML samples. A subgroup prediction model was developed, and comprehensive bioinformatics and machine learning algorithms were applied to compare immune-based subgroups in relation to clinical features, mutational landscapes, immune characterizations, drug sensitivities, and cellular hierarchies at the single-cell level.ResultsTwo immune-based AML subgroups, G1 and G2, were identified. G1 demonstrated higher immune infiltration, a more monocytic phenotype, increased proportions of monocytes/macrophages, and higher FLT3, DNMT3A, and NPM1 mutation frequencies. It was associated with a poorer prognosis, lower proportions of various immune cell types and a lower T cell infiltration score (TIS). AML T-cell-based immunotherapy target antigens, including CLEC12A, Folate receptor β, IL1RAP and TIM3, showed higher expression levels in G1, while CD117, CD244, CD96, WT and TERT exhibited higher expression levels in G2. G1 samples demonstrated higher sensitivity to elesclomol and panobinostat but increased resistance to venetoclax compared to G2 samples. Moreover, we observed a positive correlation between sample immune infiltration and sample resistance to elesclomol and panobinostat, whereas a negative correlation was found with venetoclax resistance.ConclusionOur study enriches the current AML risk stratification and provides guidance for precision medicine in AML.

Recent advances in precision medicine for acute myeloid leukemia.

Acute myeloid leukemia (AML) is a heterogeneous disease, in which treatment response and patient survival are highly conditioned by the leukemia biology. The aim of this review is to summarize recent advances in AML classification, risk stratification models, measurable residual disease (MRD) and the increasing number of treatment options that are paving the way towards precision medicine in AML. AML classification and risk stratification were recently updated by incorporating novel molecular markers that are important for diagnosis and outcome prediction. In addition, the impact of co-mutational patterns is under investigation and novel approaches using machine learning algorithms are starting to be used for individualized risk estimation. Molecular markers are also becoming useful in predicting response to non-intensive treatments. MRD informs of treatment response with high sensitivity, allowing dynamic patient risk assessment and early intervention. Finally, important advances were made in AML therapy, with an increasing number of targeted therapies becoming available and many novel treatment approaches being under development with promising early results. A better understanding of AML biology is leading to improved risk stratification and important advances in treatments, which are allowing the development of precision medicine in AML at an unprecedented pace.

A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia.

The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising therapies entering clinical translation, yet patient responses remain heterogeneous, and biomarkers for tailoring treatment are lacking. To understand how disease heterogeneity links with therapy response, we determined the leukemia cell hierarchy makeup from bulk transcriptomes of more than 1,000 patients through deconvolution using single-cell reference profiles of leukemia stem, progenitor and mature cell types. Leukemia hierarchy composition was associated with functional, genomic and clinical properties and converged into four overall classes, spanning Primitive, Mature, GMP and Intermediate. Critically, variation in hierarchy composition along the Primitive versus GMP or Primitive versus Mature axes were associated with response to chemotherapy or drug sensitivity profiles of targeted therapies, respectively. A seven-gene biomarker derived from the Primitive versus Mature axis was associated with response to 105 investigational drugs. Cellular hierarchy composition constitutes a novel framework for understanding disease biology and advancing precision medicine in AML.

Long noncoding RNAs: A novel insight in the leukemogenesis and drug resistance in acute myeloid leukemia.

Acute myeloid leukemia (AML) is a common hematological disorder with heterogeneous nature that resulted from blocked myeloid differentiation and an enhanced number of immature myeloid progenitors. During several decades, different factors, including cytogenetic, genetic, and epigenetic have been reported to contribute to the pathogenesis of AML by inhibiting the differentiation and ensuring the proliferation of myeloid blast cells. Recently, long noncoding RNAs (lncRNAs) have been considered as potential diagnostic, therapeutic, and prognostic factors in different human malignancies including AML. Altered expression of lncRNAs is correlated with the transformation of hematopoietic stem and progenitor cells into leukemic blast cells because of their distinct role in the key cellular processes. We discuss the significant role of lncRNAs in the proliferation, survival, differentiation, leukemic stem cells in AML and their involvement in different molecular pathways (insulin-like growth factor type I receptor, FLT3, c-KIT, Wnt, phosphatidylinositol 3-kinase/protein kinase-B, microRNAs), and associated mechanisms such as autophagy, apoptosis, and glucose metabolism. In addition, we aim to highlight the role of lncRNAs as reliable biomarkers for diagnosis, prognosis, and drug resistance for precision medicine in AML.

Precision medicine in acute myeloid leukemia: where are we now and what does the future hold?

ABSTRACT Introduction Precision medicine has revolutionized the diagnostic and therapeutic management of acute myeloid leukemia (AML), from standardized schemes based on chemotherapy to tailored approaches according to molecular and genetic profile and targeted therapy. Areas covered The main topics of precision medicine in AML were reviewed in MEDLINE, EMBASE, and Cochrane Central Register databases, and future directions in this therapeutic area were addressed. This review included targeted therapies, drug-sensitivity tests and predictive biomarkers, and genetic studies employing pharmacogenetic and deep sequencing strategies. Expert opinion Precision medicine has opened the door to personalized therapy for specific AML patient populations with promising results. Several targeted therapies have been approved or are being tested for specific mutations (i.e. FLT3, IDH, BCL-2, TP53), obtaining improvements in clinical outcomes and less toxicity as compared with intensive treatment, allowing potential combination therapy. Ongoing trials and real data will establish the role of these molecules in monotherapy or combined in different AML settings (front-line, relapsed/refractory, or post-transplant). Experience in drug-sensitivity predictors and pharmacogenetic biomarkers is encouraging and could be useful tools in the next years, but we need a better understanding of AML biology and pathogenesis as well as confirmatory studies to demonstrate the utility in clinical practice.

Targeting PI3K/Akt/mTOR in AML: Rationale and Clinical Evidence.

Acute myeloid leukemia (AML) is a highly heterogeneous hematopoietic malignancy characterized by excessive proliferation and accumulation of immature myeloid blasts in the bone marrow. AML has a very poor 5-year survival rate of just 16% in the UK; hence, more efficacious, tolerable, and targeted therapy is required. Persistent leukemia stem cell (LSC) populations underlie patient relapse and development of resistance to therapy. Identification of critical oncogenic signaling pathways in AML LSC may provide new avenues for novel therapeutic strategies. The phosphatidylinositol-3-kinase (PI3K)/Akt and the mammalian target of rapamycin (mTOR) signaling pathway, is often hyperactivated in AML, required to sustain the oncogenic potential of LSCs. Growing evidence suggests that targeting key components of this pathway may represent an effective treatment to kill AML LSCs. Despite this, accruing significant body of scientific knowledge, PI3K/Akt/mTOR inhibitors have not translated into clinical practice. In this article, we review the laboratory-based evidence of the critical role of PI3K/Akt/mTOR pathway in AML, and outcomes from current clinical studies using PI3K/Akt/mTOR inhibitors. Based on these results, we discuss the putative mechanisms of resistance to PI3K/Akt/mTOR inhibition, offering rationale for potential candidate combination therapies incorporating PI3K/Akt/mTOR inhibitors for precision medicine in AML.

A precision medicine approach to management of acute myeloid leukemia in older adults.

Therapy selection in older adults with acute myeloid leukemia (AML) can be challenging because of a higher incidence of high-risk cytogenetic and molecular features conferring chemoresistance and poor functional status leading to increased treatment-related toxicities. The purpose of this review is to highlight the recent advances in precision medicine in AML that have shown promise to improve outcomes of older adults. The utilization of next generation sequencing to identify and target actionable mutations can influence therapy selection in one-third of patients and can result in higher response rates as well as survival compared with those who do not receive targeted therapy. Oral targeted agents are available for AML with IDH 1, IDH2, or FLT3 mutations. Low-intensity venetoclax-based regimens have shown high rates of responses in AML, particularly among those with NPM1 and IDH2 mutations; responses are often durable and associated with minimal residual disease (MRD) negativity. Multiple studies have demonstrated the prognostic significance of flow cytometric MRD, with potential implications for subsequent therapy. Novel approaches for AML risk-stratification, MRD assessment, and a precision medicine approach offer significant promise to improve survival and quality of life of older adults.

Evaluating ivosidenib for the treatment of relapsed/refractory AML: design, development, and place in therapy

Improvements in the last decade in understanding the molecular mechanisms underlying acute myeloid leukemia (AML) have emphasized that treatment regimens should be personalized with agents that can selectively target genetic abnormalities if present. Neomorphic mutations in isoform 1 of isocitrate dehydrogenase (IDH1) result in the formation of the onco-metabolite R-2-hydroxyglutarate, which drives leukemic transformation by affecting processes such as chromatin remodeling, the cellular defense against oxidative stress and cell survival. Preclinical studies with small molecule inhibitors have validated mutant IDH1 as a molecular target, and a recent Phase 1 clinical trial with the first mutant IDH1 inhibitor ivosidenib has prompted approval by the US Food and Drug Association for the treatment of patients with IDH1-mutated AML in the relapsed and refractory setting due to impressive results. This approval has given a group of patients, that otherwise has a very poor prognosis and limited options, new hope, and it is to be expected that more indications for ivosidenib will follow soon. These developments highlight the potential of precision medicine in AML, with more agents currently under evaluation in clinical trials. Although the first reports have also already emerged describing acquired resistance for these mutant IDH inhibitors, combination treatment might overcome this problem, which could drastically change the treatment landscape of AML over the next few years.

UTX and MBD3 Epistasis Regulates Rac Gtpase Activation and Sensitizes Human Acute Myeloid Leukemia Cells to Dock Inhibition

Transcriptional plasticity is an evolving phenomenon in cancer biology. Mutational profiling alone may not suffice to dissect transcriptional dependency and underlying epigenetic vulnerabilities in tumorigenesis. Histone 3 lysine 27 (H3K27) demethylases (UTX, UTY and JMJD3) critically regulate transcriptional architecture. Recently it has been demonstrated that Utx (Kdm6a) plays tumor suppressor role in myeloid leukemogenesis through noncatalytic activity (Gozdecka M, et al., Nat Genet, 2018). Conditional (Mx1-Cre) deletion of Utx caused development of acute myeloid leukemia (AML) in ~ 60% of the mice; wherein, only Utx-/-, but not Utx+/-, aged (22 months) mice presented with AML. Paradoxically, previous report suggested that Utx conditional (Vav1-Cre) knock out male/female mice did not develop leukemia over 18 months (Tian, L., et al., Blood, 2015). In our recent report we have identified that expression of UTX is significantly increased in human primary AML, and pharmacological inhibition of H3K27 demethylase catalytic activity attenuated survival of AML cells (Boila L.D. et al,. Exp Hematol, 2017). Therefore the contribution of UTX in AML pathogenesis remains context dependent, and probably contentious, and warrants further investigations.ATP-dependent chromatin remodelers have been implicated in AML pathobiology (Chatterjee S.S., et al., Mol Cancer Res, 2018). We reported that loss of MBD3, a scaffold of NuRD chromatin remodeler, in human primary AML cells associates with nucleation of leukemic NuRD (Biswas M et al., Blood, 2017). Loss of Mbd3(Vav1-Cre) has been shown to disrupt NuRD complex integrity and causes T-cell lymphoma, suggesting tissue-specific function of NuRD (Loughran, S.J., et al., J Exp Med, 2017). Interestingly, in our present study we have identified for the first time that endogenous UTX, but not JMJD3, reversibly co-immunoprecipitates with NuRD in AML cells. These findings led us to test the hypothesis whether UTX would participate with NuRD in AML. ChIP-seq analysis in AML blasts using antibodies against UTX and CHD4 (intact ATPase component of leukemic NuRD) along with H3K27ac identified the co-localized genes. ChIP-qPCR, transcriptome, pathway analysis (P<0.001) performed in paired AML, and MBD3loss of function experiments suggested an enrichment of Dedicator of Cytokinesis (DOCK) transcripts as bona fide effectors of UTX and NuRD in AML.DOCK proteins are conserved atypical guanine nucleotide exchange factors (GEFs) for Rho GTPase activation, regulating cell motility and invasion. Earlier we had shown that small GTPases regulate myeloid leukemia cell engraftment, survival in vivo (Sengupta A et al., Blood, 2010). DOCK1 upregulation is associated with a poor prognosis in AML (Hwei, L.S., Blood, 2016). TCGA cross-cancer analysis showed that UTX is maximally expressed, whereas MBD3 is downregulated in AML among all cancer types. Consistent with this observation, DOCK expression was significantly (P<0.001) increased in MBD3loUTXhi AML cohort compared to MBD3hiUTXlo AML. Importantly, MBD3loUTXhi patients have relatively poor survival compared to MBD3hiUTXhi individuals, indicating that a combination of high UTX and low MBD3 expression could be a marker of poor prognosis in AML.Mechanistically, MBD3 deficiency caused loss of HDAC1 occupancy with a corresponding increase in UTX, CBP and H3K27ac on target DOCK loci leading to de-repression of gene expression. In agreement with this finding, loss of MBD3 resulted in ~ 2-fold increase in active Rac GTP and promoted AML cell migration to CXCL12. Interestingly, UTX silencing opposed DOCK expression, Rac activation and reversed hyper-migratory phenotype of MBD3-deficient AML cells. Together, these data account for UTX and MBD3 epistasis in regulating DOCK-Rac signalling in AML. Finally, treatment with DOCK inhibitor CPYPP dramatically inhibited survival of AML cells while having minimal effect on the survival of normal CD34+ cells. In unison, our findings highlight UTX as a putative oncogene in conjunction with leukemic NuRDand posit DOCK proteins as an important target of UTX-NuRD axis in human AML cells.To conclude, we provide evidence for MBD3-deficient NuRD in leukemia pathobiology, and inform a novel epistasis between UTX and NuRD towards maintenance of oncogenic gene expression in AML, and rationalize DOCK inhibition as a novel therapeutic modality for precision medicine in AML. DisclosuresNo relevant conflicts of interest to declare.

Proof-Of-Concept Study For Precision Medicine With Chromosome Genomic Array Testing (CGAT) For Drug Sensitivity Screening In Acute Myeloid Leukemia

Tremendous heterogeneity in acute myeloid leukemia (AML) poses a significant challenge to clinical management and effective therapy. Cytogenetics is one of the key prognostic factors for AML. New technologies, such as chromosome genomic array testing (CGAT) combining both SNP-based and non-SNP based array CGH, have allowed informative genomic profiling of chromosome abnormalities with very high resolution. Yet it remains unclear how these unique CGAT-identified clonal aberrations impact the outcome of AML patients and how they predict a patient's response to a specific medication. In this proof-of-concept study, we aim to explore the correlation of genomic abnormalities identified by CGAT with in vitrodrug sensitivity data from 30 AML patients and their clinical responses.We performed CGAT on the pre-treatment bone marrow of these AML patients using CytoScanHD, which includes 2.5 million markers, 750K of which are SNP markers. Copy number aberrations (CNA) and copy-neutral loss of heterozygosity (cnLOH) were analyzed by ChAS and Nexus software. CGAT abnormalities were enumerated based on chromosome arms affected; i.e., multiple segmental CNAs and cnLOH on the same chromosome arm were counted as one aberration. Patients' response to chemotherapy and clinical relapse were tracked. Drug sensitivity for individual patient leukemia blast samples was measured by a high-throughput in vitroassay consisting of a panel of 160 drugs, of which 45 are FDA approved and 115 investigational. Cell survival was measured by Cell Titer Glo, and data curves for 8 concentrations of each drug were generated to derive EC50 and IC50 values. Statistical correlation was analyzed by Fisher's exact test, Cox regression, and regression analysis.CGAT detected all the chromosome abnormalities identified by cytogenetics except truly balanced translocations. CGAT also identified clonal aberrations in 7 of the 13 patients with normal cytogenetics. Of the 6 uniquely CGAT abnormal patients, 3 demonstrated cnLOH only and 2 CNA only. Overall, CGAT showed 11 complex karyotypes (CK, defined as >=3 aberrations; high-risk) and 19 normal or simple abnormal cases (low/intermediate-risk), as compared to the cytogenetics classification of 9 poor-risk, 15 intermediate-risk, and 6 low-risk karyotypes. cnLOH was detected in 9 patients (30%). Complete remission (CR) rate after the first induction course in the CGAT CK group was 18% versus 68% in the non-CK group (P=0.02). There was a very high concordance (90%) between CGAT risk based on CK and conventional cytogenetics. And when cytogenetics and CGAT disagree, as for the 2 patients who had normal cytogenetics but CGAT CK, CGAT risk stratification appeared better as neither patient achieved CR. CR duration longer than 1 year occurred more (P=0.04) in the CGAT normal patients (50%) than in the CGAT abnormal patients (8.3%). Among those who achieved CR, the hazard of relapse (HR) for CGAT CK patients was 9.9 (CI: 1.6-61; P=0.02); HR for cnLOH patients was 7.1 (CI: 1.2-43; P=0.03). Considering the total aberrations (median 1.5, range 0-16), the HR for relapse among CR patients was 1.3 (CI: 1.1-1.5; P=0.01) per aberration. Six of the 48 drugs that exhibited cytotoxicity in the in vitro assay, including clofarabine (r=0.45, P=0.01) and PKI-587 (dual PI3K/mTOR inhibitor) (r=0.48, P=0.008), showed significant correlation between CGAT aberrations and EC50; i.e, the more CGAT aberrations, the higher concentration is required for a given drug to kill these CGAT-abnormal leukemic cells in vitro.In conclusion, CGAT increased the diagnostic yield by 54% among AML patients with normal cytogenetics and altered the overall risk classification by 6.7%. Complex karyotype identified by CGAT carried the same poor prognostic effect as CK by cytogenetics. Although abnormal CGAT results did not appear to predict response, increasing CGAT abnormalities are associated with early relapse, as is the presence of cnLOH. Genomic complexity detected by CGAT appeared to associate with dosage-dependent resistance to selected drugs by in vitro drug sensitivity analyses. Characterization of prognostic effect and drug response associated with each type of CGAT abnormalities will require a larger data set. Nevertheless, this study demonstrated the clinical utility of CGAT for precision medicine in AML. Disclosures:Becker:Affymetrix: Research Funding.