bims-tremyl 2022-09-25 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2022–09–25
thirty-one papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Targeting STAT5 signaling overcomes resistance to IDH inhibitors in acute myeloid leukemia through suppression of stemness.
Genomic Profiling for Clinical Decision Making in Myeloid Neoplasms and Acute Leukemia.
Implications of RAS Mutational Status in Subsets of Patients with Newly Diagnosed Acute Myeloid Leukemia Across Therapy Subtypes.
Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia.
Inhibition of O-GlcNAcase inhibits hematopoietic and leukemic stem cell self-renewal and drives dendritic cell differentiation via STAT3/5 signaling.
A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome.
Enasidenib as Maintenance following Allogeneic Hematopoietic Cell Transplantation for IDH2-Mutated Myeloid Malignancies.
Compartment-specific mutational landscape of clonal hematopoiesis.
Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia.
How I Treat TP53-Mutated Acute Myeloid Leukemia and Myelodysplastic Syndromes.
U2AF1 and EZH2 mutations are associated with nonimmune hemolytic anemia in myelodysplastic syndromes.
Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.
Contemporary evaluation of acute myeloid leukemia patients with long-term survival exceeding five years.
CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target.
Expression of the immune checkpoint modulator OX40 indicates poor survival in acute myeloid leukemia.
Activity of menin inhibitor ziftomenib (KO-539) as monotherapy or in combinations against AML cells with MLL1 rearrangement or mutant NPM1.
Targeting FOLR1 in high-risk CBF2AT3-GLIS2 Pediatric AML with STRO-002 FOLR1-Antibody-Drug Conjugate.
BCL-2 inhibitor synergizes with PI3Kδ inhibitor and overcomes FLT3 inhibitor resistance in acute myeloid leukaemia.
Characteristics and Outcomes of Secondary Acute Myeloid Leukemia and Acute Myeloid Leukemia With Myelodysplasia-Related Changes: Multicenter Study From the Thai Acute Leukemia Study Group.
Patient perspectives on testing for clonal hematopoiesis of indeterminate potential.
Germline SNPs previously implicated as prognostic biomarkers do not associate with outcomes in intensively treated AML.
Ex vivo expansion of phenotypic and transcriptomic CML stem cells.
Allogeneic hematopoietic cell transplantation can overcome the adverse prognosis indicated by secondary-type mutations in de novo acute myeloid leukemia.
Sleep exerts lasting effects on hematopoietic stem cell function and diversity.
Sensitisation of cancer cells to radiotherapy by serine and glycine starvation.
Comparative study of treosulfan plus Fludarabine (FT14) with busulfan plus Fludarabine (FB4) for acute myeloid leukemia in first or second complete remission: An analysis from the European Society for Blood and Marrow Transplantation (EBMT) Acute Leukemia Working Party (ALWP).
SF3B1, RUNX1 and TP53 Mutations Significantly Impact the Outcome of Patients With Lower-Risk Myelodysplastic Syndrome.
Deep morphology learning enhances ex vivo drug profiling-based precision medicine.
Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality.
Efficacy of JAK 1/2 inhibition in murine immune bone marrow failure.
The evolutionary dynamics of extrachromosomal DNA in human cancers.

Cancer Res. 2022 Sep 23. pii: CAN-22-1293. [Epub ahead of print]

Targeting STAT5 signaling overcomes resistance to IDH inhibitors in acute myeloid leukemia through suppression of stemness.

Alex C H Liu, Severine Cathelin, Yitong Yang, David L Dai, Dhanoop Manikoth Ayyathan, Mohsen Hosseini, Mark D Minden, Anne Tierens, Steven M Chan.

Mutant isocitrate dehydrogenase 1 (IDH1) and IDH2 block the differentiation of acute myeloid leukemia (AML) cells through production of R-2-hydroxyglutarate (R-2-HG). IDH inhibitors can induce differentiation of AML cells by lowering R-2-HG but have limited clinical efficacy as single agents. Here, we performed a genome-wide CRISPR knockout screen in an Idh1-mutated hematopoietic progenitor cell line to identify genes that increased the differentiation response to ivosidenib, an IDH1 inhibitor. The screen identified C-type lectin member 5a (Clec5a), which encodes a spleen tyrosine kinase (SYK)-coupled surface receptor, as one of the top hits. Knockout of Clec5a and Syk rendered cells more sensitive to ivosidenib-induced differentiation through a reduction in signal transducer and activator of transcription 5 (STAT5)-dependent expression of stemness-related genes, including genes in the homeobox (HOX) family. Importantly, direct inhibition of STAT5 activity was sufficient to increase the differentiation response to IDH inhibitors in primary human IDH1 and IDH2-mutated AML cells, including those harboring mutations in receptor tyrosine kinase (RTK) and mitogen-activated protein kinase (MAPK) genes that have been linked to drug resistance. In patient-derived xenograft (PDX) models of IDH1-mutated AML, combination treatment with ivosidenib and the STAT5 inhibitor pimozide was superior to each agent alone in inducing differentiation in leukemic cells without compromising normal hematopoiesis. These findings demonstrate that STAT5 is a critical mediator of resistance to IDH inhibitors and provide the rationale for combining STAT5 and IDH inhibitors in the treatment of IDH-mutated AML.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1293
Blood. 2022 Sep 21. pii: blood.2022015853. [Epub ahead of print]

Genomic Profiling for Clinical Decision Making in Myeloid Neoplasms and Acute Leukemia.

Eric J Duncavage, Adam Bagg, Robert P Hasserjian, Courtney D DiNardo, Lucy A Godley, Ilaria Iacobucci, Siddhartha Jaiswal, Luca Malcovati, Alessandro M Vannucchi, Keyur P Patel, Daniel A Arber, Maria E Arcila, Rafael Bejar, Nancy Berliner, Michael J Borowitz, Susan Branford, Anna L Brown, Catherine A Cargo, Hartmut Döhner, Brunangelo Falini, Guillermo Garcia-Manero, Torsten Haferlach, Eva Hellström-Lindberg, Annette S Kim, Jeffery M Klco, Rami S Komrokji, Mignon L Loh, Sanam Loghavi, Charles G Mullighan, Seishi Ogawa, Ayalew Tefferi, Elli Papaemmanuil, Andreas Reiter, David Morrall Ross, Michael R Savona, Akiko Shimamura, Radek C Skoda, Francesc Sole, Richard M Stone, Attilio Orazi, Matthew J Walter, David Wu, Benjamin L Ebert, Mario Cazzola.

Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. While assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the last several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole exome sequencing (WES), whole genome sequencing (WGS), and whole transcriptome sequencing (WTS) or RNAseq. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are employed not only for detecting somatically acquired gene mutations, but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias makes extensive use of genomic data. This report aims to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with these hematologic neoplasms.

DOI: https://doi.org/10.1182/blood.2022015853
Am J Hematol. 2022 Sep 18.

Implications of RAS Mutational Status in Subsets of Patients with Newly Diagnosed Acute Myeloid Leukemia Across Therapy Subtypes.

Daniel Rivera, Kunhwa Kim, Rashmi Kanagal-Shamanna, Gautam Borthakur, Guillermo Montalban-Bravo, Naval Daver, Courtney Dinardo, Nicholas J Short, Musa Yilmaz, Naveen Pemmaraju, Koichi Takahashi, Elias J Jabbour, Sherry Pierce, Marina Konopleva, Kapil Bhalla, Guillermo Garcia-Manero, Farhad Ravandi, Hagop Kantarjian, Tapan M Kadia.

Activating mutations in RAS have been reported in about 10-15% of patients with AML; previous studies have not identified a prognostic significance. However, RAS mutations have emerged as a potential resistance mechanism to treatment with inhibitors of FLT3, IDH, and BCL2. We aimed to determine the characteristics and outcomes of patients with RAS mutated (RAS-mut) AML across therapy subsets of 1410 patients newly diagnosed (ND AML). RAS-mut was observed in 273 (20%) patients. Overall, patients with RAS-mut AML had an estimated 3-year survival rate of 38% vs. 28% in those with RAS wild type (RAS-wt), p = 0.01. Among patients with RAS-mut, favorable karyotype and concomitant NPM1 mutations were associated with a higher CR/CRi rate, OR 23.2 (95% CI: 2.7-192.7; p < 0.001) and OR 2.8 (95% CI: 1.1-6.9; p = 0.02), respectively, while secondary and treated secondary (ts)-AML were associated with low response rates, OR 0.34 (95% CI: 0.1-0.9; p = 0.04) and OR 0.22 (95% CI: 0.09-0.5; p = 0.001), respectively. Intensive chemotherapy was associated with high response rates OR 5.9 (95% CI: 2.9-12.2; p < 0.001). Better median OS was observed among those with favorable karyotype, HR 0.28 (95% CI: 0.1-0.6; p = 0.002), and those treated with intensive chemotherapy, HR 0.42 (95% CI: 0.2-0.6 p < 0.001). Conversely, ts- AML and co-occurrence of mutations in TP53 were associated with poor median OS; HR 2.3 (95% CI: 1.4-3.9; p = 0.001) and HR 1.7 (95% CI: 0.9-3.1; p = 0.06), respectively. The addition of venetoclax was associated with a non-significant improvement in CR/CRi and OS. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/ajh.26731
Nat Commun. 2022 Sep 19. 13(1): 5487

Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia.

Benjamin J Huang, Jenny L Smith, Jason E Farrar, Yi-Cheng Wang, Masayuki Umeda, Rhonda E Ries, Amanda R Leonti, Erin Crowgey, Scott N Furlan, Katherine Tarlock, Marcos Armendariz, Yanling Liu, Timothy I Shaw, Lisa Wei, Robert B Gerbing, Todd M Cooper, Alan S Gamis, Richard Aplenc, E Anders Kolb, Jeffrey Rubnitz, Jing Ma, Jeffery M Klco, Xiaotu Ma, Todd A Alonzo, Timothy Triche, Soheil Meshinchi.

Relapsed or refractory pediatric acute myeloid leukemia (AML) is associated with poor outcomes and relapse risk prediction approaches have not changed significantly in decades. To build a robust transcriptional risk prediction model for pediatric AML, we perform RNA-sequencing on 1503 primary diagnostic samples. While a 17 gene leukemia stem cell signature (LSC17) is predictive in our aggregated pediatric study population, LSC17 is no longer predictive within established cytogenetic and molecular (cytomolecular) risk groups. Therefore, we identify distinct LSC signatures on the basis of AML cytomolecular subtypes (LSC47) that were more predictive than LSC17. Based on these findings, we build a robust relapse prediction model within a training cohort and then validate it within independent cohorts. Here, we show that LSC47 increases the predictive power of conventional risk stratification and that applying biomarkers in a manner that is informed by cytomolecular profiling outperforms a uniform biomarker approach.

DOI: https://doi.org/10.1038/s41467-022-33244-6
Stem Cells. 2022 Sep 19. pii: sxac068. [Epub ahead of print]

Inhibition of O-GlcNAcase inhibits hematopoietic and leukemic stem cell self-renewal and drives dendritic cell differentiation via STAT3/5 signaling.

Sudjit Luanpitpong, Napachai Rodboon, Parinya Samart, Montira Janan, Phatchanat Klaihmon, Chanchao Lorthongpanich, Yaowalak U-Pratya, Surapol Issaragrisil.

  Myeloid differentiation blockage at immature and self-renewing stages is a common hallmark across all subtypes of acute myeloid leukemia (AML), despite their genetic heterogeneity. Metabolic state is an important regulator of hematopoietic stem cell (HSC) self-renewal and lineage-specific differentiation as well as several aggressive cancers. However, how O-GlcNAcylation, a nutrient-sensitive posttranslational modification of proteins, contributes to both normal myelopoiesis and AML pathogenesis remains largely unknown. Using small molecule inhibitors and the CRISPR/Cas9 system, we reveal for the first time that inhibition of either OGA or OGT, which subsequently caused an increase or decrease in cellular O-GlcNAcylation, inhibits the self-renewal and maintenance of CD34 + hematopoietic stem/progenitor cells (HSPCs) and leukemic stem/progenitor cells and drives normal and malignant myeloid differentiation. We further unveiled the distinct roles of OGA and OGT inhibition in lineage-specific differentiation. While OGT inhibition induces macrophage differentiation, OGA inhibition promotes the differentiation of both CD34 + HSPCs and AML cells into dendritic cells (DCs), in agreement with an upregulation of a multitude of genes involved in DC development and function and their ability to induce T cell proliferation, via STAT3/5 signaling. Our novel findings provide significant basic knowledge that could be important in understanding AML pathogenesis and overcoming differentiation blockage-agnostic to the genetic background of AML. Additionally, the parallel findings in normal HSPCs may lay the groundwork for future cellular therapy as a means to improve the ex vivo differentiation of normal DCs and macrophages.

Keywords:   O-GlcNAcylation; acute myeloid leukemia; dendritic cell; differentiation therapy; hematopoiesis; hematopoietic stem cells; leukemic stem cells; macrophage; myeloid differentiation

DOI:  https://doi.org/10.1093/stmcls/sxac068
Leukemia. 2022 Sep 21.

A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome.

Héléna Boutzen, Seyed Ali Madani Tonekaboni, Michelle Chan-Seng-Yue, Alex Murison, Naoya Takayama, Nathan Mbong, Elvin Wagenblast, Elias Orouji, Andrea Arruda, Amanda Mitchell, Faiyaz Notta, Mark D Minden, Mathieu Lupien, Kerstin B Kaufmann, John E Dick.

Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission. Difficulties to isolate and undertake in vitro and in vivo experimental studies of rare CSC under conditions that preserve their original properties currently constitute a bottleneck for identifying molecular mechanisms involving coding and non-coding genomic regions that govern stemness. We focussed on acute myeloid leukemia (AML) as a paradigm of the CSC model and developed a patient-derived system termed OCI-AML22 that recapitulates the cellular hierarchy driven by leukemia stem cells (LSC). Through classical flow sorting and functional analyses, we established that a single phenotypic population is highly enriched for LSC. The LSC fraction can be easily isolated and serially expanded in culture or in xenografts while faithfully recapitulating functional, transcriptional and epigenetic features of primary LSCs. A novel non-coding regulatory element was identified with a new computational approach using functionally validated primary AML LSC fractions and its role in LSC stemness validated through efficient CRISPR editing using methods optimized for OCI-AML22 LSC. Collectively, OCI-AML22 constitutes a valuable resource to uncover mechanisms governing CSC driven malignancies.

DOI: https://doi.org/10.1038/s41375-022-01697-9
Blood Adv. 2022 Sep 23. pii: bloodadvances.2022008632. [Epub ahead of print]

Enasidenib as Maintenance following Allogeneic Hematopoietic Cell Transplantation for IDH2-Mutated Myeloid Malignancies.

Amir T Fathi, Haesook T Kim, Robert J Soiffer, Mark J Levis, Shuli Li, Annette S Kim, Alice S Mims, Zachariah DeFilipp, Areej El-Jawahri, Steven L McAfee, Andrew M Brunner, Rupa Narayan, Laura W Knight, Devon Kelley, Aj S Bottoms, Lindsey S Perry, Jonathan L Wahl, Jennifer Brock, Elayne Breton, Vincent T Ho, Yi-Bin Chen.

IDH2 (isocitrate dehydrogenase 2) mutations occur in approximately 15% of patients with acute myeloid leukemia (AML). The IDH2 inhibitor enasidenib was recently approved for IDH2-mutated relapsed or refractory AML. We conducted a multi-center, phase I trial of maintenance enasidenib following allogeneic hematopoietic cell transplantation (HCT) in patients with IDH2-mutated myeloid malignancies. Two dose levels, 50mg and 100mg daily were studied in a 3x3 dose-escalation design, with 10 additional patients treated at the recommended phase 2 dose (RP2D). Enasidenib was initiated between days 30 and 90 following HCT and continued for twelve 28-day cycles. Twenty-three patients were enrolled, of whom 19 initiated post-HCT maintenance. Two had myelodysplastic syndrome, and 17 had AML. All but 3 were in first complete remission. No dose limiting toxicities were observed, and the RP2D was established at 100 mg daily. Grade ≥3 toxicities attributable to enasidenib were rare, with the most common being cytopenias. Eight patients stopped maintenance therapy before completing 12 cycles, due to adverse events (n=3), pursuing treatment for graft versus host disease (GVHD) (n=2), clinician choice (n=1), relapse (n=1), and COVID-19 infection (n=1). No cases of grade ≥3 acute GVHD were seen, and the 12-month cumulative incidence of moderate/severe chronic GVHD was 42% (20-63%). Cumulative incidence of relapse was 16% (95% CI: 3.7-36%); only one subject relapsed while receiving maintenance enasidenib. Two-year progression-free and overall survival were 69% (95% CI: 39-86%) and 74% (950% CI, 44-90%), respectively. Enasidenib is safe, well-tolerated, with preliminary activity as maintenance therapy following HCT, and merits additional study. The study was registered at ClinicalTrials.gov (NCT03515512).

DOI: https://doi.org/10.1182/bloodadvances.2022008632
Leukemia. 2022 Sep 21.

Compartment-specific mutational landscape of clonal hematopoiesis.

Luise Hartmann, Judith S Hecker, Maja Rothenberg-Thurley, Jennifer Rivière, Madlen Jentzsch, Bianka Ksienzyk, Michèle C Buck, Mark van der Garde, Luise Fischer, Susann Winter, Martina Rauner, Elena Tsourdi, Heike Weidner, Katja Sockel, Marie Schneider, Anne S Kubasch, Martin Nolde, Dominikus Hausmann, Jörg Lützner, Szymon Goralski, Florian Bassermann, Karsten Spiekermann, Lorenz C Hofbauer, Sebastian Schwind, Uwe Platzbecker, Katharina S Götze, Klaus H Metzeler.

Clonal hematopoiesis (CH) is characterized by somatic mutations in blood cells of individuals without hematologic disease. While the mutational landscape of CH in peripheral blood (PB) has been well characterized, detailed analyses addressing its spatial and cellular distribution in the bone marrow (BM) compartment are sparse. We studied CH driver mutations in healthy individuals (n = 261) across different anatomical and cellular compartments. Variant allele frequencies were higher in BM than PB and positively correlated with the number of driver variants, yet remained stable during a median of 12 months of follow-up. In CH carriers undergoing simultaneous bilateral hip replacement, we detected ASXL1-mutant clones in one anatomical location but not the contralateral side, indicating intra-patient spatial heterogeneity. Analyses of lineage involvement in ASXL1-mutated CH showed enriched clonality in BM stem and myeloid progenitor cells, while lymphocytes were particularly involved in individuals carrying the c.1934dupG variant, indicating different ASXL1 mutations may have distinct lineage distribution patterns. Patients with overt myeloid malignancies showed higher mutation numbers and allele frequencies and a shifting mutation landscape, notably characterized by increasing prevalence of DNMT3A codon R882 variants. Collectively, our data provide novel insights into the genetics, evolution, and spatial and lineage-specific BM involvement of CH.

DOI: https://doi.org/10.1038/s41375-022-01700-3
Exp Hematol. 2022 Sep 20. pii: S0301-472X(22)00697-X. [Epub ahead of print]

Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia.

Faezeh Darbaniyan, Hong Zheng, Rashmi Kanagal-Shamanna, Pamela Lockyer, Guillermo Montalban-Bravo, Marcos Estecio, Yue Lu, Kelly A Soltysiak, Kelly S Chien, Hui Yang, Koji Sasaki, Caleb Class, Irene Ganan-Gomez, Kim-Anh Do, Guillermo Garcia-Manero, Yue Wei.

  Hypomethylating agents (HMA) are the standard of care for myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML). HMA treatment failure is a major clinical problem and its mechanisms are poorly characterized. We performed RNA-sequencing in CD34+ bone marrow stem and progenitor cells (BM-HSPCs) from 51 patients with CMML and MDS before HMA treatment and compared transcriptomic signatures between responders and non-responders. We observed very few genes with significant differential expression in HMA non-responders versus responders, and the commonly altered genes in non-responders of both azacitidine (AZA) and decitabine (DAC) treatments were immunoglobulin genes. Gene set analysis identified 78 biological pathways commonly altered in non-responders of both treatments. Among them, we demonstrated that the gamma-aminobutyric acid (GABA) receptor signalling significantly affected hematopoiesis in both human BM-HSPCs and mice, implicating that the transcriptomic signatures identified here could serve as candidate biomarkers and therapeutic targets for HMA failure in MDS and CMML.

Keywords:  Chronic Myelomonocytic Leukemia; Myelodysplastic Syndromes; hypomethylating agent; transcriptomic

DOI:  https://doi.org/10.1016/j.exphem.2022.09.002
Cancers (Basel). 2022 Sep 18. pii: 4519. [Epub ahead of print]14(18):

How I Treat TP53-Mutated Acute Myeloid Leukemia and Myelodysplastic Syndromes.

Michael Loschi, Pierre Fenaux, Thomas Cluzeau.

  TP53-mutated acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are among the myeloid malignancies with the poorest prognosis. In this review, we analyze the prognosis of these two diseases, focussing particularly on the extent of the mono or biallelic mutation status of TP53 mutation, which is largely correlated with cytogenetic complexity. We discuss the possible/potential improvement in outcome based on recent results obtained with new drugs (especially eprenetapopt and magrolimab). We also focus on the impact of allogeneic hematopoietic stem cell transplantation (aHSCT) including post aHSCT treatment.

Keywords:  AML; TP53; allogeneic stem cell transplantation; eprenetapopt; magrolimab

DOI:  https://doi.org/10.3390/cancers14184519
Blood Adv. 2022 Sep 21. pii: bloodadvances.2022007504. [Epub ahead of print]

U2AF1 and EZH2 mutations are associated with nonimmune hemolytic anemia in myelodysplastic syndromes.

Rami S Komrokji, Luis E Aguirre, Najla Al-Ali, Mohammad O Hussaini, David A Sallman, Dana E Rollison, Eric Padron.

Hemolysis is a well-recognized but poorly characterized phenomenon in a subset of patients with myelodysplastic syndromes (MDS). Its pathobiological basis seems to underpin a nonimmune etiology whose clinical significance has not been adequately characterized. Hemolysis in MDS is often attributed to either ineffective intramedullary erythropoiesis or acquired hemoglobinopathies and red blood cell (RBC) membrane defects. These heterogenous processes have not been associated with specific genetic subsets of disease. We aimed to describe the prevalence of hemolysis among MDS patients, their baseline characteristics, molecular features and resulting impact on outcomes. We considered baseline serum haptoglobin <10 mg/dl a surrogate marker for intravascular hemolysis. Among 519 patients, 10% had hemolysis. The baseline characteristics were similar among both groups. Only 13% of patients with hemolysis were Coombs-positive suggesting that hemolysis in MDS is largely not immune-mediated. Inferior survival trends were observed among lower risk MDS patients with hemolysis. Decreased response rates to erythropoiesis-stimulating agents and higher responses to hypomethylating agents (HMA) were also observed in the hemolysis group. U2AF1 and EZH2 hotspot mutations were more prevalent among those undergoing hemolysis (p<0.05). U2AF1 mutations were observed in 30% of patients with hemolysis and occurred almost exclusively at the S34 hotspot. Somatic mutations encoding splicing factors may affect erythrocyte membrane components, biochemical properties, and RBC metabolic function, which underpin the development of atypical clones from erythroid precursors in MDS presenting with hemolysis. Future studies will explore the contribution of altered splicing to the development of acquired hemoglobinopathies.

DOI: https://doi.org/10.1182/bloodadvances.2022007504
Nat Genet. 2022 Sep 22.

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.

Anna S Nam, Neville Dusaj, Franco Izzo, Rekha Murali, Robert M Myers, Tarek H Mouhieddine, Jesus Sotelo, Salima Benbarche, Michael Waarts, Federico Gaiti, Sabrin Tahri, Ross Levine, Omar Abdel-Wahab, Lucy A Godley, Ronan Chaligne, Irene Ghobrial, Dan A Landau.

Somatic mutations in cancer genes have been detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, because mutated and wild-type cells are admixed, we have limited ability to link genotypes with phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing genotype, transcriptomes and methylomes in progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations result in myeloid over lymphoid bias, and an expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate, with dysregulated expression of lineage and leukemia stem cell markers. Mutated DNMT3A leads to preferential hypomethylation of polycomb repressive complex 2 targets and a specific CpG flanking motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics paves the road to defining the downstream consequences of mutations that drive clonal mosaicism.

DOI: https://doi.org/10.1038/s41588-022-01179-9
Eur J Haematol. 2022 Sep 21.

Contemporary evaluation of acute myeloid leukemia patients with long-term survival exceeding five years.

Gabriel Heering, Maya Sasson, Dan Dominissini, Avichai Shimoni, Abraham Avigdor, Arnon Nagler, Jonathan Canaani.

   OBJECTIVES: Define clinical and laboratory attributes of acute myeloid leukemia (AML) patients with long-term survival exceeding five years and compare them with AML patients succumbing to disease within two years of diagnosis.
METHODS: A retrospective analysis of AML patients alive at least five years from the time of initial diagnosis. Baseline clinical data were compared with patients who died within two years of diagnosis.
RESULTS: The long-term cohort consisted of 93 patients treated in 2007-2016 with a median follow-up duration of 7.7 years (range 5-13.6 years). European LeukemiaNet (ELN) 2017 favorable risk patients accounted for 60% of the cohort. All long-term survivors achieved remission following induction chemotherapy. Multivariate analysis showed that compared with 132 patients experiencing death within 2 years of diagnosis, long term survivors were more likely to be of younger age [odds ratio (OR), 0.92; 95% confidence interval (CI), 0.9-0.95; p<0.001], have a lower initial WBC count (OR, 0.58; 95% CI, 0.43-0.79; p=0.0004), undergo an allogeneic stem cell transplantation (OR, 7.95; 95% CI, 3.07-20.59; p<0.0001), and harbor favorable risk cytogenetics (OR, 0.03; 95% CI, 0.006-0.23; p=0.0004).
CONCLUSIONS: Long term survival of AML is seen in a distinct demographic and biologic patient subset.

Keywords:  Acute myeloid leukemia; ELN 2017; long-term survival

DOI:  https://doi.org/10.1111/ejh.13864
J Clin Invest. 2022 Sep 22. pii: e157101. [Epub ahead of print]

CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target.

Quy Le, Brandon Hadland, Jenny L Smith, Amanda Leonti, Benjamin J Huang, Rhonda Ries, Tiffany A Hylkema, Sommer Castro, Thao T Tang, Cyd N McKay, LaKeisha Perkins, Laura Pardo, Jay Sarthy, Amy K Beckman, Robin Williams, Rhonda Idemmili, Scott Furlan, Takashi Ishida, Lindsey Call, Shivani Srivastava, Anisha M Loeb, Filippo Milano, Suzan Imren, Shelli M Morris, Fiona Pakiam, James M Olson, Michael R Loken, Lisa Eidenschink Brodersen, Stanley R Riddell, Katherine Tarlock, Irwin D Bernstein, Keith R Loeb, Soheil Meshinchi.

  Fusion oncoproteins are the initiating event in the pathogenesis of many pediatric AML. The CBFA2T3-GLIS2 (C/G) fusion is a product of a cryptic translocation primarily seen in infants and early childhood and is associated with dismal outcome. Here, we demonstrate that the expression of the C/G oncogenic fusion protein promotes the transformation of human cord blood hematopoietic stem/progenitor cells (CB HSPCs) in an endothelial cell (EC) co-culture system, that recapitulates the transcriptome, morphology and immunophenotype of C/G AML and induces highly aggressive leukemia in xenograft models. Interrogating the transcriptome of C/G-CB cells and primary C/G AML identified a library of C/G fusion-specific genes that are potential targets for therapy. We developed chimeric antigen receptor (CAR) T cells directed against one of the targets, FOLR1, and demonstrated their pre-clinical efficacy against C/G AML using in vitro and xenograft models. FOLR1 is also expressed in renal and pulmonary epithelium, raising concerns for toxicity that must be addressed for the clinical application of this therapy. Our findings underscore the role of the endothelial niche in promoting leukemic transformation of C/G-transduced CB HSPCs. Furthermore, this work has broad implications for studies of leukemogenesis applicable to a variety of oncogenic fusion-driven pediatric leukemias, providing a robust and tractable model system to characterize the molecular mechanisms of leukemogenesis and identify biomarkers for disease diagnosis and targets for therapy.

Keywords:  Cancer immunotherapy; Leukemias; Oncogenes; Oncology; Therapeutics

DOI:  https://doi.org/10.1172/JCI157101
Sci Rep. 2022 Sep 23. 12(1): 15856

Expression of the immune checkpoint modulator OX40 indicates poor survival in acute myeloid leukemia.

Maddalena Marconato, Joseph Kauer, Helmut R Salih, Melanie Märklin, Jonas S Heitmann.

Despite therapeutic advances, mortality of Acute Myeloid Leukemia (AML) is still high. Currently, the determination of prognosis which guides treatment decisions mainly relies on genetic markers. Besides molecular mechanisms, the ability of malignant cells to evade immune surveillance influences the disease outcome and, among others, the expression of checkpoints modulators contributes to this. In AML, functional expression of the checkpoint molecule OX40 was reported, but the prognostic relevance of OX40 and its ligand OX40L axis has so far not been investigated. Here we described expression and prognostic relevance of the checkpoint modulators OX40 and OX40L, analyzed on primary AML cells obtained from 92 therapy naïve patients. Substantial expression of OX40 and OX40L on AML blasts was detected in 29% and 32% of the investigated subjects, respectively, without correlation between the expression of the receptor and its ligand. Whereas OX40L expression was not associated with different survival, patients with high expression levels of the receptor (OX40high) on AML blasts survived significantly shorter than OX40low patients (p = 0.009, HR 0.46, 95% CI 0.24-0.86), which identifies OX40 as novel prognostic marker and a potential therapeutic target in AML patients.

DOI: https://doi.org/10.1038/s41598-022-19972-1
Leukemia. 2022 Sep 23.

Activity of menin inhibitor ziftomenib (KO-539) as monotherapy or in combinations against AML cells with MLL1 rearrangement or mutant NPM1.

Warren Fiskus, Naval Daver, Steffen Boettcher, Christopher P Mill, Koji Sasaki, Christine E Birdwell, John A Davis, Kaberi Das, Koichi Takahashi, Tapan M Kadia, Courtney D DiNardo, Francis Burrows, Sanam Loghavi, Joseph D Khoury, Benjamin L Ebert, Kapil N Bhalla.

DOI: https://doi.org/10.1038/s41375-022-01707-w
Blood Adv. 2022 Sep 23. pii: bloodadvances.2022008503. [Epub ahead of print]

Targeting FOLR1 in high-risk CBF2AT3-GLIS2 Pediatric AML with STRO-002 FOLR1-Antibody-Drug Conjugate.

Keith R Loeb, Quy H Le, Thao Tang, Sommer K Castro, Laura Pardo, Cyd Nourigat McKay, LaKeisha Perkins, Jenny L Smith, Danielle C Kirkey, Cristina Abrahams, Kristin Bedard, Arturo Molina, Lisa Eidenschink Brodersen, Michael R Loken, Katherine Tarlock, Soheil Meshinchi.

DOI: https://doi.org/10.1182/bloodadvances.2022008503
Am J Cancer Res. 2022 ;12(8): 3829-3842

BCL-2 inhibitor synergizes with PI3Kδ inhibitor and overcomes FLT3 inhibitor resistance in acute myeloid leukaemia.

Ming-Yue Yao, Ya-Fang Wang, Yu Zhao, Li-Jun Ling, Ye He, Jie Wen, Ming-Yue Zheng, Hua-Liang Jiang, Cheng-Ying Xie.

Inhibitors targeting the antiapoptotic molecule BCL-2 have therapeutic potential for the treatment of acute myeloid leukaemia (AML); however, BCL-2 inhibitors such as venetoclax exhibit limited monotherapy efficacy in relapsed or refractory human AML. PI3Kδ/AKT signalling has been shown to be constitutively active in AML patients. Here, we demonstrate that the combination of BCL-2 and PI3Kδ inhibitors exerts synergistic antitumour effects both in vitro and in vivo in AML. Cotreatment with venetoclax and the specific PI3Kδ inhibitor idelalisib significantly enhanced antiproliferative effects and induced caspase-dependent apoptosis in a panel of AML cell lines. The synergistic effects were mechanistically based on the inactivation of AKT/4E-BP-1 signalling and the reduction of MCL-1 expression, which diminished the binding of Bim to MCL-1. Notably, compared with the parental FLT3-ITD-positive MV-4-11, the acquired FLT3 inhibitor quizartinib-resistant xenograft model carrying the F691L mutation, exhibited a markedly higher sensitivity to venetoclax. Furthermore, venetoclax combined with idelalisib led to tumour regression in all animals in this quizartinib-resistant AML model. Thus, these data indicate that combined inhibition of BCL-2 and PI3Kδ may be a promising strategy in AML, especially for patients with FLT3-ITD and/or FLT3-TKD mutations.

Keywords: Acute myeloid leukaemia; BCL-2; FLT3; PI3Kδ; synergistic lethality
Clin Lymphoma Myeloma Leuk. 2022 Aug 23. pii: S2152-2650(22)00271-3. [Epub ahead of print]

Characteristics and Outcomes of Secondary Acute Myeloid Leukemia and Acute Myeloid Leukemia With Myelodysplasia-Related Changes: Multicenter Study From the Thai Acute Leukemia Study Group.

Chantiya Chanswangphuwana, Chantana Polprasert, Weerapat Owattanapanich, Smith Kungwankiattichai, Adisak Tantiworawit, Thanawat Rattanathammethee, Wasithep Limvorapitak, Supawee Saengboon, Pimjai Niparuck, Teeraya Puavilai, Jakrawadee Julamanee, Pirun Saelue, Chinadol Wanitpongpun, Chajchawan Nakhakes, Kannadit Prayongratana, Chantrapa Sriswasdi.

   BACKGROUND: Secondary acute myeloid leukemia (sAML) and AML with myelodysplasia-related changes (AML-MRC) both result in dismal outcomes. This retrospective study aimed to determine whether these features are poor prognostic factors independent of older age and adverse cytogenetics, which are commonly associated with a poor prognosis.
METHODS: The characteristics and real-world outcomes of sAML and AML-MRC from the Thai AML registry database were investigated.
RESULTS: From a total of 992 newly diagnosed AML patients, 315 (31.8%) patients were classified into sAML or AML-MRC subtypes. Older age, low white blood cell (WBC) count, low bone marrow blast, and adverse cytogenetic risk were commonly present in sAML and AML-MRC compared to de novo AML. Complete remission after 7 + 3 induction therapy occurred in 42.3% of patients with sAML or AML-MRC and 62.4% of de novo AML (P < .001). The median overall survival (OS) of sAML, AML-MRC, and de novo AML were 6.9, 7.0, and 12.2 months, respectively (P < .001). The independent prognostic factors for inferior OS were older age, intermediate-risk or adverse-risk cytogenetics, WBC count > 100 × 109/L, poor performance status, and a subgroup of AML-MRC with the morphologic criteria of multilineage dysplasia (AML-MRC-M). In addition, sAML, AML-MRC, and a WBC count > 100 × 109/L were pre-treatment prognostic factors associated with poor relapse-free survival (P = .006, P = .017, and P < .001, respectively).
CONCLUSION: Both sAML and AML-MRC are independently associated with poor outcomes in Thai patients. Our study supports AML-MRC-M as an adverse prognostic factor for OS.

Keywords:  Acute myeloid leukemia with antecedent hematological disease; Acute myeloid leukemia with myelodysplasia-related changes; De novo acute myeloid leukemia; Secondary acute myeloid leukemia; Therapy-related acute myeloid leukemia

DOI:  https://doi.org/10.1016/j.clml.2022.08.010
Blood Adv. 2022 Sep 21. pii: bloodadvances.2022008376. [Epub ahead of print]

Patient perspectives on testing for clonal hematopoiesis of indeterminate potential.

Tal Sella, Geoffrey G Fell, Peter Grant Miller, Christopher J Gibson, Shoshana M Rosenberg, Craig Snow, Daniel G Stover, Kathryn J Ruddy, Jeffrey M Peppercorn, Lidia Schapira, Virginia F Borges, Steven E Come, Ellen Warner, Elizabeth Frank, Donna Neuberg, Benjamin L Ebert, Ann H Partridge.

Clonal hematopoiesis of indeterminate potential (CHIP), an emerging biomarker for personalized risk-directed interventions, has increased prevalence in cancer survivors. Little is known about patients' preferences regarding CHIP testing. We surveyed participants in an ongoing prospective cohort study of young women with breast cancer (BC). The emailed survey included an introduction to CHIP and a clinical vignette eliciting participants' preferences for CHIP testing considering sequentially: 1) population-based 10-year risk of BC recurrence, hematological malignancy and heart disease; 2) increased CHIP-associated risks; 3) current CHIP management; 4) dedicated CHIP clinic; 5) hypothetical CHIP treatment. Preference changes were evaluated with McNemar's test. Survey response rate was 82.2%(528/642). Median age at survey was 46 years (range: 31-54), time from diagnosis 108 months (range: 60-168). Only 5.9% had prior knowledge of CHIP. After vignette presentation, most survivors (87.1%) recommended CHIP testing for the vignette patient. Presented next with CHIP-independent, population-based risks, 11.1% shifted their preference from testing to not testing (p<0.001). After information about CHIP-associated risks, an additional 10.1% shifted preference to testing (p<0.001). Preference for testing (p<0.001) increased if vignette patient was offered a CHIP clinic or hypothetical CHIP treatment, with 7.2% and 14.1% switching preferences towards testing, respectively. Finally, 75.8% desired CHIP testing for themselves. 28.2% reported learning about CHIP caused at least moderate anxiety. Most young survivors favored CHIP testing with preferences influenced by risk presentation and potential management strategies. Our findings highlight the importance of effective risk communication and adequate psychosocial support when considering biomarkers of future risks in cancer survivors. This trial is registered at www.clinicaltrials.gov as NCT01468246.

DOI: https://doi.org/10.1182/bloodadvances.2022008376
Blood Adv. 2022 Sep 23. pii: bloodadvances.2022007988. [Epub ahead of print]

Germline SNPs previously implicated as prognostic biomarkers do not associate with outcomes in intensively treated AML.

Aarif M N Batcha, Nele Buckup, Stefanos A Bamopoulos, Vindi Jurinovic, Maja Rothenberg-Thurley, Hanna Gittinger, Bianka Ksienzyk, Annika Dufour, Stephanie Schneider, Mika Kontro, Joseph Saad, Caroline A Heckman, Cristina M Sauerland, Dennis Görlich, Wolfgang E Berdel, Bernhard Wörmann, Utz Krug, Jan Braess, Ulrich Robert Mansmann, Wolfgang Hiddemann, Karsten Spiekermann, Klaus H Metzeler, Tobias Herold.

DOI: https://doi.org/10.1182/bloodadvances.2022007988
Exp Hematol. 2022 Sep 14. pii: S0301-472X(22)00696-8. [Epub ahead of print]

Ex vivo expansion of phenotypic and transcriptomic CML stem cells.

Sweta B Patel, Valeriya Kuznetsova, Victoria R Matkins, Alana M Franceski, Mahmoud A Bassal, Robert S Welner.

  Despite decades of research, standard therapies remain ineffective for most leukemia, pushing towards an essential unmet need for targeted drug screens. Moreover, pre-clinical drug testing is an important consideration for success of clinical trials without impacting non-transformed stem cells. Using the transgenic chronic myeloid leukemia (CML) mouse model, we show that leukemic stem cells (LSCs) are transcriptionally heterogenous with a pre-existent drug-insensitive signature. To test targeting of potentially important pathways, we establish ex vivo expanded LSCs that have long-term engraftment and give rise to multi-lineage hematopoiesis. Expanded LSCs share transcriptomic signatures with primary LSCs including enrichment in Wnt, JAK-STAT, MAPK, mTOR and TGFβ signaling pathways. Drug testing on expanded LSCs show that TGFβ and Wnt inhibitors had significant impacts on viability of LSCs, but not leukemia exposed healthy HSCs. This platform allows testing of multiple drugs at the same time to identify vulnerabilities of LSCs.

Keywords:  chronic myeloid leukemia; drug screens; ex vivo expansion; leukemic stem cells; scRNA-seq

DOI:  https://doi.org/10.1016/j.exphem.2022.09.001
Bone Marrow Transplant. 2022 Sep 23.

Allogeneic hematopoietic cell transplantation can overcome the adverse prognosis indicated by secondary-type mutations in de novo acute myeloid leukemia.

Ga-Young Song, TaeHyung Kim, Seo-Yeon Ahn, Sung-Hoon Jung, Mihee Kim, Deok-Hwan Yang, Je-Jung Lee, Seung Hyun Choi, Mi Yeon Kim, Chul Won Jung, Jun-Ho Jang, Hee Je Kim, Joon Ho Moon, Sang Kyun Sohn, Jong-Ho Won, Seong-Kyu Park, Sung-Hyun Kim, Zhaolei Zhang, Jae-Sook Ahn, Hyeoung-Joon Kim, Dennis Dong Hwan Kim.

Secondary-type mutations (STMs), namely SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, and STAG2, are more frequently detected in secondary acute myeloid leukemia (AML) than in de novo AML. Whether de novo AML with STMs should be differently managed is, however, unclear. In 394 patients diagnosed with de novo AML who had a normal karyotype, the genetic profiling via targeted deep sequencing of 45 genes revealed 59 patients carrying STMs (STM+). The STM+ group showed shorter overall survival (OS) than the STM- group (5-year OS, 15.3 vs. 31.0%) (hazard ratio [HR]: 1.975, 95% confidence interval [CI]: 1.446-2.699, p < 0.001). Among the 40 STM+ patients who achieved CR, those who received allogeneic HCT (n = 15) showed better OS (5-year OS, 40.0 vs. 12.0%) (HR: 0.423, 95% CI: 0.184-0.975, p = 0.043) and relapse-free survival (5-year, 40.0 vs. 8.0%) (HR: 0.438, 95% CI: 0.189-1.015, p = 0.054) than those who received consolidation chemotherapy only. The cumulative incidence of relapse was lower in the patients who received allogeneic HCT (5-year, 33.3 vs. 60.0%) (HR: 0.288, 95% CI: 0.111-0.746, p = 0.011), and non-relapse mortality was similar between the two groups (p = 0.935). In conclusion, STM is an independent prognostic factor for adverse outcomes in AML that can be overcome by allogeneic HCT.

DOI: https://doi.org/10.1038/s41409-022-01817-0
J Exp Med. 2022 Nov 07. pii: e20220081. [Epub ahead of print]219(11):

Sleep exerts lasting effects on hematopoietic stem cell function and diversity.

Cameron S McAlpine, Máté G Kiss, Faris M Zuraikat, David Cheek, Giulia Schiroli, Hajera Amatullah, Pacific Huynh, Mehreen Z Bhatti, Lai-Ping Wong, Abi G Yates, Wolfram C Poller, John E Mindur, Christopher T Chan, Henrike Janssen, Jeffrey Downey, Sumnima Singh, Ruslan I Sadreyev, Matthias Nahrendorf, Kate L Jeffrey, David T Scadden, Kamila Naxerova, Marie-Pierre St-Onge, Filip K Swirski.

A sleepless night may feel awful in its aftermath, but sleep's revitalizing powers are substantial, perpetuating the idea that convalescent sleep is a consequence-free physiological reset. Although recent studies have shown that catch-up sleep insufficiently neutralizes the negative effects of sleep debt, the mechanisms that control prolonged effects of sleep disruption are not understood. Here, we show that sleep interruption restructures the epigenome of hematopoietic stem and progenitor cells (HSPCs) and increases their proliferation, thus reducing hematopoietic clonal diversity through accelerated genetic drift. Sleep fragmentation exerts a lasting influence on the HSPC epigenome, skewing commitment toward a myeloid fate and priming cells for exaggerated inflammatory bursts. Combining hematopoietic clonal tracking with mathematical modeling, we infer that sleep preserves clonal diversity by limiting neutral drift. In humans, sleep restriction alters the HSPC epigenome and activates hematopoiesis. These findings show that sleep slows decay of the hematopoietic system by calibrating the hematopoietic epigenome, constraining inflammatory output, and maintaining clonal diversity.

DOI: https://doi.org/10.1084/jem.20220081
Br J Cancer. 2022 Sep 17.

Sensitisation of cancer cells to radiotherapy by serine and glycine starvation.

Mattia Falcone, Alejandro Huerta Uribe, Vasileios Papalazarou, Alice C Newman, Dimitris Athineos, Katrina Stevenson, Charles-Etienne Gabriel Sauvé, Yajing Gao, Jin K Kim, Michael Del Latto, Maria Kierstead, Chao Wu, J Joshua Smith, Paul B Romesser, Anthony J Chalmers, Karen Blyth, Oliver D K Maddocks.

BACKGROUND: Cellular metabolism is an integral component of cellular adaptation to stress, playing a pivotal role in the resistance of cancer cells to various treatment modalities, including radiotherapy. In response to radiotherapy, cancer cells engage antioxidant and DNA repair mechanisms which mitigate and remove DNA damage, facilitating cancer cell survival. Given the reliance of these resistance mechanisms on amino acid metabolism, we hypothesised that controlling the exogenous availability of the non-essential amino acids serine and glycine would radiosensitise cancer cells.
METHODS: We exposed colorectal, breast and pancreatic cancer cell lines/organoids to radiation in vitro and in vivo in the presence and absence of exogenous serine and glycine. We performed phenotypic assays for DNA damage, cell cycle, ROS levels and cell death, combined with a high-resolution untargeted LCMS metabolomics and RNA-Seq.
RESULTS: Serine and glycine restriction sensitised a range of cancer cell lines, patient-derived organoids and syngeneic mouse tumour models to radiotherapy. Comprehensive metabolomic and transcriptomic analysis of central carbon metabolism revealed that amino acid restriction impacted not only antioxidant response and nucleotide synthesis but had a marked inhibitory effect on the TCA cycle.
CONCLUSION: Dietary restriction of serine and glycine is a viable radio-sensitisation strategy in cancer.

DOI: https://doi.org/10.1038/s41416-022-01965-6
Bone Marrow Transplant. 2022 Sep 22.

Comparative study of treosulfan plus Fludarabine (FT14) with busulfan plus Fludarabine (FB4) for acute myeloid leukemia in first or second complete remission: An analysis from the European Society for Blood and Marrow Transplantation (EBMT) Acute Leukemia Working Party (ALWP).

Eleni Gavriilaki, Myriam Labopin, Ioanna Sakellari, Urpu Salmenniemi, Ibrahim Yakoub-Agha, Victoria Potter, Ana Berceanu, Alessandro Rambaldi, Inken Hilgendorf, Nicolaus Kröger, Stephan Mielke, Tsila Zuckerman, Jaime Sanz, Alessandro Busca, Hakan Ozdogu, Achilles Anagnostopoulos, Bipin Savani, Sebastian Giebel, Ali Bazarbachi, Alexandros Spyridonidis, Arnon Nagler, Mohamad Mohty.

Different doses of treosulfan plus fludarabine have shown advantage over reduced intensity regimens. However, data comparing higher doses of treosulfan to myeloablative busulfan are limited. Thus, we compared outcomes between FT14 (fludarabine 150/160 mg/m2 and treosulfan 42 g/m2, or FT14) over FB4 (fludarabine 150/160 mg/m2 and busulfan 12.8 mg/kg). We retrospectively studied patients from European Society for Blood and Marrow Transplantation registry: a) adults diagnosed with acute myeloid leukemia (AML), b) recipients of first allogeneic hematopoietic stem cell transplantation (HSCT) from unrelated or sibling donor (2010-2020), c) HSCT at first or second complete remission, d) conditioning with FT14 or FB4. FT14 recipients (n = 678) were older, with higher rates of secondary AML, unrelated donors, peripheral blood grafts, and adverse cytogenetics, but lower percentage of female donor to male recipient compared to FB4 (n = 2025). Analysis was stratified on age. In patients aged < 55 years, FT14 was associated with higher relapse incidence (RI) and lower Leukemia-Free Survival (LFS). In patients aged≥55 years, acute GVHD CI was higher in FB4, without significant differences in other outcomes. Although FT14 has been used for higher-risk HSCT patients, our large real-world multicenter study suggests that FB4 is associated with better outcomes compared to FT14 in younger patients.

DOI: https://doi.org/10.1038/s41409-022-01830-3
Clin Lymphoma Myeloma Leuk. 2022 Aug 27. pii: S2152-2650(22)00269-5. [Epub ahead of print]

SF3B1, RUNX1 and TP53 Mutations Significantly Impact the Outcome of Patients With Lower-Risk Myelodysplastic Syndrome.

Jose F Falantes, Francisco J Márquez-Malaver, Estrella Carrillo, Marta García Culebras, Rosario Morales, Concepción Prats, Maria T Vargas, Teresa Caballero, Eduardo Rodríguez-Arbolí, Ildefonso Espigado, Jose Antonio Pérez-Simón.

   INTRODUCTION: Prognosis of patients with myelodysplastic syndrome (MDS), particularly the group with lower-risk disease (LR-MDS) is very heterogeneous. Several studies have described the prognostic value of recurrent somatic mutations in MDS including all risk categories. Recently, the incorporation of genomic data to clinical parameters defined the new Molecular International Prognostic Scoring System (IPSS-M).
MATERIALS AND METHODS: In this study, we evaluated the impact of molecular profile in a series of 181 patients with LR-MDS and non-proliferative chronic myelomonocytic leukemia.
RESULTS: Epigenetic regulators (TET2, ASXL1) and splicing (SF3B1) were the most recurrent mutated pathways. In univariate analysis, RUNX1 or TP53 mutations correlated with lower median overall survival (OS). In contrast, SF3B1 mutation was associated with prolonged median OS [95 months (95% IC, 32-157) vs. 33 months (95% CI, 19-46) in unmutated patients (P < 0.01)]. In a multivariate Cox regression model, RUNX1 mutations independently associated with shorter OS, while SF3B1 mutation retained its favorable impact on outcome (HR: 0.24, 95% CI, 0.1-0.5; P = 0.001). In addition, TP53 or RUNX1 mutations were identified as predictive covariates for the probability of leukemic progression (P < 0.001).
CONCLUSION: Incorporation of molecular testing in LR-MDS identified a subset of patients with expected poorer outcome, either due to lower survival or probability of leukemic progression.

Keywords:  Genetics; Leukemic progression; Myelodysplasia; Prognosis

DOI:  https://doi.org/10.1016/j.clml.2022.08.012
Blood Cancer Discov. 2022 Sep 13. pii: BCD-21-0219. [Epub ahead of print]

Deep morphology learning enhances ex vivo drug profiling-based precision medicine.

Tim Heinemann, Christoph Kornauth, Yannik Severin, Gregory I Vladimer, Tea Pemovska, Emir Hadzijusufovic, Hermine Agis, Maria-Theresa Krauth, Wolfgang R Sperr, Peter Valent, Ulrich Jager, Ingrid Simonitsch-Klupp, Giulio Superti-Furga, Philipp B Staber, Berend Snijder.

Image-based drug testing in patient biopsies has recently been shown to identify potent treatments for patients suffering from relapsed or refractory hematological cancers. Here we investigate the use of weakly-supervised deep learning on cell morphologies (DML) to complement immunofluorescence (IF) in the classification of cancer and healthy cells in such drug testing. Across 390 biopsies from 289 patients with diverse blood cancers, DML-based drug responses show improved reproducibility and clustering of drugs with the same mode of action. DML does so by adapting to batch effects and by autonomously recognizing disease-associated cell morphologies. In a post-hoc analysis of 66 patients, DML-recommended treatments led to improved progression free survival compared to IF-based recommendations and physician's choice-based treatments. Treatments recommended by both IF and DML enriched for patients achieving exceptional clinical responses. Thus, DML-enhanced ex vivo drug screening is a promising new tool in the identification of effective personalized treatments.

DOI: https://doi.org/10.1158/2643-3230.BCD-21-0219
Science. 2022 Sep 23. 377(6613): 1413-1419

Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality.

Samuel J Wattrus, Mackenzie L Smith, Cecilia Pessoa Rodrigues, Elliott J Hagedorn, Ji Wook Kim, Bogdan Budnik, Leonard I Zon.

Tissue-specific stem cells persist for a lifetime and can differentiate to maintain homeostasis or transform to initiate cancer. Despite their importance, there are no described quality assurance mechanisms for newly formed stem cells. We observed intimate and specific interactions between macrophages and nascent blood stem cells in zebrafish embryos. Macrophage interactions frequently led to either removal of cytoplasmic material and stem cell division or complete engulfment and stem cell death. Stressed stem cells were marked by surface Calreticulin, which stimulated macrophage interactions. Using cellular barcoding, we found that Calreticulin knock-down or embryonic macrophage depletion reduced the number of stem cell clones that established adult hematopoiesis. Our work supports a model in which embryonic macrophages determine hematopoietic clonality by monitoring stem cell quality.

DOI: https://doi.org/10.1126/science.abo4837
Blood. 2022 Sep 21. pii: blood.2022015898. [Epub ahead of print]

Efficacy of JAK 1/2 inhibition in murine immune bone marrow failure.

Emma M Groarke, Xingmin Feng, Nidhi Aggarwal, Ash Lee Telisa Manley, Zhijie Wu, Shouguo Gao, Bhavisha A Patel, Jichun Chen, Neal S Young.

Immune aplastic anemia (AA) is a severe blood disease characterized by T-lymphocyte mediated stem cell destruction. Hematopoietic stem cell transplant and immunosuppression are effective but entail costs and risks and are not always successful. The Janus Kinase (JAK) 1/2 inhibitor ruxolitinib (RUX) suppresses cytotoxic T cell activation and inhibits cytokine production in models of graft-versus-host disease. We tested RUX in murine immune AA for potential therapeutic benefit. After infusion of lymph node (LN) cells mismatched at the major histocompatibility complex [C67BL/6 (B6)ÞCByB6F1], RUX, administered as a food additive (Rux-chow), attenuated bone marrow hypoplasia, ameliorated peripheral blood pancytopenia, preserved hematopoietic progenitors, and prevented mortality, when used either prophylactically or therapeutically. RUX suppressed the infiltration, proliferation, and activation of effector T cells in the bone marrow and mitigated Fas-mediated apoptotic destruction of target hematopoietic cells. Similar effects were obtained when Rux-chow was fed to C.B10 mice in a minor histocompatibility antigen mismatched (B6ÞC.B10) AA model. RUX only modestly suppressed lymphoid and erythroid hematopoiesis in normal and irradiated CByB6F1 mice. Our data supports clinical trials of JAK/STAT inhibitors in human AA and other immune bone marrow failure syndromes.

DOI: https://doi.org/10.1182/blood.2022015898
Nat Genet. 2022 Sep 19.

The evolutionary dynamics of extrachromosomal DNA in human cancers.

Joshua T Lange, John C Rose, Celine Y Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L Hung, Kathryn E Yost, Quanming Shi, Marcella L Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner-Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y Chang, Vineet Bafna, Anton G Henssen, Benjamin Werner, Paul S Mischel.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

DOI: https://doi.org/10.1038/s41588-022-01177-x