bims-tremyl 2021-06-06 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2021‒06‒06
twenty-five papers selected by
Paolo Gallipoli
Barts Cancer Institute, Queen Mary University of London

Machine Learning Integrates Genomic Signatures for Subclassification Beyond Primary and Secondary Acute Myeloid Leukemia.
ATF3 coordinates serine and nucleotide metabolism to drive cell cycle progression in acute myeloid leukemia.
What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort.
Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells.
Acute myeloid leukemia with IDH1 and IDH2 mutations: 2021 treatment algorithm.
The Mutational Landscape of Acute Myeloid Leukaemia Predicts Responses and Outcomes in Elderly Patients from the PETHEMA-FLUGAZA Phase 3 Clinical Trial.
Acute Myeloid Leukemia: Is It T Time?
Mitochondrial metabolism: powering new directions in acute myeloid leukemia.
Allogenic Stem Cell Transplantation Abrogates Negative Impact on Outcome of AML Patients with KMT2A Partial Tandem Duplication.
Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients.
HOXA11 plays critical roles in disease progression and response to cytarabine in AML.
Prognostic value of measurable residual disease monitoring by next-generation sequencing before and after allogeneic hematopoietic cell transplantation in acute myeloid leukemia.
Efficacy and Safety of Imatinib Treatment in Elderly Patients With Chronic Myeloid Leukemia: Real-Life Data and a Single-Center Experience.
Identification of RHOBTB2 aberration as an independent prognostic indicator in acute myeloid leukemia.
MLKL promotes cellular differentiation in myeloid leukemia by facilitating the release of G-CSF.
Allogeneic stem cell transplantation for AML patients with RUNX1 mutation in first complete remission: a study on behalf of the acute leukemia working party of the EBMT.
N 6-Methyladenosine mRNA Forms Condensates to Promote AML Cell Survival.
Gupta V, Kim S, Hu Z-H, et al. Comparison of outcomes of HCT in blast phase of BCR-ABL1- MPN with de novo AML and with AML following MDS. Blood Adv. 2020;4(19):4748-4757.
Clinical Relevance of ABCB1, ABCG2, and ABCC2 Gene Polymorphisms in Chronic Myeloid Leukemia Patients Treated With Nilotinib.
A KDM4A-PAF1-mediated epigenomic network is essential for acute myeloid leukemia cell self-renewal and survival.
An evaluation of venetoclax in combination with azacitidine, decitabine, or low-dose cytarabine as therapy for acute myeloid leukemia.
Clinical and histopathological features of myeloid neoplasms with concurrent Janus kinase 2 (JAK2) V617F and KIT proto-oncogene, receptor tyrosine kinase (KIT) D816V mutations.
Harnessing the Therapeutic Value of Venetoclax: A Breakthrough Therapy in Acute Myeloid Leukemia.
Apc-mutant cells act as supercompetitors in intestinal tumour initiation.
NOTUM from Apc-mutant cells biases clonal competition to initiate cancer.

Blood. 2021 Jun 01. pii: blood.2020010603. [Epub ahead of print]

Machine Learning Integrates Genomic Signatures for Subclassification Beyond Primary and Secondary Acute Myeloid Leukemia.

Hassan Awada, Arda Durmaz, Carmelo Gurnari, Ashwin Kishtagari, Manja Meggendorfer, Cassandra M Kerr, Teodora Kuzmanovic, Jibran Durrani, Jacob Shreve, Yasunobu Nagata, Tomas Radivoyevitch, Anjali S Advani, Farhad Ravandi, Hetty E Carraway, Aziz Nazha, Claudia Haferlach, Yogen Saunthararajah, Jacob G Scott, Valeria Visconte, Hagop Meguerditch Kantarjian, Tapan Mahendra Kadia, Mikkael A Sekeres, Torsten Haferlach, Jaroslaw P Maciejewski.

While genomic alterations drive the pathogenesis of acute myeloid leukemia (AML), traditional classifications are largely based on morphology and prototypic genetic founder lesions define only a small proportion of AML patients. The historical subdivision of primary/de novo AML (pAML) and secondary AML (sAML) has shown to variably correlate with genetic patterns. Perhaps, the combinatorial complexity and heterogeneity of AML genomic architecture have precluded, so far, the genomic-based subclassification to identify distinct molecularly-defined subtypes more reflective of shared pathogenesis. We integrated cytogenetic and gene sequencing data from a multicenter cohort of 6,788 AML patients that were analyzed using standard and machine learning methods to generate a novel AML molecular subclassification with biological correlates corresponding to underlying pathogenesis. Standard supervised analyses resulted in modest cross-validation accuracy when attempting to use molecular patterns to predict traditional pathomorphological AML classifications. We performed unsupervised analysis by applying Bayesian Latent Class method that identified 4 unique genomic clusters of distinct prognoses. Invariant genomic features driving each cluster were extracted and resulted in 97% cross-validation accuracy when used for genomic subclassification. Subclasses of AML defined by molecular signatures overlapped current pathomorphological and clinically-defined AML subtypes. We internally and externally validated our results and share an open-access molecular classification scheme for AML patients. Although the heterogeneity inherent in the genomic changes across nearly 7,000 AML patients is too vast for traditional prediction methods, however, machine learning methods allowed for the definition of novel genomic AML subclasses indicating that traditional pathomorphological definitions may be less reflective of overlapping pathogenesis.

DOI: https://doi.org/10.1182/blood.2020010603
Mol Cell. 2021 May 25. pii: S1097-2765(21)00365-8. [Epub ahead of print]

ATF3 coordinates serine and nucleotide metabolism to drive cell cycle progression in acute myeloid leukemia.

Daniela Di Marcantonio, Esteban Martinez, Joice S Kanefsky, Jacklyn M Huhn, Rashid Gabbasov, Anushk Gupta, John J Krais, Suraj Peri, YinFei Tan, Tomasz Skorski, Adrienne Dorrance, Ramiro Garzon, Aaron R Goldman, Hsin-Yao Tang, Neil Johnson, Stephen M Sykes.

  Metabolic reprogramming is a common feature of many human cancers, including acute myeloid leukemia (AML). However, the upstream regulators that promote AML metabolic reprogramming and the benefits conferred to leukemia cells by these metabolic changes remain largely unknown. We report that the transcription factor ATF3 coordinates serine and nucleotide metabolism to maintain cell cycling, survival, and the differentiation blockade in AML. Analysis of mouse and human AML models demonstrate that ATF3 directly activates the transcription of genes encoding key enzymatic regulators of serine synthesis, one-carbon metabolism, and de novo purine and pyrimidine synthesis. Total steady-state polar metabolite and heavy isotope tracing analyses show that ATF3 inhibition reduces de novo serine synthesis, impedes the incorporation of serine-derived carbons into newly synthesized purines, and disrupts pyrimidine metabolism. Importantly, exogenous nucleotide supplementation mitigates the anti-leukemia effects of ATF3 inhibition. Together, these findings reveal the dependence of AML on ATF3-regulated serine and nucleotide metabolism.

Keywords:  AML; ATF3; ATF4; cell cycle; differentiation; leukemia; metabolism; purines; pyrimidines; serine

DOI:  https://doi.org/10.1016/j.molcel.2021.05.008
Genes (Basel). 2021 May 21. pii: 792. [Epub ahead of print]12(6):

What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort.

Morten Krogh Herlin, Sara A Yones, Eigil Kjeldsen, Linda Holmfeldt, Henrik Hasle.

  Normal karyotype acute myeloid leukemia (NK-AML) constitutes 20-25% of pediatric AML and detailed molecular analysis is essential to unravel the genetic background of this group. Using publicly available sequencing data from the TARGET-AML initiative, we investigated the mutational landscape of NK-AML in comparison with abnormal karyotype AML (AK-AML). In 164 (97.6%) of 168 independent NK-AML samples, at least one somatic protein-coding mutation was identified using whole-genome or targeted capture sequencing. We identified a unique mutational landscape of NK-AML characterized by a higher prevalence of mutated CEBPA, FLT3, GATA2, NPM1, PTPN11, TET2, and WT1 and a lower prevalence of mutated KIT, KRAS, and NRAS compared with AK-AML. Mutated CEBPA often co-occurred with mutated GATA2, whereas mutated FLT3 co-occurred with mutated WT1 and NPM1. In multivariate regression analysis, we identified younger age, WBC count ≥50 × 109/L, FLT3-internal tandem duplications, and mutated WT1 as independent predictors of adverse prognosis and mutated NPM1 and GATA2 as independent predictors of favorable prognosis in NK-AML. In conclusion, NK-AML in children is characterized by a unique mutational landscape which impacts the disease outcome.

Keywords:  cancer genetics; cytogenetically normal; cytogenetics; diagnosis; molecular genetics; mutational landscape; normal karyotype; pediatric acute myeloid leukemia; prognosis; survival

DOI:  https://doi.org/10.3390/genes12060792
Blood. 2021 Jun 01. pii: blood.2020009707. [Epub ahead of print]

Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells.

Julie A I Thoms, Peter Truong, Shruthi Subramanian, Kathy Knezevic, Gregory Harvey, Yizhou Huang, Janith A Seneviratne, Daniel R Carter, Swapna Joshi, Joanna Skhinas, Diego Chacon, Anushi Shah, Ineke de Jong, Dominik Beck, Bertie Gottgens, Jonas Larsson, Jason Wing Hon Wong, Fabio Zanini, John E Pimanda.

Changes in gene regulation and expression govern orderly transitions from hematopoietic stem cells to terminally differentiated blood cell types. These transitions are disrupted during leukemic transformation but knowledge of the gene regulatory changes underpinning this process is elusive. We hypothesised that identifying core gene regulatory networks in healthy hematopoietic and leukemic cells could provide insights into network alterations that perturb cell state transitions. A heptad of transcription factors (LYL1, TAL1, LMO2, FLI1, ERG, GATA2, RUNX1) bind key hematopoietic genes in human CD34+ haematopoietic stem and progenitor cells (HSPCs) and have prognostic significance in acute myeloid leukemia (AML). These factors also form a densely interconnected circuit by binding combinatorially at their own, and each other's, regulatory elements. However, their mutual regulation during normal haematopoiesis and in AML cells, and how perturbation of their expression levels influences cell fate decisions remains unclear. Here, we integrated bulk and single cell data and found that the fully connected heptad circuit identified in healthy HSPCs persists with only minor alterations in AML, and that chromatin accessibility at key heptad regulatory elements was predictive of cell identity in both healthy progenitors and in leukemic cells. The heptad factors GATA2, TAL1 and ERG formed an integrated sub-circuit that regulates stem cell to erythroid transition in both healthy and leukemic cells. Components of this triad could be manipulated to facilitate erythroid transition providing a proof of concept that such regulatory circuits could be harnessed to promote specific cell type transitions and overcome dysregulated haematopoiesis.

DOI: https://doi.org/10.1182/blood.2020009707
Blood Cancer J. 2021 Jun 03. 11(6): 107

Acute myeloid leukemia with IDH1 and IDH2 mutations: 2021 treatment algorithm.

Ghayas C Issa, Courtney D DiNardo.

Acute myeloid leukemia is a genetically heterogeneous hematologic malignancy; approximately 20% of AML harbors a mutation in the isocitrate dehydrogenase (IDH) genes, IDH1 or IDH2. These recurrent mutations in key metabolic enzymes lead to the production of the oncometabolite 2-hydroxyglutarate, which promotes leukemogenesis through a block in normal myeloid differentiation. Since this discovery, selective oral inhibitors of mutant IDH1 and IDH2 have subsequently been developed and are now approved as single agent therapy, based on clinical efficacy observed within the original first-in-human trials. The investigation of IDH inhibitors in combination with standard therapies such as azacytidine, with intensive chemotherapy, and with other small molecule targeted therapies in rational combinations are currently under evaluation to further improve upon clinical efficacy.

DOI: https://doi.org/10.1038/s41408-021-00497-1
Cancers (Basel). 2021 May 18. pii: 2458. [Epub ahead of print]13(10):

The Mutational Landscape of Acute Myeloid Leukaemia Predicts Responses and Outcomes in Elderly Patients from the PETHEMA-FLUGAZA Phase 3 Clinical Trial.

Rosa Ayala, Inmaculada Rapado, Esther Onecha, David Martínez-Cuadrón, Gonzalo Carreño-Tarragona, Juan Miguel Bergua, Susana Vives, Jesus Lorenzo Algarra, Mar Tormo, Pilar Martinez, Josefina Serrano, Pilar Herrera, Fernando Ramos, Olga Salamero, Esperanza Lavilla, Cristina Gil, Jose Luis López Lorenzo, María Belén Vidriales, Jorge Labrador, José Francisco Falantes, María José Sayas, Bruno Paiva, Eva Barragán, Felipe Prosper, Miguel Ángel Sanz, Joaquín Martínez-López, Pau Montesinos, On Behalf Of The Programa Para El Estudio de la Terapeutica En Hemopatias Malignas Pethema Cooperative Study Group.

  We sought to predict treatment responses and outcomes in older patients with newly diagnosed acute myeloid leukemia (AML) from our FLUGAZA phase III clinical trial (PETHEMA group) based on mutational status, comparing azacytidine (AZA) with fludarabine plus low-dose cytarabine (FLUGA). Mutational profiling using a custom 43-gene next-generation sequencing panel revealed differences in profiles between older and younger patients, and several prognostic markers that were useful in young patients were ineffective in older patients. We examined the associations between variables and overall responses at the end of the third cycle. Patients with mutated DNMT3A or EZH2 were shown to benefit from azacytidine in the treatment-adjusted subgroup analysis. An analysis of the associations with tumor burden using variant allele frequency (VAF) quantification showed that a higher overall response was associated with an increase in TET2 VAF (odds ratio (OR), 1.014; p = 0.030) and lower TP53 VAF (OR, 0.981; p = 0.003). In the treatment-adjusted multivariate survival analyses, only the NRAS (hazard ratio (HR), 1.9, p = 0.005) and TP53 (HR, 2.6, p = 9.8 × 10-7) variants were associated with shorter overall survival (OS), whereas only mutated BCOR (HR, 3.6, p = 0.0003) was associated with a shorter relapse-free survival (RFS). Subgroup analyses of OS according to biological and genomic characteristics showed that patients with low-intermediate cytogenetic risk (HR, 1.51, p = 0.045) and mutated NRAS (HR, 3.66, p = 0.047) benefited from azacytidine therapy. In the subgroup analyses, patients with mutated TP53 (HR, 4.71, p = 0.009) showed a better RFS in the azacytidine arm. In conclusion, differential mutational profiling might anticipate the outcomes of first-line treatment choices (AZA or FLUGA) in older patients with AML. The study is registered at ClinicalTrials.gov as NCT02319135.

Keywords:  NGS; acute; azacytidine; clinical trials and observations; complete remission; cytarabine; genetic risk; leukemia; leukemic cells; myelocytic; myeloid neoplasia; older adults; prognostic factors; variants

DOI:  https://doi.org/10.3390/cancers13102458
Cancers (Basel). 2021 May 14. pii: 2385. [Epub ahead of print]13(10):

Acute Myeloid Leukemia: Is It T Time?

Meriem Ben Khoud, Tiziano Ingegnere, Bruno Quesnel, Suman Mitra, Carine Brinster.

  Acute myeloid leukemia (AML) is a heterogeneous disease driven by impaired differentiation of hematopoietic primitive cells toward myeloid lineages (monocytes, granulocytes, red blood cells, platelets), leading to expansion and accumulation of "stem" and/or "progenitor"-like or differentiated leukemic cells in the bone marrow and blood. AML progression alters the bone marrow microenvironment and inhibits hematopoiesis' proper functioning, causing sustained cytopenia and immunodeficiency. This review describes how the AML microenvironment influences lymphoid lineages, particularly T lymphocytes that originate from the thymus and orchestrate adaptive immune response. We focus on the elderly population, which is mainly affected by this pathology. We discuss how a permissive AML microenvironment can alter and even worsen the thymic function, T cells' peripheral homeostasis, phenotype, and functions. Based on the recent findings on the mechanisms supporting that AML induces quantitative and qualitative changes in T cells, we suggest and summarize current immunotherapeutic strategies and challenges to overcome these anomalies to improve the anti-leukemic immune response and the clinical outcome of patients.

Keywords:  T cells; acute myeloid leukemia; immunotherapy; thymus function

DOI:  https://doi.org/10.3390/cancers13102385
Leuk Lymphoma. 2021 Jun 01. 1-11

Mitochondrial metabolism: powering new directions in acute myeloid leukemia.

Ryan J Stubbins, Irina A Maksakov, David S Sanford, Arefeh Rouhi, Florian Kuchenbauer.

  There has been an explosion of knowledge about the role of metabolism and the mitochondria in acute myeloid leukemia (AML). We have also recently seen several waves of novel therapies change the treatment landscape for AML, such as the selective B-cell lymphoma 2 (BCL-2) inhibitor venetoclax. In this new context, we review the rapidly advancing literature on the role of metabolism and the mitochondria in AML pathogenesis, and how these are interwoven with the mechanisms of action for novel therapeutics in AML. We also review the role of oxidative phosphorylation (OxPhos) in maintaining leukemia stem cells (LSCs), how recurrent genomic alterations in AML alter downstream metabolism, and focus on how the BCL-2 pathway and the mitochondria are inextricably linked in AML. Thus, we provide an overview of the mitochondria and metabolism in the context of our new therapeutic world for AML and outline how targeting these vulnerabilities may produce novel therapeutic strategies.

Keywords:  Acute myeloid leukemia; BCL-2; OxPhos; mitochondria; venetoclax therapy resistance

DOI:  https://doi.org/10.1080/10428194.2021.1910685
Cancers (Basel). 2021 May 10. pii: 2272. [Epub ahead of print]13(9):

Allogenic Stem Cell Transplantation Abrogates Negative Impact on Outcome of AML Patients with KMT2A Partial Tandem Duplication.

Gabriel Antherieu, Audrey Bidet, Sarah Huet, Sandrine Hayette, Marina Migeon, Lisa Boureau, Pierre Sujobert, Xavier Thomas, Hervé Ghesquières, Arnaud Pigneux, Mael Heiblig.

  Recently, a new subset of acute myeloid leukemia (AML) presenting a direct partial tandem duplication (PTD) of the KMT2A gene was described. The consequences of this alteration in terms of outcome and response to treatment remain unclear. We analyzed retrospectively a cohort of KMT2A-PTD-mutated patients with newly diagnosed AML. With a median follow-up of 3.6 years, the median overall survival was 12.1 months. KMT2A-PTD-mutated patients were highly enriched in mutations affecting epigenetic actors and the RTK/RAS signaling pathway. Integrating KMT2A-PTD in ELN classification abrogates its predictive value on survival suggesting that this mutation may overcome other genomic marker effects. In patients receiving intensive chemotherapy, hematopoietic stem cell transplantation (HSCT) significantly improved the outcome compared to non-transplanted patients. In the multivariate analysis, only HSCT at any time in complete remission (HR = 2.35; p = 0.034) and FLT3-ITD status (HR = 0.29; p = 0.014) were independent variables associated with overall survival, whereas age was not. In conclusion, our results emphasize that KMT2A-PTD should be considered as a potential adverse prognostic factor. However, as KMT2A-PTD-mutated patients are usually considered an intermediate risk group, upfront HSCT should be considered in first CR due to the high relapse rate observed in this subset of patients.

Keywords:  KMT2A; acute myeloid leukemia; transplantation

DOI:  https://doi.org/10.3390/cancers13092272
Eur J Haematol. 2021 May 30.

Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients.

Lok Lam Ngai, Connie Y Ma, Orla Maguire, An D Do, Alberto Robert, Aaron C Logan, Elizabeth A Griffiths, Michael J Nemeth, Cherie Green, Tony Pourmohamad, Bo J van Kuijk, Alexander N Snel, Zinia W Kwidama, Bianca Venniker-Punt, James Cooper, Markus G Manz, Bjørn T Gjertsen, Linda Smit, Gert J Ossenkoppele, Jeroen J W M Janssen, Jacqueline Cloos, Teiko Sumiyoshi.

  OBJECTIVES: This study aims to retrospectively assess C-lectin like molecule 1 (CLL-1) bimodal expression on CD34+ blasts in AML patients (total N=306) and explore potential CLL-1 bimodal associations with leukemia and patient specific characteristics.METHODS: Flow cytometry assays were performed to assess the deeper immunophenotyping of CLL-1 bimodality. Cytogenetic analysis was performed to characterize the gene mutation on CLL-1 negative sub-population of CLL-1 bimodal AML samples.
RESULTS: The frequency of a bimodal pattern of CLL-1 expression of CD34+ blasts ranged from 8-65% in the different cohorts. Bimodal CLL-1 expression was most prevalent in patients with MDS related AML (p=0.011), ELN adverse risk (p=0.002), NPM1 wild type (WT, p=0.049), FLT3 WT (p=0.035) and relatively low percentages of leukemia associated immunophenotypes (p=0.006). Additional immunophenotyping analysis revealed the CLL-1- sub-population may consist of pre-B cells, immature myeloblasts and hematopoietic stem cells. Furthermore, (pre)-leukemic mutations were detected in both CLL-1+ and CLL-1- subfractions of bimodal samples (N=3).
CONCLUSIONS: CLL-1 bimodality occurs in about 25% of AML patients and the CLL-1- cell population still contains malignant cells, hence it may potentially limit the effectiveness of CLL-1 targeted therapies and warrant further investigation.

Keywords:  CD34+ blasts; CLL-1; acute myeloid leukemia; bimodality; bone marrow aspirates; flow cytometry

DOI:  https://doi.org/10.1111/ejh.13672
Oncol Rep. 2021 Jul;pii: 150. [Epub ahead of print]46(1):

HOXA11 plays critical roles in disease progression and response to cytarabine in AML.

Jen-Fen Fu, Lee-Yung Shih, Tzung-Hai Yen.

  Lysine methyltransferase 2A (KMT2A, also known as MLL) translocations (MLL‑t) are frequently associated with mutations in RAS pathway genes in acute myeloid leukemia (AML). Previous findings with a mouse model showed that cooperation of MLL/AF10 with tyrosine‑protein phosphatase non‑receptor type 11 (PTPN11)G503A accelerated leukemia development, but increased cytarabine (Ara‑C) sensitivity of leukemia cells. To identify the genes responsible for reduced survival and Ara‑C resistance, transcriptomic profiling between six pairs of mouse MLL/AF10(OM‑LZ) leukemia cells harboring activating and wild‑type KRAS or PTPN11 was compared. A total of 23 differentially expressed genes (DEGs) with >1.5‑fold‑change between the paired cell lines were identified. The Gene Ontology (GO) terms overrepresented in these 23 DEGs included 'immune system process', 'actin filament binding', 'cellular response to interferon‑alpha' and 'sequence‑specific DNA'. Among the four genes (Hoxa11, PR domain zinc finger protein 5, Iroquois‑class homeodomain protein IRX‑5 and homeobox protein PKNOX2) mapped to the GO term 'sequence‑specific DNA', HOXA11 upregulation was associated with AML harboring MLL‑t and RAS signaling mutations based on a meta‑analysis using data deposited in Oncomine™ and analysis of the clinical samples in the present study. Microarray data revealed that only Hoxa11 was upregulated in those cells harboring activating PTPN11. Functional studies of Hoxa11 knockdown or overexpression in MLL/AF10(OM‑LZ) cells revealed that Hoxa11 expression levels were associated with survival in vivo and Ara‑C sensitivity/apoptosis in vitro. In addition, Hoxa11 regulated the expression of the apoptosis‑related genes, NF‑κB inhibitor α, transcription factor p65 and transformation‑related protein p53. Furthermore, the results of a meta‑analysis using Heuser's AML dataset supported the finding that chemotherapy responders have higher expression levels of HOXA11. These results indicated that the expression of HOXA11 increased cell apoptosis and predicted an improved response to Ara‑C in AML.

Keywords:  Hoxa11; MLL translocation; activating tyrosine‑protein phosphatase non‑receptor type 11 mutation; acute myeloid leukemia; cytarabine sensitivity; survival

DOI:  https://doi.org/10.3892/or.2021.8101
Blood Cancer J. 2021 Jun 04. 11(6): 109

Prognostic value of measurable residual disease monitoring by next-generation sequencing before and after allogeneic hematopoietic cell transplantation in acute myeloid leukemia.

Hee-Je Kim, Yonggoo Kim, Dain Kang, Hoon Seok Kim, Jong-Mi Lee, Myungshin Kim, Byung-Sik Cho.

Given limited studies on next-generation sequencing-based measurable residual disease (NGS-MRD) in acute myeloid leukemia (AML) patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT), we longitudinally collected samples before and after allo-HSCT from two independent prospective cohorts (n = 132) and investigated the prognostic impact of amplicon-based NGS assessment. Persistent mutations were detected pre-HSCT (43%) and 1 month after HSCT (post-HSCT-1m, 20%). All persistent mutations at both pre-HSCT and post-HSCT-1m were significantly associated with post-transplant relapse and worse overall survival. Changes in MRD status from pre-HSCT to post-HSCT-1m indicated a higher risk for relapse and death. Isolated detectable mutations in genes associated with clonal hematopoiesis were also significant predictors of post-transplant relapse. The optimal time point of NGS-MRD assessment depended on the conditioning intensity (pre-HSCT for myeloablative conditioning and post-HSCT-1m for reduced-intensity conditioning). Serial NGS-MRD monitoring revealed that most residual clones at both pre-HSCT and post-HSCT-1m in patients who never relapsed disappeared after allo-HSCT. Reappearance of mutant clones before overt relapse was detected by the NGS-MRD assay. Taken together, NGS-MRD detection has a prognostic value at both pre-HSCT and post-HSCT-1m, regardless of the mutation type, depending on the conditioning intensity. Serial NGS-MRD monitoring was feasible to compensate for the limited performance of the NGS-MRD assay.

DOI: https://doi.org/10.1038/s41408-021-00500-9
Clin Lymphoma Myeloma Leuk. 2021 Apr 20. pii: S2152-2650(21)00148-8. [Epub ahead of print]

Efficacy and Safety of Imatinib Treatment in Elderly Patients With Chronic Myeloid Leukemia: Real-Life Data and a Single-Center Experience.

Ahmet Emre Eşkazan, Deniz Özmen, Mert Öztaş, Fatih Bektaş, Eşref Alperen Bayraktar, Sevil Sadri, Dilek Keskin, Nurgül Özgür Yurttaş, Tuğrul Elverdi, Ayşe Salihoğlu, Muhlis Cem Ar, Şeniz Öngören, Zafer Başlar, Yıldız Aydın, Teoman Soysal.

  BACKGROUND: In the era of tyrosine kinase inhibitors (TKIs), chronic myeloid leukemia (CML) patients generally live close to a normal lifespan, and the number of elderly patients with CML with comorbidities is increasing.PATIENTS AND METHODS: We retrospectively compared the efficacy and safety of frontline imatinib between elderly patients (≥60 years old) and younger patients (<60 years old) with CML.
RESULTS: The study included 33 elderly and 125 younger patients. Elderly patients had significantly higher Charlson comorbidity index (CCI) scores. Efficacy and toxicity were comparable among the older patients with CCI scores of 0 and ≥1. There were significantly more hematologic adverse events (AEs) in elderly patients (P = .005). Although not significant, nonhematologic AEs were also more common in older cases (P = .056). Elderly patients had significantly higher rates of imatinib dose reduction (P < .001). Cumulative response rates were similar in both groups. Event-free survival was comparable, and overall survival (OS)-when non-CML-related deaths were censored-was also similar. In the multivariate analysis, age at diagnosis and CCI were associated with OS, and patients ≥ 60 years of age had a 5.998-times higher risk of death compared with the patients < 60 years of age (P = .011). Similarly, patients with CCI scores ≥ 2 had a 3.758-times higher risk of death compared with patients with a CCI score of 0 (P = .033).
CONCLUSIONS: Upfront imatinib was generally well tolerated among elderly Turkish patients with CML with non-inferior responses and long-term outcomes when compared with younger patients. Comorbidities can be problematic in elderly patients, and today the survival of patients with CML is determined mostly by comorbidities.

Keywords:  Age; Charlson comorbidity index (CCI); Chronic myeloid leukemia; Comorbidity; Imatinib

DOI:  https://doi.org/10.1016/j.clml.2021.04.005
Aging (Albany NY). 2021 Jun 01. 13

Identification of RHOBTB2 aberration as an independent prognostic indicator in acute myeloid leukemia.

Peng Liu, Qinghai Ma, Hanxiang Chen, Li Zhang, Xiaoning Zhang.

  Rho-related BTB domain (RhoBTB) proteins belong to Rho guanosine triphosphatases (GTPases). Their putative role implicated in carcinogenesis has been supported by accumulating evidence. However, their expression pattern and potential role in acute myeloid leukemia (AML) remain unclear. We profiled RHOBTB mRNA expression via the Gene Expression Profiling Interactive Analysis 2 (GEPIA2) database. Survival analysis was conducted with GEPIA2 and UALCAN. Univariate and multivariate Cox regression analyses were performed to validate RHOBTB genes as independent prognostic indicators in the LAML cohort from The Cancer Genome Atlas (TCGA). Data regarding expression in different subtypes and relationships with common disease-related genes were retrieved from UALCAN. Co-expressed genes were screened out and subsequently subjected to functional enrichment analysis. We observed aberrant transcription levels of RHOBTB genes in AML patients. RHOBTB2 was identified as a prognostic candidate for overall survival (OS), independent of prognosis-related clinical factors and genetic abnormalities. Moreover, RHOBTB2 expression was increased in non-acute promyelocytic leukemia (APL) subtypes, patients without FLT3 mutation and PML/RAR fusion, and imparted a positive correlation with the expression of FLT3, FHL1, and RUNXs. Co-expressed genes of RHOBTB2 were enriched in functional pathways in AML. Our findings suggest that RHOBTB2 might be a novel biomarker and independent prognostic indicator in AML and provide insights into the leukemogenesis and molecular network of AML.

Keywords:  Rho-related BTB domain-containing protein 2 Gene; acute myeloid leukemia; bioinformatics analysis; prognosis

DOI:  https://doi.org/10.18632/aging.203087
Cell Death Differ. 2021 Jun 02.

MLKL promotes cellular differentiation in myeloid leukemia by facilitating the release of G-CSF.

Xin Wang, Uris Ros, Deepti Agrawal, Eva C Keller, Julia Slotta-Huspenina, Veronika Dill, Bo Shen, Run Shi, Tobias Herold, Claus Belka, Ritu Misra, Florian Bassermann, Ana J Garcia-Saez, Philipp J Jost.

The blockade of cellular differentiation represents a hallmark of acute myeloid leukemia (AML), which is largely attributed to the dysfunction of lineage-specific transcription factors controlling cellular differentiation. However, alternative mechanisms of cellular differentiation programs in AML remain largely unexplored. Here we report that mixed lineage kinase domain-like protein (MLKL) contributes to the cellular differentiation of transformed hematopoietic progenitor cells in AML. Using gene-targeted mice, we show that MLKL facilitates the release of granulocyte colony-stimulating factor (G-CSF) by controlling membrane permeabilization in leukemic cells. Mlkl-/- hematopoietic stem and progenitor cells released reduced amounts of G-CSF while retaining their capacity for CSF3 (G-CSF) mRNA expression, G-CSF protein translation, and G-CSF receptor signaling. MLKL associates with early endosomes and controls G-CSF release from intracellular storage by plasma membrane pore formation, whereas cell death remained unaffected by loss of MLKL. Of note, MLKL expression was significantly reduced in AML patients, specifically in those with a poor-risk AML subtype. Our data provide evidence that MLKL controls myeloid differentiation in AML by controlling the release of G-CSF from leukemic progenitor cells.

DOI: https://doi.org/10.1038/s41418-021-00811-1
Bone Marrow Transplant. 2021 May 31.

Allogeneic stem cell transplantation for AML patients with RUNX1 mutation in first complete remission: a study on behalf of the acute leukemia working party of the EBMT.

Johanna Waidhauser, Myriam Labopin, Jordi Esteve, Nicolaus Kröger, Jan Cornelissen, Tobias Gedde-Dahl, Gwendolyn Van Gorkom, Jürgen Finke, Montserrat Rovira, Nicolaas Schaap, Eefke Petersen, Dietrich Beelen, Donald Bunjes, Bipin Savani, Christoph Schmid, Arnon Nagler, Mohamad Mohty, .

Acute myeloid leukemia with runt-related transcription factor 1 gene mutation (RUNX1+ AML) is associated with inferior response rates and outcome after conventional chemotherapy. We performed a retrospective, registry-based analysis to elucidate the prognostic value of RUNX1 mutation after allogeneic stem cell transplantation (alloSCT). All consecutive adults undergoing alloSCT for AML in first complete remission (CR1) between 2013 and 2019 with complete information on conventional cytogenetics and RUNX1 mutational status were included. Endpoints of interest were cumulative relapse incidence, non-relapse mortality, overall and leukemia-free survival (OS/LFS), and GvHD-free/relapse-free survival. A total of 674 patients (183 RUNX1+, 491 RUNX1-) were identified, with >85% presenting as de novo AML. Median follow-up was 16.4 (RUNX1+) and 21.9 (RUNX1-) months. Survival rates showed no difference between RUNX1+ and RUNX1- patients either in univariate or multivariate analysis (2-year OS: 67.7 vs. 66.1%, p = 0.7; 2-year LFS: 61.1 vs. 60.8%, p = 0.62). Multivariate analysis identified age, donor type and poor cytogenetics as risk factors for inferior outcome. Among patients with RUNX+ AML, older age, reduced intensity conditioning and minimal residual disease at alloSCT predicted inferior outcome. Our data provide evidence that the negative influence of RUNX1 mutations in patients with AML can be overcome by transplantation in CR1.

DOI: https://doi.org/10.1038/s41409-021-01322-w
Cancer Discov. 2021 Jun 04.

N 6-Methyladenosine mRNA Forms Condensates to Promote AML Cell Survival.

In myeloid leukemia, nuclear reader YTHDC1 bound m6A-modified mRNA, forming nuclear condensates.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2021-079
Blood Adv. 2021 Jun 08. 5(11): 2515

Gupta V, Kim S, Hu Z-H, et al. Comparison of outcomes of HCT in blast phase of BCR-ABL1- MPN with de novo AML and with AML following MDS. Blood Adv. 2020;4(19):4748-4757.

DOI: https://doi.org/10.1182/bloodadvances.2021005066
Front Oncol. 2021 ;11 672287

Clinical Relevance of ABCB1, ABCG2, and ABCC2 Gene Polymorphisms in Chronic Myeloid Leukemia Patients Treated With Nilotinib.

Federica Loscocco, Giuseppe Visani, Annamaria Ruzzo, Irene Bagaloni, Fabio Fuligni, Sara Galimberti, Antonello Di Paolo, Fabio Stagno, Patrizia Pregno, Mario Annunziata, Antonella Gozzini, Sara Barulli, Elisa Gabucci, Mauro Magnani, Alessandro Isidori.

  Tyrosine kinase inhibitors (TKIs) have radically changed the outcome of chronic myeloid leukemia (CML) patients in the last 20 years. Moreover, the advent of second generation TKIs, namely nilotinib and dasatinib, have largely increased the number of CML patients achieving deep and sustained molecular responses. However, the possible mechanisms capable of influencing the maintenance of the long-term molecular response are not yet fully known and understood. In this light, polymorphisms in MDR-ABC transporters may influence the efficacy and safety of TKIs. In this study, we examined seven single nucleotide polymorphisms (SNPs) in four ABC transporter genes: ABCC1 rs212090 (5463T>A), ABCC2 rs3740066 (3972C>T), ABCC2 rs4148386 G>A, ABCC2 rs1885301 (1549G>A), ABCG2 rs2231137 (34G>A), ABCG2 rs2231142 G>C, ABCB1 rs1045642 (3435C>T), to determine their effect on the achievement and/or loss of molecular response in 90 CML patients treated with nilotinib. We found that ABCC2 rs3740066 CC and CT as well as the ABCB1 rs1045642 TT genotypes correlated with a higher probability to achieve MR3 in a shorter time (p=0.02, p=0.004, and p=0.01), whereas ABCG2 rs2231137 GG was associated with lower probability of MR3 achievement (p=0.005). Moreover, ABCC2 rs3740066 CC genotype, the ABCB1 rs1045642 CC and TT genotypes were positively correlated with MR4 achievement (p=0.02, p=0.007, and p=0.003). We then generated a predictive model incorporating the information of four genotypes, to evaluate the combined effect of the SNPs. The combination of SNPs present in the model affected the probability and the time to molecular response. This model had a high prognostic significance for both MR3 and MR4 (p=0.005 and p=0.008, respectively). Finally, we found ABCG2 rs2231142 GG genotype to be associated with a decrease risk of MR3 loss. In conclusion, MDR-transporters SNPs may significantly affect the achievement and loss of molecular response in CML patients treated with nilotinib.

Keywords:  MDR-ABC transporters; chronic myeloid leukemia; drug resistance; molecular response; nilotinib; polymorphisms

DOI:  https://doi.org/10.3389/fonc.2021.672287
Cell Death Dis. 2021 Jun 03. 12(6): 573

A KDM4A-PAF1-mediated epigenomic network is essential for acute myeloid leukemia cell self-renewal and survival.

Matthew E Massett, Laura Monaghan, Shaun Patterson, Niamh Mannion, Roderick P Bunschoten, Alex Hoose, Sandra Marmiroli, Robert M J Liskamp, Heather G Jørgensen, David Vetrie, Alison M Michie, Xu Huang.

Epigenomic dysregulation is a common pathological feature in human hematological malignancies. H3K9me3 emerges as an important epigenomic marker in acute myeloid leukemia (AML). Its associated methyltransferases, such as SETDB1, suppress AML leukemogenesis, whilst H3K9me3 demethylases KDM4C is required for mixed-lineage leukemia rearranged AML. However, the specific role and molecular mechanism of action of another member of the KDM4 family, KDM4A has not previously been clearly defined. In this study, we delineated and functionally validated the epigenomic network regulated by KDM4A. We show that selective loss of KDM4A is sufficient to induce apoptosis in a broad spectrum of human AML cells. This detrimental phenotype results from a global accumulation of H3K9me3 and H3K27me3 at KDM4A targeted genomic loci thereby causing downregulation of a KDM4A-PAF1 controlled transcriptional program essential for leukemogenesis, distinct from that of KDM4C. From this regulatory network, we further extracted a KDM4A-9 gene signature enriched with leukemia stem cell activity; the KDM4A-9 score alone or in combination with the known LSC17 score, effectively stratifies high-risk AML patients. Together, these results establish the essential and unique role of KDM4A for AML self-renewal and survival, supporting further investigation of KDM4A and its targets as a potential therapeutic vulnerability in AML.

DOI: https://doi.org/10.1038/s41419-021-03738-0
Expert Rev Hematol. 2021 Jun 02.

An evaluation of venetoclax in combination with azacitidine, decitabine, or low-dose cytarabine as therapy for acute myeloid leukemia.

Tamer A Othman, Matthew E Tenold, Benjamin N Moskoff, Tali Azenkot, Brian A Jonas.

  INTRODUCTION: Older patients with acute myeloid leukemia (AML) ineligible for conventional chemotherapy have historically received low-intensity treatments, if any, and have had dismal outcomes. Recent phase III data have demonstrated significant efficacy of venetoclax-based combinations and have begun to address the unmet need in this patient population. As venetoclax-based combinations become increasingly used in the clinical setting, it is important to understand their development, current use, and future directions.AREAS COVERED: This review covers the clinical development of venetoclax-based combinations for the management of AML, and their current and future use. A search of PubMed and ashpublications.org using the keywords "venetoclax", "AML", and "hypomethylating agents" as the search terms was undertaken to identify the most pertinent publications.
EXPERT OPINION: While venetoclax-based combinations have shown excellent responses and improved survival in patients with untreated AML, further studies are required to understand how to expand on their frontline use, manage patients who fail venetoclax-based combinations, and their true efficacy in the relapsed/refractory setting. Management of AML with venetoclax-based combinations is expected to evolve over the next few years.

Keywords:  AML; HMA; LDAC; acute myeloid leukemia; azacitidine; cytarabine; decitabine; hypomethylating agent; venetoclax

DOI:  https://doi.org/10.1080/17474086.2021.1938533
Br J Haematol. 2021 Jun 01.

Clinical and histopathological features of myeloid neoplasms with concurrent Janus kinase 2 (JAK2) V617F and KIT proto-oncogene, receptor tyrosine kinase (KIT) D816V mutations.

Nicole Naumann, Johannes Lübke, William Shomali, Lukas Reiter, Hans-Peter Horny, Mohamad Jawhar, Vito Dangelo, Alice Fabarius, Georgia Metzgeroth, Sebastian Kreil, Karl Sotlar, Claire Oni, Claire Harrison, Wolf-Karsten Hofmann, Nicholas C P Cross, Peter Valent, Deepti Radia, Jason Gotlib, Andreas Reiter, Juliana Schwaab.

  We report on 45 patients with myeloid neoplasms and concurrent Janus kinase 2 (JAK2) V617F and KIT proto-oncogene, receptor tyrosine kinase (KIT) D816V (JAK2pos . /KITpos . ) mutations, which are individually identified in >60% of patients with classical myeloproliferative neoplasms (MPN) and >90% of patients with systemic mastocytosis (SM) respectively. In SM, the concurrent presence of a clonal non-mast cell neoplasm [SM with associated haematological neoplasm (SM-AHN)] usually constitutes a distinct subtype associated with poor survival. All 45 patients presented with a heterogeneous combination of clinical/morphological features typical of the individual disorders (e.g. leuco-/erythro-/thrombocytosis and elevated lactate dehydrogenase for MPN; elevated serum tryptase and alkaline phosphatase for SM). Overlapping features identified in 70% of patients included splenomegaly, cytopenia(s), bone marrow fibrosis and additional somatic mutations. Molecular dissection revealed discordant development of variant allele frequency for both mutations and absence of concurrently positive single-cell derived colonies, indicating disease evolution in two independent clones rather than monoclonal disease in >60% of patients examined. Overall survival of JAK2pos . /KITpos . patients without additional somatic high-risk mutations [HRM, e.g. in serine and arginine-rich splicing factor 2 (SRSF2), additional sex combs like-1 (ASXL1) or Runt-related transcription factor 1 (RUNX1)] at 5 years was 77%, indicating that the mutual impact of JAK2 V617F and KIT D816V on prognosis is fundamentally different from the adverse impact of additional HRM in the individual disorders.

Keywords:   JAK2 V617F ; KIT D816V ; mixed phenotype; multi-mutated myeloid neoplasm; myeloproliferative neoplasm; systemic mastocytosis

DOI:  https://doi.org/10.1111/bjh.17567
J Clin Oncol. 2021 Jun 04. JCO2100080

Harnessing the Therapeutic Value of Venetoclax: A Breakthrough Therapy in Acute Myeloid Leukemia.

Andrew H Wei, Gail J Roboz, Hagop M Kantarjian.

DOI: https://doi.org/10.1200/JCO.21.00080
Nature. 2021 Jun 02.

Apc-mutant cells act as supercompetitors in intestinal tumour initiation.

Sanne M van Neerven, Nina E de Groot, Lisanne E Nijman, Brendon P Scicluna, Milou S van Driel, Maria C Lecca, Daniël O Warmerdam, Vaishali Kakkar, Leandro F Moreno, Felipe A Vieira Braga, Delano R Sanches, Prashanthi Ramesh, Sanne Ten Hoorn, Arthur S Aelvoet, Marouska F van Boxel, Lianne Koens, Przemek M Krawczyk, Jan Koster, Evelien Dekker, Jan Paul Medema, Douglas J Winton, Maarten F Bijlsma, Edward Morrissey, Nicolas Léveillé, Louis Vermeulen.

A delicate equilibrium of WNT agonists and antagonists in the intestinal stem cell (ISC) niche is critical to maintaining the ISC compartment, as it accommodates the rapid renewal of the gut lining. Disruption of this balance by mutations in the tumour suppressor gene APC, which are found in approximately 80% of all human colon cancers, leads to unrestrained activation of the WNT pathway1,2. It has previously been established that Apc-mutant cells have a competitive advantage over wild-type ISCs3. Consequently, Apc-mutant ISCs frequently outcompete all wild-type stem cells within a crypt, thereby reaching clonal fixation in the tissue and initiating cancer formation. However, whether the increased relative fitness of Apc-mutant ISCs involves only cell-intrinsic features or whether Apc mutants are actively involved in the elimination of their wild-type neighbours remains unresolved. Here we show that Apc-mutant ISCs function as bona fide supercompetitors by secreting WNT antagonists, thereby inducing differentiation of neighbouring wild-type ISCs. Lithium chloride prevented the expansion of Apc-mutant clones and the formation of adenomas by rendering wild-type ISCs insensitive to WNT antagonists through downstream activation of WNT by inhibition of GSK3β. Our work suggests that boosting the fitness of healthy cells to limit the expansion of pre-malignant clones may be a powerful strategy to limit the formation of cancers in high-risk individuals.

DOI: https://doi.org/10.1038/s41586-021-03558-4
Nature. 2021 Jun 02.

NOTUM from Apc-mutant cells biases clonal competition to initiate cancer.

Dustin J Flanagan, Nalle Pentinmikko, Kalle Luopajärvi, Nicky J Willis, Kathryn Gilroy, Alexander P Raven, Lynn Mcgarry, Johanna I Englund, Anna T Webb, Sandra Scharaw, Nadia Nasreddin, Michael C Hodder, Rachel A Ridgway, Emma Minnee, Nathalie Sphyris, Ella Gilchrist, Arafath K Najumudeen, Beatrice Romagnolo, Christine Perret, Ann C Williams, Hans Clevers, Pirjo Nummela, Marianne Lähde, Kari Alitalo, Ville Hietakangas, Ann Hedley, William Clark, Colin Nixon, Kristina Kirschner, E Yvonne Jones, Ari Ristimäki, Simon J Leedham, Paul V Fish, Jean-Paul Vincent, Pekka Katajisto, Owen J Sansom.

The tumour suppressor APC is the most commonly mutated gene in colorectal cancer. Loss of Apc in intestinal stem cells drives the formation of adenomas in mice via increased WNT signalling1, but reduced secretion of WNT ligands increases the ability of Apc-mutant intestinal stem cells to colonize a crypt (known as fixation)2. Here we investigated how Apc-mutant cells gain a clonal advantage over wild-type counterparts to achieve fixation. We found that Apc-mutant cells are enriched for transcripts that encode several secreted WNT antagonists, with Notum being the most highly expressed. Conditioned medium from Apc-mutant cells suppressed the growth of wild-type organoids in a NOTUM-dependent manner. Furthermore, NOTUM-secreting Apc-mutant clones actively inhibited the proliferation of surrounding wild-type crypt cells and drove their differentiation, thereby outcompeting crypt cells from the niche. Genetic or pharmacological inhibition of NOTUM abrogated the ability of Apc-mutant cells to expand and form intestinal adenomas. We identify NOTUM as a key mediator during the early stages of mutation fixation that can be targeted to restore wild-type cell competitiveness and provide preventative strategies for people at a high risk of developing colorectal cancer.

DOI: https://doi.org/10.1038/s41586-021-03525-z