bims-tremyl 2023-08-20 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2023–08–20
38 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Clinical impact of the genomic landscape and leukemogenic trajectories in non-intensively treated elderly acute myeloid leukemia patients.
Measurable Residual IDH1 before Allogeneic Transplant for Acute Myeloid Leukemia.
PPM1D modulates hematopoietic cell fitness and response to DNA damage and is a therapeutic target in myeloid malignancy.
Fractionated Versus Single Dose Gemtuzumab Ozogamicin with Determinants of Benefit in Older AML: UK NCRI AML18 Trial.
RUNX1 loss renders hematopoietic and leukemic cells dependent on interleukin-3 and sensitive to JAK inhibition.
miR-30e-5p regulates leukemia stem cell self-renewal through the Cyb561/ROS signaling pathway.
Pyruvate anaplerosis is a targetable vulnerability in persistent leukaemic stem cells.
Risk assessment according to IPSS-M is superior to AML ELN risk classification in MDS/AML overlap patients defined by ICC.
Standardising acute myeloid leukaemia classification systems: a perspective from a panel of international experts.
Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths.
Phase 1 Results of Bromodomain and Extraterminal Inhibitor PLX51107 in Combination with Azacitidine in Patients with Relapsed/Refractory Myeloid Malignancies.
French Retrospective Database Analysis of Patient Characteristics and Treatment Patterns in Patients with R/R FLT3-Mutated AML: A Registry-Based Cohort Study.
Midostaurin plus daunorubicin or idarubicin for young and elderly adults with FLT3-mutated AML: a Phase 3b trial.
Cell fate determinant Llgl1 is required for propagation of acute myeloid leukemia.
Use of tamibarotene, a potent and selective RARα agonist, in combination with azacitidine in patients with relapsed and refractory AML with RARA gene overexpression.
CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny.
Overcoming adaptive resistance in AML by synergistically targeting FOXO3A-GNG7-mTOR axis with FOXO3A inhibitor Gardenoside and rapamycin.
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.
RNA m6A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression.
Phase I study evaluating the Fc-optimized FLT3 antibody FLYSYN in AML patients with measurable residual disease.
LepR+ niche cell-derived AREG compromises hematopoietic stem cell maintenance under conditions of DNA repair deficiency and aging.
Myeloablative dose of busulfan and fludarabine combined with in vivo T-cell depletion is a safe and effective conditioning for acute myeloid leukaemia and myelodysplastic syndrome patients.
miRNAs as prognostic predictors in acute myeloid leukemia.
In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis.
The maintenance mechanism of hematopoietic stem cell dormancy: role for a subset of macrophages.
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.
Genetic mutations and leukapheresis in acute myeloid leukemia: is there a link?
FANCA deficiency promotes leukaemic progression by allowing the emergence of cells carrying oncogenic driver mutations.
AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology.
FASN deficiency induces a cytosol-to-mitochondria citrate flux to mitigate detachment-induced oxidative stress.
Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS.
Single-cell RNA-seq reveals a microenvironment and an exhaustion state of T/NK cells in acute myeloid leukemia.
Core-binding factor abnormalities involving chromosome 16 in acute myeloid leukaemia: prognostic and therapeutic implications.
Comparison of efficacy between homoharringtonine, aclarubicin, cytarabine (HAA) and idarubicin, cytarabine (IA) regimens as induction therapy in patients with de novo core binding factor acute myeloid leukemia.
Spontaneous remission and loss of monosomy 7: a window of opportunity for young children with SAMD9L syndrome.
Myelodysplastic neoplasm-associated U2AF1 mutations induce host defense defects by compromising neutrophil chemotaxis.
Nuclear genetic control of mtDNA copy number and heteroplasmy in humans.
GATA2 mitotic bookmarking is required for definitive haematopoiesis.

Leukemia. 2023 Aug 17.

Clinical impact of the genomic landscape and leukemogenic trajectories in non-intensively treated elderly acute myeloid leukemia patients.

Ekaterina Jahn, Maral Saadati, Pierre Fenaux, Marco Gobbi, Gail J Roboz, Lars Bullinger, Pavlo Lutsik, Anna Riedel, Christoph Plass, Nikolaus Jahn, Claudia Walter, Karlheinz Holzmann, Yong Hao, Sue Naim, Nicholas Schreck, Julia Krzykalla, Axel Benner, Harold N Keer, Mohammad Azab, Konstanze Döhner, Hartmut Döhner.

To characterize the genomic landscape and leukemogenic pathways of older, newly diagnosed, non-intensively treated patients with AML and to study the clinical implications, comprehensive genetics analyses were performed including targeted DNA sequencing of 263 genes in 604 patients treated in a prospective Phase III clinical trial. Leukemic trajectories were delineated using oncogenetic tree modeling and hierarchical clustering, and prognostic groups were derived from multivariable Cox regression models. Clonal hematopoiesis-related genes (ASXL1, TET2, SRSF2, DNMT3A) were most frequently mutated. The oncogenetic modeling algorithm produced a tree with five branches with ASXL1, DDX41, DNMT3A, TET2, and TP53 emanating from the root suggesting leukemia-initiating events which gave rise to further subbranches with distinct subclones. Unsupervised clustering mirrored the genetic groups identified by the tree model. Multivariable analysis identified FLT3 internal tandem duplications (ITD), SRSF2, and TP53 mutations as poor prognostic factors, while DDX41 mutations exerted an exceptionally favorable effect. Subsequent backwards elimination based on the Akaike information criterion delineated three genetic risk groups: DDX41 mutations (favorable-risk), DDX41wildtype/FLT3-ITDneg/TP53wildtype (intermediate-risk), and FLT3-ITD or TP53 mutations (high-risk). Our data identified distinct trajectories of leukemia development in older AML patients and provide a basis for a clinically meaningful genetic outcome stratification for patients receiving less intensive therapies.

DOI: https://doi.org/10.1038/s41375-023-01999-6
medRxiv. 2023 Aug 01. pii: 2023.07.28.23293166. [Epub ahead of print]

Measurable Residual IDH1 before Allogeneic Transplant for Acute Myeloid Leukemia.

Gege Gui, Laura W Dillon, Niveditha Ravindra, Pranay S Hegde, Georgia Andrew, Devdeep Mukherjee, Zoë Wong, Jeffery Auletta, Firas El Chaer, Evan Chen, Yi-Bin Chen, Adam Corner, Steven M Devine, Sunil Iyer, Antonio Martin Jimenez Jimenez, Marcos J G De Lima, Mark R Litzow, Partow Kebriaei, Stephen R Spellman, Scott L Zeger, Kristin M Page, Christopher S Hourigan.

Measurable residual disease (MRD) in adults with acute myeloid leukemia (AML) in complete remission is an important prognostic marker, but detection methodology requires optimization. The persistence of mutated NPM1 or FLT3 -ITD in the blood of adult patients with AML in first complete remission (CR1) prior to allogeneic hematopoetic cell transplant (alloHCT) has been established as associated with increased relapse and death after transplant. The prognostic implications of persistence of other common AML-associated mutations, such as IDH1 , at this treatment landmark however remains incompletely defined. We performed testing for residual IDH1 variants ( IDH1 m) in pre-transplant CR1 blood of 148 adult patients undergoing alloHCT for IDH1 -mutated AML at a CIBMTR site between 2013-2019. No post-transplant differences were observed between those testing IDH1 m positive (n=53, 36%) and negative pre-transplant (overall survival: p = 0.4; relapse: p = 0.5). For patients with IDH1 mutated AML co-mutated with NPM1 and/or FLT3 -ITD, only detection of persistent mutated NPM1 and/or FLT3 -ITD was associated with significantly higher rates of relapse (p = 0.01). These data, from the largest study to date, do not support the detection of IDH1 mutation in CR1 blood prior to alloHCT as evidence of AML MRD or increased post-transplant relapse risk.

DOI: https://doi.org/10.1101/2023.07.28.23293166
Blood. 2023 Aug 18. pii: blood.2023020331. [Epub ahead of print]

PPM1D modulates hematopoietic cell fitness and response to DNA damage and is a therapeutic target in myeloid malignancy.

Peter Grant Miller, Adam S Sperling, Christina Mayerhofer, Marie McConkey, Jana Maria Ellegast, Carmen Da Silva, Drew Nathaniel Cohen, Chuqi Wang, Azeem Sharda, Ni Yan, Subha Saha, Cameron Schluter, Ilexa Ashley Schechter, Mikołaj Słabicki, Brittany Sandoval, Josephine Kahn, Steffen Boettcher, Christopher J Gibson, David T Scadden, Kimberly Stegmaier, Shruti Bhatt, R Coleman Lindsley, Benjamin L Ebert.

PPM1D encodes a phosphatase that is recurrently activated across cancer, most notably in therapy-related myeloid neoplasms. However, the function of PPM1D in hematopoiesis and its contribution to tumor cell growth remain incompletely understood. Using conditional mouse models, we uncover a central role for Ppm1d in hematopoiesis and validate its potential as a therapeutic target. We find that Ppm1d regulates the competitive fitness and self-renewal of hematopoietic stem cells (HSCs) with and without exogenous genotoxic stresses. We also show that while Ppm1d activation confers cellular resistance to cytotoxic therapy, it does so to a lesser degree than p53 loss, informing the clonal competition phenotypes often observed in human studies. Notably, loss of Ppm1d sensitizes leukemias to cytotoxic therapies in vitro and in vivo, even in the absence of a Ppm1d mutation. Vulnerability to PPM1D inhibition is observed across many cancer types and dependent on p53 activity. Importantly, organism-wide loss of Ppm1d in adult mice is well tolerated, supporting the tolerability of pharmacologically targeting PPM1D. Our data link PPM1D gain-of-function mutations to the clonal expansion of HSCs, inform human genetic observations, and support the therapeutic targeting of PPM1D in cancer.

DOI: https://doi.org/10.1182/blood.2023020331
Blood. 2023 Aug 18. pii: blood.2023020630. [Epub ahead of print]

Fractionated Versus Single Dose Gemtuzumab Ozogamicin with Determinants of Benefit in Older AML: UK NCRI AML18 Trial.

Sylvie D Freeman, Abin Thomas, Ian Thomas, Robert K Hills, Paresh Vyas, Amanda Frances Gilkes, Marlen Metzner, Niels Asger Jakobsen, Alison Kennedy, Amy Rachel Moore, Nuria Marquez-Almuina, Sarah Burns, Sophie King, Georgia Andrew, Kathleen M E Gallagher, Rob S Sellar, Paul A Cahalin, Duruta Weber, Mike Dennis, Priyanka Mehta, Steven Knapper, Nigel H Russell.

Addition of gemtuzumab ozogamicin (GO) to induction chemotherapy improves outcomes in older patients with acute myeloid leukemia (AML) but it is uncertain whether a fractionated schedule provides additional benefit to a single dose. We randomised 852 older adults (median age 68yrs) with AML/high risk myelodysplasia to GO on day 1 (GO1), or on days 1 and 4 (GO2) of course-1 induction. Median follow-up was 50.2 months. While complete remission rates post course 1 did not significantly differ between arms (GO2 63%, GO1 57%, OR 0.78 (0.59-1.03), P=0.08), there were significantly more patients who achieved CR with MRD <0.1% (50% vs 41% OR 0.72 (0.54-0.96) P=0.027). This differential MRD reduction with GO2 varied across molecular subtypes being greatest for IDH mutations. 5yr overall survival (OS) was 29% for GO2 and 24% for GO1 patients (HR 0.89, P=0.14). In a sensitivity analysis excluding patients found to have adverse cytogenetics /TP53 mutations, 5yr OS was 33% for GO2 and 26% for GO1 (HR 0.83, P=0.045). 228 (27%) patients received an allo-transplant in first remission. OS was superior for transplanted patients on the GO2 arm (HR 0.67, 95%CI 0.47-0.97, P=0.033) however this benefit was lost when patients were censored at transplant. In conclusion, GO2 was associated with greater reduction in MRD and improved survival in older adults with non-adverse risk genetics. This benefit from GO2 was dependent on allo-transplant to translate the better leukemia clearance into improved survival. CT# ISRCTN 31682779.

DOI: https://doi.org/10.1182/blood.2023020630
J Clin Invest. 2023 Aug 15. pii: e167053. [Epub ahead of print]

RUNX1 loss renders hematopoietic and leukemic cells dependent on interleukin-3 and sensitive to JAK inhibition.

Amy C Fan, Yusuke Nakauchi, Lawrence Bai, Armon Azizi, Kevin A Nuno, Feifei Zhao, Thomas Köhnke, Daiki Karigane, David Cruz-Hernandez, Andreas Reinisch, Purvesh Khatri, Ravindra Majeti.

  Disease-initiating mutations in the transcription factor RUNX1 occur as germline and somatic events that cause leukemias with particularly poor prognosis. However, the role of RUNX1 in leukemogenesis is not fully understood and effective therapies for RUNX1-mutant leukemias remain elusive. Here, we use primary patient samples and a RUNX1 knockout model in primary human hematopoietic cells to investigate how RUNX1 loss contributes to leukemic progression and to identify targetable vulnerabilities. Surprisingly, we found that RUNX1 loss decreased proliferative capacity and stem cell function. However, RUNX1-deficient cells selectively upregulated the interleukin-3 (IL-3) receptor. Exposure to IL-3, but not other JAK/STAT cytokines, rescued RUNX1 KO proliferative and competitive defects. Further, we demonstrated that RUNX1 loss repressed JAK/STAT signaling and rendered RUNX1-deficient cells sensitive to JAK inhibitors. Our study identifies a dependency of RUNX1-mutant leukemias on IL-3/JAK/STAT signaling, which may enable these aggressive blood cancers to be targeted with existing agents.

Keywords:  Hematology; Hematopoietic stem cells; Human stem cells; Inflammation; Leukemias

DOI:  https://doi.org/10.1172/JCI167053
Haematologica. 2023 Aug 16.

miR-30e-5p regulates leukemia stem cell self-renewal through the Cyb561/ROS signaling pathway.

Yanwen Ge, Mei Hong, Yu Zhang, Jiachen Wang, Lei Li, Hongkai Zhu, Yue Sheng, Wen-Shu Wu, Zhonghui Zhang.

Leukemia stem cells (LSCs) represent a crucial and rare subset of cells within acute myeloid leukemia (AML) that play a pivotal role in the initiation, maintenance, and relapse of AML. Targeting LSCs holds great promise for preventing AML relapse and improving long-term outcomes. However, the precise molecular mechanisms governing LSC self-renewal are still poorly understood. Here, we present compelling evidence that miR-30e-5p, a potential tumorsuppressive microRNA, exhibits significantly lower expression in AML samples compared to healthy bone marrow samples. Forced expression of miR-30e effectively inhibits leukemogenesis, impairs LSC self-renewal, and delays leukemia progression. Mechanistically, Cyb561 acts as a direct target of miR-30e-5p in LSCs, and its deficiency restricts the selfrenewal of LSCs by activating ROS signaling and markedly prolongs recipient survival. Moreover, genetic or pharmacological overexpression of miR-30e-5p or knockdown of Cyb561 suppresses the growth of human AML cells. In conclusion, our findings establish the crucial role of the miR-30e-5p/Cyb561/ROS axis in finely regulating LSC self-renewal, highlighting Cyb561 as a potential therapeutic target for LSC-directed therapies.

DOI: https://doi.org/10.3324/haematol.2023.282837
Nat Commun. 2023 Aug 17. 14(1): 4634

Pyruvate anaplerosis is a targetable vulnerability in persistent leukaemic stem cells.

Kevin M Rattigan, Zuzana Brabcova, Daniele Sarnello, Martha M Zarou, Kiron Roy, Ryan Kwan, Lucie de Beauchamp, Amy Dawson, Angela Ianniciello, Ahmed Khalaf, Eric R Kalkman, Mary T Scott, Karen Dunn, David Sumpton, Alison M Michie, Mhairi Copland, Saverio Tardito, Eyal Gottlieb, G Vignir Helgason.

Deregulated oxidative metabolism is a hallmark of leukaemia. While tyrosine kinase inhibitors (TKIs) such as imatinib have increased survival of chronic myeloid leukaemia (CML) patients, they fail to eradicate disease-initiating leukemic stem cells (LSCs). Whether TKI-treated CML LSCs remain metabolically deregulated is unknown. Using clinically and physiologically relevant assays, we generate multi-omics datasets that offer unique insight into metabolic adaptation and nutrient fate in patient-derived CML LSCs. We demonstrate that LSCs have increased pyruvate anaplerosis, mediated by increased mitochondrial pyruvate carrier 1/2 (MPC1/2) levels and pyruvate carboxylase (PC) activity, in comparison to normal counterparts. While imatinib reverses BCR::ABL1-mediated LSC metabolic reprogramming, stable isotope-assisted metabolomics reveals that deregulated pyruvate anaplerosis is not affected by imatinib. Encouragingly, genetic ablation of pyruvate anaplerosis sensitises CML cells to imatinib. Finally, we demonstrate that MSDC-0160, a clinical orally-available MPC1/2 inhibitor, inhibits pyruvate anaplerosis and targets imatinib-resistant CML LSCs in robust pre-clinical CML models. Collectively these results highlight pyruvate anaplerosis as a persistent and therapeutically targetable vulnerability in imatinib-treated CML patient-derived samples.

DOI: https://doi.org/10.1038/s41467-023-40222-z
Leukemia. 2023 Aug 12.

Risk assessment according to IPSS-M is superior to AML ELN risk classification in MDS/AML overlap patients defined by ICC.

Sandra Huber, Constance Baer, Stephan Hutter, Frank Dicker, Irene Fuhrmann, Manja Meggendorfer, Christian Pohlkamp, Wolfgang Kern, Torsten Haferlach, Claudia Haferlach, Gregor Hoermann.

DOI: https://doi.org/10.1038/s41375-023-02004-w
Lancet Haematol. 2023 Aug 09. pii: S2352-3026(23)00159-X. [Epub ahead of print]

Standardising acute myeloid leukaemia classification systems: a perspective from a panel of international experts.

Rory M Shallis, Naval Daver, Jessica K Altman, Rami S Komrokji, Daniel A Pollyea, Talha Badar, Jan P Bewersdorf, Vijaya R Bhatt, Stéphane de Botton, Adolfo de la Fuente Burguera, Hetty E Carraway, Pinkal Desai, Richard Dillon, Nicolas Duployez, Firas El Chaer, Amir T Fathi, Sylvie D Freeman, Ivana Gojo, Michael R Grunwald, Brian A Jonas, Marina Konopleva, Tara L Lin, Gabriel N Mannis, John Mascarenhas, Laura C Michaelis, Alice S Mims, Pau Montesinos, Olga Pozdnyakova, Keith W Pratz, Andre C Schuh, Mikkael A Sekeres, Catherine C Smith, Maximilian Stahl, Marion Subklewe, Geoffrey L Uy, Maria Teresa Voso, Roland B Walter, Eunice S Wang, Joshua F Zeidner, Andrius Žučenka, Amer M Zeidan.

The existence of two acute myeloid leukaemia classification systems-one put forth by WHO and one by the International Consensus Classification in 2022-is concerning. Although both systems appropriately move towards genomic disease definitions and reduced emphasis on blast enumeration, there are consequential disagreements between the two systems on what constitutes a diagnosis of acute myeloid leukaemia. This fundamental problem threatens the ability of heath-care providers to diagnose acute myeloid leukaemia, communicate with patients and other health-care providers, and deliver appropriate and consistent management strategies for patients with the condition. Clinical trial eligibility, standardised response assessments, and eventual drug development and regulatory pathways might also be negatively affected by the discrepancies. In this Viewpoint, we review the merits and limitations of both classification systems and illustrate how the coexistence, as well as application of both systems is an undue challenge to patients, clinicians, hematopathologists, sponsors of research, and regulators. Lastly, we emphasise the urgency and propose a roadmap, by which the two divergent classification systems can be harmonised.

DOI: https://doi.org/10.1016/S2352-3026(23)00159-X
Cell Stem Cell. 2023 Aug 09. pii: S1934-5909(23)00257-6. [Epub ahead of print]

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths.

Mariela Cortés-López, Paulina Chamely, Allegra G Hawkins, Robert F Stanley, Ariel D Swett, Saravanan Ganesan, Tarek H Mouhieddine, Xiaoguang Dai, Lloyd Kluegel, Celine Chen, Kiran Batta, Nili Furer, Rahul S Vedula, John Beaulaurier, Alexander W Drong, Scott Hickey, Neville Dusaj, Gavriel Mullokandov, Adam M Stasiw, Jiayu Su, Ronan Chaligné, Sissel Juul, Eoghan Harrington, David A Knowles, Catherine J Potenski, Daniel H Wiseman, Amos Tanay, Liran Shlush, Robert C Lindsley, Irene M Ghobrial, Justin Taylor, Omar Abdel-Wahab, Federico Gaiti, Dan A Landau.

  RNA splicing factors are recurrently mutated in clonal blood disorders, but the impact of dysregulated splicing in hematopoiesis remains unclear. To overcome technical limitations, we integrated genotyping of transcriptomes (GoT) with long-read single-cell transcriptomics and proteogenomics for single-cell profiling of transcriptomes, surface proteins, somatic mutations, and RNA splicing (GoT-Splice). We applied GoT-Splice to hematopoietic progenitors from myelodysplastic syndrome (MDS) patients with mutations in the core splicing factor SF3B1. SF3B1mut cells were enriched in the megakaryocytic-erythroid lineage, with expansion of SF3B1mut erythroid progenitor cells. We uncovered distinct cryptic 3' splice site usage in different progenitor populations and stage-specific aberrant splicing during erythroid differentiation. Profiling SF3B1-mutated clonal hematopoiesis samples revealed that erythroid bias and cell-type-specific cryptic 3' splice site usage in SF3B1mut cells precede overt MDS. Collectively, GoT-Splice defines the cell-type-specific impact of somatic mutations on RNA splicing, from early clonal outgrowths to overt neoplasia, directly in human samples.

Keywords:  BAX; RNA-seq; SF3B1; clonal hematopoiesis; genotyping; long-read sequencing; multi-omics; myelodysplastic syndrome; single cell; splicing

DOI:  https://doi.org/10.1016/j.stem.2023.07.012
Clin Cancer Res. 2023 Aug 16. pii: CCR-23-1429. [Epub ahead of print]

Phase 1 Results of Bromodomain and Extraterminal Inhibitor PLX51107 in Combination with Azacitidine in Patients with Relapsed/Refractory Myeloid Malignancies.

Jayastu Senapati, Warren C Fiskus, Naval Daver, Nathaniel R Wilson, Farhad Ravandi, Guillermo Garcia-Manero, Tapan Kadia, Courtney D DiNardo, Elias Jabbour, Jan Burger, Nicholas J Short, Yesid Alvarado, Nitin Jain, Lucia Masarova, Ghayas C Issa, Wei Qiao, Joseph D Khoury, Sherry Pierce, Darla Miller, Koji Sasaki, Marina Konopleva, Kapil N Bhalla, Gautam Borthakur, Naveen Pemmaraju.

PURPOSE: Treatment outcomes in patients with relapsed/refractory (R/R) MDS and AML remains dismal. Based on both extensive pre-clinical data and emerging clinical data, treatment with bromodomain and extra-terminal domain inhibitors (BETi) is a potential approach for patients with high-risk myeloid malignancies.
PATIENTS AND METHODS: We conducted a phase I trial to study the safety and efficacy of PLX51107 (BETi) and azacitidine combination therapy in patients with R/R AML and high-risk (HR) MDS and studied mechanisms of resistance to the combination therapy.
RESULTS: Thirty-seven patients with HR R/R MDS (n=4) and R/R AML (n=33) were treated. Sixteen patients (43%) had MECOM gene rearrangement and 7 other patients had TP53 mutation. Median prior number of therapies was three (range 1-9); 97% had received prior hypomethylating agent and 84% prior venetoclax. Overall response rate was 8/37 (22%): complete remission with incomplete platelet recovery (n=1); morphological leukemia-free state (n=2); hematologic improvement (n=5). The most common non-hematological toxicities were febrile neutropenia and pneumonia in 12 (32%) patients each; 6 patients (17%) had severe hyperbilirubinemia. RNA-Sequencing analysis of mononuclear cells harvested on treatment (day 3) vs pre-treatment showed significant changes in mRNA expressions in responders: downregulation of MYC, BCL2, IL7R and CDK6 and upregulation of HEXIM1, CD93, DCXR and CDKN1A. Immunoblot analyses confirmed reduction in protein levels of c-Myc, CDK6, BCL2 and BCL-xL, and induction of BRD4 and HEXIM1 protein levels in responders.
CONCLUSIONS: In a heavily pre-treated patient cohort with R/R MDS and AML, PLX51107+ azacitidine was well-tolerated and resulted in modest clinical benefit.

DOI: https://doi.org/10.1158/1078-0432.CCR-23-1429
Oncol Ther. 2023 Aug 14.

French Retrospective Database Analysis of Patient Characteristics and Treatment Patterns in Patients with R/R FLT3-Mutated AML: A Registry-Based Cohort Study.

Andy Garnham, Franck Bruon, Céline Berthon, Delphine Lebon, Mounika Parimi, Rosalind Polya, Kahina M Makhloufi, Marie-Hélène Dramard-Goasdoue.

   INTRODUCTION: There is a dearth of evidence to document treatment of FMS-like tyrosine kinase 3 (FLT3)-mutated acute myeloid leukemia (AML) in real-world settings before the introduction of FLT3 inhibitors. A retrospective cohort study was conducted to understand treatment practices prior to the availability of FLT3 inhibitors in patients with FLT3-mutated AML from two registries in France.
METHODS: Patient data from January 1, 2009 to December 31, 2017 were collected from the Hauts-de-France and Midi-Pyrénées registries. Patients aged ≥ 18 years at diagnosis with FLT3-mutated AML were included. Demographic and disease characteristics of patients with FLT3-mutated AML and relapsed or refractory (R/R) FLT3-mutated AML were documented. Treatment regimens, overall survival (OS), and event-free survival were assessed in patients with R/R FLT3-mutated AML who did not participate in clinical trials.
RESULTS: Overall, 819 and 1244 adult patients with AML from the Midi-Pyrénées and Hauts-de-France cohorts, respectively, underwent FLT3 mutation testing; 172 (21.0%) and 263 (21.1%) patients, respectively, had a FLT3 mutation. Primary R/R status was identified in 41.3% (n = 71/172) of the Midi-Pyrénées and 34.6% (n = 91/263) of the Hauts-de-France cohorts. Before R/R AML diagnosis, 82.0% and 97.5% of patients in the Midi-Pyrénées and Hauts-de-France cohorts, respectively, achieved complete remission (CR) or CR with incomplete hematologic recovery (CRi) following induction chemotherapy; after diagnosis of R/R AML, CR/CRi rates with salvage therapy were 33.3% and 28.1%, respectively. Median OS (interquartile range) in patients receiving salvage therapy (n = 49, n = 78) was 5.2 (2.3-11.1) and 6.1 (2.5-35.2) months, in the Midi-Pyrénées and Hauts-de-France cohorts, respectively. Across both cohorts, patients with R/R FLT3-mutated AML had low rates of CR/CRi with salvage therapy and a median OS of approximately 6 months.
CONCLUSION: Before FLT3 inhibitor availability, real-world treatment patterns and outcomes in French patients with R/R FLT3-mutated AML were consistent with clinical trial data, highlighting a poor prognosis and unmet need for effective treatment.

Keywords:  FLT3 mutations; Real-world evidence; Relapsed or refractory acute myeloid leukemia; Treatment patterns

DOI:  https://doi.org/10.1007/s40487-023-00239-2
Blood Adv. 2023 Aug 15. pii: bloodadvances.2023009847. [Epub ahead of print]

Midostaurin plus daunorubicin or idarubicin for young and elderly adults with FLT3-mutated AML: a Phase 3b trial.

Jorge Sierra, Pau Montesinos, Xavier Thomas, Laimonas Griskevicius, Thomas Cluzeau, Denis Caillot, Ollivier Legrand, Clara Minotti, Mario Luppi, Firas Farkas, Bourras-Rezki Bengoudifa, Geralyn Gilotti, Sejla Hodzic, Alessandro Rambaldi, Adriano Venditti.

The pivotal RATIFY study demonstrated midostaurin (50 mg b.i.d.) with standard chemotherapy significantly reducing mortality in adult patients (<60 years) with newly diagnosed (ND) FLT3mut acute myeloid leukemia (AML). Considering that AML often present in older patients who show poor response to chemotherapy, this open-label, multicenter Phase 3b trial was designed to further assess safety and efficacy of midostaurin plus chemotherapy in induction, consolidation, and maintenance monotherapy in young (60 years) and older (>60 years) patients with FLT3mut ND-AML. Compared with RATIFY, this study extended midostaurin treatment from 14 days to 21 days, substituted anthracyclines (idarubicin or daunorubicin), and introduced variation in standard combination chemotherapy dosing ("7+3" or "5+2" in more fragile patients). Total 301 patients (47.2% >60 years, 82.7% with FLT3-ITDmut) of median age 59 years entered induction phase. Overall, 295 patients (98.0%) had at least 1 adverse event (AE), including 254 patients (84.4%) with grade ≥3 AE. The grade ≥3 serious AEs occurred in 134 patients. No difference was seen in AE frequency between age groups, but grade ≥3AE frequency was higher in older patients. Overall, complete remission (CR) rate including incomplete hematological recovery (CR+CRi) (80.7% [95%CI: 75.74, 84.98]) was comparable between age groups (≤60 years [83.5%]; >60 to ≤70 years [82.5%]; little less in patients >70 years [64.1%]) and the type of anthracycline used in induction. CR+CRi rate was lower in males (76.4%) than females (84.4%). Overall, safety and efficacy of midostaurin remains consistent with previous findings, regardless of age, gender, or induction regimen. The trial is registered at clinicaltrials.gov: NCT03379727.

DOI: https://doi.org/10.1182/bloodadvances.2023009847
Leukemia. 2023 Aug 16.

Cell fate determinant Llgl1 is required for propagation of acute myeloid leukemia.

Theresa Eifert, Chen-Jen Hsu, Alicia L Becker, Sarah Graessle, Arik Horne, Franziska Bemmann, Qirui Zhang, Michael Heuser, Valeri Vasioukhin, Sebastian Scholl, Andreas Hochhaus, Florian Siegerist, Nicole Endlich, Lars Bullinger, Steven W Lane, Simon Haas, Tina M Schnoeder, Florian H Heidel.

Scribble complex proteins can influence cell fate decisions and self-renewal capacity of hematopoietic cells. While specific cellular functions of Scribble complex members are conserved in mammalian hematopoiesis, they appear to be highly context dependent. Using CRISPR/Cas9-based genetic screening, we have identified Scribble complex-related liabilities in AML including LLGL1. Despite its reported suppressive function in HSC self-renewal, inactivation of LLGL1 in AML confirms its relevant role for proliferative capacity and development of AML. Its function was conserved in human and murine models of AML and across various genetic backgrounds. Inactivation of LLGL1 results in loss of stemness-associated gene-expression including HoxA-genes and induces a GMP-like phenotype in the leukemia stem cell compartment. Re-expression of HoxA9 facilitates functional and phenotypic rescue. Collectively, these data establish LLGL1 as a specific dependency and putative target in AML and emphasizes its cell-type specific functions.

DOI: https://doi.org/10.1038/s41375-023-02005-9
Leuk Lymphoma. 2023 Aug 12. 1-10

Use of tamibarotene, a potent and selective RARα agonist, in combination with azacitidine in patients with relapsed and refractory AML with RARA gene overexpression.

Eytan M Stein, Stephane de Botton, Thomas Cluzeau, Arnaud Pigneux, Jane L Liesveld, Rachel J Cook, Philippe Rousselot, David A Rizzieri, Thorsten Braun, Gail J Roboz, Delphine Lebon, Mael Heiblig, Kristen Baker, Angela Volkert, Sofia Paul, Nisha Rajagopal, David A Roth, Michael Kelly, Pierre Peterlin.

  Tamibarotene-based therapy is a novel targeted approach for the treatment of relapsed/refractory (R/R) acute myeloid leukemia (AML) with retinoic acid receptor alpha (RARA) gene overexpression. Approximately, 50% of higher-risk myelodysplastic syndrome (MDS) patients and approximately 30% of AML patients are positive for RARA overexpression using a blood-based biomarker test that measures RARA expression in peripheral blasts. A phase 2 study investigating the activity of tamibarotene in patients with RARA overexpression was conducted in patients with AML and MDS (NCT02807558). In 28 patients with R/R AML and RARA overexpression treated with tamibarotene in combination with azacitidine, the median overall survival was 5.9 months. In 21 response-evaluable patients, the complete remission/complete remission with incomplete hematologic recovery (CR/CRi) rate was 19%, and median time to initial CR/CRi was 1.2 months. The favorable safety profile and preliminary clinical activity support the development of combination therapies with tamibarotene in myeloid malignancies with RARA overexpression.

Keywords:  Biomarker; RARA; SY-1425; retinoid; tamibarotene

DOI:  https://doi.org/10.1080/10428194.2023.2243356
Proc Natl Acad Sci U S A. 2023 08 22. 120(34): e2300224120

CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny.

Emily A Saunderson, Hector Huerga Encabo, Julie Devis, Kevin Rouault-Pierre, Marion Piganeau, Christopher G Bell, John G Gribben, Dominique Bonnet, Gabriella Ficz.

  Aging is associated with an abnormal increase in DNA methylation (DNAm) in human gene promoters, including in bone marrow stem cells. DNAm patterns are further perturbed in hematological malignancies such as acute myeloid leukemia but the physiological significance of such epigenetic changes is unknown. Using epigenetic editing of human stem/progenitor cells (HSPCs), we show that p15 methylation affects hematopoiesis in vivo. We edited the CDKN2B (p15) promoter and ARF (p14) using dCas9-3A3L and observed DNAm spreading beyond the gRNA location. We find that despite a transient delivery system, DNAm is maintained during myeloid differentiation in vitro, and hypermethylation of the p15 promoter reduces gene expression. In vivo, edited human HSPCs can engraft the bone marrow of mice and targeted DNAm is maintained in HSPCs long term. Moreover, epigenetic changes are conserved and inherited in both myeloid and lymphoid lineages. Although the proportion of myeloid (CD33+) and lymphoid (CD19+) cells is unaffected, monocyte (CD14+) populations decreased and granulocytes (CD66b+) increased in mice engrafted with p15 hypermethylated HSPCs. Monocytes derived from p15 hypermethylated HSPCs appear to be activated and show increased inflammatory transcriptional programs. We believe these findings have clinical relevance since we found p15 promoter methylation in the peripheral blood of patients with clonal hematopoiesis. Our study shows DNAm can be targeted and maintained in human HSPCs and demonstrated functional relevance of aberrant DNAm on the p15 locus. As such, other aging-associated aberrant DNAm may impact hematopoiesis in vivo.

Keywords:  CRISPR; epigenetic editing; hematopoiesis

DOI:  https://doi.org/10.1073/pnas.2300224120
Genes Dis. 2024 Jan;11(1): 397-412

Overcoming adaptive resistance in AML by synergistically targeting FOXO3A-GNG7-mTOR axis with FOXO3A inhibitor Gardenoside and rapamycin.

Zhe Chen, Qian Guo, Shichen Huang, Lei Li, Feng Wu, Zhilong Liu, Zhigang Li, Tao Chen, Guanbin Song, Shuangnian Xu, Jieping Chen, Yu Hou.

  Therapeutic targeting FOXO3A (a forkhead transcription factor) represents a promising strategy to suppress acute myeloid leukemia (AML). However, the effective inhibitors that target FOXO3A are lacking and the adaptive response signaling weakens the cytotoxic effect of FOXO3A depletion on AML cells. Here, we show that FOXO3A deficiency induces a compensatory response involved in the reactive activation of mTOR that leads to signaling rebound and adaptive resistance. Mitochondrial metabolism acts downstream of mTOR to provoke activation of JNK/c-JUN via reactive oxygen species (ROS). At the molecular level, FOXO3A directly binds to the promoter of G protein gamma subunit 7 (GNG7) and preserves its expression, while GNG7 interacts with mTOR and restricts phosphorylated activation of mTOR. Consequently, combinatorial inhibition of FOXO3A and mTOR show a synergistic cytotoxic effect on AML cells and prolongs survival in a mouse model of AML. Through a structure-based virtual screening, we report one potent small-molecule FOXO3A inhibitor (Gardenoside) that exhibits a strong effect of anti-FOXO3A DNA binding. Gardenoside synergizes with rapamycin to substantially reduce tumor burden and extend survival in AML patient-derived xenograft model. These results demonstrate that mTOR can mediate adaptive resistance to FOXO3A inhibition and validate a combinatorial approach for treating AML.

Keywords:  AML; Combinatorial inhibition; FOXO3A; GNG7; mTOR

DOI:  https://doi.org/10.1016/j.gendis.2023.01.002
bioRxiv. 2023 Jul 31. pii: 2023.07.29.551111. [Epub ahead of print]

Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.

Ataur Katebi, Xiaowen Chen, Sheng Li, Mingyang Lu.

Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a novel optimization procedure to identify the optimal network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
Significance: A combined bioinformatics and systems-biology modeling approach is designed to model a transcriptional regulatory network for AML with IDH mutations. Network modeling identifies key regulators DNMT1 and E2F1, which is supported by patient survival data.

DOI: https://doi.org/10.1101/2023.07.29.551111
Genes Dis. 2024 Jan;11(1): 382-396

RNA m6A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression.

Zheng Zhang, Keren Zhou, Li Han, Andrew Small, Jianhuang Xue, Huilin Huang, Hengyou Weng, Rui Su, Brandon Tan, Chao Shen, Wei Li, Zhicong Zhao, Ying Qing, Xi Qin, Kitty Wang, Keith Leung, Mark Boldin, Chun-Wei Chen, David Ann, Zhijian Qian, Xiaolan Deng, Jianjun Chen, Zhenhua Chen.

  As the most common internal modification of mRNA, N6-methyladenosine (m6A) and its regulators modulate gene expression and play critical roles in various biological and pathological processes including tumorigenesis. It was reported previously that m6A methyltransferase (writer), methyltransferase-like 3 (METTL3) adds m6A in primary microRNAs (pri-miRNAs) and facilitates its processing into precursor miRNAs (pre-miRNAs). However, it is unknown whether m6A modification also plays a role in the maturation process of pre-miRNAs and (if so) whether such a function contributes to tumorigenesis. Here, we found that YTHDF2 is aberrantly overexpressed in acute myeloid leukemia (AML) patients, especially in relapsed patients, and plays an oncogenic role in AML. Moreover, YTHDF2 promotes expression of miR-126-3p (also known as miR-126, as it is the main product of precursor miR-126 (pre-miR-126)), a miRNA that was reported as an oncomiRNA in AML, through facilitating the processing of pre-miR-126 into mature miR-126. Mechanistically, YTHDF2 recognizes m6A modification in pre-miR-126 and recruits AGO2, a regulator of pre-miRNA processing, to promote the maturation of pre-miR-126. YTHDF2 positively and negatively correlates with miR-126 and miR-126's downstream target genes, respectively, in AML patients, and forced expression of miR-126 could largely rescue YTHDF2/Ythdf2 depletion-mediated suppression on AML cell growth/proliferation and leukemogenesis, indicating that miR-126 is a functionally important target of YTHDF2 in AML. Overall, our studies not only reveal a previously unappreciated YTHDF2/miR-126 axis in AML and highlight the therapeutic potential of targeting this axis for AML treatment, but also suggest that m6A plays a role in pre-miRNA processing that contributes to tumorigenesis.

Keywords:  AML; N6-methyladenosine; Pre-miRNA maturation; YTHDF2; miR-126

DOI:  https://doi.org/10.1016/j.gendis.2023.01.016
J Hematol Oncol. 2023 Aug 17. 16(1): 96

Phase I study evaluating the Fc-optimized FLT3 antibody FLYSYN in AML patients with measurable residual disease.

Jonas S Heitmann, Richard F Schlenk, Daniela Dörfel, Sabine Kayser, Konstanze Döhner, Michael Heuser, Felicitas Thol, Silke Kapp-Schwoerer, Jannik Labrenz, Dominic Edelmann, Melanie Märklin, Wichard Vogel, Wolfgang Bethge, Juliane S Walz, Ludger Große-Hovest, Martin Steiner, Gundram Jung, Helmut R Salih.

   BACKGROUND: About half of AML patients achieving complete remission (CR) display measurable residual disease (MRD) and eventually relapse. FLYSYN is an Fc-optimized antibody for eradication of MRD directed to FLT3/CD135, which is abundantly expressed on AML cells.
METHODS: This first-in-human, open-label, single-arm, multicenter trial included AML patients in CR with persisting or increasing MRD and evaluated safety/tolerability, pharmacokinetics and preliminary efficacy of FLYSYN at different dose levels administered intravenously (cohort 1-5: single dose of 0.5 mg/m2, 1.5 mg/m2, 5 mg/m2, 15 mg/m2, 45 mg/m2; cohort 6: 15 mg/m2 on day 1, 15 and 29). Three patients were treated per cohort except for cohorts 4 and 6, which were expanded to nine and ten patients, respectively. Primary objective was safety, and secondary efficacy objective was ≥ 1 log MRD reduction or negativity in bone marrow.
RESULTS: Overall, 31 patients were treated, of whom seven patients (22.6%) experienced a transient decrease in neutrophil count (two grade 3, others ≤ grade 2). No infusion-related reaction or dose-limiting toxicity was observed. Adverse events (AEs) were mostly mild to moderate, with the most frequent AEs being hematologic events and laboratory abnormalities. Response per predefined criteria was documented in 35% of patients, and two patients maintained MRD negativity until end of study. Application of 45 mg/m2 FLYSYN as single or cumulative dose achieved objective responses in 46% of patients, whereas 28% responded at lower doses.
CONCLUSIONS: FLYSYN monotherapy is safe and well-tolerated in AML patients with MRD. Early efficacy data are promising and warrant further evaluation in an up-coming phase II trial. Trial registration This clinical is registered on clinicaltrials.gov (NCT02789254).

Keywords:  AML; FLT3; Fc-optimized antibody; Immunotherapy; MRD

DOI:  https://doi.org/10.1186/s13045-023-01490-w
Blood. 2023 Aug 15. pii: blood.2022018212. [Epub ahead of print]

LepR+ niche cell-derived AREG compromises hematopoietic stem cell maintenance under conditions of DNA repair deficiency and aging.

Limei Wu, Qiqi Lin, Srinivas Chatla, Surya Prakash Amarachintha, Andrew F Wilson, Neha Atale, Zhenxia J Gao, Jonathan Joseph, Emily Wolff, Wei Du.

The crosstalk between extrinsic niche-derived and intrinsic hematopoietic stem cell (HSC) factors controlling HSC maintenance remain elusive. Here we demonstrate that amphiregulin (AREG) from bone marrow (BM) leptin receptor (LepR+) niche cells is an important factor that mediates the crosstalk between BM niche and HSCs in stem cell maintenance. Mice deficient for the DNA repair gene Brca2 specifically in LepR+ cells (LepR-Cre;Brca2fl/fl) exhibit increased frequencies of total and myeloid-biased HSCs. Furthermore, HSCs from LepR-Cre;Brca2fl/fl mice show compromised repopulation, increased expansion of donor-derived myeloid-biased HSCs and myeloid output. Brca2-deficient BM LepR+ cells exhibit persistent DNA damage-inducible overproduction of AREG. Ex vivo treatment of WT HSCs, or systemic treatment of C57BL/6 mice, with recombinant AREG impairs repopulation, leading to HSC exhaustion. Conversely, inhibition of AREG by anti-AREG neutralizing antibody or deletion of the Areg gene in LepR-Cre;Brca2fl/fl mice rescues the HSC defects caused by AREG. Mechanistically, AREG activates the PI3K/AKT/mTOR pathway, promotes HSC cycling and compromises HSC quiescence. Finally, we demonstrate that BM LepR+ niche cells from other DNA repair-deficient and aged mice also show persistent DNA damage-associated overexpression of AREG, which exerts similar negative effects on HSC maintenance. We have therefore identified an important factor regulating HSCs function under conditions of DNA repair deficiency and aging.

DOI: https://doi.org/10.1182/blood.2022018212
Transplant Cell Ther. 2023 Aug 12. pii: S2666-6367(23)01469-0. [Epub ahead of print]

Myeloablative dose of busulfan and fludarabine combined with in vivo T-cell depletion is a safe and effective conditioning for acute myeloid leukaemia and myelodysplastic syndrome patients.

Daniele Avenoso, Varun Mehra, Liron Barnea Slonim, Madson de Farias, Hassan Alshehri, Styliani Bouziana, Pramila Krishnamurthy, Austin Kulasekararaj, Francesco Dazzi, Henry Wood, Michelle Kenyon, Ye Ting Leung, Sandra Anteh, Mili Naresh Shah, Guy Hannah, Fabio Serpenti, Amna Gameil, Christianne Bourlon, Oana Diana Dragoi, Antonio Pagliuca, Victoria Potter.

   BACKGROUND: Allogeneic haematopoietic stem cell transplant (HSCT) is a curative strategy for acute myeloid leukaemia (AML) and myelodysplastic syndromes (MDS). The prediction of transplant related mortality (TRM) using the HCT-CI score and an arbitrary upper limit of 55 years for administering myeloablative conditioning (MAC) are common strategies to ensure a safe procedure. Reduced toxicity conditioning regimens are additional methods to deliver safe and effective myeloablation.
OBJECTIVES: Herein we report the outcome of AML and MDS patients conditioned with fludarabine and a myeloablative dose of busulfan (FB4) stratified by age and HCT-CI score. The primary objective was overall survival (OS) for patients aged ≥55 years. Secondary objectives were total OS, TRM, graft versus-host disease (GVHD) and GVHD-relapse-free survival (GRFS).
RESULTS: The two years' OS in patients aged < 55 and aged ≥ 55 were 72% and 51%, respectively. In patients aged ≥55 with an HCT-CI <2, the estimated two years' OS was 64%, with median OS not reached. In those with HCT-CI ≥2, the two-year OS was 43%, with median OS of 14 months. The total cumulative incidence of relapse was 30% regardless of age or HCT-CI score.
CONCLUSIONS: FB4 conditioning regimen offers a high rate of prolonged remission with a relapse rate similar to that reported in previous studies. These positive outcomes suggest that this conditioning platform can be offered to patients aged ≥55 in absence of comorbidities, and that age should not be the sole determinate of conditioning intensity.

Keywords:  AML; CAMPATH; FB4; MDS

DOI:  https://doi.org/10.1016/j.jtct.2023.08.012
Transl Cancer Res. 2023 Jul 31. 12(7): 1656-1659

miRNAs as prognostic predictors in acute myeloid leukemia.

João Agostinho Machado-Neto, Jorge Antonio Elias Godoy Carlos, Keli Lima.



Keywords:  Acute myeloid leukemia (AML); chemotherapy; microRNAs; prognosis

DOI:  https://doi.org/10.21037/tcr-23-716
Nat Genet. 2023 Aug 14.

In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis.

David Lara-Astiaso, Ainhoa Goñi-Salaverri, Julen Mendieta-Esteban, Nisha Narayan, Cynthia Del Valle, Torsten Gross, George Giotopoulos, Tumas Beinortas, Mar Navarro-Alonso, Laura Pilar Aguado-Alvaro, Jon Zazpe, Francesco Marchese, Natalia Torrea, Isabel A Calvo, Cecile K Lopez, Diego Alignani, Aitziber Lopez, Borja Saez, Jake P Taylor-King, Felipe Prosper, Nikolaus Fortelny, Brian J P Huntly.

Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.

DOI: https://doi.org/10.1038/s41588-023-01471-2
BMB Rep. 2023 Aug 14. pii: 5960. [Epub ahead of print]

The maintenance mechanism of hematopoietic stem cell dormancy: role for a subset of macrophages.

Cheong-Whan Chae, Gun Choi, You Ji Kim, Mingug Cho, Yoo-Wook Kwon, Hyo-Soo Kim.

Hematopoiesis is regulated by crosstalk between long-term repopulating hematopoietic stem cells (LT-HSCs) and supporting niche cells in the bone marrow (BM). Here, we describe the role of KAI1, which is mainly expressed on LT-HSCs and rarely on other hematopoietic stem-progenitor cells (HSPCs), in nichemediated LT-HSC maintenance. KAI1 activates TGF-β1/Smad3 signal in LT-HSCs, leading to the induction of CDK inhibitors and inhibition of the cell cycle. The KAI1-binding partner DARC is expressed on macrophages and stabilizes KAI1 on LT-HSCs, promoting their quiescence. Conversely, when DARC+ BM macrophages were absent, the level of surface KAI1 on LT-HSCs decreases, leading to cell-cycle entry, proliferation, and differentiation. Thus, KAI1 acts as a functional surface marker of LTHSCs that regulates dormancy through interaction with DARCexpressing macrophages in the BM stem cell niche. Recently, we showed very special and rare macrophages expressing α-SMA+ COX2+ & DARC+ induce not only dormancy of LTHSC through interaction of KAI1-DARC but also protect HSCs by down-regulating ROS through COX2 signaling. In the near future, the strategy to combine KAI1-positive LT-HSCs and α-SMA/Cox2/DARC triple-positive macrophages will improve the efficacy of stem cell transplantation after the ablative chemo-therapy for hematological disorders including leukemia.
Blood. 2023 Aug 18. pii: blood.2023021120. [Epub ahead of print]

Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.

Shruthi Subramanian, Julie A I Thoms, Yizhou Huang, Carina Paola Cornejo Paramo, Forrest Charles Koch, Sebastien Jacquelin, Sylvie Shen, Emma Song, Swapna Joshi, Christopher Peter Brownlee, Petter S Woll, Diego Chacon-Fajardo, Dominik Beck, David J Curtis, Kenneth Yehson, Vicki Antonenas, Tracey O'Brien, Annette Trickett, Jason A Powell, Ian D Lewis, Stuart M Pitson, Maher K Gandhi, Steven W Lane, Fatemeh Vafaee, Emily Wong, Berthold Gottgens, Hamid Rokny, Jason Wing Hon Wong, John E Pimanda.

Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remained unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (the Heptad, PU.1, CTCF, and STAG2) in HSPC subsets (HSC-MPP, CMP, GMP, MEP) and found that TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs such as PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type-specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of specific TF complexes was at least partially regulated by features encoded in specific DNA sequence motifs. Taken together, this study provides a comprehensive characterisation of the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying datasets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analysing aberrant regulatory networks in leukemic cells.

DOI: https://doi.org/10.1182/blood.2023021120
Ann Hematol. 2023 Aug 17.

Genetic mutations and leukapheresis in acute myeloid leukemia: is there a link?

Andrea Corbingi, Rossana Putzulu, Giuseppina Massini, Maria Colangelo, Gessica Minnella, Patrizia Chiusolo, Simona Sica, Nicola Piccirillo.

  Acute myeloid leukemia is the most common acute leukemia in adults and up to 20% of patients present with hyperleukocytosis at the onset of the disease. The therapeutic approach involves medical support, cytoreductive treatment, and/or leukapheresis. Despite WBC count greater than 100.000/μL, not all patients develop symptoms. To clarify the role of leukapheresis in the setting of hyperleukocytotic AML, we aimed to find associations between AML morphologic subtypes and molecular alterations on presence or absence of leukostasis symptoms (and hence therapeutic vs prophylactic leukapheresis) and clinical outcomes in the cohort of 41 patients at our single center who underwent leukapheresis for hyperleukocytotic AML. There was a trend for increased WBC count, 30-day mortality, M4-M5 AML subtypes, and number of leukapheresis procedures performed in symptomatic hyperleukocytotic pts. No molecular marker was significantly associated with presence or absence of leukostasis symptoms due to small sample size, though there was a trend for increased NPM1-mutated and NPM1 + FLT3-mutated AML in asymptomatic patients and a greater proportion of symptomatic patients who were negative for all assessed molecular alterations. In conclusion, leukapheresis combined with cytoreductive treatment represents a synergic and efficient approach in the management of hyperleukocytosis especially in symptomatic patients considering the higher mortality independently from the presence of specific clonal markers whose distribution among the two groups may result more considerable with a higher number of patients.

Keywords:  Acute myeloid leukemia; Genetic mutations; Leukapheresis

DOI:  https://doi.org/10.1007/s00277-023-05414-z
Oncogene. 2023 Aug 12.

FANCA deficiency promotes leukaemic progression by allowing the emergence of cells carrying oncogenic driver mutations.

Patrycja Pawlikowska, Laure Delestré, Sebastian Gregoricchio, Alessia Oppezzo, Michela Esposito, M' Boyba Diop, Filippo Rosselli, Christel Guillouf.

Leukaemia is caused by the clonal evolution of a cell that accumulates mutations/genomic rearrangements, allowing unrestrained cell growth. However, recent identification of leukaemic mutations in the blood cells of healthy individuals revealed that additional events are required to expand the mutated clones for overt leukaemia. Here, we assessed the functional consequences of deleting the Fanconi anaemia A (Fanca) gene, which encodes a DNA damage response protein, in Spi1 transgenic mice that develop preleukaemic syndrome. FANCA loss increases SPI1-associated disease penetrance and leukaemic progression without increasing the global mutation load of leukaemic clones. However, a high frequency of leukaemic FANCA-depleted cells display heterozygous activating mutations in known oncogenes, such as Kit or Nras, also identified but at low frequency in FANCA-WT mice with preleukaemic syndrome, indicating that FANCA counteracts the emergence of oncogene mutated leukaemic cells. A unique transcriptional signature is associated with the leukaemic status of FANCA-depleted cells, leading to activation of MDM4, NOTCH and Wnt/β-catenin pathways. We show that NOTCH signalling improves the proliferation capacity of FANCA-deficient leukaemic cells. Collectively, our observations indicate that loss of the FANC pathway, known to control genetic instability, fosters the expansion of leukaemic cells carrying oncogenic mutations rather than mutation formation. FANCA loss may contribute to this leukaemogenic progression by reprogramming transcriptomic landscape of the cells.

DOI: https://doi.org/10.1038/s41388-023-02800-9
Blood Adv. 2023 Aug 15. pii: bloodadvances.2023010887. [Epub ahead of print]

AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology.

Marius-Konstantin Klever, Eric Sträng, Sara Hetzel, Julius Jungnitsch, Anna Dolnik, Robert Schöpflin, Jens-Florian F Schrezenmeier, Felix Schick, Olga Blau, Jörg Westermann, Frank G Rücker, Zuyao Xia, Konstanze Döhner, Hubert Schrezenmeier, Malte Spielmann, Alexander Meissner, Uira Souto Melo, Stefan Mundlos, Lars Bullinger.

Acute myeloid leukemia with complex karyotype (CK-AML) is associated with poor prognosis, which is only in part explained by underlying TP53 mutations. Especially in the presence of complex chromosomal rearrangements, such as chromothripsis, the outcome of CK-AML is dismal. However, this degree of complexity of genomic rearrangements contributes to the leukemogenic phenotype and treatment resistance of CK-AML remains largely unknown. Applying an integrative workflow for the detection of structural variants (SVs) based on Oxford Nanopore (ONT) genomic DNA long-read sequencing (gDNA-LRS) and high-throughput chromosome confirmation capture (Hi-C) in a well-defined cohort of CK-AML identified regions with an extreme density of SVs. These rearrangements consisted to a large degree of focal amplifications enriched in the proximity of mammalian-wide interspersed repeat (MIR) elements, which often result in oncogenic fusion transcripts, such as USP7::MVD, or the deregulation of oncogenic driver genes as confirmed by RNA-seq and ONT direct cDNA sequencing. We termed this novel phenomenon chromocataclysm. Thus, our integrative SV detection workflow combing gDNA-LRS and Hi-C enables to unravel complex genomic rearrangements at a very high resolution in regions hard to analyze by conventional sequencing technology, thereby providing an important tool to identify novel important drivers underlying cancer with complex karyotypic changes.

DOI: https://doi.org/10.1182/bloodadvances.2023010887
Cell Rep. 2023 Aug 12. pii: S2211-1247(23)00982-8. [Epub ahead of print]42(8): 112971

FASN deficiency induces a cytosol-to-mitochondria citrate flux to mitigate detachment-induced oxidative stress.

Wenting Dai, Zhichao Wang, Guan Wang, Qiong A Wang, Ralph DeBerardinis, Lei Jiang.

  Fatty acid synthase (FASN) maintains de novo lipogenesis (DNL) to support rapid growth in most proliferating cancer cells. Lipogenic acetyl-coenzyme A (CoA) is primarily produced from carbohydrates but can arise from glutamine-dependent reductive carboxylation. Here, we show that reductive carboxylation also occurs in the absence of DNL. In FASN-deficient cells, reductive carboxylation is mainly catalyzed by isocitrate dehydrogenase-1 (IDH1), but IDH1-generated cytosolic citrate is not utilized for supplying DNL. Metabolic flux analysis (MFA) shows that FASN deficiency induces a net cytosol-to-mitochondria citrate flux through mitochondrial citrate transport protein (CTP). Previously, a similar pathway has been shown to mitigate detachment-induced oxidative stress in anchorage-independent tumor spheroids. We further report that tumor spheroids show reduced FASN activity and that FASN-deficient cells acquire resistance to oxidative stress in a CTP- and IDH1-dependent manner. Collectively, these data indicate that by inducing a cytosol-to-mitochondria citrate flux, anchorage-independent malignant cells can gain redox capacity by trading off FASN-supported rapid growth.

Keywords:  CP: Metabolism; CP: Molecular biology; DNL; FASN inhibitor; IDH1 inhibitor; MFA; SLC25A1; anchorage-independent growth; cytosol-to-mitochondria citrate flux; de novo lipogenesis; metabolic flux analysis; redox; reductive carboxylation

DOI:  https://doi.org/10.1016/j.celrep.2023.112971
Cell Rep Med. 2023 Aug 15. pii: S2666-3791(23)00313-0. [Epub ahead of print]4(8): 101160

Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS.

Zhijie Wu, Shouguo Gao, Qingyan Gao, Bhavisha A Patel, Emma M Groarke, Xingmin Feng, Ash Lee Manley, Haoran Li, Daniela Ospina Cardona, Sachiko Kajigaya, Lemlem Alemu, Diego Quinones Raffo, Amanda K Ombrello, Marcela A Ferrada, Peter C Grayson, Katherine R Calvo, Daniel L Kastner, David B Beck, Neal S Young.

  VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a pleiotropic, severe autoinflammatory disease caused by somatic mutations in the ubiquitin-like modifier activating enzyme 1 (UBA1) gene. To elucidate VEXAS pathophysiology, we performed transcriptome sequencing of single bone marrow mononuclear cells and hematopoietic stem and progenitor cells (HSPCs) from VEXAS patients. HSPCs are biased toward myeloid (granulocytic) differentiation, and against lymphoid differentiation in VEXAS. Activation of multiple inflammatory pathways (interferons and tumor necrosis factor alpha) occurs ontogenically early in primitive hematopoietic cells and particularly in the myeloid lineage in VEXAS, and inflammation is prominent in UBA1-mutated cells. Dysregulation in protein degradation likely leads to higher stress response in VEXAS HSPCs, which positively correlates with inflammation. TCR usage is restricted and there are increased cytotoxicity and IFN-γ signaling in T cells. In VEXAS syndrome, both aberrant inflammation and myeloid predominance appear intrinsic to hematopoietic stem cells mutated in UBA1.

Keywords:  VEXAS; clonal hematopoiesis; inflammation; single-cell RNA sequencing

DOI:  https://doi.org/10.1016/j.xcrm.2023.101160
Cancer Sci. 2023 Aug 17.

Single-cell RNA-seq reveals a microenvironment and an exhaustion state of T/NK cells in acute myeloid leukemia.

Zhiyong Zhang, Cong Deng, Pei Zhu, Danlin Yao, Jinlong Shi, Tiansheng Zeng, Wenhui Huang, Zeyong Huang, Zhihua Wu, Junyi Li, Min Xiao, Lin Fu.

  Acute myeloid leukemia (AML) is a heterogeneous blood cancer. Effective immunotherapies for AML are hindered by a lack of understanding of the tumor microenvironment (TME). Here, we retrieved published single-cell RNA sequencing data for 128,688 cells derived from 29 bone marrow aspirates, including 21 AML patients and eight healthy donors. We established a global tumor ecosystem including nine main cell types. Myeloid, T, and NK cells were further re-clustered and annotated. Developmental trajectory analysis indicated that exhausted CD8+ T cells might develop via tissue residual memory T cells (TRM) in the AML TME. Significantly higher expression levels of exhaustion molecules in AML TRM cells suggested that these cells were influenced by the TME and entered an exhausted state. Meanwhile, the upregulation of checkpoint molecules and downregulation of granzyme were also observed in AML NK cells, suggesting an exhaustion state. In conclusion, our comprehensive profiling of T/NK subpopulations provides deeper insights into the AML immunosuppressive ecosystem, which is critical for immunotherapies.

Keywords:  NK-cell exhaustion; T-cell exhaustion; acute myeloid leukemia; single-cell RNA sequencing; tumor microenvironment

DOI:  https://doi.org/10.1111/cas.15932
BMJ Case Rep. 2023 Aug 17. pii: e252915. [Epub ahead of print]16(8):

Core-binding factor abnormalities involving chromosome 16 in acute myeloid leukaemia: prognostic and therapeutic implications.

Chinmayee Panigrahi, Nakul Tikare, Prabodha Kumar Das, Somanath Padhi.

  Core-binding factor (CBF) abnormality-associated myeloid neoplasms incorporate acute myeloid leukaemia (AML) (CBF-AML) with translocation t(8;21)(q22;q22.1) (AML1/ETO fusion) and inv(16)(p13.1q22) or translocation t(16;16)(p13.1;q22) (CBFB/MYH11 fusion) abnormalities which confer a favourable prognosis following cytarabine-based induction chemotherapy. Accumulating evidence from the molecular studies have stratified CBF-AML into favourable and unfavourable subgroups based on the associated cooperating mutations that impact the outcome. We describe a case of acute myelomonocytic leukaemia with abnormal eosinophils (M4Eo) in a woman in her 20s who was found to have CBFβ/MYH11 fusion along with mutated c-KIT (exon 17) and KRAS (exon 2) genes by next-generation sequencing. She had an aggressive clinical course following initiation of cytarabine-based induction chemotherapy. The underlying mutational landscape may significantly influence the biological behaviour of otherwise favourable risk of CBF-AML cases.

Keywords:  Cancer - see Oncology; Haematology (incl blood transfusion); Pathology

DOI:  https://doi.org/10.1136/bcr-2022-252915
Ann Hematol. 2023 Aug 12.

Comparison of efficacy between homoharringtonine, aclarubicin, cytarabine (HAA) and idarubicin, cytarabine (IA) regimens as induction therapy in patients with de novo core binding factor acute myeloid leukemia.

Wenbing Duan, Sen Yang, Ting Zhao, Lijuan Hu, Yazhen Qin, Jinsong Jia, Jing Wang, Shengye Lu, Hao Jiang, Xiaohui Zhang, Lanping Xu, Yu Wang, Yueyun Lai, Hongxia Shi, Xiaojun Huang, Qian Jiang.

  To compare efficacy between homoharringtonine combined with cytarabine and aclarubicin (HAA) and idarubicin and cytarabine (IA) regimens as first induction chemotherapy in patients with core binding factor acute myeloid leukemia (CBF-AML). Cox regression model and propensity score matching (PSM) were used to identify the regimen associated with a better remission rate and outcomes. In total, 374 patients with CBF-AML (243 with RUNX1::RUXN1T1 and 131 with CBFB::MYH11) were included in this study. The patients received the HAA or IA regimen (187 each) as the first induction therapy. For patients with RUNX1::RUXN1T1, multivariate analyses showed that the HAA regimen was significantly associated with a higher CR/CRi rate after the first induction (hazard ratio [HR] = 5.3 [95% CI 2.3, 12.2]; p < 0.001) and more favorable relapse-free survival (RFS) (HR = 0.5 [0.3, 0.8], p = 0.01). In PSM analysis, the HAA regimen also had a higher CR/CRi rate (96% vs. 77%, p < 0.001), especially for those harboring wild-type KIT (KITWT) (96% vs. 83%, p = 0.02) or non-D816 KIT mutation (100% vs. 63%, p = 0.002), as well as more favorable RFS (p = 0.01), compared with the IA regimen. However, there was no difference in the remission rate or outcomes between the two regimens for patients with CBFB::MYH11. The HAA regimen as first induction chemotherapy resulted in a higher CR/CRi rate in AML patients with RUNX1::RUNX1T1, especially those harboring KITWT and non-D816 KIT mutation, and a more favorable RFS compared with the IA regimen. The efficacy between the two regimens did not differ in those with CBFB::MYH11.

Keywords:  Acute myeloid leukemia; Core binding factor; HAA; IA; The first induction chemotherapy

DOI:  https://doi.org/10.1007/s00277-023-05400-5
Haematologica. 2023 Aug 16.

Spontaneous remission and loss of monosomy 7: a window of opportunity for young children with SAMD9L syndrome.

Miriam Erlacher, Felicia Andresen, Martina Sukova, Jan Stary, Barbara De Moerloose, Jutte van der Werff Ten Bosch, Michael Dworzak, Markus G Seidel, Sophia Polychronopoulou, Rita Beier, Christian M Kratz, Michaela Nathrath, Michael C Frühwald, Gudrun Göhring, Anke K Bergmann, Christina Mayerhofer, Dirk Lebrecht, Senthilkumar Ramamoorthy, Ayami Yoshimi, Brigitte Strahm, Marcin W Wlodarski, Charlotte M Niemeyer.

Monosomy 7 is the most common cytogenetic abnormality in pediatric myelodysplastic syndrome (MDS) and associated with a high risk of disease progression. However, in young children, spontaneous loss of monosomy 7 with concomitant hematologic recovery has been described, especially in the presence of germline mutations in SAMD9 and SAMD9L genes. Here, we report on our experience of close surveillance instead of upfront hematopoietic stem cell transplantation (HSCT) in seven patients diagnosed with SAMD9L syndrome and monosomy 7 at a median age of 0.6 years (0.4-2.9). Within 14 months from diagnosis, three children experienced spontaneous hematological remission accompanied by a decrease in monosomy 7 clone size. Subclones with somatic SAMD9L mutations in cis were identified in five patients, three of whom attained hematological remission. Two patients acquired RUNX1 and EZH2 mutations during the observation period, of whom one progressed to MDS with excess of blasts (MDS-EB). Four patients underwent allogeneic HSCT at a median time of 26 months (14-40) from diagnosis for MDS-EB, necrotizing granulomatous lymphadenitis, persistent monosomy 7, and severe neutropenia. At last follow-up, six patients were alive, while one passed away due to transplant-related causes. These data confirm previous observations that monosomy 7 can be transient in young children with SAMD9L syndrome. However, they also indicate that delaying HSCT poses a substantial risk of severe infection and disease progression. Finally, surveillance of patients with SAMD9L syndrome and monosomy 7 is critical to define the evolving genetic landscape and to determine the appropriate timing of HSCT.

DOI: https://doi.org/10.3324/haematol.2023.283591
Leukemia. 2023 Aug 17.

Myelodysplastic neoplasm-associated U2AF1 mutations induce host defense defects by compromising neutrophil chemotaxis.

Natalia J Gurule, Kenneth C Malcolm, Chelsea Harris, Jennifer R Knapp, Brian P O'Connor, Jazalle McClendon, William J Janssen, Frank Fang Yao Lee, Caitlin Price, Jackson Osaghae-Nosa, Emily A Wheeler, Christine M McMahon, Eric M Pietras, Daniel A Pollyea, Scott Alper.

Myelodysplastic neoplasm (MDS) is a hematopoietic stem cell disorder that may evolve into acute myeloid leukemia. Fatal infection is among the most common cause of death in MDS patients, likely due to myeloid cell cytopenia and dysfunction in these patients. Mutations in genes that encode components of the spliceosome represent the most common class of somatically acquired mutations in MDS patients. To determine the molecular underpinnings of the host defense defects in MDS patients, we investigated the MDS-associated spliceosome mutation U2AF1-S34F using a transgenic mouse model that expresses this mutant gene. We found that U2AF1-S34F causes a profound host defense defect in these mice, likely by inducing a significant neutrophil chemotaxis defect. Studies in human neutrophils suggest that this effect of U2AF1-S34F likely extends to MDS patients as well. RNA-seq analysis suggests that the expression of multiple genes that mediate cell migration are affected by this spliceosome mutation and therefore are likely drivers of this neutrophil dysfunction.

DOI: https://doi.org/10.1038/s41375-023-02007-7
Nature. 2023 Aug 16.

Nuclear genetic control of mtDNA copy number and heteroplasmy in humans.

Rahul Gupta, Masahiro Kanai, Timothy J Durham, Kristin Tsuo, Jason G McCoy, Anna V Kotrys, Wei Zhou, Patrick F Chinnery, Konrad J Karczewski, Sarah E Calvo, Benjamin M Neale, Vamsi K Mootha.

Mitochondrial DNA (mtDNA) is a maternally inherited, high-copy-number genome required for oxidative phosphorylation1. Heteroplasmy refers to the presence of a mixture of mtDNA alleles in an individual and has been associated with disease and ageing. Mechanisms underlying common variation in human heteroplasmy, and the influence of the nuclear genome on this variation, remain insufficiently explored. Here we quantify mtDNA copy number (mtCN) and heteroplasmy using blood-derived whole-genome sequences from 274,832 individuals and perform genome-wide association studies to identify associated nuclear loci. Following blood cell composition correction, we find that mtCN declines linearly with age and is associated with variants at 92 nuclear loci. We observe that nearly everyone harbours heteroplasmic mtDNA variants obeying two principles: (1) heteroplasmic single nucleotide variants tend to arise somatically and accumulate sharply after the age of 70 years, whereas (2) heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles. As an illustrative example, we identify a length variant carried by more than 50% of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching2,3. We find that this variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch. Our study suggests that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.

DOI: https://doi.org/10.1038/s41586-023-06426-5
Nat Commun. 2023 Aug 14. 14(1): 4645

GATA2 mitotic bookmarking is required for definitive haematopoiesis.

Rita Silvério-Alves, Ilia Kurochkin, Anna Rydström, Camila Vazquez Echegaray, Jakob Haider, Matthew Nicholls, Christina Rode, Louise Thelaus, Aida Yifter Lindgren, Alexandra Gabriela Ferreira, Rafael Brandão, Jonas Larsson, Marella F T R de Bruijn, Javier Martin-Gonzalez, Carlos-Filipe Pereira.

In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.

DOI: https://doi.org/10.1038/s41467-023-40391-x