bims-tremyl Biomed News
on Therapy resistance biology in myeloid leukemia
Issue of 2021–07–11
thirty-one papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London
  1. SIRT5 Is a Druggable Metabolic Vulnerability in Acute Myeloid Leukemia.
  2. Sphingosine-1-Phosphate Receptor 3 Potentiates Inflammatory Programs in Normal and Leukemia Stem Cells to Promote Differentiation.
  3. Patterns of Resistance Differ in Patients with Acute Myeloid Leukemia Treated with Type I versus Type II FLT3 Inhibitors.
  4. TFEB Links MYC Signaling to Epigenetic Control of Myeloid Differentiation and Acute Myeloid Leukemia.
  5. A Therapeutic Strategy for Preferential Targeting of TET2-Mutant and TET Dioxygenase-Deficient Cells in Myeloid Neoplasms.
  6. Embelin potentiates venetoclax-induced apoptosis in acute myeloid leukemia cells.
  7. A method for overcoming plasma protein inhibition of tyrosine kinase inhibitors.
  8. Avadomide Induces Degradation of ZMYM2 Fusion Oncoproteins in Hematologic Malignancies.
  9. Understanding FLT3 Inhibitor Resistance to Rationalize Combinatorial AML Therapies.
  10. A dual inhibitor overcomes drug-resistant FLT3-ITD acute myeloid leukemia.
  11. The AML-associated K313 mutation enhances C/EBPα activity by leading to C/EBPα overexpression.
  12. Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis.
  13. Mutation signatures of pediatric acute myeloid leukemia and normal blood progenitors associated with differential patient outcomes.
  14. MYC and TFEB Control DNA Methylation and Differentiation in AML.
  15. Non-oncogene Addiction to SIRT5 in Acute Myeloid Leukemia.
  16. Monocytic differentiation and AHR signaling as Primary Nodes of BET Inhibitor Response in Acute Myeloid Leukemia.
  17. Precision oncology in AML: validation of the prognostic value of the knowledge bank approach and suggestions for improvement.
  18. The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations.
  19. Ectopic Humanized Mesenchymal Niche in Mice Enables Robust Engraftment of Myelodysplastic Stem Cells.
  20. A Novel Function of Sphingolipid Signaling via S1PR3 in Hematopoietic and Leukemic Stem Cells.
  21. Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers.
  22. An Evolutionary Approach to Clonally Complex Hematologic Disorders.
  23. PML/RARA destabilization by hyperthermia: a new model for oncogenic fusion protein degradation?
  24. Rapamycin pretreatment rescues the bone marrow AML cell elimination capacity of CAR-T cells.
  25. Menin inhibition decreases Bcl-2 and synergizes with venetoclax in NPM1/FLT3-mutated AML.
  26. Increased donor inhibitory KIR with known HLA interactions provide protection from relapse following HLA matched unrelated donor HCT for AML.
  27. Enzymatic activation of pyruvate kinase increases cytosolic oxaloacetate to inhibit the Warburg effect.
  28. Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis.
  29. Survival in Primary Myelofibrosis: A Population-based Analysis in the Netherlands.
  30. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia.
  31. Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS.
  1. Cancer Discov. 2021 May;2(3): 266-287
    SIRT5 Is a Druggable Metabolic Vulnerability in Acute Myeloid Leukemia.
    Dongqing Yan, Anca Franzini, Anthony D Pomicter, Brayden J Halverson, Orlando Antelope, Clinton C Mason, Jonathan M Ahmann, Anna V Senina, Nadeem A Vellore, Courtney L Jones, Matthew S Zabriskie, Hein Than, Michael J Xiao, Alexandria van Scoyk, Ami B Patel, Phillip M Clair, William L Heaton, Shawn C Owen, Joshua L Andersen, Christina M Egbert, Julie A Reisz, Angelo D'Alessandro, James E Cox, Kevin C Gantz, Hannah M Redwine, Siddharth M Iyer, Jamshid S Khorashad, Nima Rajabi, Christian A Olsen, Thomas O'Hare, Michael W Deininger.
      We discovered that the survival and growth of many primary acute myeloid leukemia (AML) samples and cell lines, but not normal CD34+ cells, are dependent on SIRT5, a lysine deacylase implicated in regulating multiple metabolic pathways. Dependence on SIRT5 is genotype agnostic and extends to RAS- and p53-mutated AML. Results were comparable between SIRT5 knockdown and SIRT5 inhibition using NRD167, a potent and selective SIRT5 inhibitor. Apoptosis induced by SIRT5 disruption is preceded by reductions in oxidative phosphorylation and glutamine utilization, and an increase in mitochondrial superoxide that is attenuated by ectopic superoxide dismutase 2. These data indicate that SIRT5 controls and coordinates several key metabolic pathways in AML and implicate SIRT5 as a vulnerability in AML. SIGNIFICANCE: Reducing SIRT5 activity is detrimental to the survival of AML cells regardless of genotype, yet well tolerated by healthy hematopoietic cells. In mouse models, disrupting SIRT5 inhibits AML progression. SIRT5 controls several metabolic pathways that are required for leukemia cell survival. These results identify SIRT5 as a therapeutic target in AML.See related commentary by Li and Melnick, p. 198.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0168
  2. Cancer Discov. 2021 Jan;2(1): 32-53
    Sphingosine-1-Phosphate Receptor 3 Potentiates Inflammatory Programs in Normal and Leukemia Stem Cells to Promote Differentiation.
    Stephanie Z Xie, Kerstin B Kaufmann, Weijia Wang, Michelle Chan-Seng-Yue, Olga I Gan, Elisa Laurenti, Laura Garcia-Prat, Shin-Ichiro Takayanagi, Stanley W K Ng, ChangJiang Xu, Andy G X Zeng, Liqing Jin, Jessica McLeod, Elvin Wagenblast, Amanda Mitchell, James A Kennedy, Qiang Liu, Héléna Boutzen, Melissa Kleinau, Joseph Jargstorf, Gareth Holmes, Yang Zhang, Veronique Voisin, Gary D Bader, Jean C Y Wang, Yusuf A Hannun, Chiara Luberto, Timm Schroeder, Mark D Minden, John E Dick.
      Acute myeloid leukemia (AML) is a caricature of normal hematopoiesis driven from leukemia stem cells (LSC) that share some hematopoietic stem cell (HSC) programs including responsiveness to inflammatory signaling. Although inflammation dysregulates mature myeloid cells and influences stemness programs and lineage determination in HSCs by activating stress myelopoiesis, such roles in LSCs are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator that drives myeloid differentiation and activates inflammatory programs in both HSCs and LSCs. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across cohorts of patients with AML, each with distinct phenotypic and clinical properties. S1PR3 was high in LSCs and blasts of mature myeloid samples with linkages to chemosensitivity, whereas S1PR3 activation in primitive samples promoted LSC differentiation leading to eradication. Our studies open new avenues for therapeutic target identification specific for each AML subset. SIGNIFICANCE: S1PR3 is a novel regulator of myeloid fate in normal hematopoiesis that is heterogeneously expressed in AML. S1PR3 marks a subset of less primitive AML cases with a distinct inflammatory signature and therefore has clinical implications as both a therapeutic target and a biomarker to distinguish primitive from mature AML.See related commentary by Yang et al., p. 3.This article is highlighted in the In This Issue feature, p. 1.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0155
  3. Cancer Discov. 2021 Mar;2(2): 125-134
    Patterns of Resistance Differ in Patients with Acute Myeloid Leukemia Treated with Type I versus Type II FLT3 Inhibitors.
    Ahmad S Alotaibi, Musa Yilmaz, Rashmi Kanagal-Shamanna, Sanam Loghavi, Tapan M Kadia, Courtney D DiNardo, Gautam Borthakur, Marina Konopleva, Sherry A Pierce, Sa A Wang, Guilin Tang, Veronica Guerra, Bachar Samra, Naveen Pemmaraju, Elias Jabbour, Nicholas J Short, Ghayas C Issa, Maro Ohanian, Guillermo Garcia-Manero, Kapil N Bhalla, Keyur P Patel, Koichi Takahashi, Michael Andreeff, Jorge E Cortes, Hagop M Kantarjian, Farhad Ravandi, Naval Daver.
      Despite promising results with FLT3 inhibitors (FLT3i), response durations remain short. We studied pretreatment and relapse bone marrow samples from patients with FLT3-mutated acute myeloid leukemia (AML) treated with FLT3i-based therapies (secondary resistance cohort), and pretreatment bone marrow samples from patients with no response to FLT3i-based therapies (primary resistance cohort). Targeted next-generation sequencing (NGS) at relapse identified emergent mutations involving on-target FLT3, epigenetic modifiers, RAS/MAPK pathway, and less frequently WT1 and TP53. RAS/MAPK and FLT3-D835 mutations emerged most commonly following type I and II FLT3i-based therapies, respectively. Patients with emergent mutations at relapse had inferior overall survival compared with those without emergent mutations. Among pretreatment RAS-mutated patients, pretreatment cohort-level variant allelic frequencies for RAS were higher in nonresponders, particularly with type I FLT3i-based therapies, suggesting a potential role in primary resistance as well. These data demonstrate distinct pathways of resistance in FLT3-mutated AML treated with type I versus II FLT3i. SIGNIFICANCE: Sequential NGS-based mutational analysis at relapse after FLT3i-based therapies showed distinct pathways of secondary resistance between type I and II FLT3i. FLT3 mutations may be lost at relapse after FLT3i-based therapies. Pretreatment RAS/MAPK mutations may also be associated with primary resistance in patients treated with type I FLT3i.See related commentary by Shastri et al., p. 113.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0143
  4. Cancer Discov. 2021 Mar;2(2): 162-185
    TFEB Links MYC Signaling to Epigenetic Control of Myeloid Differentiation and Acute Myeloid Leukemia.
    Seongseok Yun, Nicole D Vincelette, Xiaoqing Yu, Gregory W Watson, Mario R Fernandez, Chunying Yang, Taro Hitosugi, Chia-Ho Cheng, Audrey R Freischel, Ling Zhang, Weimin Li, Hsinan Hou, Franz X Schaub, Alexis R Vedder, Ling Cen, Kathy L McGraw, Jungwon Moon, Daniel J Murphy, Andrea Ballabio, Scott H Kaufmann, Anders E Berglund, John L Cleveland.
      MYC oncoproteins regulate transcription of genes directing cell proliferation, metabolism, and tumorigenesis. A variety of alterations drive MYC expression in acute myeloid leukemia (AML), and enforced MYC expression in hematopoietic progenitors is sufficient to induce AML. Here we report that AML and myeloid progenitor cell growth and survival rely on MYC-directed suppression of Transcription Factor EB (TFEB), a master regulator of the autophagy-lysosome pathway. Notably, although originally identified as an oncogene, TFEB functions as a tumor suppressor in AML, where it provokes AML cell differentiation and death. These responses reflect TFEB control of myeloid epigenetic programs by inducing expression of isocitrate dehydrogenase-1 (IDH1) and IDH2, resulting in global hydroxylation of 5-methycytosine. Finally, activating the TFEB-IDH1/IDH2-TET2 axis is revealed as a targetable vulnerability in AML. Thus, epigenetic control by an MYC-TFEB circuit dictates myeloid cell fate and is essential for maintenance of AML. SIGNIFICANCE: Alterations in epigenetic control are a hallmark of AML. This study establishes that a MYC-TFEB circuit controls AML differentiation and epigenetic programs by inducing IDH1/IDH2 and hydroxylation of 5-methylcytosine, that TFEB functions as a tumor suppressor in AML, and that this circuit is a targetable vulnerability in AML.See related commentary by Wu and Eisenman, p. 116.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0029
  5. Cancer Discov. 2021 Mar;2(2): 146-161
    A Therapeutic Strategy for Preferential Targeting of TET2-Mutant and TET Dioxygenase-Deficient Cells in Myeloid Neoplasms.
    Yihong Guan, Anand D Tiwari, James G Phillips, Metis Hasipek, Dale R Grabowski, Simona Pagliuca, Priyanka Gopal, Cassandra M Kerr, Vera Adema, Tomas Radivoyevitch, Yvonne Parker, Daniel J Lindner, Manja Meggendorfer, Mohamed Abazeed, Mikkeal A Sekeres, Omar Y Mian, Torsten Haferlach, Jaroslaw P Maciejewski, Babal K Jha.
      TET2 is frequently mutated in myeloid neoplasms. Genetic TET2 deficiency leads to skewed myeloid differentiation and clonal expansion, but minimal residual TET activity is critical for survival of neoplastic progenitor and stem cells. Consistent with mutual exclusivity of TET2 and neomorphic IDH1/2 mutations, here we report that IDH1/2 mutant-derived 2-hydroxyglutarate is synthetically lethal to TET dioxygenase-deficient cells. In addition, a TET-selective small-molecule inhibitor decreases cytosine hydroxymethylation and restricted clonal outgrowth of TET2 mutant but not normal hematopoietic precursor cells in vitro and in vivo. Although TET inhibitor phenocopied somatic TET2 mutations, its pharmacologic effects on normal stem cells are, unlike mutations, reversible. Treatment with TET inhibitor suppresses the clonal evolution of TET2-mutant cells in murine models and TET2-mutated human leukemia xenografts. These results suggest that TET inhibitors may constitute a new class of targeted agents in TET2-mutant neoplasia. SIGNIFICANCE: Loss-of-function somatic TET2 mutations are among the most frequent lesions in myeloid neoplasms and associated disorders. Here we report a strategy for selective targeting of residual TET dioxygenase activity in TET-deficient clones that results in restriction of clonal evolution in vitro and in vivo.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0173
  6. Toxicol In Vitro. 2021 Jun 30. pii: S0887-2333(21)00132-6. [Epub ahead of print] 105207
    Embelin potentiates venetoclax-induced apoptosis in acute myeloid leukemia cells.
    Catarina Sofia Mateus Reis E Silva, Paola Cristina Branco, Keli Lima, Fabiana Lima Silva, Paulo Roberto Hrihorowitsch Moreno, Victor Guallar, Leticia Veras Costa-Lotufo, João Agostinho Machado-Neto.
      Acute myeloid leukemia (AML) belongs to a group of hematological cancer whose relapse cases are often associated with chemoresistance that impairs treatment success and contributes to a poor outcome. For this reason, there is an urgent need for the development of new therapeutic strategies. Herein, we explore the combination of venetoclax, a BCL2 inhibitor, and embelin, an XIAP inhibitor, in the AML cell lines. Combinatory treatment of venetoclax and embelin potentiated cytotoxic effects of these drugs, demonstrating that both in combination present lower IC50 values than single treatment of either venetoclax or embelin alone in both cell lines analyzed. The combinatory treatment further increased the apoptosis-inducing properties of both compounds. Computer simulations suggest that embelin binds to both BIR2 and BIR3 domains of XIAP, reinforcing this inhibitory apoptosis protein as an embelin target. Although all AML cell lines presented similar basal levels of XIAP, the combinatory treatment effectively inhibited XIAP expression in OCI-AML3 cells. In conclusion, the inhibition of both apoptosis inhibitory players, BCL2 and XIAP, by venetoclax and embelin, respectively, potentiated their cytotoxic effects in AML cell lines.
    Keywords:  Acute myeloid leukemia; Apoptosis; Embelin; Venetoclax
    DOI:  https://doi.org/10.1016/j.tiv.2021.105207
  7. Cancer Discov. 2021 Jul 02. pii: bloodcandisc.0119.2020. [Epub ahead of print]
    A method for overcoming plasma protein inhibition of tyrosine kinase inhibitors.
    David J Young, Bao Nguyen, Li Li, Tomoyasu Higashimoto, Mark J Levis, Jun O Liu, Donald Small.
      FMS-like tyrosine kinase 3 (FLT3) is the most frequently-mutated gene in acute myeloid leukemia and a target for tyrosine kinase inhibitors (TKI). FLT3 TKI have yielded limited improvements to clinical outcomes. One reason for this is TKI inhibition by endogenous factors. We characterized plasma protein binding of FLT3 TKI, specifically staurosporine-derivatives (STS-TKI) by alpha-1-acid glycoprotein (AGP); simulating its effects upon drug efficacy. Human AGP inhibits the anti-proliferative activity of STS-TKI in FLT3-ITD-dependent cells, with IC50 shifts higher than clinically achievable. This is not seen with non-human plasma. Mifepristone co-treatment, with its higher AGP affinity, improves TKI activity despite AGP, yielding IC50s predicted to be clinically effective. In a mouse model of AGP drug inhibition, mifepristone restores midostaurin activity. This suggests combinatorial methods for overcoming plasma protein inhibition of existing TKIs for leukemia as well as providing a platform for investigating the drug-protein interaction space for developing more potent small-molecule agents.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0119
  8. Cancer Discov. 2021 May;2(3): 250-265
    Avadomide Induces Degradation of ZMYM2 Fusion Oncoproteins in Hematologic Malignancies.
    Aline Renneville, Jessica A Gasser, Daniel E Grinshpun, Pierre M Jean Beltran, Namrata D Udeshi, Mary E Matyskiela, Thomas Clayton, Marie McConkey, Kaushik Viswanathan, Alexander Tepper, Andrew A Guirguis, Rob S Sellar, Sophie Cotteret, Christophe Marzac, Véronique Saada, Stéphane De Botton, Jean-Jacques Kiladjian, Jean-Michel Cayuela, Mark Rolfe, Philip P Chamberlain, Steven A Carr, Benjamin L Ebert.
      Thalidomide analogues exert their therapeutic effects by binding to the CRL4CRBN E3 ubiquitin ligase, promoting ubiquitination and subsequent proteasomal degradation of specific protein substrates. Drug-induced degradation of IKZF1 and IKZF3 in B-cell malignancies demonstrates the clinical utility of targeting disease-relevant transcription factors for degradation. Here, we found that avadomide (CC-122) induces CRBN-dependent ubiquitination and proteasomal degradation of ZMYM2 (ZNF198), a transcription factor involved in balanced chromosomal rearrangements with FGFR1 and FLT3 in aggressive forms of hematologic malignancies. The minimal drug-responsive element of ZMYM2 is a zinc-chelating MYM domain and is contained in the N-terminal portion of ZMYM2 that is universally included in the derived fusion proteins. We demonstrate that avadomide has the ability to induce proteasomal degradation of ZMYM2-FGFR1 and ZMYM2-FLT3 chimeric oncoproteins, both in vitro and in vivo. Our findings suggest that patients with hematologic malignancies harboring these ZMYM2 fusion proteins may benefit from avadomide treatment. SIGNIFICANCE: We extend the potential clinical scope of thalidomide analogues by the identification of a novel avadomide-dependent CRL4CRBN substrate, ZMYM2. Avadomide induces ubiquitination and degradation of ZMYM2-FGFR1 and ZMYM2-FLT3, two chimeric oncoproteins involved in hematologic malignancies, providing a proof of concept for drug-induced degradation of transcription factor fusion proteins by thalidomide analogues.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0105
  9. Cancer Discov. 2021 Mar;2(2): 113-115
    Understanding FLT3 Inhibitor Resistance to Rationalize Combinatorial AML Therapies.
    Aditi Shastri, Jesus Gonzalez-Lugo, Amit Verma.
      Patients treated with Fms-like tyrosine kinase 3 (FLT3) inhibitor-based acute myeloid leukemia therapies nearly always develop resistance. In this issue, Alotaibi and colleagues describe the patterns of mutations that emerge upon relapse after FLT3 inhibitor therapy after initial response, as well as in treatment-refractory disease in a single-institution study; the findings offer insights for sequential therapies targeting the dominant clone at the time of relapse.See related article by Alotaibi et al., p. 125.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0210
  10. J Hematol Oncol. 2021 Jul 03. 14(1): 105
    A dual inhibitor overcomes drug-resistant FLT3-ITD acute myeloid leukemia.
    Peihong Wang, Xinhua Xiao, Yuyin Zhang, Baoyuan Zhang, Donghe Li, Mingzhu Liu, Xi Xie, Chenxuan Liu, Ping Liu, Ruibao Ren.
      FLT3 mutations are the most frequently identified genetic alterations in acute myeloid leukemia (AML) and are associated with poor prognosis. Multiple FLT3 inhibitors are in various stages of clinical evaluation. However, resistance to FLT3 inhibitors resulting from acquired point mutations in tyrosine kinase domain (TKD) have limited the sustained efficacy of treatments, and a "gatekeeper" mutation (F691L) is resistant to most available FLT3 inhibitors. Thus, new FLT3 inhibitors against both FLT3 internal tandem duplication (FLT3-ITD) and FLT3-TKD mutations (including F691L) are urgently sought. Herein, we identified KX2-391 as a dual FLT3 and tubulin inhibitor and investigated its efficacy and mechanisms in overcoming drug-resistant FLT3-ITD-TKD mutations in AML. KX2-391 exhibited potent growth inhibitory and apoptosis promoting effects on diverse AML cell lines harboring FLT3-ITD mutations and AC220-resistant mutations at the D835 and F691 residues in TKD and inhibited FLT3 phosphorylation and its downstream signaling targets. Orally administered KX2-391 significantly prolonged the survival of a murine leukemia model induced by FLT3-ITD-F691L. KX2-391 also significantly inhibited the growth of 4 primary AML cells expressing FLT3-ITD and 2 primary AML cells expressing FLT3-ITD-D835Y. Our preclinical data highlight KX2-391 as a promising FLT3 inhibitor for the treatment of AML patients harboring FLT3 mutations, especially refractory/relapsed patients with F691L and other FLT3-TKD mutations.
    Keywords:  AC220; Acute myeloid leukemia; FLT3 resistance mutation; FLT3-ITD; KX2-391
    DOI:  https://doi.org/10.1186/s13045-021-01098-y
  11. Cell Death Dis. 2021 Jul 05. 12(7): 675
    The AML-associated K313 mutation enhances C/EBPα activity by leading to C/EBPα overexpression.
    Ian Edward Gentle, Isabel Moelter, Mohamed Tarek Badr, Konstanze Döhner, Michael Lübbert, Georg Häcker.
      Mutations in the transcription factor C/EBPα are found in ~10% of all acute myeloid leukaemia (AML) cases but the contribution of these mutations to leukemogenesis is incompletely understood. We here use a mouse model of granulocyte progenitors expressing conditionally active HoxB8 to assess the cell biological and molecular activity of C/EBPα-mutations associated with human AML. Both N-terminal truncation and C-terminal AML-associated mutations of C/EBPα substantially altered differentiation of progenitors into mature neutrophils in cell culture. Closer analysis of the C/EBPα-K313-duplication showed expansion and prolonged survival of mutant C/EBPα-expressing granulocytes following adoptive transfer into mice. C/EBPα-protein containing the K313-mutation further showed strongly enhanced transcriptional activity compared with the wild-type protein at certain promoters. Analysis of differentially regulated genes in cells overexpressing C/EBPα-K313 indicates a strong correlation with genes regulated by C/EBPα. Analysis of transcription factor enrichment in the differentially regulated genes indicated a strong reliance of SPI1/PU.1, suggesting that despite reduced DNA binding, C/EBPα-K313 is active in regulating target gene expression and acts largely through a network of other transcription factors. Strikingly, the K313 mutation caused strongly elevated expression of C/EBPα-protein, which could also be seen in primary K313 mutated AML blasts, explaining the enhanced C/EBPα activity in K313-expressing cells.
    DOI:  https://doi.org/10.1038/s41419-021-03948-6
  12. Cancer Discov. 2021 Jul;2(4): 319-325
    Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis.
    Laura W Dillon, Jack Ghannam, Chidera Nosiri, Gege Gui, Meghali Goswami, Katherine R Calvo, Katherine E Lindblad, Karolyn A Oetjen, Matthew D Wilkerson, Anthony R Soltis, Gauthaman Sukumar, Clifton L Dalgard, Julie Thompson, Janet Valdez, Christin B DeStefano, Catherine Lai, Adam Sciambi, Robert Durruthy-Durruthy, Aaron Llanso, Saurabh Gulati, Shu Wang, Aik Ooi, Pradeep K Dagur, J Philip McCoy, Patrick Burr, Yuesheng Li, Christopher S Hourigan.
      Genetic mutations associated with acute myeloid leukemia (AML) also occur in age-related clonal hematopoiesis, often in the same individual. This makes confident assignment of detected variants to malignancy challenging. The issue is particularly crucial for AML posttreatment measurable residual disease monitoring, where results can be discordant between genetic sequencing and flow cytometry. We show here that it is possible to distinguish AML from clonal hematopoiesis and to resolve the immunophenotypic identity of clonal architecture. To achieve this, we first design patient-specific DNA probes based on patient's whole-genome sequencing and then use them for patient-personalized single-cell DNA sequencing with simultaneous single-cell antibody-oligonucleotide sequencing. Examples illustrate AML arising from DNMT3A- and TET2-mutated clones as well as independently. The ability to personalize single-cell proteogenomic assessment for individual patients based on leukemia-specific genomic features has implications for ongoing AML precision medicine efforts. SIGNIFICANCE: This study offers a proof of principle of patient-personalized customized single-cell proteogenomics in AML including whole-genome sequencing-defined structural variants, currently unmeasurable by commercial "off-the-shelf" panels. This approach allows for the definition of genetic and immunophenotype features for an individual patient that would be best suited for measurable residual disease tracking.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-21-0046
  13. Cancer Discov. 2021 Jul 02. pii: bloodcandisc.0010.2021. [Epub ahead of print]
    Mutation signatures of pediatric acute myeloid leukemia and normal blood progenitors associated with differential patient outcomes.
    Arianne M Brandsma, Eline J M Bertrums, Markus J van Roosmalen, Damon A Hofman, Rurika Oka, Mark Verheul, Freek Manders, Joske Ubels, Mirjam E Belderbos, Ruben van Boxtel.
      Acquisition of oncogenic mutations with age is believed to be rate limiting for carcinogenesis. However, the incidence of leukemia in children is higher than in young adults. Here we compare somatic mutations across pediatric acute myeloid leukemia (pAML) patient-matched leukemic blasts and hematopoietic stem and progenitor cells (HSPCs), as well as HSPCs from age-matched healthy donors. HSPCs in the leukemic bone marrow have limited genetic relatedness and share few somatic mutations with the cell-of-origin of the malignant blasts, suggesting polyclonal hematopoiesis in pAML patients. Compared to normal HSPCs, a subset of pAML cases harbored more somatic mutations and a distinct composition of mutational process signatures. We hypothesize these cases might have arisen from a more committed progenitor. This subset had better outcomes than pAML cases with mutation burden comparable to age-matched healthy HSPCs. Our study provides insights into the etiology and patient stratification of pAML.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-21-0010
  14. Cancer Discov. 2021 Mar;2(2): 116-118
    MYC and TFEB Control DNA Methylation and Differentiation in AML.
    Xiaoying Wu, Robert N Eisenman.
      Although the MYC transcription factor has been consistently implicated in acute myeloid leukemia (AML), its gene targets and precise role in leukemogenesis remain unknown. In this issue of Blood Cancer Discovery, Yun and colleagues provide evidence that MYC directly suppresses the expression of TFEB, an mTORC1-regulated transcription factor. They show that, in the context of the myelocytic/granulocytic lineage, TFEB acts as a tumor suppressor by inducing the IDH1/2-TET pathway, which in turn, leads to altered DNA methylation and increased expression of genes involved in myeloid differentiation and apoptosis. Therefore, high levels of MYC suppress an epigenetic pathway that should normally act to attenuate leukemic progression. Identification of the components of this pathway is likely to inform new therapeutic tactics for AML and possibly other cancers.See related article by Yun et al., p. 162.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0230
  15. Cancer Discov. 2021 May;2(3): 198-200
    Non-oncogene Addiction to SIRT5 in Acute Myeloid Leukemia.
    Meng Li, Ari M Melnick.
      In this issue of Blood Cancer Discovery, Yan and colleagues discovered that mitochondrial deacylase, SIRT5, is required in AML cells to support mitochondrial oxidative phosphorylation, maintain redox homeostasis, and drive glutaminolysis. The new SIRT5 inhibitor, NRD167, can efficiently target SIRT5 in AMLs at micromolar range and may constitute a novel therapeutic approach to improve clinical outcomes of patients with AML.See related article by Yan et al., p. 266.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-21-0026
  16. Cancer Discov. 2021 Jul 01. pii: bloodcandisc.0012.2021. [Epub ahead of print]
    Monocytic differentiation and AHR signaling as Primary Nodes of BET Inhibitor Response in Acute Myeloid Leukemia.
    Kyle A Romine, Tamilla Nechiporuk, Daniel Bottomly, Sophia Jeng, Shannon K McWeeney, Andy Kaempf, M Ryan Corces, Ravindra Majeti, Jeffrey W Tyner.
      To understand mechanisms of response to BET inhibitors (BETi), we mined the Beat AML functional genomic dataset and performed genome-wide CRISPR screens on BETi- sensitive and BETi- resistant AML cells. Both strategies revealed regulators of monocytic differentiation, SPI1, JUNB, FOS, and aryl-hydrocarbon receptor signaling (AHR/ARNT), as determinants of BETi response. AHR activation synergized with BETi while inhibition antagonized BETi-mediated cytotoxicity. Consistent with BETi sensitivity dependence on monocytic differentiation, ex vivo sensitivity to BETi in primary AML patient samples correlated with higher expression of monocytic markers CSF1R, LILRs, and VCAN. In addition, HL-60 cell line differentiation enhanced its sensitivity to BETi. Further, screens to rescue BETi sensitivity identified BCL2 and CDK6 as druggable vulnerabilities.¬¬ Finally, monocytic AML patient samples refractory to venetoclax ex vivo were significantly more sensitive to combined BETi + venetoclax. Together, our work highlights mechanisms that could predict BETi response and identifies combination strategies to overcome resistance.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-21-0012
  17. J Hematol Oncol. 2021 Jul 06. 14(1): 107
    Precision oncology in AML: validation of the prognostic value of the knowledge bank approach and suggestions for improvement.
    Marius Bill, Krzysztof Mrózek, Brian Giacopelli, Jessica Kohlschmidt, Deedra Nicolet, Dimitrios Papaioannou, Ann-Kathrin Eisfeld, Jonathan E Kolitz, Bayard L Powell, Andrew J Carroll, Richard M Stone, Ramiro Garzon, John C Byrd, Clara D Bloomfield, Christopher C Oakes.
      Recently, a novel knowledge bank (KB) approach to predict outcomes of individual patients with acute myeloid leukemia (AML) was developed using unbiased machine learning. To validate its prognostic value, we analyzed 1612 adults with de novo AML treated on Cancer and Leukemia Group B front-line trials who had pretreatment clinical, cytogenetics, and mutation data on 81 leukemia/cancer-associated genes available. We used receiver operating characteristic (ROC) curves and the area under the curve (AUC) to evaluate the predictive values of the KB algorithm and other risk classifications. The KB algorithm predicted 3-year overall survival (OS) probability in the entire patient cohort (AUCKB = 0.799), and both younger (< 60 years) (AUCKB = 0.747) and older patients (AUCKB = 0.770). The KB algorithm predicted non-remission death (AUCKB = 0.860) well but was less accurate in predicting relapse death (AUCKB = 0.695) and death in first complete remission (AUCKB = 0.603). The KB algorithm's 3-year OS predictive value was higher than that of the 2017 European LeukemiaNet (ELN) classification (AUC2017ELN = 0.707, p < 0.001) and 2010 ELN classification (AUC2010ELN = 0.721, p < 0.001) but did not differ significantly from that of the 17-gene stemness score (AUC17-gene = 0.732, p = 0.10). Analysis of additional cytogenetic and molecular markers not included in the KB algorithm revealed that taking into account atypical complex karyotype, infrequent recurrent balanced chromosome rearrangements and mutational status of the SAMHD1, AXL and NOTCH1 genes may improve the KB algorithm. We conclude that the KB algorithm has a high predictive value that is higher than those of the 2017 and 2010 ELN classifications. Inclusion of additional genetic features might refine the KB algorithm.
    Keywords:  Acute myeloid leukemia; Clinical outcome; Gene mutations; Knowledge bank; Next-generation sequencing
    DOI:  https://doi.org/10.1186/s13045-021-01118-x
  18. Nat Commun. 2021 07 05. 12(1): 4130
    The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations.
    Brianna J Klein, Anagha Deshpande, Khan L Cox, Fan Xuan, Mohamad Zandian, Karina Barbosa, Sujita Khanal, Qiong Tong, Yi Zhang, Pan Zhang, Amit Sinha, Stefan K Bohlander, Xiaobing Shi, Hong Wen, Michael G Poirier, Aniruddha J Deshpande, Tatiana G Kutateladze.
      Chromosomal translocations of the AF10 (or MLLT10) gene are frequently found in acute leukemias. Here, we show that the PZP domain of AF10 (AF10PZP), which is consistently impaired or deleted in leukemogenic AF10 translocations, plays a critical role in blocking malignant transformation. Incorporation of functional AF10PZP into the leukemogenic CALM-AF10 fusion prevents the transforming activity of the fusion in bone marrow-derived hematopoietic stem and progenitor cells in vitro and in vivo and abrogates CALM-AF10-mediated leukemogenesis in vivo. Crystallographic, biochemical and mutagenesis studies reveal that AF10PZP binds to the nucleosome core particle through multivalent contacts with the histone H3 tail and DNA and associates with chromatin in cells, colocalizing with active methylation marks and discriminating against the repressive H3K27me3 mark. AF10PZP promotes nuclear localization of CALM-AF10 and is required for association with chromatin. Our data indicate that the disruption of AF10PZP function in the CALM-AF10 fusion directly leads to transformation, whereas the inclusion of AF10PZP downregulates Hoxa genes and reverses cellular transformation. Our findings highlight the molecular mechanism by which AF10 targets chromatin and suggest a model for the AF10PZP-dependent CALM-AF10-mediated leukemogenesis.
    DOI:  https://doi.org/10.1038/s41467-021-24418-9
  19. Cancer Discov. 2021 Mar;2(2): 135-145
    Ectopic Humanized Mesenchymal Niche in Mice Enables Robust Engraftment of Myelodysplastic Stem Cells.
    Syed A Mian, Ander Abarrategi, Kar Lok Kong, Kevin Rouault-Pierre, Henry Wood, Caroline A Oedekoven, Alexander E Smith, Antoniana Batsivari, Linda Ariza-McNaughton, Peter Johnson, Thomas Snoeks, Ghulam J Mufti, Dominique Bonnet.
      Myelodysplastic syndromes (MDS) are clonal stem cell diseases characterized mainly by ineffective hematopoiesis. Here, we present an approach that enables robust long-term engraftment of primary MDS stem cells (MDS-SC) in mice by implantation of human mesenchymal cell-seeded scaffolds. Critically for modeling MDS, where patient sample material is limiting, mononuclear bone marrow cells containing as few as 104 CD34+ cells can be engrafted and expanded by this approach with the maintenance of the genetic make-up seen in the patients. Noninvasive high-resolution ultrasound imaging shows that these scaffolds are fully perfused. Our data show that the human microenvironment but not mouse is essential to MDS-SC homing and engraftment. Notably, the alternative niche provided by healthy donor mesenchymal stromal cells enhances engraftment of MDS-SCs. This study characterizes a new tool to model MDS human disease with the level of engraftment previously unattainable in mice and offers insights into human-specific determinants of the MDS-SC microenvironment. SIGNIFICANCE: These findings are significant for understanding the niche dependence of MDS. This report provides the evidence of the migratory behavior of hematopoietic stem cells in myeloid cancers. Our model offers a unique opportunity to study the clonal behavior of the myeloid/lymphoid cancers and delineate how cancer cells interact with different niches.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0161
  20. Cancer Discov. 2021 Jan;2(1): 3-5
    A Novel Function of Sphingolipid Signaling via S1PR3 in Hematopoietic and Leukemic Stem Cells.
    Chong Yang, Masayuki Yamashita, Toshio Suda.
      In this issue of Blood Cancer Discovery, Xie and colleagues describe a novel function of sphingosine-1-phosphate receptor 3 (S1PR3) to regulate myeloid differentiation and activate inflammatory programs in both human hematopoietic stem cells and leukemic stem cells. They propose S1PR3 as a major downstream signaling pathway of a TNFα-NF-κB axis in this study and unlock potential therapeutic opportunities to improve outcomes of patients with acute myeloid leukemia by modulating sphingolipid signaling via S1PR3.See related article by Xie et al., p. 32.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0200
  21. Cancer Discov. 2021 May;2(3): 226-237
    Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers.
    Julie E Feusier, Sasi Arunachalam, Tsewang Tashi, Monika J Baker, Chad VanSant-Webb, Amber Ferdig, Bryan E Welm, Juan L Rodriguez-Flores, Christopher Ours, Lynn B Jorde, Josef T Prchal, Clinton C Mason.
      Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detectable hematopoietic-associated gene mutations in a person without evidence of hematologic malignancy. We sought to identify additional cancer-presenting mutations usable for CHIP detection by performing a data mining analysis of 48 somatic mutation landscape studies reporting mutations at diagnoses of 7,430 adult and pediatric patients with leukemia or other hematologic malignancy. Following extraction of 20,141 protein-altering mutations, we identified 434 significantly recurrent mutation hotspots, 364 of which occurred at loci confidently assessable for CHIP. We then performed an additional large-scale analysis of whole-exome sequencing data from 4,538 persons belonging to three noncancer cohorts for clonal mutations. We found the combined cohort prevalence of CHIP with mutations identical to those reported at blood cancer mutation hotspots to be 1.8%, and that some of these CHIP mutations occurred in children. Our findings may help to improve CHIP detection and precancer surveillance for both children and adults. SIGNIFICANCE: This study identifies frequently occurring mutations across several blood cancers that may drive hematologic malignancies and signal increased risk for cancer when detected in healthy persons. We find clonal mutations at these hotspots in a substantial number of individuals from noncancer cohorts, including children, showcasing potential for improved precancer surveillance.See related commentary by Spitzer and Levine, p. 192.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0094
  22. Cancer Discov. 2021 May;2(3): 201-215
    An Evolutionary Approach to Clonally Complex Hematologic Disorders.
    Emily Schwenger, Ulrich Steidl.
      Emerging clonal complexity has brought into question the way in which we perceive and, in turn, treat disorders of the hematopoietic system. Former models of cell-intrinsic clonal dominance driven by acquisition of driver genes in a stereotypic sequence are often insufficient in explaining observations such as clonal hematopoiesis, and new paradigms are in order. Here, we review the evidence within the hematologic malignancy field and also borrow from perspectives rooted in evolutionary biology to reframe pathogenesis of hematologic disorders as dynamic processes involving complex interplays of genetic and nongenetic subclones and the tissue microenvironment in which they reside. SIGNIFICANCE: Hematopoietic malignant and premalignant syndromes exhibit vast clonal diversity that is subject to selection imposed by the tissue microenvironment, as well as artificial selection by therapy. Tackling these disorders requires an appreciation of heterogeneity at both genetic and nongenetic levels, which can be borrowed from evolutionary biology principles. Models and drug development strategies that veer away from targeting solely dominant clones and, instead, embrace this complexity to outsmart it are required for long-term remission.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0219
  23. Blood Cancer Discov. 2021 Jun 10. 2 300-301
    PML/RARA destabilization by hyperthermia: a new model for oncogenic fusion protein degradation?
    Hsin Chieh Wu, Domitille Rérolle, Hugues de Thé.
      In this issue, Maimaitiyiming and colleagues demonstrate thermic stress-induced PML/RARA oncogenic fusion protein destabilization driven by corepressor aggregation. Hyperthermia synergizes with PML/RARA degradation by ATO and may circumvent ATO-resistance in historical APL patients. This novel approach could be extended to other corepressor-associated oncogenic fusion proteins.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-21-0071
  24. Clin Cancer Res. 2021 Jul 07. pii: clincanres.0452.2021. [Epub ahead of print]
    Rapamycin pretreatment rescues the bone marrow AML cell elimination capacity of CAR-T cells.
    Zhigang Nian, Xiaohu Zheng, Yingchao Dou, Xianghui Du, Li Zhou, Binqing Fu, Rui Sun, Zhigang Tian, Haiming Wei.
       PURPOSE: Ongoing clinical trials show limited efficacy for Chimeric antigen receptor (CAR) T treatment for acute myeloid leukemia (AML). The aim of the present study was to identify potential causes of the reported limited efficacy from CAR-T therapies against AML.
    EXPERIMENTAL DESIGN: We generated CAR-T cells targeting Epithelial cell adhesion molecule (EpCAM) and evaluated their killing activity against AML cells. We examined the impacts of modulating mTORC1 and mTORC2 signaling in CAR-T cells in terms of CXCR4 levels. We examined the effects of a rapamycin pretreatment of EpCAM CAR-T cells and assessed the in vivo antitumor efficacy of rapamycin pretreated EpCAM CAR-T cells and CD33 CAR-T cells in leukemia xenograft mouse models.
    RESULTS: EpCAM CAR-T exhibited killing activity against AML cells but failed to eliminate AML cells in bone marrow. Subsequent investigations revealed that aberrantly activated mTORC1 signaling in CAR-T cells results in decreased bone marrow infiltration and decreased the levels of the rapamycin target CXCR4. Attenuating mTORC1 activity with the rapamycin pretreatment increased the capacity of CAR-T cells to infiltrate bone marrow and enhanced the extent of bone marrow AML cell elimination in leukemia xenograft mouse models. CXCR4 knockdown experiments showed that CXCR4 contributes to the enhanced bone marrow infiltration capacity of EpCAM CAR-T cells and the observed reduction in bone marrow AML cell.
    CONCLUSIONS: Our study reveals a potential cause for the limited efficacy of CAR-T reported from current AML clinical trials and illustrates an easy-to-implement pretreatment strategy which enhances the anti-AML efficacy of CAR-T cells.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-0452
  25. Blood. 2021 Jul 07. pii: blood.2021011917. [Epub ahead of print]
    Menin inhibition decreases Bcl-2 and synergizes with venetoclax in NPM1/FLT3-mutated AML.
    Bing Z Carter, Wenjing Tao, Po Yee Mak, Lauren B Ostermann, Duncan H Mak, Gerard M McGeehan, Peter Ordentlich, Michael Andreeff.
      
    DOI:  https://doi.org/10.1182/blood.2021011917
  26. Bone Marrow Transplant. 2021 Jul 07.
    Increased donor inhibitory KIR with known HLA interactions provide protection from relapse following HLA matched unrelated donor HCT for AML.
    Elizabeth Krieger, Rehan Qayyum, Armand Keating, Amir Toor.
      Killer immunoglobulin-like receptor (KIR) and KIR-ligand (KIRL) interactions play an important role in natural killer cell-mediated graft versus leukemia effect (GVL) after hematopoietic cell transplant (HCT) for AML. Accounting for known KIR-KIRL interactions may identify donors with optimal NK cell-mediated alloreactivity and GVL. A retrospective study of 2359 donor-recipient pairs (DRP) who underwent unrelated donor (URD) HCT for AML was performed. KIR-KIRL combinations were determined and associations with clinical outcomes examined. Relapse risk was reduced in DRP with both higher inhibitory KIR-KIRL (iKIR) and missing KIRL (mKIR) scores, with HR 0.86 (P = 0.01) & HR 0.84 (P = 0.02) respectively. The iKIR and mKIR score components were summed to give a maximal inhibitory KIR ligand (IM-KIR) score for each donor, which if it was 5, as opposed to <5, was also associated with a lower relapse risk, SHR 0.8 (P = 0.004). All IM = 5 donors possess KIR Haplotype B/x. Transplant-related mortality was increased among those with IM-KIR = 5, HR, 1.32 (P = 0.01). In a subset analysis of those transplanted with 8/8 HLA-matched DRP, anti-thymocyte globulin recipients with IM-KIR = 5, had a lower relapse rate HR, 0.61 (p = 0.001). This study demonstrates that HLA-matched unrelated donors with the highest inhibitory KIR content confer relapse protection, albeit with increased TRM. These donors all have KIR haplotype B. Clinical trials utilizing donors with a higher iKIR content in conjunction with novel strategies to reduce TRM should be considered for URD HCT in recipients with AML to optimize clinical outcomes.
    DOI:  https://doi.org/10.1038/s41409-021-01393-9
  27. Nat Metab. 2021 Jul 05.
    Enzymatic activation of pyruvate kinase increases cytosolic oxaloacetate to inhibit the Warburg effect.
    Elizabeth K Wiese, Sadae Hitosugi, Sharon T Loa, Annapoorna Sreedhar, Lindsey G Andres-Beck, Kiran Kurmi, Yuan-Ping Pang, Larry M Karnitz, Wilson I Gonsalves, Taro Hitosugi.
      Pharmacological activation of the glycolytic enzyme PKM2 or expression of the constitutively active PKM1 isoform in cancer cells results in decreased lactate production, a phenomenon known as the PKM2 paradox in the Warburg effect. Here we show that oxaloacetate (OAA) is a competitive inhibitor of human lactate dehydrogenase A (LDHA) and that elevated PKM2 activity increases de novo synthesis of OAA through glutaminolysis, thereby inhibiting LDHA in cancer cells. We also show that replacement of human LDHA with rabbit LDHA, which is relatively resistant to OAA inhibition, eliminated the paradoxical correlation between the elevated PKM2 activity and the decreased lactate concentration in cancer cells treated with a PKM2 activator. Furthermore, rabbit LDHA-expressing tumours, compared to human LDHA-expressing tumours in mice, displayed resistance to the PKM2 activator. These findings describe a mechanistic explanation for the PKM2 paradox by showing that OAA accumulates and inhibits LDHA following PKM2 activation.
    DOI:  https://doi.org/10.1038/s42255-021-00424-5
  28. Nat Med. 2021 Jul 08.
    Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis.
    Ryunosuke Saiki, Yukihide Momozawa, Yasuhito Nannya, Masahiro M Nakagawa, Yotaro Ochi, Tetsuichi Yoshizato, Chikashi Terao, Yutaka Kuroda, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Atsushi Niida, Seiya Imoto, Koichi Matsuda, Takayuki Morisaki, Yoshinori Murakami, Yoichiro Kamatani, Shuichi Matsuda, Michiaki Kubo, Satoru Miyano, Hideki Makishima, Seishi Ogawa.
      Clonal hematopoiesis (CH) in apparently healthy individuals is implicated in the development of hematological malignancies (HM) and cardiovascular diseases. Previous studies of CH analyzed either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here, using a combination of targeted sequencing of 23 CH-related genes and array-based CNA detection of blood-derived DNA, we have delineated the landscape of CH-related SNVs/indels and CNAs in 11,234 individuals without HM from the BioBank Japan cohort, including 672 individuals with subsequent HM development, and studied the effects of these somatic alterations on mortality from HM and cardiovascular disease, as well as on hematological and cardiovascular phenotypes. The total number of both types of CH-related lesions and their clone size positively correlated with blood count abnormalities and mortality from HM. CH-related SNVs/indels and CNAs exhibited statistically significant co-occurrence in the same individuals. In particular, co-occurrence of SNVs/indels and CNAs affecting DNMT3A, TET2, JAK2 and TP53 resulted in biallelic alterations of these genes and was associated with higher HM mortality. Co-occurrence of SNVs/indels and CNAs also modulated risks for cardiovascular mortality. These findings highlight the importance of detecting both SNVs/indels and CNAs in the evaluation of CH.
    DOI:  https://doi.org/10.1038/s41591-021-01411-9
  29. Hemasphere. 2021 Jul;5(7): e595
    Survival in Primary Myelofibrosis: A Population-based Analysis in the Netherlands.
    Stefanie Slot, Avinash G Dinmohamed, Otto Visser, Peter A W Te Boekhorst, Sonja Zweegman.
      
    DOI:  https://doi.org/10.1097/HS9.0000000000000595
  30. Nat Commun. 2021 Jul 06. 12(1): 4164
    Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia.
    Quentin Van Thillo, Jolien De Bie, Janith A Seneviratne, Sofie Demeyer, Sofia Omari, Anushree Balachandran, Vicki Zhai, Wai L Tam, Bram Sweron, Ellen Geerdens, Olga Gielen, Sarah Provost, Heidi Segers, Nancy Boeckx, Glenn M Marshall, Belamy B Cheung, Kiyotaka Isobe, Itaru Kato, Junko Takita, Timothy G Amos, Ira W Deveson, Hannah McCalmont, Richard B Lock, Ethan P Oxley, Maximilian M Garwood, Ross A Dickins, Anne Uyttebroeck, Daniel R Carter, Jan Cools, Charles E de Bock.
      Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
    DOI:  https://doi.org/10.1038/s41467-021-24442-9
  31. Cancer Discov. 2021 May;2(3): 238-249
    Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS.
    Oscar E Brück, Susanna E Lallukka-Brück, Helena R Hohtari, Aleksandr Ianevski, Freja T Ebeling, Panu E Kovanen, Soili I Kytölä, Tero A Aittokallio, Pedro M Ramos, Kimmo V Porkka, Satu M Mustjoki.
      In myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN), bone marrow (BM) histopathology is assessed to identify dysplastic cellular morphology, cellularity, and blast excess. Yet, other morphologic findings may elude the human eye. We used convolutional neural networks to extract morphologic features from 236 MDS, 87 MDS/MPN, and 11 control BM biopsies. These features predicted genetic and cytogenetic aberrations, prognosis, age, and gender in multivariate regression models. Highest prediction accuracy was found for TET2 [area under the receiver operating curve (AUROC) = 0.94] and spliceosome mutations (0.89) and chromosome 7 monosomy (0.89). Mutation prediction probability correlated with variant allele frequency and number of affected genes per pathway, demonstrating the algorithms' ability to identify relevant morphologic patterns. By converting regression models to texture and cellular composition, we reproduced the classical del(5q) MDS morphology consisting of hypolobulated megakaryocytes. In summary, this study highlights the potential of linking deep BM histopathology with genetics and clinical variables. SIGNIFICANCE: Histopathology is elementary in the diagnostics of patients with MDS, but its high-dimensional data are underused. By elucidating the association of morphologic features with clinical variables and molecular genetics, this study highlights the vast potential of convolutional neural networks in understanding MDS pathology and how genetics is reflected in BM morphology.See related commentary by Elemento, p. 195.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0162
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