bims-tremyl 2020-11-01 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2020–11–01
thirty papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Clinical characteristics and outcomes in patients with acute myeloid leukemia with concurrent FLT3-ITD and IDH mutations.
Mutant Isocitrate Dehydrogenase 1 Inhibitor Ivosidenib in Combination With Azacitidine for Newly Diagnosed Acute Myeloid Leukemia.
Precision medicine treatment in acute myeloid leukemia using prospective genomic profiling: feasibility and preliminary efficacy of the Beat AML Master Trial.
Venetoclax with azacitidine or decitabine in patients with newly diagnosed acute myeloid leukemia: long term follow-up from a Phase 1b study.
Single-cell mutation analysis of clonal evolution in myeloid malignancies.
Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia.
Extinguishing the Embers: Targeting AML Metabolism.
New directions for emerging therapies in acute myeloid leukemia: the next chapter.
Acute myeloid leukemia-induced remodeling of the human bone marrow niche predicts clinical outcome.
Profiling of Metabolic Differences between Hematopoietic Stem Cells and Acute/Chronic Myeloid Leukemia.
Combined Expression of CD34 and FLT3-Internal Tandem Duplication Mutation Predicts Poor Response to Treatment in Acute Myeloid Leukemia.
FLT3-ITD and CD135 Over-Expression are Frequent Findings of Poor Survival in Adult Patients With Acute Leukemias.
The IL1-IL1RAP axis plays an important role in the inflammatory leukemic niche that favors acute myeloid leukemia proliferation over normal hematopoiesis.
Emerging epigenetic therapeutics for myeloid leukemia: modulating demethylase activity with ascorbate.
Detection of residual disease in chronic myeloid leukemia utilizing genomic next generation sequencing reveals persistence of differentiated Ph+ B cells but not bone marrow stem/progenitors.
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity.
Cancer therapy shapes the fitness landscape of clonal hematopoiesis.
Systemic mastocytosis with acute myeloid leukemia occurs from mutually exclusive clones expressing KITD816V and FLT3-ITD.
ANGPTL2-containing small extracellular vesicles from vascular endothelial cells accelerate leukemia progression.
Metabolic reprogramming of donor T cells enhances graft-versus-leukemia effects in mice and humans.
Outcome of patients with IDH1/2-mutated post-myeloproliferative neoplasm AML in the era of IDH inhibitors.
Phase 2 study of ruxolitinib and decitabine in patients with myeloproliferative neoplasm in accelerated and blast phase.
New strategies to treat AML: novel insights into AML survival pathways and combination therapies.
Integrated analysis of patient samples identifies biomarkers for venetoclax efficacy and combination strategies in acute myeloid leukemia.
Detection of Pathogenic Isoforms of IKZF1 in Leukemic Cell Lines and Acute Lymphoblastic Leukemia Samples: Identification of a Novel Truncated IKZF1 Transcript in SUP-B15.
Acute myeloid leukemia with mutated NPM1 mimics acute promyelocytic leukemia presentation.
In Vitro Recapitulation of Murine Thymopoiesis from Single Hematopoietic Stem Cells.
New Drug for Chronic Myeloid Leukemia Might Stimulate the Market.
Oligomonocytic and overt chronic myelomonocytic leukemia show similar clinical, genomic, and immunophenotypic features.
Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes.

Cancer. 2020 Oct 29.

Clinical characteristics and outcomes in patients with acute myeloid leukemia with concurrent FLT3-ITD and IDH mutations.

Mahran Shoukier, Tapan Kadia, Marina Konopleva, Ahmad S Alotaibi, Mansour Alfayez, Sanam Loghavi, Keyur P Patel, Rashmi Kanagal-Shamanna, Jorge Cortes, Bachar Samra, Elias Jabbour, Guillermo Garcia-Manero, Koichi Takahashi, Sherry Pierce, Nicholas J Short, Musa Yilmaz, Koji Sasaki, Lucia Masarova, Naveen Pemmaraju, Gautam Borthakur, Hagop M Kantarjian, Farhad Ravandi, Courtney D DiNardo, Naval Daver.

   BACKGROUND: Isocitrate dehydrogenase (IDH1 and IDH2) mutations commonly co-occur with FMS-like tyrosine kinase 3 (FLT3) mutations in patients with acute myeloid leukemia (AML).
METHODS: The authors reviewed cases of patients with FLT3-internal tandem duplication (FLT3-ITD)-mutated AML with concurrent IDH mutations diagnosed between January 2011 and December 2018.
RESULTS: A total of 91 patients with FLT3-ITD and IDH1 or IDH2 "double-mutated" AML were identified; 36 patients had concurrent FLT3-ITD/IDH1 mutations (18 in the frontline and 18 in the recurrent and/or refractory [R/R] setting) and 55 patients had concurrent FLT3-ITD/IDH2 mutations (37 in the frontline and 18 in the R/R setting). FLT3 and/or IDH inhibitors (FLT3Is and/or IDHIs) were given as a single agent or in combination with cytotoxic chemotherapy (CCT) or low-intensity therapy (LIT). Rates of complete remission (CR) plus CR with incomplete count recovery (CRi) with the use of CCT and FLT3Is were 100% and 64%, respectively, in patients in the frontline and R/R settings. CCT with IDHIs was given in 2 frontline patients and both achieved a CR. LIT with FLT3Is in the frontline and R/R settings demonstrated CR and CRi rates of 67% and 28%, respectively. Single-agent FLT3Is and IDHIs demonstrated limited activity with a CR and/or CRi rate of 14% in patients with disease in the R/R setting.
CONCLUSIONS: The combination of FLT3I-based therapy with CCT or LIT appeared to be effective in both the frontline and R/R settings among patients with FLT3-ITD/IDH co-mutated disease. Fewer patients with double-mutated disease received CCT or LIT with IDH1/2 inhibitor in the frontline setting; however, high response rates also were noted with this approach.
LAY SUMMARY: The prognostic influence of FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) and isocitrate dehydrogenase (IDH) co-mutation status on outcomes in patients with acute myeloid leukemia receiving an FLT3 inhibitor, non-FLT3/IDH inhibitor-based regimens, or an IDH inhibitor is unclear. This is an important clinical question because multiple targeted therapies for FLT3 and IDH1/2 mutations have become available. The results of the current study demonstrated that a combination of a FLT3 inhibitor with cytotoxic chemotherapy or low-intensity therapy appears to be an effective approach in patients with FLT3-ITD/IDH co-mutated disease in both the frontline and recurrent and/or refractory settings. Fewer dual-mutated patients received cytotoxic chemotherapy or low-intensity therapy with an IDH1/2 inhibitor in the frontline setting; however, excellent responses also were observed with this approach.

Keywords:  FLT3 and/or IDH inhibitors; FMS-like tyrosine kinase 3 (FLT3) with the internal tandem duplication (ITD) mutation; acute myeloid leukemia; isocitrate dehydrogenase (IDH) mutations

DOI:  https://doi.org/10.1002/cncr.33293
J Clin Oncol. 2020 Oct 29. JCO2001632

Mutant Isocitrate Dehydrogenase 1 Inhibitor Ivosidenib in Combination With Azacitidine for Newly Diagnosed Acute Myeloid Leukemia.

Courtney D DiNardo, Anthony S Stein, Eytan M Stein, Amir T Fathi, Olga Frankfurt, Andre C Schuh, Hartmut Döhner, Giovanni Martinelli, Prapti A Patel, Emmanuel Raffoux, Peter Tan, Amer M Zeidan, Stéphane de Botton, Hagop M Kantarjian, Richard M Stone, Mark G Frattini, Frederik Lersch, Jing Gong, Diego A Gianolio, Vickie Zhang, Aleksandra Franovic, Bin Fan, Meredith Goldwasser, Scott Daigle, Sung Choe, Bin Wu, Thomas Winkler, Paresh Vyas.

PURPOSE: Ivosidenib is an oral inhibitor of the mutant isocitrate dehydrogenase 1 (IDH1) enzyme, approved for treatment of IDH1-mutant (mIDH1) acute myeloid leukemia (AML). Preclinical work suggested that addition of azacitidine to ivosidenib enhances mIDH1 inhibition-related differentiation and apoptosis.
PATIENTS AND METHODS: This was an open-label, multicenter, phase Ib trial comprising dose-finding and expansion stages to evaluate safety and efficacy of combining oral ivosidenib 500 mg once daily continuously with subcutaneous azacitidine 75 mg/m2 on days 1-7 in 28-day cycles in patients with newly diagnosed mIDH1 AML ineligible for intensive induction chemotherapy (ClinicalTrials.gov identifier: NCT02677922).
RESULTS: Twenty-three patients received ivosidenib plus azacitidine (median age, 76 years; range, 61-88 years). Treatment-related grade ≥ 3 adverse events occurring in > 10% of patients were neutropenia (22%), anemia (13%), thrombocytopenia (13%), and electrocardiogram QT prolongation (13%). Adverse events of special interest included all-grade IDH differentiation syndrome (17%), all-grade electrocardiogram QT prolongation (26%), and grade ≥ 3 leukocytosis (9%). Median treatment duration was 15.1 months (range, 0.3-32.2 months); 10 patients remained on treatment as of February 19, 2019. The overall response rate was 78.3% (18/23 patients; 95% CI, 56.3% to 92.5%), and the complete remission rate was 60.9% (14/23 patients; 95% CI, 38.5% to 80.3%). With median follow-up of 16 months, median duration of response in responders had not been reached. The 12-month survival estimate was 82.0% (95% CI, 58.8% to 92.8%). mIDH1 clearance in bone marrow mononuclear cells by BEAMing (beads, emulsion, amplification, magnetics) digital polymerase chain reaction was seen in 10/14 patients (71.4%) achieving complete remission.
CONCLUSION: Ivosidenib plus azacitidine was well tolerated, with an expected safety profile consistent with monotherapy with each agent. Responses were deep and durable, with most complete responders achieving mIDH1 mutation clearance.

DOI: https://doi.org/10.1200/JCO.20.01632
Nat Med. 2020 Oct 26.

Precision medicine treatment in acute myeloid leukemia using prospective genomic profiling: feasibility and preliminary efficacy of the Beat AML Master Trial.

Amy Burd, Ross L Levine, Amy S Ruppert, Alice S Mims, Uma Borate, Eytan M Stein, Prapti Patel, Maria R Baer, Wendy Stock, Michael Deininger, William Blum, Gary Schiller, Rebecca Olin, Mark Litzow, James Foran, Tara L Lin, Brian Ball, Michael Boyiadzis, Elie Traer, Olatoyosi Odenike, Martha Arellano, Alison Walker, Vu H Duong, Tibor Kovacsovics, Robert Collins, Abigail B Shoben, Nyla A Heerema, Matthew C Foster, Jo-Anne Vergilio, Tim Brennan, Christine Vietz, Eric Severson, Molly Miller, Leonard Rosenberg, Sonja Marcus, Ashley Yocum, Timothy Chen, Mona Stefanos, Brian Druker, John C Byrd.

Acute myeloid leukemia (AML) is the most common diagnosed leukemia. In older adults, AML confers an adverse outcome1,2. AML originates from a dominant mutation, then acquires collaborative transformative mutations leading to myeloid transformation and clinical/biological heterogeneity. Currently, AML treatment is initiated rapidly, precluding the ability to consider the mutational profile of a patient's leukemia for treatment decisions. Untreated patients with AML ≥ 60 years were prospectively enrolled on the ongoing Beat AML trial (ClinicalTrials.gov NCT03013998), which aims to provide cytogenetic and mutational data within 7 days (d) from sample receipt and before treatment selection, followed by treatment assignment to a sub-study based on the dominant clone. A total of 487 patients with suspected AML were enrolled; 395 were eligible. Median age was 72 years (range 60-92 years; 38% ≥75 years); 374 patients (94.7%) had genetic and cytogenetic analysis completed within 7 d and were centrally assigned to a Beat AML sub-study; 224 (56.7%) were enrolled on a Beat AML sub-study. The remaining 171 patients elected standard of care (SOC) (103), investigational therapy (28) or palliative care (40); 9 died before treatment assignment. Demographic, laboratory and molecular characteristics were not significantly different between patients on the Beat AML sub-studies and those receiving SOC (induction with cytarabine + daunorubicin (7 + 3 or equivalent) or hypomethylation agent). Thirty-day mortality was less frequent and overall survival was significantly longer for patients enrolled on the Beat AML sub-studies versus those who elected SOC. A precision medicine therapy strategy in AML is feasible within 7 d, allowing patients and physicians to rapidly incorporate genomic data into treatment decisions without increasing early death or adversely impacting overall survival.

DOI: https://doi.org/10.1038/s41591-020-1089-8
Am J Hematol. 2020 Oct 29.

Venetoclax with azacitidine or decitabine in patients with newly diagnosed acute myeloid leukemia: long term follow-up from a Phase 1b study.

Daniel A Pollyea, Keith Pratz, Anthony Letai, Brian A Jonas, Andrew H Wei, Vinod Pullarkat, Marina Konopleva, Michael J Thirman, Martha Arellano, Pamela S Becker, Brenda Chyla, Wan-Jen Hong, Qi Jiang, Jalaja Potluri, Courtney D DiNardo.

This analysis represents the longest-term follow-up for patients with acute myeloid leukemia (AML) treated with 400 mg of venetoclax plus azacitidine or decitabine. Adults with newly diagnosed AML ineligible for intensive chemotherapy were enrolled in an open-label, non-randomized, multicenter phase 1b trial of venetoclax with azacitidine (AZA; 75 mg/m2 ; days 1-7) or decitabine (DEC; 20 mg/m2 ; days 1-5). Endpoints included safety, response rates (complete remission [CR], CR with incomplete blood count recovery [CRi]), response duration and overall survival (OS). The median follow-up time was 29 and 40 months for patients treated with venetoclax plus AZA and DEC combinations, respectively. Key Grade ≥3 AEs (AZA and DEC) were febrile neutropenia (39% and 65%), anemia (30% and 26%), thrombocytopenia (25% and 23%), and neutropenia (20% and 10%). The CR/CRi rate was 71% for venetoclax plus AZA and 74% for venetoclax plus DEC. The median duration of CR/CRi was 21.9 months and 15.0 months, and the median OS was 16.4 months and 16.2 months, for venetoclax plus AZA and DEC, respectively. These results support venetoclax plus hypomethylating agents as highly effective frontline AML therapies for patients unfit for intensive chemotherapy. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/ajh.26039
Nature. 2020 Oct 28.

Single-cell mutation analysis of clonal evolution in myeloid malignancies.

Linde A Miles, Robert L Bowman, Tiffany R Merlinsky, Isabelle S Csete, Aik T Ooi, Robert Durruthy-Durruthy, Michael Bowman, Christopher Famulare, Minal A Patel, Pedro Mendez, Chrysanthi Ainali, Benjamin Demaree, Cyrille L Delley, Adam R Abate, Manimozhi Manivannan, Sombeet Sahu, Aaron D Goldberg, Kelly L Bolton, Ahmet Zehir, Raajit Rampal, Martin P Carroll, Sara E Meyer, Aaron D Viny, Ross L Levine.

Myeloid malignancies, including acute myeloid leukaemia (AML), arise from the expansion of haematopoietic stem and progenitor cells that acquire somatic mutations. Bulk molecular profiling has suggested that mutations are acquired in a stepwise fashion: mutant genes with high variant allele frequencies appear early in leukaemogenesis, and mutations with lower variant allele frequencies are thought to be acquired later1-3. Although bulk sequencing can provide information about leukaemia biology and prognosis, it cannot distinguish which mutations occur in the same clone(s), accurately measure clonal complexity, or definitively elucidate the order of mutations. To delineate the clonal framework of myeloid malignancies, we performed single-cell mutational profiling on 146 samples from 123 patients. Here we show that AML is dominated by a small number of clones, which frequently harbour co-occurring mutations in epigenetic regulators. Conversely, mutations in signalling genes often occur more than once in distinct subclones, consistent with increasing clonal diversity. We mapped clonal trajectories for each sample and uncovered combinations of mutations that synergized to promote clonal expansion and dominance. Finally, we combined protein expression with mutational analysis to map somatic genotype and clonal architecture with immunophenotype. Our findings provide insights into the pathogenesis of myeloid transformation and how clonal complexity evolves with disease progression.

DOI: https://doi.org/10.1038/s41586-020-2864-x
J Clin Invest. 2020 Oct 27. pii: 129115. [Epub ahead of print]

Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia.

Alhomidi Almotiri, Hamed Ahmad A Alzahrani, Juan Bautista Menendez-Gonzalez, Ali Abdelfattah, Badi Alotaibi, Lubaid Saleh, Adelle Greene, Mia R F Georgiou, Alex Gibbs, Amani Salem Alsayari, Sarab Taha, Leigh-Anne Thomas, Dhruv Shah, Sarah Edkins, Peter J Giles, Marc P Stemmler, Simone Brabletz, Thomas Brabletz, Ashleigh S Boyd, Florian A Siebzehnrubl, Neil P Rodrigues.

  Zeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal (EMT) transcription factor, confers properties of 'stemness', such as self-renewal, in cancer. Yet little is known about the function of Zeb1 in adult stem cells. Here, we used the hematopoietic system, as a well-established paradigm of stem cell biology, to evaluate Zeb1 mediated regulation of adult stem cells. We employed a conditional genetic approach using the Mx1-Cre system to specifically knockout (KO) Zeb1 in adult hematopoietic stem cells (HSCs) and their downstream progeny. Acute genetic deletion of Zeb1 led to rapid onset thymic atrophy and apoptosis driven loss of thymocytes and T cells. A profound cell-autonomous self-renewal defect and multi-lineage differentiation block was observed in Zeb1 KO HSCs. Loss of Zeb1 in HSCs activated transcriptional programs of deregulated HSC maintenance and multi-lineage differentiation genes, and of cell polarity, consisting of cytoskeleton, lipid metabolism/lipid membrane and cell adhesion related genes. Notably, Epithelial cell adhesion molecule (EpCAM) expression was prodigiously upregulated in Zeb1 KO HSCs, which correlated with enhanced cell survival, diminished mitochondrial metabolism, ribosome biogenesis, and differentiation capacity and an activated transcriptomic signature associated with acute myeloid leukemia (AML) signaling. ZEB1 expression was downregulated in AML patients and Zeb1 KO in the malignant counterparts of HSCs - leukemic stem cells (LSCs) - accelerated MLL-AF9 and Meis1a/Hoxa9-driven AML progression, implicating Zeb1 as a tumor suppressor in AML LSCs. Thus, Zeb1 acts as a transcriptional regulator in hematopoiesis, critically co-ordinating HSC self-renewal, apoptotic and multi-lineage differentiation fates required to suppress leukemic potential in AML.

Keywords:  Bone marrow differentiation; Hematology; Stem cells

DOI:  https://doi.org/10.1172/JCI129115
Trends Mol Med. 2020 Oct 26. pii: S1471-4914(20)30262-8. [Epub ahead of print]

Extinguishing the Embers: Targeting AML Metabolism.

Rachel Culp-Hill, Angelo D'Alessandro, Eric M Pietras.

  Acute myeloid leukemia (AML) is a cancer derived from the myeloid lineage of blood cells, characterized by overproduction of leukemic blasts. Although therapeutic improvements have made a significant impact on the outcomes of patients with AML, survival rates remain low due to a high incidence of relapse. Similar to how wildfires can reignite from hidden embers not extinguished from an initial round of firefighting, leukemic stem cells (LSCs) are the embers remaining after completion of traditional chemotherapeutic treatments. LSCs exhibit a unique metabolic profile and contain metabolically distinct subpopulations. In this review, we detail the metabolic features of LSCs and how these characteristics promote resistance to traditional chemotherapy. We also discuss new therapeutic approaches that target metabolic vulnerabilities of LSC to selectively eradicate them.

Keywords:  AML; LSC; acute myeloid leukemia; leukemic stem cells; mitochondrial metabolism; oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.molmed.2020.10.001
Blood Cancer J. 2020 Oct 30. 10(10): 107

New directions for emerging therapies in acute myeloid leukemia: the next chapter.

Naval Daver, Andrew H Wei, Daniel A Pollyea, Amir T Fathi, Paresh Vyas, Courtney D DiNardo.

Conventional therapy for acute myeloid leukemia is composed of remission induction with cytarabine- and anthracycline-containing regimens, followed by consolidation therapy, including allogeneic stem cell transplantation, to prolong remission. In recent years, there has been a significant shift toward the use of novel and effective, target-directed therapies, including inhibitors of mutant FMS-like tyrosine kinase 3 (FLT3) and isocitrate dehydrogenase (IDH), the B-cell lymphoma 2 inhibitor venetoclax, and the hedgehog pathway inhibitor glasdegib. In older patients the combination of a hypomethylating agent or low-dose cytarabine, venetoclax achieved composite response rates that approximate those seen with standard induction regimens in similar populations, but with potentially less toxicity and early mortality. Preclinical data suggest synergy between venetoclax and FLT3- and IDH-targeted therapies, and doublets of venetoclax with inhibitors targeting these mutations have shown promising clinical activity in early stage trials. Triplet regimens involving the hypomethylating agent and venetoclax with FLT3 or IDH1/2 inhibitor, the TP53-modulating agent APR-246 and magrolimab, myeloid cell leukemia-1 inhibitors, or immune therapies such as CD123 antibody-drug conjugates and programmed cell death protein 1 inhibitors are currently being evaluated. It is hoped that such triplets, when applied in appropriate patient subsets, will further enhance remission rates, and more importantly remission durations and survival.

DOI: https://doi.org/10.1038/s41408-020-00376-1
Blood Adv. 2020 Oct 27. 4(20): 5257-5268

Acute myeloid leukemia-induced remodeling of the human bone marrow niche predicts clinical outcome.

Yiyang Chen, Lina Marie Hoffmeister, Yasmin Zaun, Lucas Arnold, Kurt Werner Schmid, Bernd Giebel, Ludger Klein-Hitpass, Helmut Hanenberg, Anthony Squire, H Christian Reinhardt, Ulrich Dührsen, Stefanie Bertram, Maher Hanoun.

Murine models of myeloid neoplasia show how leukemia infiltration alters the hematopoietic stem cell (HSC) niche to reinforce malignancy at the expense of healthy hematopoiesis. However, little is known about the bone marrow architecture in humans and its impact on clinical outcome. Here, we dissect the bone marrow niche in patients with acute myeloid leukemia (AML) at first diagnosis. We combined immunohistochemical stainings with global gene expression analyses from these AML patients and correlated them with clinical features. Mesenchymal stem and progenitor cells (MSPCs) lost quiescence and significantly expanded in the bone marrow of AML patients. Strikingly, their HSC- and niche-regulating capacities were impaired with significant inhibition of osteogenesis and bone formation in a cell contact-dependent manner through inhibition of cytoplasmic β-catenin. Assessment of bone metabolism by quantifying peripheral blood osteocalcin levels revealed 30% lower expression in AML patients at first diagnosis than in non-leukemic donors. Furthermore, patients with osteocalcin levels ≤11 ng/mL showed inferior overall survival with a 1-year survival rate of 38.7% whereas patients with higher osteocalcin levels reached a survival rate of 66.8%. These novel insights into the human AML bone marrow microenvironment help translate findings from preclinical models and detect new targets which might pave the way for niche-targeted therapies in AML patients.

DOI: https://doi.org/10.1182/bloodadvances.2020001808
Metabolites. 2020 Oct 26. pii: E427. [Epub ahead of print]10(11):

Profiling of Metabolic Differences between Hematopoietic Stem Cells and Acute/Chronic Myeloid Leukemia.

Byung Hoo Song, Su Young Son, Hyun Kyu Kim, Tae Won Ha, Jeong Suk Im, Aeli Ryu, Hyeji Jeon, Hee Yong Chung, Jae Sang Oh, Choong Hwan Lee, Man Ryul Lee.

  Although many studies have been conducted on leukemia, only a few have analyzed the metabolomic profiles of various leukemic cells. In this study, the metabolomes of THP-1, U937, KG-1 (acute myelogenous leukemia, AML), K562 (chronic myelogenous leukemia, CML), and cord blood-derived CD34-positive hematopoietic stem cells (HSC) were analyzed using gas chromatography-mass spectrometry, and specific metabolic alterations were found using multivariate statistical analysis. Compared to HSCs, leukemia cell metabolomes were found to have significant alterations, among which three were related to amino acids, three to sugars, and five to fatty acids. Compared to CML, four metabolomes were observed specifically in AML. Given that overall more metabolites are present in leukemia cells than in HSCs, we observed that the activation of glycolysis and oxidative phosphorylation (OXPHOS) metabolism facilitated the incidence of leukemia and the proliferation of leukemic cells. Analysis of metabolome profiles specifically present in HSCs and leukemia cells greatly increases our basic understanding of cellular metabolic characteristics, which is valuable fundamental knowledge for developing novel anticancer drugs targeting leukemia metabolism.

Keywords:  K562; KG-1; THP-1; U937; acute myelogenous leukemia; chronic myelogenous leukemia; hematopoietic stem cells; metabolome

DOI:  https://doi.org/10.3390/metabo10110427
Int J Gen Med. 2020 ;13 867-879

Combined Expression of CD34 and FLT3-Internal Tandem Duplication Mutation Predicts Poor Response to Treatment in Acute Myeloid Leukemia.

Mona S Abdellateif, Amira B Kassem, Yomna M El-Meligui.

   Background: Acute myeloid leukemia (AML) is a common hematological malignancy associated with different cytogenetic and genetic abnormalities.
Methods: FLT3-internal tandem duplication (FLT3/ITD) mutation and CD34 expression levels were assessed in the bone marrow (BM) aspirates of 153 de novo AML patients. Data were correlated with relevant clinic-pathological features of the patients, response to treatment, disease-free survival (DFS), and overall free survival (OS) rates.
Results: FLT3-ITD mutation was detected in 27/153 (17.6%) AML patients (P=0.001), and CD34 was expressed in 83/153 (54.2%) patients (P=0.293) compared to those with wild FLT3 and CD34- expression, respectively. Patients with FLT3-ITD mutation showed increased peripheral blood and BM blast cells, abnormal cytogenetics, poor DFS and OS compared to those with wild FLT3 (P=0.013, P<0.001, P=0.010, P=0.008 and P=0.004, respectively), while there was no significant association with response to treatment (P=0.081). There was no significant association between CD34 expression and response to treatment, DFS, and OS (P>0.05). FLT3-ITD mutation and FAB subtypes were independent prognostic factors for DFS. Older age ≥39 years, HB <7 mg/dL PB blast ≥54%, and FLT3-ITD mutation were independent prognostic factors for poor OS in AML patients. The presence of both FLT3-ITD mutation and CD34 expression associated significantly with resistance to therapy (P=0.024), short DFS and OS rates (P=0.006, P=0.037, respectively).
Conclusion: Combined expression of both FLT3-ITD mutation and CD34 expression is an important prognostic and predictive factor for poor disease outcome in AML patients.

Keywords:  AML; CD34; FLT3-ITD; acute myeloid leukemia

DOI:  https://doi.org/10.2147/IJGM.S276138
Arch Med Res. 2020 Oct 24. pii: S0188-4409(20)30227-7. [Epub ahead of print]

FLT3-ITD and CD135 Over-Expression are Frequent Findings of Poor Survival in Adult Patients With Acute Leukemias.

Jorge Vela-Ojeda, Pamela Vazquez Cardenas, Miriam A Garcia-Ruiz Esparza, Laura Arcelia Montiel Cervantes, Jaime Garcia Chavez, Alvaro Hernandez Caballero, Abraham Majluf-Cruz, Armando Vega-López, Elba Reyes-Maldonado.

   BACKGROUND: Fms-like tyrosine kinase 3 (FLT3) expression and mutation have been considered a poor prognostic factor in acute myeloid leukemia (AML). FLT3-ITD mutation is present in 30% of adult patients with AML and 2-5% in childhood acute lymphoblastic leukemia (ALL). The impact of these mutations on the prognosis of ALL patients, has not yet been established. Moreover, a limited number of publications regarding the level of expression of the FLT3 receptor (CD135) in both leukemias exist. This study aimed to analyze the clinical outcomes associated to the presence of FLT3-ITD mutation and the expression of CD135.
METHODS: 82 adult patients with newly diagnosed acute leukemia (39 with AML and 43 with ALL) were included. Flow cytometry and RT-PCR were done to analyze the expression of CD135 and the presence of FLT3 ITD mutation, respectively.
RESULTS: FLT3-ITD was present in 14 (36%) of AML and 15 (35%) of ALL patients. Disease free survival (DFS) and overall survival (OS) were lower in ALL patients having a CD135 expression >3000 cells/μL. There was a trend for poor OS in AML patients expressing FLT3 ITD. OS was worse in AML patients with high expression of CD135.
CONCLUSION: A higher (35%) frequency of FLT3-ITD was found in adult ALL patients. The presence of FLT3-ITD was associated with a trend of poor OS in AML cases, and overexpression of CD135 was correlated with poor DFS in ALL cases and poor OS in both acute leukemias.

Keywords:  CD135; FLT3 ITD; Lymphoblastic leukemia; Myeloblastic leukemia; Prognostic factors; Survival

DOI:  https://doi.org/10.1016/j.arcmed.2020.10.013
Haematologica. 2020 Oct 29. Online ahead of print 0

The IL1-IL1RAP axis plays an important role in the inflammatory leukemic niche that favors acute myeloid leukemia proliferation over normal hematopoiesis.

Bauke De Boer, Sofia Sheveleva, Katja Apelt, Edo Vellenga, Andre B Mulder, Gerwin Huls Schuringa, Jan Jacob.

Upregulation of the plasma membrane receptor IL1RAP in Acute Myeloid Leukemia (AML) has been reported but its role in the context of the leukemic bone marrow niche is unclear. Here, we studied the signaling events downstream of IL1RAP in relation to leukemogenesis and normal hematopoiesis. High IL1RAP expression was associated with a leukemic GMP-like state, and knockdown of IL1RAP in AML reduced colony-forming capacity. Stimulation with IL1β resulted in the induction of multiple chemokines and an inflammatory secretome via the p38 MAPK and NFκB signaling pathways in IL1RAP-expressing AML cells, but IL1β-induced signaling was dispensable for AML cell proliferation and NFκB-driven survival. IL1RAP was also expressed in stromal cells where IL1β induced expression of inflammatory chemokines and cytokines as well. Intriguingly, the IL1β-induced inflammatory secretome of IL1RAPexpressing AML cells grown on a stromal layer of mesenchymal stem cells affected normal hematopoiesis including hematopoietic stem/progenitor cells while AML cell proliferation was not affected. The addition of Anakinra, an FDA-approved IL1 receptor antagonist, could reverse this effect. Therefore, blocking the IL1-IL1RAP signaling axis might be a good therapeutic approach to reduce inflammation in the bone marrow niche and thereby promote normal hematopoietic recovery over AML proliferation after chemotherapy.

DOI: https://doi.org/10.3324/haematol.2020.254987
Haematologica. 2020 Oct 22. Online ahead of print

Emerging epigenetic therapeutics for myeloid leukemia: modulating demethylase activity with ascorbate.

Andrew B Das, Carlos C Smith-Díaz, Margreet C M Vissers.

The past decade has seen a proliferation of drugs that target epigenetic pathways. Many of these drugs were developed to treat acute myeloid leukemia, a condition in which dysregulation of the epigenetic landscape is well established. While these drugs have shown promise, critical issues persist. Specifically, patients with the same mutations respond quite differently to treatment. This is true even with highly specific drugs that are designed to target the underlying oncogenic driver mutations. Furthermore, patients who do respond may eventually develop resistance. There is now evidence that epigenetic heterogeneity contributes, in part, to these issues. Cancer cells also have a remarkable capacity to 'rewire' themselves at the epigenetic level in response to drug treatment, and thereby maintain expression of key oncogenes. This epigenetic plasticity is a promising new target for drug development. It is therefore important to consider combination therapy in cases in which both driver mutations and epigenetic plasticity are targeted. Using ascorbate as an example of an emerging epigenetic therapeutic, we review the evidence for its potential use in both of these modes. We provide an overview of 2-oxoglutarate dependent dioxygenases with DNA, histone and RNA demethylase activity, focusing on those which require ascorbate as a cofactor. We also evaluate their role in the development and maintenance of acute myeloid leukemia. Using this information, we highlight situations in which the use of ascorbate to restore 2-oxoglutarate dependent dioxygenase activity could prove beneficial, in contrast to contexts in which targeted inhibition of specific enzymes might be preferred. Finally, we discuss how these insights could be incorporated into the rational design of future clinical trials.

DOI: https://doi.org/10.3324/haematol.2020.259283
Leuk Lymphoma. 2020 Oct 26. 1-9

Detection of residual disease in chronic myeloid leukemia utilizing genomic next generation sequencing reveals persistence of differentiated Ph+ B cells but not bone marrow stem/progenitors.

Daiki Karigane, Hidenori Kasahara, Kouhei Shiroshita, Shinya Fujita, Hiroshi Kobayashi, Shinpei Tamaki, Rie Yamazaki, Kaori Yahagi, Yoko Yatabe, Naomi Kondoh, Tomoko Arai, Hisako Katagiri, Nobuko Shimizu, Masatoshi Sakurai, Taku Kikuchi, Jun Kato, Takayuki Shimizu, Taeko Hayakawa, Tomonori Yaguchi, Maiko Matsushita, Hideaki Nakajima, Yutaka Kawakami, Mitsuru Murata, Takehiko Mori, Takashi Sasaki, Shinichiro Okamoto, Keiyo Takubo.

  Persistence of leukemic stem cells (LSCs) results in the recurrence of chronic myeloid leukemia (CML) after the administration of tyrosine kinase inhibitors (TKIs). Thus, the detection of minimal residual disease (MRD) with LSC potential can improve prognosis. Here, we analyzed 115 CML patients and found that CD25 was preferentially expressed on the phenotypic stem and progenitor cells (SPCs), and TKI therapy decreased the number of CD25-positive cells in the SPC fraction. To detect MRD harboring BCR-ABL1 fusion DNA, we developed a highly-sensitive method using patient-specific primers and next-generation sequencing. By using this method, we identified that in patients who achieved molecular remission, almost all residual CD25-positive SPCs were BCR-ABL1-negative. Moreover, in some patients BCR-ABL1 was detectable in peripheral B cells but not in SPCs. We conclude that CD25 marks LSCs at diagnosis but does not mark MRD following TKI treatment and that analysis of peripheral B cells can allow sensitive detection of MRD.

Keywords:  CD25; Chronic myeloid leukemia; minimal residual disease; tyrosine kinase inhibitor

DOI:  https://doi.org/10.1080/10428194.2020.1837366
Nat Genet. 2020 Nov;52(11): 1208-1218

Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity.

Gabriela S Kinker, Alissa C Greenwald, Rotem Tal, Zhanna Orlova, Michael S Cuoco, James M McFarland, Allison Warren, Christopher Rodman, Jennifer A Roth, Samantha A Bender, Bhavna Kumar, James W Rocco, Pedro A C M Fernandes, Christopher C Mader, Hadas Keren-Shaul, Alexander Plotnikov, Haim Barr, Aviad Tsherniak, Orit Rozenblatt-Rosen, Valery Krizhanovsky, Sidharth V Puram, Aviv Regev, Itay Tirosh.

Cultured cell lines are the workhorse of cancer research, but the extent to which they recapitulate the heterogeneity observed among malignant cells in tumors is unclear. Here we used multiplexed single-cell RNA-seq to profile 198 cancer cell lines from 22 cancer types. We identified 12 expression programs that are recurrently heterogeneous within multiple cancer cell lines. These programs are associated with diverse biological processes, including cell cycle, senescence, stress and interferon responses, epithelial-mesenchymal transition and protein metabolism. Most of these programs recapitulate those recently identified as heterogeneous within human tumors. We prioritized specific cell lines as models of cellular heterogeneity and used them to study subpopulations of senescence-related cells, demonstrating their dynamics, regulation and unique drug sensitivities, which were predictive of clinical response. Our work describes the landscape of heterogeneity within diverse cancer cell lines and identifies recurrent patterns of heterogeneity that are shared between tumors and specific cell lines.

DOI: https://doi.org/10.1038/s41588-020-00726-6
Nat Genet. 2020 Nov;52(11): 1219-1226

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Kelly L Bolton, Ryan N Ptashkin, Teng Gao, Lior Braunstein, Sean M Devlin, Daniel Kelly, Minal Patel, Antonin Berthon, Aijazuddin Syed, Mariko Yabe, Catherine C Coombs, Nicole M Caltabellotta, Mike Walsh, Kenneth Offit, Zsofia Stadler, Diana Mandelker, Jessica Schulman, Akshar Patel, John Philip, Elsa Bernard, Gunes Gundem, Juan E Arango Ossa, Max Levine, Juan S Medina Martinez, Noushin Farnoud, Dominik Glodzik, Sonya Li, Mark E Robson, Choonsik Lee, Paul D P Pharoah, Konrad H Stopsack, Barbara Spitzer, Simon Mantha, James Fagin, Laura Boucai, Christopher J Gibson, Benjamin L Ebert, Andrew L Young, Todd Druley, Koichi Takahashi, Nancy Gillis, Markus Ball, Eric Padron, David M Hyman, Jose Baselga, Larry Norton, Stuart Gardos, Virginia M Klimek, Howard Scher, Dean Bajorin, Eder Paraiso, Ryma Benayed, Maria E Arcila, Marc Ladanyi, David B Solit, Michael F Berger, Martin Tallman, Montserrat Garcia-Closas, Nilanjan Chatterjee, Luis A Diaz, Ross L Levine, Lindsay M Morton, Ahmet Zehir, Elli Papaemmanuil.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies.

DOI: https://doi.org/10.1038/s41588-020-00710-0
Leukemia. 2020 Oct 26.

Systemic mastocytosis with acute myeloid leukemia occurs from mutually exclusive clones expressing KITD816V and FLT3-ITD.

Jose-Mario Capo-Chichi, Elizabeth Kagotho, Rakesh Nayyar, Davidson Zhao, Mark Minden, Hong Chang.

DOI: https://doi.org/10.1038/s41375-020-01073-5
J Clin Invest. 2020 Oct 27. pii: 138986. [Epub ahead of print]

ANGPTL2-containing small extracellular vesicles from vascular endothelial cells accelerate leukemia progression.

Dan Huang, Guohuan Sun, Xiaoxin Hao, Xiaoxiao He, Zhaofeng Zheng, Chiqi Chen, Zhuo Yu, Li Xie, Shihui Ma, Ligen Liu, Bo O Zhou, Hui Cheng, Junke Zheng, Tao Cheng.

  Small extracellular vesicles (SEVs) are functional messengers of certain cellular niches to permit non-contact cell communications. Whether niche-specific SEVs fulfill this role in cancer is unclear. Here, we used seven cell-type specific mouse Cre lines to conditionally knockout Vps33b in Cdh5+ or Tie2+ endothelial cells (ECs), Lepr+ bone marrow perivascular cells, Osx+ osteo-progenitor cells (OPCs), Pf4+ megakaryocytes and Tcf21+ spleen stromal cells. We then examined the effects of reduced SEV secretion on progression of MLL-AF9 induced acute myeloid leukemia (AML) as well as normal hematopoiesis. Blocking SEV secretion from ECs, but not perivascular cells, megakaryocytes or spleen stromal cells, markedly delayed the leukemia progression. Notably, reducing SEV production from ECs had no effect on normal hematopoiesis. Protein analysis showed that EC-derived SEVs contained a high level of ANGPTL2, which accelerated leukemia progression via binding to LILRB2 receptor. Moreover, ANGPTL2-SEVs released from ECs were governed by VPS33B. Importantly, ANGPTL2-SEVs were also required for primary human AML cell maintenance. These findings demonstrate a role of niche-specific SEVs in cancer development and suggest that targeting ANGPTL2-SEVs from ECs might be a potential strategy to interfere certain types of AML.

Keywords:  Hematology; Leukemias; Stem cells

DOI:  https://doi.org/10.1172/JCI138986
Sci Transl Med. 2020 Oct 28. pii: eabb8969. [Epub ahead of print]12(567):

Metabolic reprogramming of donor T cells enhances graft-versus-leukemia effects in mice and humans.

Franziska M Uhl, Sophia Chen, David O'Sullivan, Joy Edwards-Hicks, Gesa Richter, Eileen Haring, Geoffroy Andrieux, Sebastian Halbach, Petya Apostolova, Jörg Büscher, Sandra Duquesne, Wolfgang Melchinger, Barbara Sauer, Khalid Shoumariyeh, Annette Schmitt-Graeff, Marina Kreutz, Michael Lübbert, Justus Duyster, Tilman Brummer, Melanie Boerries, Tobias Madl, Bruce R Blazar, Olaf Groß, Erika L Pearce, Robert Zeiser.

Acute myeloid leukemia (AML) relapse after allogeneic hematopoietic cell transplantation (allo-HCT) has a dismal prognosis. We found that T cells of patients relapsing with AML after allo-HCT exhibited reduced glycolysis and interferon-γ production. Functional studies in multiple mouse models of leukemia showed that leukemia-derived lactic acid (LA) interfered with T cell glycolysis and proliferation. Mechanistically, LA reduced intracellular pH in T cells, led to lower transcription of glycolysis-related enzymes, and decreased activity of essential metabolic pathways. Metabolic reprogramming by sodium bicarbonate (NaBi) reversed the LA-induced low intracellular pH, restored metabolite concentrations, led to incorporation of LA into the tricarboxylic acid cycle as an additional energy source, and enhanced graft-versus-leukemia activity of murine and human T cells. NaBi treatment of post-allo-HCT patients with relapsed AML improved metabolic fitness and interferon-γ production in T cells. Overall, we show that metabolic reprogramming of donor T cells is a pharmacological strategy for patients with relapsed AML after allo-HCT.

DOI: https://doi.org/10.1126/scitranslmed.abb8969
Blood Adv. 2020 Nov 10. 4(21): 5336-5342

Outcome of patients with IDH1/2-mutated post-myeloproliferative neoplasm AML in the era of IDH inhibitors.

Helen T Chifotides, Lucia Masarova, Mansour Alfayez, Naval Daver, Yesid Alvarado, Elias Jabbour, Marina Konopleva, Hagop M Kantarjian, Keyur P Patel, Courtney D DiNardo, Srdan Verstovsek.

DOI: https://doi.org/10.1182/bloodadvances.2020001528
Blood Adv. 2020 Oct 27. 4(20): 5246-5256

Phase 2 study of ruxolitinib and decitabine in patients with myeloproliferative neoplasm in accelerated and blast phase.

John O Mascarenhas, Raajit K Rampal, Heidi E Kosiorek, Rupali Bhave, Elizabeth Hexner, Eunice S Wang, Aaron Gerds, Camille N Abboud, Marina Kremyanskaya, Dimitry Berenzon, Olatoyosi Odenike, Noushin Farnoud, Aishwarya Krishnan, Rona Singer Weinberg, Erin McGovern, Mohamed E Salama, Vesna Najfeld, Juan S Medina-Martinez, Juan E Arango Ossa, Max F Levine, Yangyu Zhou, Lonette Sandy, Mark L Heaney, Ross L Levine, Ruben A Mesa, Amylou C Dueck, Ronald Hoffman.

Myeloproliferative neoplasms (MPN) that have evolved into accelerated or blast phase disease (MPN-AP/BP) have poor outcomes with limited treatment options and therefore represent an urgent unmet need. We have previously demonstrated in a multicenter, phase 1 trial conducted through the Myeloproliferative Neoplasms Research Consortium that the combination of ruxolitinib and decitabine is safe and tolerable and is associated with a favorable overall survival (OS). In this phase 2 trial, 25 patients with MPN-AP/BP were treated at the recommended phase 2 dose of ruxolitinib 25 mg twice daily for the induction cycle followed by 10 mg twice daily for subsequent cycles in combination with decitabine 20 mg/m2 for 5 consecutive days in a 28-day cycle. Nineteen patients died during the study follow-up. The median OS for all patients on study was 9.5 months (95% confidence interval, 4.3-12.0). Overall response rate (complete remission + incomplete platelet recovery + partial remission) was 11/25 (44%) and response was not associated with improved survival. We conclude that the combination of decitabine and ruxolitinib was well tolerated, demonstrated favorable OS, and represents a therapeutic option for this high-risk patient population. This trial was registered at www.clinicaltrials.gov as #NCT02076191.

DOI: https://doi.org/10.1182/bloodadvances.2020002119
Leukemia. 2020 Oct 29.

New strategies to treat AML: novel insights into AML survival pathways and combination therapies.

Ramya Nair, Alejandro Salinas-Illarena, Hanna-Mari Baldauf.

The effective treatment of acute myeloid leukemia (AML) is very challenging. Due to the immense heterogeneity of this disease, treating it using a "one size fits all" approach is ineffective and only benefits a subset of patients. Instead, there is a shift towards more personalized treatment based on the patients' genomic signature. This shift has facilitated the increased revelation of novel insights into pathways that lead to the survival and propagation of AML cells. These AML survival pathways are involved in drug resistance, evasion of the immune system, reprogramming metabolism, and impairing differentiation. In addition, based on the reports of enhanced clinical efficiencies when combining drugs or treatments, deeper investigation into possible pathways, which can be targeted together to increase treatment response in a wider group of patients, is warranted. In this review, not only is a comprehensive summary of targets involved in these pathways provided, but also insights into the potential of targeting these molecules in combination therapy will be discussed.

DOI: https://doi.org/10.1038/s41375-020-01069-1
Nat Cancer. 2020 Aug;1(8): 826-839

Integrated analysis of patient samples identifies biomarkers for venetoclax efficacy and combination strategies in acute myeloid leukemia.

Haijiao Zhang, Yusuke Nakauchi, Thomas Köhnke, Melissa Stafford, Daniel Bottomly, Rozario Thomas, Beth Wilmot, Shannon K McWeeney, Ravindra Majeti, Jeffrey W Tyner.

Deregulation of the BCL2 gene family plays an important role in the pathogenesis of acute myeloid leukemia (AML). The BCL2 inhibitor, venetoclax, has received FDA approval for the treatment of AML. However, upfront and acquired drug resistance ensues due, in part, to the clinical and genetic heterogeneity of AML, highlighting the importance of identifying biomarkers to stratify patients onto the most effective therapies. By integrating clinical characteristics, exome and RNA sequencing, and inhibitor data from primary AML patient samples, we determined that myelomonocytic leukemia, upregulation of BCL2A1 and CLEC7A, as well as mutations of PTPN11 and KRAS conferred resistance to venetoclax and multiple venetoclax combinations. Venetoclax in combination with an MCL1 inhibitor AZD5991 induced synthetic lethality and circumvented venetoclax resistance.

DOI: https://doi.org/10.1038/s43018-020-0103-x
Cancers (Basel). 2020 Oct 28. pii: E3161. [Epub ahead of print]12(11):

Detection of Pathogenic Isoforms of IKZF1 in Leukemic Cell Lines and Acute Lymphoblastic Leukemia Samples: Identification of a Novel Truncated IKZF1 Transcript in SUP-B15.

Weiqiang Zhao, Ying Li, Chenjiao Yao, Guojuan Zhang, Kevin Y Zhao, Wei Chen, Peng Ru, Xiaokang Pan, Huolin Tu, Daniel Jones.

  Leukemia-associated alternative splicing of IKZF1 can result in proteins with loss of one to four copies of its N-terminal zinc finger domains (N-ZnF). The best characterized pathogenic splice isoforms, Ik-6 and Ik-8, have been commonly found in BCR-ABL1+ acute lymphoblastic leukemia (ALL) and a subset of BCR-ABL1-like ALL. Infantile and childhood ALL that express these pathogenic IKZF1 isoforms have shown inferior clinical outcomes and can be resistant to tyrosine kinase inhibitors. Using ALL cell lines, we designed and validated a method to detect abnormal IKZF1 transcripts. In the SUP-B15 leukemia cell line, we noted novel IKZF1 transcripts that include both an Ik-6 splice and a transcript with a 14 base pair insertion at the C-terminus. There was also increased IKZF2 protein in SUP-B15 as compared to other ALL lines. Expression of Ik-6 could be suppressed by treatment with the pro-apoptotic type II histone deacetylase inhibitor givinostat. In 17 adult ALL samples, we noted the Ik-6 isoforms in 6 of 15 BCR-ABL1-, and 1 of 2 BCR-ABL1+ cases, with Ik-8 also expressed in one case. Cases with Ik-6 expression showed inferior survival as well as older age at presentation, lower expression of CD10 and more commonly a diploid karyotype.

Keywords:  ALL; IKZF1; Ik-6; Ik-8; isoforms; survival

DOI:  https://doi.org/10.3390/cancers12113161
Int J Lab Hematol. 2020 Oct 25.

Acute myeloid leukemia with mutated NPM1 mimics acute promyelocytic leukemia presentation.

Manuel J Arana Rosainz, Nghia Nguyen, Amer Wahed, Laura C Lelenwa, Nfn Aakash, Karen Schaefer, Adan Rios, Zeyad Kanaan, Lei Chen.

   OBJECTIVES: To investigate clinicopathological and molecular features of NPM1-mutated acute myeloid leukemia that presented with infrequent acute promyelocytic leukemia (APL)-like phenotype and clinical presentation.
METHODS: Cases with both de novo or secondary Acute Myeloid Leukemia (AML) were retrieved. Data from flow cytometry immunophenotyping, cytogenetics, molecular studies, and clinical presentation were analyzed.
RESULTS: Cases presented with abnormal coagulation parameters and low platelets count; four of them showed a DIC index compatible with overt DIC. Two cases showed Auer rods. In all cases, immunophenotypes mimicked APL: blasts expressed CD33, CD13, and cytoplasmic MPO but did not express CD34, HLA-DR, or CD11b. Notably, CD4 expression was observed in all cases. Neither t(15;17) nor PML/RARα gene rearrangement was detected. NPM1 gene mutation was identified in all cases. In four cases, TET2 or IDH2 co-mutations were identified.
CONCLUSIONS: Our findings provide additional evidence of association between NPM1-mutated AML with TET2 or IDH2 co-mutations and the APL-like immunophenotype. This AML subset was found to exist in both de novo and secondary AML. High WBC count and blasts with low to moderate side scatter and significant expression of CD4 are observed features that could assist in the differential diagnosis with APL. The occurrence of significant elevated D-dimer levels, or even overt DIC observed at diagnosis in these cases could be relevant for this AML subtype.

Keywords:   NPM1 ; APL-like immunophenotype; acute myeloid leukemia with mutated NPM1; disseminated intravascular coagulation

DOI:  https://doi.org/10.1111/ijlh.13357
Cell Rep. 2020 Oct 27. pii: S2211-1247(20)31309-7. [Epub ahead of print]33(4): 108320

In Vitro Recapitulation of Murine Thymopoiesis from Single Hematopoietic Stem Cells.

Amélie Montel-Hagen, Victoria Sun, David Casero, Steven Tsai, Alexandre Zampieri, Nicholas Jackson, Suwen Li, Shawn Lopez, Yuhua Zhu, Brent Chick, Chongbin He, Stéphanie C de Barros, Christopher S Seet, Gay M Crooks.

  We report a serum-free, 3D murine artificial thymic organoid (M-ATO) system that mimics normal murine thymopoiesis with the production of all T cell stages, from early thymic progenitors to functional single-positive (CD8SP and CD4SP) TCRαβ and TCRγδ cells. RNA sequencing aligns M-ATO-derived populations with phenotypically identical primary thymocytes. M-ATOs initiated with Rag1-/- marrow produce the same differentiation block as seen in the endogenous thymus, and Notch signaling patterns in M-ATOs mirror primary thymopoiesis. M-ATOs initiated with defined hematopoietic stem cells (HSCs) and lymphoid progenitors from marrow and thymus generate each of the downstream differentiation stages, allowing the kinetics of T cell differentiation to be tracked. Remarkably, single HSCs deposited into each M-ATO generate the complete trajectory of T cell differentiation, producing diverse TCR repertoires across clones that largely match endogenous thymus. M-ATOs represent a highly reproducible and efficient experimental platform for the interrogation of clonal thymopoiesis from HSCs.

Keywords:  Hematopoietic stem and progenitor cells; T-cells; Thymopoiesis; in vitro T-cell development; single cell; thymic organoids

DOI:  https://doi.org/10.1016/j.celrep.2020.108320
Clin Cancer Res. 2020 Oct 27. pii: clincanres.3684.2020. [Epub ahead of print]

New Drug for Chronic Myeloid Leukemia Might Stimulate the Market.

Martin C Müller.

The evolution of treatment options over the past 20 years has provided for a normal life expectancy for most patients with chronic myeloid leukemia. Currently approved tyrosine kinase inhibitors mainly differ in potency and side effect profile. Flumatinib goes for deep responses and good tolerability.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-3684
Blood Adv. 2020 Oct 27. 4(20): 5285-5296

Oligomonocytic and overt chronic myelomonocytic leukemia show similar clinical, genomic, and immunophenotypic features.

Xavier Calvo, Nieves Garcia-Gisbert, Ivonne Parraga, Joan Gibert, Lourdes Florensa, Marcio Andrade-Campos, Brayan Merchan, Sara Garcia-Avila, Sara Montesdeoca, Concepción Fernández-Rodríguez, Marta Salido, Anna Puiggros, Blanca Espinet, Luís Colomo, David Roman-Bravo, Beatriz Bellosillo, Ana Ferrer, Leonor Arenillas.

Oligomonocytic chronic myelomonocytic leukemia (OM-CMML) is defined as those myelodysplastic syndromes (MDSs) or myelodysplastic/myeloproliferative neoplasms, unclassifiable with relative monocytosis (≥10% monocytes) and a monocyte count of 0.5 to <1 × 109/L. These patients show clinical and genomic features similar to those of overt chronic myelomonocytic leukemia (CMML), although most of them are currently categorized as MDS, according to the World Health Organization 2017 classification. We analyzed the clinicopathologic features of 40 patients with OM-CMML with well-annotated immunophenotypic and molecular data and compared them to those of 56 patients with overt CMML. We found similar clinical, morphological, and cytogenetic features. In addition, OM-CMML mirrored the well-known complex molecular profile of CMML, except for the presence of a lower percentage of RAS pathway mutations. In this regard, of the different genes assessed, only CBL was found to be mutated at a significantly lower frequency. Likewise, the OM-CMML immunophenotypic profile, assessed by the presence of >94% classical monocytes (MO1s) and CD56 and/or CD2 positivity in peripheral blood monocytes, was similar to overt CMML. The MO1 percentage >94% method showed high accuracy for predicting CMML diagnosis (sensitivity, 90.7%; specificity, 92.2%), even when considering OM-CMML as a subtype of CMML (sensitivity, 84.9%; specificity, 92.1%) in our series of 233 patients (39 OM-CMML, 54 CMML, 23 MDS, and 15 myeloproliferative neoplasms with monocytosis and 102 reactive monocytosis). These results support the consideration of OM-CMML as a distinctive subtype of CMML.

DOI: https://doi.org/10.1182/bloodadvances.2020002206
Front Oncol. 2020 ;10 578933

Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes.

Yuanyuan Zhang, Shengling Ma, Moran Wang, Wei Shi, Yu Hu.

  Background: Metabolic reprogramming is the core characteristic of tumors during the development of tumors, and cancer cells can rely on metabolic changes to support their rapid growth. Nevertheless, an overall analysis of metabolic markers in acute myeloid leukemia (AML) is absent and urgently needed. Methods: Within this work, genetic expression, mutation data and clinical data of AML were queried from Genotype-Tissue Expression (GTEx) database, The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. The tumor samples of TCGA were randomly divided into a training group (64 samples) and an internal validation group (64 samples) at one time, and the tumor samples of GEO served as two external validation groups (99 samples, 374 samples). According to the expression levels of survival-associated metabolic genes, we divided all TCGA tumor samples into high, medium and low metabolism groups, and evaluated the immune cell activity in the tumor microenvironment of the three metabolism groups by single-sample gene set enrichment analysis (ssGSEA) algorithm. Finally, we examined the mutations and prognostic effects of each model gene. Results: Four metabolism-related genes were screened and applied to construct a prognostic model for AML, giving excellent results. As for the area under the curve (AUC) value of receiver operating characteristic (ROC) curve, the training group was up to 0.902 (1-year), 0.81 (3-year), and 0.877 (5-year); and the internal and external validation groups also met the expected standards, showing high potency in predicting patient outcome. Univariate and multivariate prognostic analyses indicated that the riskScore obtained from our prognostic model was an independent prognostic factor. ssGSEA analysis revealed the high metabolism group had higher immune activity. Single and multiple gene survival analysis validated that each model gene had significant effects on the overall survival of AML patients. Conclusions: In our study, a high-efficiency prognostic prediction model was built and validated for AML patients. The results showed that metabolism-related genes could become potential prognostic biomarkers for AML.

Keywords:  acute myeloid leukemia; bioinformatic analysis; metabolism; prognosis; survival

DOI:  https://doi.org/10.3389/fonc.2020.578933