bims-tremyl 2023-10-22 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2023–10–22
33 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Targeting metabolic vulnerabilities to overcome resistance to therapy in acute myeloid leukemia.
A gain-of-function p53 mutant synergizes with oncogenic NRAS to promote acute myeloid leukemia in mice.
CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition.
SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.
Current State and Future Prospects of Diagnosis and Management of TP53 Mutated Myeloid Neoplasms.
Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation.
Venetoclax with hypomethylating agents might lead to eradication of measurable residual disease (MRD) persisting after intensive chemotherapy in acute myeloid leukemia (AML) patients with mutated NPM1 and rearranged CBF.
Unveiling T cell evasion mechanisms to immune checkpoint inhibitors in acute myeloid leukemia.
Immune Surveillance of Acute Myeloid Leukemia Is Mediated by HLA-Presented Antigens on Leukemia Progenitor Cells.
The prognostic contribution of CBL, NRAS, KRAS, RUNX1, and TP53 mutations to mutation-enhanced international prognostic score systems (MIPSS70/plus/plus v2.0) for primary myelofibrosis.
Non-genetic mechanisms of drug resistance in acute leukemias.
Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis.
Immunologic Targets in AML.
The history of oral decitabine/cedazuridine and its potential role in acute myeloid leukemia.
Machine Learning Improves Risk Stratification in Myelodysplastic Neoplasms: An Analysis of the Spanish Group of Myelodysplastic Syndromes.
Aspartyl-tRNA synthetase 2 orchestrates iron-sulfur metabolism in hematopoietic stem cells via fine-tuning alternative RNA splicing.
RAS-pathway mutations are common in patients with ruxolitinib refractory/intolerant myelofibrosis: molecular analysis of the PAC203 cohort.
Cutaneous manifestations of myeloid neoplasms exhibit broad and divergent morphologic and immunophenotypic features, but share ancestral clonal mutations with bone marrow.
Complete miRNA-15/16 loss in mice promotes hematopoietic progenitor expansion and a myeloid-biased hyperproliferative state.
Evolution of clonal hematopoiesis.
A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
The effect of small molecule inhibitor NSC348884 on nucleophosmin 1-mutated acute myeloid leukemia cells.
Differential transcriptional control of hematopoiesis in congenital and cycling neutropenia patients harboring ELANE mutations.
Familial Clonal Hematopoiesis in a Long Telomere Syndrome.
Effect of donor age in patients with acute myeloid leukemia undergoing haploidentical hematopoietic cell transplantation vary by conditioning intensity and recipient age.
Making normal hematopoiesis invisible to CAR T cells.
Familial Clonal Hematopoiesis in a Long Telomere Syndrome. Reply.
Identification of multivariable microRNA and clinical biomarker panels to predict imatinib response in chronic myeloid leukemia at diagnosis.
The PD-1- and LAG-3-targeting bispecific molecule tebotelimab in solid tumors and hematologic cancers: a phase 1 trial.
Chromatin compartmentalization regulates the response to DNA damage.
Iron overload induces dysplastic erythropoiesis and features of myelodysplasia in Nrf2-deficient mice.
Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration.
Quantitative interpretation of bone marrow biopsies in MPN-What's the point in a molecular age?

Cancer Drug Resist. 2023 ;6(3): 567-589

Targeting metabolic vulnerabilities to overcome resistance to therapy in acute myeloid leukemia.

Priyanka Sharma, Gautam Borthakur.

  Malignant hematopoietic cells gain metabolic plasticity, reorganize anabolic mechanisms to improve anabolic output and prevent oxidative damage, and bypass cell cycle checkpoints, eventually outcompeting normal hematopoietic cells. Current therapeutic strategies of acute myeloid leukemia (AML) are based on prognostic stratification that includes mutation profile as the closest surrogate to disease biology. Clinical efficacy of targeted therapies, e.g., agents targeting mutant FMS-like tyrosine kinase 3 (FLT3) and isocitrate dehydrogenase 1 or 2, are mostly limited to the presence of relevant mutations. Recent studies have not only demonstrated that specific mutations in AML create metabolic vulnerabilities but also highlighted the efficacy of targeting metabolic vulnerabilities in combination with inhibitors of these mutations. Therefore, delineating the functional relationships between genetic stratification, metabolic dependencies, and response to specific inhibitors of these vulnerabilities is crucial for identifying more effective therapeutic regimens, understanding resistance mechanisms, and identifying early response markers, ultimately improving the likelihood of cure. In addition, metabolic changes occurring in the tumor microenvironment have also been reported as therapeutic targets. The metabolic profiles of leukemia stem cells (LSCs) differ, and relapsed/refractory LSCs switch to alternative metabolic pathways, fueling oxidative phosphorylation (OXPHOS), rendering them therapeutically resistant. In this review, we discuss the role of cancer metabolic pathways that contribute to the metabolic plasticity of AML and confer resistance to standard therapy; we also highlight the latest promising developments in the field in translating these important findings to the clinic and discuss the tumor microenvironment that supports metabolic plasticity and interplay with AML cells.

Keywords:  DHODH; IDH; OXPHOS; leukemia stem cells; mesenchymal stromal cells

DOI:  https://doi.org/10.20517/cdr.2023.12
J Clin Invest. 2023 Oct 17. pii: e173116. [Epub ahead of print]

A gain-of-function p53 mutant synergizes with oncogenic NRAS to promote acute myeloid leukemia in mice.

Adhithi Rajagopalan, Yubin Feng, Meher B Gayatri, Erik A Ranheim, Taylor Klungness, Daniel R Matson, Moon Hee Lee, Mabel Minji Jung, Yun Zhou, Xin Gao, Kalyan Vg Nadiminti, David T Yang, Vu L Tran, Eric Padron, Shigeki Miyamoto, Emery H Bresnick, Jing Zhang.

  We previously demonstrated that a subset of acute myeloid leukemia (AML) patients with concurrent RAS pathway and TP53 mutations have extremely poor prognosis, and most of these TP53 mutations are missense mutations. Here, we report that in contrast to mixed AML and T-cell malignancy developed in NrasG12D/+; p53-/- (NP-/-) mice, NrasG12D/+; p53R172H/+ (NPmut) mice rapidly developed an inflammation-associated AML. Under the inflammatory conditions, NPmut hematopoietic stem and progenitor cells (HSPCs) displayed imbalanced myelopoiesis and lymphopoiesis and largely normal cell proliferation despite MEK/ERK hyperactivation. RNA-Seq analysis revealed that oncogenic NRAS signaling and mutant p53 synergize to establish an NPmut-AML transcriptome distinct from that of NP-/- cells. The NPmut-AML transcriptome showed GATA2 downregulation and elevated expression of inflammatory genes, including those linked to NFκB signaling. NFκB was also upregulated in human NRAS;TP53 AML. Exogenous expression of GATA2 in human NPmut KY821 AML cells downregulated inflammatory gene expression. Mouse and human NPmut AML cells were sensitive to MEK and NFκB inhibition in vitro. The proteasome inhibitor bortezomib stabilized NFκB inhibitory protein IκBα reduced inflammatory gene expression, and potentiated the survival benefit of a MEK inhibitor in NPmut mice. Our study demonstrates that a p53 structural mutant synergizes with oncogenic NRAS to promote AML through mechanisms distinct from p53 loss.

Keywords:  Hematology; Leukemias

DOI:  https://doi.org/10.1172/JCI173116
Hemasphere. 2023 Oct;7(10): e958

CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition.

Anja S Swoboda, Vanessa C Arfelli, Anna Danese, Roland Windisch, Paul Kerbs, Enric Redondo Monte, Johannes W Bagnoli, Linping Chen-Wichmann, Alessandra Caroleo, Monica Cusan, Stefan Krebs, Helmut Blum, Michael Sterr, Wolfgang Enard, Tobias Herold, Maria Colomé-Tatché, Christian Wichmann, Philipp A Greif.

Activating colony-stimulating factor-3 receptor gene (CSF3R) mutations are recurrent in acute myeloid leukemia (AML) with t(8;21) translocation. However, the nature of oncogenic collaboration between alterations of CSF3R and the t(8;21) associated RUNX1-RUNX1T1 fusion remains unclear. In CD34+ hematopoietic stem and progenitor cells from healthy donors, double oncogene expression led to a clonal advantage, increased self-renewal potential, and blast-like morphology and distinct immunophenotype. Gene expression profiling revealed hedgehog signaling as a potential mechanism, with upregulation of GLI2 constituting a putative pharmacological target. Both primary hematopoietic cells and the t(8;21) positive AML cell line SKNO-1 showed increased sensitivity to the GLI inhibitor GANT61 when expressing CSF3R T618I. Our findings suggest that during leukemogenesis, the RUNX1-RUNXT1 fusion and CSF3R mutation act in a synergistic manner to alter hedgehog signaling, which can be exploited therapeutically.

DOI: https://doi.org/10.1097/HS9.0000000000000958
Cell Stem Cell. 2023 Oct 16. pii: S1934-5909(23)00358-2. [Epub ahead of print]

SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.

Chun-Wei Chen, Linda Zhang, Ravi Dutta, Abhishek Niroula, Peter G Miller, Christopher J Gibson, Alexander G Bick, Jaime M Reyes, Yi-Tang Lee, Ayala Tovy, Tianpeng Gu, Sarah Waldvogel, Yi-Hung Chen, Bryan J Venters, Pierre-Olivier Estève, Sriharsa Pradhan, Michael-Christopher Keogh, Pradeep Natarajan, Koichi Takahashi, Adam S Sperling, Margaret A Goodell.

  Somatic mutations accumulate in all cells with age and can confer a selective advantage, leading to clonal expansion over time. In hematopoietic cells, mutations in a subset of genes regulating DNA repair or epigenetics frequently lead to clonal hematopoiesis (CH). Here, we describe the context and mechanisms that lead to enrichment of hematopoietic stem cells (HSCs) with mutations in SRCAP, which encodes a chromatin remodeler that also influences DNA repair. We show that SRCAP mutations confer a selective advantage in human cells and in mice upon treatment with the anthracycline-class chemotherapeutic doxorubicin and bone marrow transplantation. Furthermore, Srcap mutations lead to a lymphoid-biased expansion, driven by loss of SRCAP-regulated H2A.Z deposition and increased DNA repair. Altogether, we demonstrate that SRCAP operates at the intersection of multiple pathways in stem and progenitor cells, offering a new perspective on the functional impact of genetic variants that promote stem cell competition in the hematopoietic system.

Keywords:  DNA damage; H2A.Z; SRCAP; chromatin remodeling; clonal hematopoiesis; hematopoietic stem cells; lymphoid

DOI:  https://doi.org/10.1016/j.stem.2023.09.011
Pathobiology. 2023 Oct 13.

Current State and Future Prospects of Diagnosis and Management of TP53 Mutated Myeloid Neoplasms.

Sangeetha Venugopal, Sanam Loghavi.

TP53 mutated myeloid neoplasms including acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are notoriously treatment resistant with uniformly poor outcomes. TP53 status is an important prognostic indicator and early knowledge of the of TP53 mutation/allelic state may assist in appropriate management including clinical trial enrollment for eligible patients. Thus far, no therapy has shown to demonstrate durable response or incremental survival benefit in TP53 mutated AML or MDS. Therefore, there is an urgent need for innovative therapies to improve the outcomes in this notoriously recalcitrant genomic subset. In this review, we dissect the biology, classification,prognosis, current treatment landscape, and the early phase evaluation of investigational agents in TP53 mutated AML and MDS.

DOI: https://doi.org/10.1159/000534566
Leukemia. 2023 Oct 14.

Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation.

Ming Yan, Mengdan Liu, Amanda G Davis, Samuel A Stoner, Dong-Er Zhang.

T(8;21)(q22;q22), which generates the AML1-ETO fusion oncoprotein, is a common chromosomal abnormality in acute myeloid leukemia (AML) patients. Despite having favorable prognosis, 40% of patients will relapse, highlighting the need for innovative models and application of the newest technologies to study t(8;21) leukemogenesis. Currently, available AML1-ETO mouse models have limited utility for studying the pre-leukemic stage because AML1-ETO produces mild hematopoietic phenotypes and no leukemic transformation. Conversely, overexpression of a truncated variant, AML1-ETO9a (AE9a), promotes fully penetrant leukemia and is too potent for studying pre-leukemic changes. To overcome these limitations, we devised a germline-transmitted Rosa26 locus AE9a knock-in mouse model that moderately overexpressed AE9a and developed leukemia with long latency and low penetrance. We observed pre-leukemic alterations in AE9a mice, including skewing of progenitors towards granulocyte/monocyte lineages and replating of stem and progenitor cells. Next, we performed single-cell RNA sequencing to identify specific cell populations that contribute to these pre-leukemic phenotypes. We discovered a subset of common myeloid progenitors that have heightened granulocyte/monocyte bias in AE9a mice. We also observed dysregulation of key hematopoietic transcription factor target gene networks, blocking cellular differentiation. Finally, we identified Sox4 activation as a potential contributor to stem cell self-renewal during the pre-leukemic stage.

DOI: https://doi.org/10.1038/s41375-023-02063-z
Leuk Res. 2023 Sep 30. pii: S0145-2126(23)00668-9. [Epub ahead of print]135 107403

Venetoclax with hypomethylating agents might lead to eradication of measurable residual disease (MRD) persisting after intensive chemotherapy in acute myeloid leukemia (AML) patients with mutated NPM1 and rearranged CBF.

Carlos Jiménez-Vicente, Alexandra Martínez-Roca, Helena Pomares, Sandra Castaño-Diez, Francesca Guijarro, Mònica López-Guerra, Alex Bataller, Daniel Esteban, Albert Cortés-Bullich, Amanda Isabel Pérez-Valencia, Ares Guardia-Torrelles, Inés Zugasti, Montserrat Rovira, Francesc Fernández-Avilés, Dolors Colomer, Montserrat Arnan, Marina Díaz-Beyá, Jordi Esteve.



Keywords:  AML; MRD; Preemptive treatment

DOI:  https://doi.org/10.1016/j.leukres.2023.107403
Cancer Drug Resist. 2023 ;6(3): 674-687

Unveiling T cell evasion mechanisms to immune checkpoint inhibitors in acute myeloid leukemia.

Lindsay Gurska, Kira Gritsman.

  Acute myeloid leukemia (AML) is a heterogeneous and aggressive hematologic malignancy that is associated with a high relapse rate and poor prognosis. Despite advances in immunotherapies in solid tumors and other hematologic malignancies, AML has been particularly difficult to treat with immunotherapies, as their efficacy is limited by the ability of leukemic cells to evade T cell recognition. In this review, we discuss the common mechanisms of T cell evasion in AML: (1) increased expression of immune checkpoint molecules; (2) downregulation of antigen presentation molecules; (3) induction of T cell exhaustion; and (4) creation of an immunosuppressive environment through the increased frequency of regulatory T cells. We also review the clinical investigation of immune checkpoint inhibitors (ICIs) in AML. We discuss the limitations of ICIs, particularly in the context of T cell evasion mechanisms in AML, and we describe emerging strategies to overcome T cell evasion, including combination therapies. Finally, we provide an outlook on the future directions of immunotherapy research in AML, highlighting the need for a more comprehensive understanding of the complex interplay between AML cells and the immune system.

Keywords:  Acute myeloid leukemia; T cells; immune checkpoint; immune evasion

DOI:  https://doi.org/10.20517/cdr.2023.39
Blood Cancer Discov. 2023 Oct 17. OF1-OF22

Immune Surveillance of Acute Myeloid Leukemia Is Mediated by HLA-Presented Antigens on Leukemia Progenitor Cells.

Annika Nelde, Heiko Schuster, Jonas S Heitmann, Jens Bauer, Yacine Maringer, Melissa Zwick, Jens-Peter Volkmer, James Y Chen, Anna M Paczulla Stanger, Ariane Lehmann, Bismark Appiah, Melanie Märklin, Elke Rücker-Braun, Helmut R Salih, Malte Roerden, Sarah M Schroeder, Max-Felix Häring, Andreas Schlosser, Johannes Schetelig, Marc Schmitz, Melanie Boerries, Natalie Köhler, Claudia Lengerke, Ravindra Majeti, Irving L Weissman, Hans-Georg Rammensee, Juliane S Walz.

Therapy-resistant leukemia stem and progenitor cells (LSC) are a main cause of acute myeloid leukemia (AML) relapse. LSC-targeting therapies may thus improve outcome of patients with AML. Here we demonstrate that LSCs present HLA-restricted antigens that induce T-cell responses allowing for immune surveillance of AML. Using a mass spectrometry-based immunopeptidomics approach, we characterized the antigenic landscape of patient LSCs and identified AML- and AML/LSC-associated HLA-presented antigens absent from normal tissues comprising nonmutated peptides, cryptic neoepitopes, and neoepitopes of common AML driver mutations of NPM1 and IDH2. Functional relevance of shared AML/LSC antigens is illustrated by presence of their cognizant memory T cells in patients. Antigen-specific T-cell recognition and HLA class II immunopeptidome diversity correlated with clinical outcome. Together, these antigens shared among AML and LSCs represent prime targets for T cell-based therapies with potential of eliminating residual LSCs in patients with AML.
SIGNIFICANCE: The elimination of therapy-resistant leukemia stem and progenitor cells (LSC) remains a major challenge in the treatment of AML. This study identifies and functionally validates LSC-associated HLA class I and HLA class II-presented antigens, paving the way to the development of LSC-directed T cell-based immunotherapeutic approaches for patients with AML. See related commentary by Ritz, p. 437 .

DOI: https://doi.org/10.1158/2643-3230.BCD-23-0020
Am J Hematol. 2023 Oct 17.

The prognostic contribution of CBL, NRAS, KRAS, RUNX1, and TP53 mutations to mutation-enhanced international prognostic score systems (MIPSS70/plus/plus v2.0) for primary myelofibrosis.

Giuseppe G Loscocco, Giada Rotunno, Francesco Mannelli, Giacomo Coltro, Francesca Gesullo, Fabiana Pancani, Leonardo Signori, Chiara Maccari, Maria Esposito, Chiara Paoli, Alessandro M Vannucchi, Paola Guglielmelli.

Contemporary risk models in primary myelofibrosis (PMF) include the mutation (MIPSS70) and mutation/karyotype enhanced (MIPSS70 plus/v2.0) international prognostic scoring systems. High molecular risk (HMR) mutations incorporated in one or both of these models include ASXL1, SRSF2, EZH2, IDH1/2, and U2AF1Q157; the current study examines additional prognostic contribution from more recently described HMR mutations, including CBL, NRAS, KRAS, RUNX1, and TP53. In a cohort of 363 informative cases (median age 58 years; 60% males), mutations included JAK2 61%, CALR 24%, MPL 6%, ASXL1 29%, SRSF2 10%, U2AF1Q157 5%, EZH2 10%, IDH1/2 4%, TP53 5%, CBL 5%, NRAS 7%, KRAS 4%, and RUNX1 4%. At a median follow-up of 4.6 years, 135 (37%) deaths and 42 (11.6%) leukemic transformations were recorded. Univariate analysis confirmed significant survival impact from the original MIPSS70/plus/v2.0 HMR mutations as well as CBL (HR 2.8; p < .001), NRAS (HR 2.4; p < .001), KRAS (HR 2.1; p = .01), and TP53 (HR 2.4; p = .004), but not RUNX1 mutations (HR 1.8; p = .08). Multivariate analysis (MVA) that included both the original and more recently described HMR mutations confirmed independent prognostic contribution from ASXL1 (HR 1.8; p = .007), SRSF2 (HR 4.3; p < .001), U2AF1Q157 (HR 2.9, p = .004), and EZH2 (HR 2.4; p < .001), but not from IDH1/2 (p = .3), TP53 (p = .2), CBL (p = .3), NRAS (p = .8) or KRAS (p = .2) mutations. The lack of additional prognostic value from CBL, NRAS, KRAS, RUNX1, and TP53 was further demonstrated in the setting of (i) MVA of mutations and karyotype, (ii) MVA of MIPSS70/plus/v2.0 composite scores and each one of the recently described HMR mutations, except TP53, and iii) modified MIPSS70/plus/plus v2.0 that included CBL, NRAS, KRAS, and TP53 as part of the HMR constituency, operationally referred to as "HMR+" category. Furthermore, "HMR+" enhancement of MIPSS70/plus/plus v2.0 did not result in improved model performance, as measured by C-statistics. We conclude that prognostic integrity of MIPSS70/plus/plus v2.0, as well as their genetic components, was sustained and their value not significantly upgraded by the inclusion of more recently described HMR mutations, including CBL, NRAS, KRAS, and RUNX1. Additional studies are needed to clarify the apparent additional prognostic value of TP53 mutation and its allelic state.

DOI: https://doi.org/10.1002/ajh.27136
Trends Cancer. 2023 Oct 13. pii: S2405-8033(23)00187-5. [Epub ahead of print]

Non-genetic mechanisms of drug resistance in acute leukemias.

Alexander Calderon, Cuijuan Han, Sadik Karma, Eric Wang.

  Acute leukemia is characterized by clonal heterogeneity that contributes to poor drug responses in patients. Despite treatment advances, the occurrence of relapse remains a major barrier to achieving cures as current therapeutic approaches are inadequate to effectively prevent or overcome resistance. Given that only a few genetic mutations are associated with relapse in acute leukemia patients, there is a growing focus on 'non-genetic' mechanisms that affect the hallmarks of cancer to allow leukemic cells to survive post therapy. In this review, we provide an overview of the therapeutic landscape in acute leukemias. Importantly, we discuss non-genetic mechanisms exploited by leukemic cells to promote their survival after treatment. Last, we present current strategies to prevent or overcome drug resistance in this disease.

Keywords:  AML; acute leukemia; drug resistance; immunotherapy; non-genetic; targeted therapy

DOI:  https://doi.org/10.1016/j.trecan.2023.09.003
EMBO J. 2023 Oct 17. e113527

Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis.

Karolina Vanickova, Mirko Milosevic, Irina Ribeiro Bas, Monika Burocziova, Asumi Yokota, Petr Danek, Srdjan Grusanovic, Mateusz Chiliński, Dariusz Plewczynski, Jakub Rohlena, Hideyo Hirai, Katerina Rohlenova, Meritxell Alberich-Jorda.

  Emergency granulopoiesis is the enhanced and accelerated production of granulocytes that occurs during acute infection. The contribution of hematopoietic stem cells (HSCs) to this process was reported; however, how HSCs participate in emergency granulopoiesis remains elusive. Here, using a mouse model of emergency granulopoiesis we observe transcriptional changes in HSCs as early as 4 h after lipopolysaccharide (LPS) administration. We observe that the HSC identity is changed towards a myeloid-biased HSC and show that CD201 is enriched in lymphoid-biased HSCs. While CD201 expression under steady-state conditions reveals a lymphoid bias, under emergency granulopoiesis loss of CD201 marks the lymphoid-to-myeloid transcriptional switch. Mechanistically, we determine that lymphoid-biased CD201+ HSCs act as a first response during emergency granulopoiesis due to direct sensing of LPS by TLR4 and downstream activation of NF-κΒ signaling. The myeloid-biased CD201- HSC population responds indirectly during an acute infection by sensing G-CSF, increasing STAT3 phosphorylation, and upregulating LAP/LAP* C/EBPβ isoforms. In conclusion, HSC subpopulations support early phases of emergency granulopoiesis due to their transcriptional rewiring from a lymphoid-biased to myeloid-biased population and thus establishing alternative paths to supply elevated numbers of granulocytes.

Keywords:  CD201; emergency granulopoiesis; lymphoid-biased HSC; myeloid-biased HSC

DOI:  https://doi.org/10.15252/embj.2023113527
Blood Cancer Discov. 2023 Oct 17. OF1-OF3

Immunologic Targets in AML.

Jerome Ritz.

SUMMARY: In this issue of Blood Cancer Discovery, Nelde and colleagues used a sensitive mass spectrometry-based immunopeptidomics approach to characterize the antigenic landscape of acute myeloid leukemia (AML) and were able to identify immunogenic peptides presented by both leukemia stem cells (LSC) and bulk primary AML blasts. These immunogenic peptides elicit primarily CD4 T-cell responses and the diversity of the HLA class II immunopeptidome and presence of CD4 memory T-cell responses were both associated with improved clinical outcome. See related article by Nelde et al., p. 468 (1) .

DOI: https://doi.org/10.1158/2643-3230.BCD-23-0161
Ther Adv Hematol. 2023 ;14 20406207231205429

The history of oral decitabine/cedazuridine and its potential role in acute myeloid leukemia.

Robert Briski, Guillermo Garcia-Manero, Hagop Kantarjian, Farhad Ravandi.

  Decitabine, a member of the 5-azanucleosides, has a dose-dependent mechanism of action in vitro: termination of DNA replication at high doses, and inhibition of DNA methyltransferase at low doses. The alteration of DNA methylation patterns by low-dose decitabine is hypothesized to upregulate genes, which promote myeloblast differentiation. In a phase III clinical trial, low-dose decitabine achieved a superior overall response rate (ORR) when compared with 'treatment choice' [consisting of low-dose cytarabine (80%) and supportive care (20%)] as a frontline treatment for elderly patients with acute myeloid leukemia (AML). Despite an improved ORR, the median overall survival (OS) for elderly patients with AML was poor, <1 year. In turn, venetoclax was added to low-dose decitabine, the combination of which significantly improved the ORR and median OS in elderly patients with AML. Currently, hypomethylating agents are being combined with other novel therapies as investigational strategies for elderly and unfit patients with AML. They are also being evaluated as components of maintenance therapy in patients achieving remission. An oral formulation of decitabine has been developed which relies on the concomitant use of oral cedazuridine to protect against first pass metabolism. This oral formulation, which has been approved in myelodysplastic syndrome, is intended to increase convenience of use and therefore compliance in patients. This review characterizes the evolution of decitabine, its oral formulation, and its future in the treatment of AML.

Keywords:  5-azanucleosides decitabine; acute myeloid leukemia; decitabine/cedazuridine; epigenetics; hypomethylating agents; hypomethylation; novel combination therapy for AML; oral decitabine; oral therapy for AML; therapy for elderly and unfit patients with AML

DOI:  https://doi.org/10.1177/20406207231205429
Hemasphere. 2023 Oct;7(10): e961

Machine Learning Improves Risk Stratification in Myelodysplastic Neoplasms: An Analysis of the Spanish Group of Myelodysplastic Syndromes.

Adrian Mosquera Orgueira, Manuel Mateo Perez Encinas, Nicolas A Diaz Varela, Elvira Mora, Marina Díaz-Beyá, María Julia Montoro, Helena Pomares, Fernando Ramos, Mar Tormo, Andres Jerez, Josep F Nomdedeu, Carlos De Miguel Sanchez, Arenillas Leonor, Paula Cárcel, Maria Teresa Cedena Romero, Blanca Xicoy, Eugenia Rivero, Rafael Andres Del Orbe Barreto, Maria Diez-Campelo, Luis E Benlloch, Davide Crucitti, David Valcárcel.

Myelodysplastic neoplasms (MDS) are a heterogeneous group of hematological stem cell disorders characterized by dysplasia, cytopenias, and increased risk of acute leukemia. As prognosis differs widely between patients, and treatment options vary from observation to allogeneic stem cell transplantation, accurate and precise disease risk prognostication is critical for decision making. With this aim, we retrieved registry data from MDS patients from 90 Spanish institutions. A total of 7202 patients were included, which were divided into a training (80%) and a test (20%) set. A machine learning technique (random survival forests) was used to model overall survival (OS) and leukemia-free survival (LFS). The optimal model was based on 8 variables (age, gender, hemoglobin, leukocyte count, platelet count, neutrophil percentage, bone marrow blast, and cytogenetic risk group). This model achieved high accuracy in predicting OS (c-indexes; 0.759 and 0.776) and LFS (c-indexes; 0.812 and 0.845). Importantly, the model was superior to the revised International Prognostic Scoring System (IPSS-R) and the age-adjusted IPSS-R. This difference persisted in different age ranges and in all evaluated disease subgroups. Finally, we validated our results in an external cohort, confirming the superiority of the Artificial Intelligence Prognostic Scoring System for MDS (AIPSS-MDS) over the IPSS-R, and achieving a similar performance as the molecular IPSS. In conclusion, the AIPSS-MDS score is a new prognostic model based exclusively on traditional clinical, hematological, and cytogenetic variables. AIPSS-MDS has a high prognostic accuracy in predicting survival in MDS patients, outperforming other well-established risk-scoring systems.

DOI: https://doi.org/10.1097/HS9.0000000000000961
Cell Rep. 2023 Oct 13. pii: S2211-1247(23)01276-7. [Epub ahead of print]42(10): 113264

Aspartyl-tRNA synthetase 2 orchestrates iron-sulfur metabolism in hematopoietic stem cells via fine-tuning alternative RNA splicing.

Xuan Gu, Kailing Li, Meng Zhang, Yandan Chen, Jingchao Zhou, Chunxu Yao, Yong Zang, Jiefeng He, Jun Wan, Bin Guo.

  Aspartyl-tRNA synthetase 2 (Dars2) is involved in the regulation of mitochondrial protein synthesis and tissue-specific mitochondrial unfolded protein response (UPRmt). The role of Dars2 in the self-renewal and differentiation of hematopoietic stem cells (HSCs) is unknown. Here, we show that knockout (KO) of Dars2 significantly impairs the maintenance of hematopoietic stem and progenitor cells (HSPCs) without involving its tRNA synthetase activity. Dars2 KO results in significantly reduced expression of Srsf2/3/6 and impairs multiple events of mRNA alternative splicing (AS). Dars2 directly localizes to Srsf3-labeled spliceosomes in HSPCs and regulates the stability of Srsf3. Dars2-deficient HSPCs exhibit aberrant AS of mTOR and Slc22a17. Dars2 KO greatly suppresses the levels of labile ferrous iron and iron-sulfur cluster-containing proteins, which dampens mitochondrial metabolic activity and DNA damage repair pathways in HSPCs. Our study reveals that Dars2 plays a crucial role in the iron-sulfur metabolism and maintenance of HSPCs by modulating RNA splicing.

Keywords:  CP: Metabolism; CP: Stem cell research

DOI:  https://doi.org/10.1016/j.celrep.2023.113264
Leukemia. 2023 Oct 20.

RAS-pathway mutations are common in patients with ruxolitinib refractory/intolerant myelofibrosis: molecular analysis of the PAC203 cohort.

J M O'Sullivan, J Taylor, A Gerds, S Buckley, C N Harrison, S Oh, A F List, K Howard, H Dreau, A Hamblin, A J Mead.

DOI: https://doi.org/10.1038/s41375-023-02027-3
Mod Pathol. 2023 Oct 13. pii: S0893-3952(23)00257-0. [Epub ahead of print] 100352

Cutaneous manifestations of myeloid neoplasms exhibit broad and divergent morphologic and immunophenotypic features, but share ancestral clonal mutations with bone marrow.

Sam Sadigh, Daniel J DeAngelo, Jacqueline S Garcia, Robert P Hasserjian, Christopher B Hergott, Andrew A Lane, Scott B Lovitch, Fabienne Lucas, Marlise R Luskin, Elizabeth A Morgan, Geraldine S Pinkus, Olga Pozdnyakova, Scott J Rodig, Vignesh Shanmugam, Harrison K Tsai, Eric S Winer, David Zemmour, Annette S Kim.

In this study, we performed comprehensive molecular analysis of paired skin and peripheral blood (PB)/bone marrow (BM) samples from 17 patients with cutaneous myeloid or cutaneous histiocytic-dendritic neoplasms (CHDN). The cutaneous manifestations included 10 patients with cutaneous acute myeloid leukemia (c-AML), 2 patients with full or partial Langerhans cell differentiation (LCH), 2 patients with blastic plasmacytoid dendritic dell neoplasms (BPDCN), 1 patient with both LCH and BPDCN and 2 patients with full or partial indeterminate dendritic cell differentiation. Seven of 10 patients (70%) exhibited concurrent or subsequent marrow involvement by AML, with all seven cases (100%) demonstrating shared clonal mutations in the skin and BM, and clonal relatedness documented in one additional case that never had any BM involvement. NPM1 mutations were identified in 7 of 10 (70%) of these c-AML cases while one had KMT2A rearrangement and one showed inv(16). All 3 patients (100%) with Langerhans cell neoplasms, both patients with BPDCN (100%), and one of two patients (50%) with other cutaneous dendritic cell neoplasms also demonstrated shared mutations between skin and a concurrent or subsequent myeloid neoplasm. Both BM and cutaneous AML shared identical founding drivers with a predominance of NPM1, DNMT3A, and translocations associated with monocytic differentiation with common cutaneous only mutations involve genes in the signal transduction and epigenetic pathways. Cutaneous histiocytic-dendritic neoplasms shared founding drivers in ASXL1, TET2, and/or SRSF2 with recurrent secondary RAS pathway hits in the Langerhans cell histiocytosis or histiocytic sarcoma cases and copy number or structural variants in the cutaneous BPDCN cases. These results enrich and broaden our understanding of clonally related cutaneous manifestations of myeloid neoplasms, and further illuminate the highly diverse spectrum of morphologic and immunophenotypic features they exhibit.

DOI: https://doi.org/10.1016/j.modpat.2023.100352
Proc Natl Acad Sci U S A. 2023 Oct 24. 120(43): e2308658120

Complete miRNA-15/16 loss in mice promotes hematopoietic progenitor expansion and a myeloid-biased hyperproliferative state.

Anita Ng, Francesca Lovat, Andrew J Shih, Yuhong Ma, Yuri Pekarsky, Frank DiCaro, Lita Crichton, Esha Sharma, Xiao Jie Yan, Daqian Sun, Tengfei Song, Yong-Rui Zou, Britta Will, Carlo M Croce, Nicholas Chiorazzi.

  Dysregulated apoptosis and proliferation are fundamental properties of cancer, and microRNAs (miRNA) are critical regulators of these processes. Loss of miR-15a/16-1 at chromosome 13q14 is the most common genomic aberration in chronic lymphocytic leukemia (CLL). Correspondingly, the deletion of either murine miR-15a/16-1 or miR-15b/16-2 locus in mice is linked to B cell lymphoproliferative malignancies. However, unexpectedly, when both miR-15/16 clusters are eliminated, most double knockout (DKO) mice develop acute myeloid leukemia (AML). Moreover, in patients with CLL, significantly reduced expression of miR-15a, miR-15b, and miR-16 associates with progression of myelodysplastic syndrome to AML, as well as blast crisis in chronic myeloid leukemia. Thus, the miR-15/16 clusters have a biological relevance for myeloid neoplasms. Here, we demonstrate that the myeloproliferative phenotype in DKO mice correlates with an increase of hematopoietic stem and progenitor cells (HSPC) early in life. Using single-cell transcriptomic analyses, we presented the molecular underpinning of increased myeloid output in the HSPC of DKO mice with gene signatures suggestive of dysregulated hematopoiesis, metabolic activities, and cell cycle stages. Functionally, we found that multipotent progenitors (MPP) of DKO mice have increased self-renewing capacities and give rise to significantly more progeny in the granulocytic compartment. Moreover, a unique transcriptomic signature of DKO MPP correlates with poor outcome in patients with AML. Together, these data point to a unique regulatory role for miR-15/16 during the early stages of hematopoiesis and to a potentially useful biomarker for the pathogenesis of myeloid neoplasms.

Keywords:  CITE-seq; acute myeloid leukemia; hematopoietic stem cell; miR-15/16 clusters; microRNA

DOI:  https://doi.org/10.1073/pnas.2308658120
Clin Transl Med. 2023 Oct;13(10): e1444

Evolution of clonal hematopoiesis.

Isabelle A van Zeventer, Aniek O de Graaf, Joop H Jansen, Gerwin Huls.

DOI: https://doi.org/10.1002/ctm2.1444
Cell. 2023 Oct 12. pii: S0092-8674(23)01040-1. [Epub ahead of print]

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.

Li Li, Sarah Bowling, Sean E McGeary, Qi Yu, Bianca Lemke, Karel Alcedo, Yuemeng Jia, Xugeng Liu, Mark Ferreira, Allon M Klein, Shou-Wen Wang, Fernando D Camargo.

  Cellular lineage histories and their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have insufficient barcode diversity and single-cell lineage coverage for profiling tissues composed of millions of cells. Here, we developed DARLIN, an inducible Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) and 30 CRISPR target sites. DARLIN is inducible, generates massive lineage barcodes across tissues, and enables the detection of edited barcodes in ∼70% of profiled single cells. Using DARLIN, we examined fate bias within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we established a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN and found that cellular clonal memory is associated with genome-wide DNA methylation rather than gene expression or chromatin accessibility. DARLIN will enable the high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts.

Keywords:  DNA methylation; hematopoiesis; lineage tracing; multiomics; single cell

DOI:  https://doi.org/10.1016/j.cell.2023.09.019
Eur Rev Med Pharmacol Sci. 2023 Oct;pii: 33940. [Epub ahead of print]27(19): 9145-9151

The effect of small molecule inhibitor NSC348884 on nucleophosmin 1-mutated acute myeloid leukemia cells.

J-F Zhu, L-L Han, Y Ma, Y-X Wang, F Zhang.

OBJECTIVE: Nucleophosmin 1 (NPM1) is a common shuttling protein. Mutation in the NPM1 gene is the most frequent gene alteration in acute myeloid leukemia (AML). This study aims to explore the inhibitory effects of small molecule NSC348884 on wild-type and NPM1-mutated AML cells.
MATERIALS AND METHODS: Immunofluorescence was used to determine the intracellular localization of NPM1 protein in wild-type (OCI-AML2) and NPM1-mutated (OCI-AML3) AML cell lines. The oligomerization state of NPM1 was assessed by Western blot analysis, and the inhibitory effect of NSC348884 on the proliferation of AML cells was evaluated by Cell-counting kit-8 (CCK-8). Flow cytometry was used to detect the proapoptotic effect of NSC348884 on AML cells.
RESULTS: Western blot results showed a significant reduction in the levels of the oligomeric NPM1 protein after the treatment with NSC348884. NSC348884 had an inhibitory effect on the proliferation of both wild-type and NPM1-mutant AML cells. The inhibitory effect on OCI-AML3 cells was stronger, compared to OCI-AML2 cells. Flow cytometry showed that NSC348884 could significantly induce AML cell apoptosis and had a stronger proapoptotic effect on OCI-AML3 cells.
CONCLUSIONS: NSC348884 had inhibitory and proapoptotic effects on both wild-type and NPM1-mutated AML cells. The effect of NSC348884 on AML cells, carrying NPM1 mutation was significantly stronger.

DOI: https://doi.org/10.26355/eurrev_202310_33940
Haematologica. 2023 Oct 19.

Differential transcriptional control of hematopoiesis in congenital and cycling neutropenia patients harboring ELANE mutations.

Alexander Zeidler, Natalia Borbaran-Bravo, Benjamin Dannenmann, Malte Ritter, Masoud Nasri, Maksim Klimiankou, Sergey Kandabarau, Azadeh Zahabi, Josef König, Cornelia Zeidler, Julia Skokowa, Karl Welte.

Mutations in the ELANE gene, encoding the neutrophil elastase (NE) protein, are responsible for most CyN cases and approximately 25 % of CN cases. In CN and in CyN, a median of 2.8 % of CD34+ cells were early CD49f+ hematopoietic stem cells (eHSC) that did not express ELANE and thus escape from the unfolded protein response (UPR) caused by mutated NE. In CyN, the CD49f+ cells respond to G-CSF with a significant upregulation of the hematopoietic stem-cell-specific transcription factors, C/EBP/, MLL1, HOXA9, MEIS1, and HLF during the ascending arm of the cycle, resulting in the differentiation of myeloid cells to mature neutrophils at the cycle peak. However, NE protein released by neutrophils at the cycle's peak caused a negative feedback loop on granulopoiesis through the proteolytic digestion of G-CSF. In contrast, in CN patients, CD49f+ cells failed to express mRNA levels of HSC-specific transcription factors mentioned above. Rescue of C/EBP//expression in CN restored granulopoiesis.

DOI: https://doi.org/10.3324/haematol.2023.284033
N Engl J Med. 2023 Oct 19. pii: 10.1056/NEJMc2309139#sa1. [Epub ahead of print]389(16): 1535

Familial Clonal Hematopoiesis in a Long Telomere Syndrome.

Tetsushi Nakao, Pradeep Natarajan.

DOI: https://doi.org/10.1056/NEJMc2309139
Am J Hematol. 2023 Oct 18.

Effect of donor age in patients with acute myeloid leukemia undergoing haploidentical hematopoietic cell transplantation vary by conditioning intensity and recipient age.

Rima M Saliba, Christopher G Kanakry, Shahinaz Gadalla, Partow Kebriaei, Katayoun Rezvani, Richard E Champlin, Elizabeth J Shpall, Daniel Weisdorf, Rohtesh S Mehta.

We investigated the impact of donor age (younger [≤35 years] vs. older [>35 years]) after accounting for other non-HLA and HLA factors on outcomes of patients with acute myeloid leukemia undergoing HLA-haploidentical hematopoietic cell transplantation (n = 790). The effect differed by conditioning-partly related to the differences in the recipient age in myeloablative (MAC; median 46 years) versus reduced-intensity/non-myeloablative conditioning (RIC/NMA; median 61 years) groups. With MAC (n = 320), donor age had no impact on acute graft-versus-host disease (GVHD), but older donors were associated with a significantly higher risk of chronic GVHD (hazard ratio [HR]: 1.6, 95% confidence interval [CI]: 1.10-2.30, p = .02) independent of recipient age and other factors. Donor age had no impact on either relapse or non-relapse mortality (NRM). The impact of donor/recipient age on overall survival changed over time. Older donors were associated with significantly higher late overall mortality (>6 months) in younger recipients (≤ 50 years; HR: 2.2, 95% CI: 1.03-4.6, p = .04) but not older recipients. With RIC/NMA (n = 470), neither recipient's nor donor's age influenced the risk of GVHD. Donor age had no significant impact on the risk of relapse, but older donors were associated with a significantly higher risk of NRM (HR: 1.6, 95% CI: 1.02-2.6, p = .04) independent of recipient age. Older donor age was associated with significantly higher late overall mortality (>9 months) in older recipients (>50 years; HR: 1.66, 95% CI: 1.0-2.67; p = .049) but not in younger recipients. Donor selection based on donor age may require a tailored approach for a particular recipient.

DOI: https://doi.org/10.1002/ajh.27126
Trends Cancer. 2023 Oct 18. pii: S2405-8033(23)00212-1. [Epub ahead of print]

Making normal hematopoiesis invisible to CAR T cells.

Miriam Y Kim.

  Two recent studies, by Casirati et al. and Wellhausen et al., report genetically engineering normal hematopoietic stem and progenitor cells (HSPCs) to be resistant to chimeric antigen receptor (CAR)-T cells, by changing a single amino acid in the target protein that abrogates CAR binding, without compromising protein function. This allows for selective targeting of cancer cells without harming normal hematopoietic cells.

Keywords:  CAR T cells; HSPCs; epitope editing

DOI:  https://doi.org/10.1016/j.trecan.2023.10.001
N Engl J Med. 2023 Oct 19. pii: 10.1056/NEJMc2309139#sa2. [Epub ahead of print]389(16): 1535-1536

Familial Clonal Hematopoiesis in a Long Telomere Syndrome. Reply.

Mary Armanios.

DOI: https://doi.org/10.1056/NEJMc2309139
Leukemia. 2023 Oct 17.

Identification of multivariable microRNA and clinical biomarker panels to predict imatinib response in chronic myeloid leukemia at diagnosis.

Andrew Wu, Ryan Yen, Sarah Grasedieck, Hanyang Lin, Helen Nakamoto, Donna L Forrest, Connie J Eaves, Xiaoyan Jiang.

Imatinib Mesylate (imatinib) was once hailed as the magic bullet for chronic myeloid leukemia (CML) and remains a front-line therapy for CML to this day alongside other tyrosine kinase inhibitors (TKIs). However, TKI treatments are rarely curative and patients are often required to receive life-long treatment or otherwise risk relapse. Thus, there is a growing interest in identifying biomarkers in patients which can predict TKI response upon diagnosis. In this study, we analyze clinical data and differentially expressed miRNAs in CD34+ CML cells from 80 patients at diagnosis who were later classified as imatinib-responders or imatinib-nonresponders. A Cox Proportional Hazard (CoxPH) analysis identified 16 miRNAs that were associated with imatinib nonresponse and differentially expressed in these patients. We also trained a machine learning model with different combinations of the 16 miRNAs with and without clinical parameters and identified a panel with high predictive performance based on area-under-curve values of receiver-operating-characteristic and precision-recall curves. Interestingly, the multivariable panel consisting of both miRNAs and clinical features performed better than either miRNA or clinical panels alone. Thus, our findings may inform future studies on predictive biomarkers and serve as a tool to develop more optimized treatment plans for CML patients in the clinic.

DOI: https://doi.org/10.1038/s41375-023-02062-0
Nat Med. 2023 Oct 19.

The PD-1- and LAG-3-targeting bispecific molecule tebotelimab in solid tumors and hematologic cancers: a phase 1 trial.

Jason J Luke, Manish R Patel, George R Blumenschein, Erika Hamilton, Bartosz Chmielowski, Susanna V Ulahannan, Roisin M Connolly, Cesar A Santa-Maria, Jie Wang, Shakeela W Bahadur, Andrew Weickhardt, Adam S Asch, Girish Mallesara, Philip Clingan, Monika Dlugosz-Danecka, Monika Tomaszewska-Kiecana, Halyna Pylypenko, Nada Hamad, Hedy L Kindler, Bradley J Sumrow, Patrick Kaminker, Francine Z Chen, Xiaoyu Zhang, Kalpana Shah, Douglas H Smith, Anushka De Costa, Jonathan Li, Hua Li, Jichao Sun, Paul A Moore.

Tebotelimab, a bispecific PD-1×LAG-3 DART molecule that blocks both PD-1 and LAG-3, was investigated for clinical safety and activity in a phase 1 dose-escalation and cohort-expansion clinical trial in patients with solid tumors or hematologic malignancies and disease progression on previous treatment. Primary endpoints were safety and maximum tolerated dose of tebotelimab when administered as a single agent (n = 269) or in combination with the anti-HER2 antibody margetuximab (n = 84). Secondary endpoints included anti-tumor activity. In patients with advanced cancer treated with tebotelimab monotherapy, 68% (184/269) experienced treatment-related adverse events (TRAEs; 22% were grade ≥3). No maximum tolerated dose was defined; the recommended phase 2 dose (RP2D) was 600 mg once every 2 weeks. There were tumor decreases in 34% (59/172) of response-evaluable patients in the dose-escalation cohorts, with objective responses in multiple solid tumor types, including PD-1-refractory disease, and in LAG-3+ non-Hodgkin lymphomas, including CAR-T refractory disease. To enhance potential anti-tumor responses, we tested margetuximab plus tebotelimab. In patients with HER2+ tumors treated with tebotelimab plus margetuximab, 74% (62/84) had TRAEs (17% were grade ≥3). The RP2D was 600 mg once every 3 weeks. The confirmed objective response rate in these patients was 19% (14/72), including responses in patients typically not responsive to anti-HER2/anti-PD-1 combination therapy. ClinicalTrials.gov identifier: NCT03219268 .

DOI: https://doi.org/10.1038/s41591-023-02593-0
Nature. 2023 Oct 18.

Chromatin compartmentalization regulates the response to DNA damage.

Coline Arnould, Vincent Rocher, Florian Saur, Aldo S Bader, Fernando Muzzopappa, Sarah Collins, Emma Lesage, Benjamin Le Bozec, Nadine Puget, Thomas Clouaire, Thomas Mangeat, Raphael Mourad, Nadav Ahituv, Daan Noordermeer, Fabian Erdel, Martin Bushell, Aline Marnef, Gaëlle Legube.

The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated1,2, the contribution of chromosome folding to these processes remains unclear3. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1. This compartment forms by a mechanism that is consistent with polymer-polymer phase separation rather than liquid-liquid phase separation. The D compartment arises mostly in G1 phase, is independent of cohesin and is enhanced after pharmacological inhibition of DNA-dependent protein kinase (DNA-PK) or R-loop accumulation. Importantly, R-loop-enriched DNA-damage-responsive genes physically localize to the D compartment, and this contributes to their optimal activation, providing a function for DSB clustering in the DNA damage response. However, DSB-induced chromosome reorganization comes at the expense of an increased rate of translocations, also observed in cancer genomes. Overall, we characterize how DSB-induced compartmentalization orchestrates the DNA damage response and highlight the critical impact of chromosome architecture in genomic instability.

DOI: https://doi.org/10.1038/s41586-023-06635-y
Leukemia. 2023 Oct 19.

Iron overload induces dysplastic erythropoiesis and features of myelodysplasia in Nrf2-deficient mice.

Tiago L Duarte, Marta Lopes, Mónica Oliveira, Ana G Santos, Catarina Vasco, Joana P Reis, Ana Rita Antunes, Andreia Gonçalves, Sérgio Chacim, Cláudia Oliveira, Beatriz Porto, Maria José Teles, Ana C Moreira, André M N Silva, Ron Schwessinger, Hal Drakesmith, Rui Henrique, Graça Porto, Delfim Duarte.

Iron overload (IOL) is hypothesized to contribute to dysplastic erythropoiesis. Several conditions, including myelodysplastic syndrome, thalassemia and sickle cell anemia, are characterized by ineffective erythropoiesis and IOL. Iron is pro-oxidant and may participate in the pathophysiology of these conditions by increasing genomic instability and altering the microenvironment. There is, however, lack of in vivo evidence demonstrating a role of IOL and oxidative damage in dysplastic erythropoiesis. NRF2 transcription factor is the master regulator of antioxidant defenses, playing a crucial role in the cellular response to IOL in the liver. Here, we crossed Nrf2-/- with hemochromatosis (Hfe-/-) or hepcidin-null (Hamp1-/-) mice. Double-knockout mice developed features of ineffective erythropoiesis and myelodysplasia including macrocytic anemia, splenomegaly, and accumulation of immature dysplastic bone marrow (BM) cells. BM cells from Nrf2/Hamp1-/- mice showed increased in vitro clonogenic potential and, upon serial transplantation, recipients disclosed cytopenias, despite normal engraftment, suggesting defective differentiation. Unstimulated karyotype analysis showed increased chromosome instability and aneuploidy in Nrf2/Hamp1-/- BM cells. In HFE-related hemochromatosis patients, NRF2 promoter SNP rs35652124 genotype TT (predicted to decrease NRF2 expression) associated with increased MCV, consistent with erythroid dysplasia. Our results suggest that IOL induces ineffective erythropoiesis and dysplastic hematologic features through oxidative damage in Nrf2-deficient cells.

DOI: https://doi.org/10.1038/s41375-023-02067-9
Nat Genet. 2023 Oct 19.

Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration.

Hiroyuki Hirakawa, Longfei Gao, Daniel Naveed Tavakol, Gordana Vunjak-Novakovic, Lei Ding.

Hematopoietic stem cells (HSCs) regenerate after myeloablation, a procedure that adversely disrupts the bone marrow and drives leptin receptor-expressing cells, a key niche component, to differentiate extensively into adipocytes. Regeneration of the bone marrow niche is associated with the resolution of adipocytes, but the mechanisms remain poorly understood. Using Plin1-creER knock-in mice, we followed the fate of adipocytes in the regenerating niche in vivo. We found that bone marrow adipocytes were highly dynamic and dedifferentiated to leptin receptor-expressing cells during regeneration after myeloablation. Bone marrow adipocytes could give rise to osteolineage cells after skeletal injury. The cellular fate of steady-state bone marrow adipocytes was also plastic. Deletion of adipose triglyceride lipase (Atgl) from bone marrow stromal cells, including adipocytes, obstructed adipocyte dedifferentiation and led to severely compromised regeneration of HSCs as well as impaired B lymphopoiesis after myeloablation, but not in the steady state. Thus, the regeneration of HSCs and their niche depends on the cellular plasticity of bone marrow adipocytes.

DOI: https://doi.org/10.1038/s41588-023-01528-2
Br J Haematol. 2023 Oct 19.

Quantitative interpretation of bone marrow biopsies in MPN-What's the point in a molecular age?

Hosuk Ryou, Oliver Lomas, Helen Theissen, Emily Thomas, Jens Rittscher, Daniel Royston.

  The diagnosis of myeloproliferative neoplasms (MPN) requires the integration of clinical, morphological, genetic and immunophenotypic findings. Recently, there has been a transformation in our understanding of the cellular and molecular mechanisms underlying disease initiation and progression in MPN. This has been accompanied by the widespread application of high-resolution quantitative molecular techniques. By contrast, microscopic interpretation of bone marrow biopsies by haematologists/haematopathologists remains subjective and qualitative. However, advances in tissue image analysis and artificial intelligence (AI) promise to transform haematopathology. Pioneering studies in bone marrow image analysis offer to refine our understanding of the boundaries between reactive samples and MPN subtypes and better capture the morphological correlates of high-risk disease. They also demonstrate potential to improve the evaluation of current and novel therapeutics for MPN and other blood cancers. With increased therapeutic targeting of diverse molecular, cellular and extra-cellular components of the marrow, these approaches can address the unmet need for improved objective and quantitative measures of disease modification in the context of clinical trials. This review focuses on the state-of-the-art in image analysis/AI of bone marrow tissue, with an emphasis on its potential to complement and inform future clinical studies and research in MPN.

Keywords:  artificial intelligence; bone marrow biopsy; clinical trials; marrow fibrosis; megakaryocytes; myeloproliferative neoplasm

DOI:  https://doi.org/10.1111/bjh.19154