bims-tremyl 2023-11-19 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2023‒11‒19
29 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Survival outcomes in patients with acute myeloid leukaemia who received subsequent therapy for relapse in QUAZAR AML-001.
LAIR-1 agonism as a therapy for acute myeloid leukemia.
Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease.
Perspective on measurable residual disease testing in acute myeloid leukemia.
Validation of the transplant conditioning intensity (TCI) index for allogeneic hematopoietic cell transplantation.
How low can you go?: Methodologic considerations in clonal hematopoiesis variant calling.
Perspectives and challenges of small molecule inhibitor therapy for FLT3-mutated acute myeloid leukemia.
Fractionated vs single-dose gemtuzumab for AML.
Bone marrow stromal cells reduce low-dose cytarabine-induced differentiation of acute myeloid leukemia.
Acute myeloid leukemia with mixed phenotype is characterized by stemness transcriptomic signatures and limited lineage plasticity.
R-loop accumulation in spliceosome mutant leukemias confers sensitivity to PARP1 inhibition by triggering transcription-replication conflicts.
Missense mutations in Myc Box I influence MYC cellular localization, mRNA partitioning and turnover to promote leukemogenesis.
Acid Ceramidase Inhibitor LCL-805 Antagonizes Akt Signaling and Promotes Iron-Dependent Cell Death in Acute Myeloid Leukemia.
Mutation spectrum, expression profiling, and prognosis evaluation of Fanconi anemia signaling pathway genes for 4259 patients with myelodysplastic syndromes or acute myeloid leukemia.
Deep Learning Predicts Therapy-Relevant Genetics in Acute Myeloid Leukemia from Pappenheim-stained Bone Marrow Smears.
Outcomes and Characteristics of Non-Melanoma Skin Cancers in Patients with Myeloproliferative Neoplasms on Ruxolitinib.
A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies.
A combinatorial therapeutic approach to enhance FLT3-ITD AML treatment.
Proof of concept of triple COMBI therapy to prohibit MPN progression to AML.
Monitoring clone dynamics and reversibility in clonal haematopoiesis and myelodysplastic neoplasm associated with PARP inhibitor therapy-a role for early monitoring and intervention.
High-fat diet promotes Acute Promyelocytic Leukemia through PPARδ-enhanced self-renewal of preleukemic progenitors.
A longitudinal single-cell atlas of treatment response in pediatric AML.
Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia.
Clonal haematopoiesis of indeterminate potential predicts incident cardiac arrhythmias.
JAK2V617F and ischemic stroke: CHIP or CMD-NBV?
A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics.
Sphingolipids and HSC fitness: enigma no more.
Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms.
Haematopoietic stem cell numbers are not solely determined by niche availability.

Br J Haematol. 2023 Nov 12.

Survival outcomes in patients with acute myeloid leukaemia who received subsequent therapy for relapse in QUAZAR AML-001.

Farhad Ravandi, Hartmut Döhner, Andrew H Wei, Pau Montesinos, Michael Pfeilstöcker, Cristina Papayannidis, Yinzhi Lai, Kefeng Wang, Wendy L See, Daniel Lopes de Menezes, Erica Petrlik, Thomas Prebet, Gail J Roboz.

  In the phase 3 QUAZAR AML-001 trial (NCT01757535) of patients with acute myeloid leukaemia (AML) in remission following intensive chemotherapy (IC) and ineligible for haematopoietic stem cell transplant (HSCT), oral azacitidine (Oral-AZA) maintenance significantly prolonged overall survival (OS) versus placebo. The impact of subsequent treatment following maintenance has not been evaluated. In this post hoc analysis, OS was estimated for patients who received subsequent AML therapy, and by regimen received (IC or lower-intensity therapy). First subsequent therapy (FST) was administered after treatment discontinuation in 134/238 Oral-AZA and 173/234 placebo patients. OS from randomization in patients who received FST after Oral-AZA versus placebo was 17.8 versus 12.9 months (HR: 0.82 [95% CI: 0.64-1.04], median follow-up: 56.7 months); OS from FST was similar between arms. Among patients who received injectable hypomethylating agents as FST, median OS was 8.2 versus 4.9 months in the Oral-AZA versus placebo groups (HR: 0.66 [95% CI: 0.41-1.06]). Forty-eight patients (16/238 Oral-AZA, 32/234 placebo) received HSCT following treatment discontinuation, including six Oral-AZA patients still in first remission; Oral-AZA OS benefit persisted when censoring these patients. Oral-AZA maintenance can prolong AML remission duration without negatively impacting survival outcomes after salvage therapies.

Keywords:  acute myeloid leukaemia; haematopoietic stem cell transplant; maintenance treatment; oral azacitidine; subsequent treatment

DOI:  https://doi.org/10.1111/bjh.19202
J Clin Invest. 2023 Nov 15. pii: e169519. [Epub ahead of print]133(22):

LAIR-1 agonism as a therapy for acute myeloid leukemia.

Rustin R Lovewell, Junshik Hong, Subhadip Kundu, Carly M Fielder, Qianni Hu, Kwang Woon Kim, Haley E Ramsey, Agnieszka E Gorska, Londa S Fuller, Linjie Tian, Priyanka Kothari, Ana Paucarmayta, Emily F Mason, Ingrid Meza, Yanira Manzanarez, Jason Bosiacki, Karla Maloveste, Ngan Mitchell, Emilia A Barbu, Aaron Morawski, Sebastien Maloveste, Zac Cusumano, Shashank J Patel, Michael R Savona, Solomon Langermann, Han Myint, Dallas B Flies, Tae Kon Kim.

  Effective eradication of leukemic stem cells (LSCs) remains the greatest challenge in treating acute myeloid leukemia (AML). The immune receptor LAIR-1 has been shown to regulate LSC survival; however, the therapeutic potential of this pathway remains unexplored. We developed a therapeutic LAIR-1 agonist antibody, NC525, that induced cell death of LSCs, but not healthy hematopoietic stem cells in vitro, and killed LSCs and AML blasts in both cell- and patient-derived xenograft models. We showed that LAIR-1 agonism drives a unique apoptotic signaling program in leukemic cells that was enhanced in the presence of collagen. NC525 also significantly improved the activity of azacitidine and venetoclax to establish LAIR-1 targeting as a therapeutic strategy for AML that may synergize with standard-of-care therapies.

Keywords:  Leukemias; Oncology

DOI:  https://doi.org/10.1172/JCI169519
Nat Med. 2023 Nov 16.

Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease.

Michael Spencer Chapman, Alyssa H Cull, Marioara F Ciuculescu, Erica B Esrick, Emily Mitchell, Hyunchul Jung, Laura O'Neill, Kirsty Roberts, Margarete A Fabre, Nicholas Williams, Jyoti Nangalia, Joanne Quinton, James M Fox, Danilo Pellin, Julie Makani, Myriam Armant, David A Williams, Peter J Campbell, David G Kent.

Gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms.

DOI: https://doi.org/10.1038/s41591-023-02636-6
Leukemia. 2023 Nov 16.

Perspective on measurable residual disease testing in acute myeloid leukemia.

Roland B Walter.

DOI: https://doi.org/10.1038/s41375-023-02084-8
Bone Marrow Transplant. 2023 Nov 17.

Validation of the transplant conditioning intensity (TCI) index for allogeneic hematopoietic cell transplantation.

Alexandros Spyridonidis, Myriam Labopin, Tobias Gedde-Dahl, Arnold Ganser, Matthias Stelljes, Charles Craddock, Eva Maria Wagner-Drouet, Jurjen Versluis, Thomas Schroeder, Igor Wolfgang Blau, Gerald G Wulf, Peter Dreger, Gitte Olesen, Henrik Sengeloev, Nicolaus Kröger, Victoria Potter, Edouard Forcade, Jakob Passweg, Régis Peffault de Latour, Johan Maertens, Keith M O Wilson, Jean Henri Bourhis, Juergen Finke, Eolia Brissot, Ali Bazarbachi, Sebastian Giebel, Bipin P Savani, Arnon Nagler, Fabio Ciceri, Mohamad Mohty.

The intensity of the conditioning regimen given before allogeneic hematopoietic cell transplantation (allo-HCT) can vary substantially. To confirm the ability of the recently developed transplant conditioning intensity (TCI) score to stratify the preparative regimens of allo-HCT, we used an independent and contemporary patient cohort of 4060 transplant recipients with acute myeloid leukemia meeting inclusion criteria from the discovery study (allo-HCT in first complete remission, matched donor), but who were allografted in a more recent period (2018-2021) and were one decade older (55-75 years, median 63.4 years), we assigned them to a TCI category (low n = 1934, 48%; intermediate n = 1948, 48%, high n = 178, 4%) according to the calculated TCI score ([1-2], [2.5-3.5], [4-6], respectively), and examined the validity of the TCI category in predicting early non-relapse mortality (NRM), 2-year NRM and relapse (REL). In the unadjusted comparison, the TCI index provided a significant risk stratification for d100 and d180 NRM, NRM and REL risk. In the multivariate analysis adjusted for significant variables, there was an independent association of TCI with early NRM, NRM and REL. In summary, we confirm in contemporary treated patients that TCI reflects the conditioning regimen related morbidity and anti-leukemic efficacy satisfactorily and across other established prognostic factors.

DOI: https://doi.org/10.1038/s41409-023-02139-5
Leuk Res. 2023 Nov 02. pii: S0145-2126(23)00684-7. [Epub ahead of print]135 107419

How low can you go?: Methodologic considerations in clonal hematopoiesis variant calling.

J Scott Beeler, Kelly L Bolton.

  Clonal hematopoiesis (CH) is defined by the presence of an expanded clonal hematopoietic cell population due to an acquired mutation conferring a selective growth advantage and is known to predispose to hematologic malignancy. In this review, we discuss sequencing methods for CH detection in bulk sequencing data and corresponding bioinformatic approaches for variant calling, filtering, and curation. We detail practical recommendations for CH calling. Finally, we discuss how improvements in CH sequencing and bioinformatic approaches will enable the characterization of CH trajectories, its impact on human health, and therapeutic approaches to mitigate its adverse effects.

Keywords:  Clonal hematopoiesis; DNA sequencing; Myeloid neoplasm; Sequencing errors; Somatic variant calling; Unique molecular identifiers

DOI:  https://doi.org/10.1016/j.leukres.2023.107419
Ann Hematol. 2023 Nov 17.

Perspectives and challenges of small molecule inhibitor therapy for FLT3-mutated acute myeloid leukemia.

Coen J Lap, Marwa Sh Abrahim, Samah Nassereddine.

  Acute myeloid leukemia (AML) is a heterogeneous clonal disease characterized overall by an aggressive clinical course. The underlying genetic abnormalities present in leukemic cells contribute significantly to the AML phenotype. Mutations in FMS-like tyrosine kinase 3 (FLT3) are one of the most common genetic abnormalities identified in AML, and the presence of these mutations strongly influences disease presentation and negatively impacts prognosis. Since mutations in FLT3 were identified in AML, they have been recognized as a valid therapeutic target resulting in decades of research to develop effective small molecule inhibitor treatment that could improve outcome for these patients. Despite the approval of several FLT3 inhibitors over the last couple of years, the treatment of patients with FLT3-mutated AML remains challenging and many questions still need to be addressed. This review will provide an up-to-date overview of our current understanding of FLT3-mutated AML and discuss what the current status is of the available FLT3 inhibitors for the day-to-day management of this aggressive disease.

Keywords:  AML; FLT3; Gilteritinib; Midostaurin; Precision medicine; Quizartinib; Treatment

DOI:  https://doi.org/10.1007/s00277-023-05545-3
Blood. 2023 Nov 16. 142(20): 1759

Fractionated vs single-dose gemtuzumab for AML.

DOI: https://doi.org/10.1182/blood.2023022657
Front Pharmacol. 2023 ;14 1258151

Bone marrow stromal cells reduce low-dose cytarabine-induced differentiation of acute myeloid leukemia.

Tomislav Smoljo, Barbara Tomic, Hrvoje Lalic, Vilma Dembitz, Josip Batinic, Antonio Bedalov, Dora Visnjic.

  Low-dose cytarabine (LDAC) is a standard therapy for elderly acute myeloid leukemia (AML) patients unfit for intensive chemotherapy. While high doses of cytarabine induce cytotoxicity, the precise mechanism of action of LDAC in AML remains elusive. In vitro studies have demonstrated LDAC-induced differentiation; however, such differentiation is seldom observed in vivo. We hypothesize that this discrepancy may be attributed to the influence of bone marrow (BM) stromal cells on AML cells. Thus, this study aimed to investigate the impact of BM stromal cells on LDAC-induced differentiation of AML cell lines and primary samples. Our results demonstrate that the presence of MS-5 stromal cells prevented LDAC-induced cell cycle arrest, DNA damage signaling and differentiation of U937 and MOLM-13 cell lines. Although transcriptomic analysis revealed that the stroma reduces the expression of genes involved in cytokine signaling and oxidative stress, data obtained with pharmacological inhibitors and neutralizing antibodies did not support the role for CXCL12, TGF-β1 or reactive oxygen species. The presence of stromal cells reduces LDAC-induced differentiation in primary samples from AML-M4 and myelodysplastic syndrome/AML patients. In conclusion, our study demonstrates that BM stroma reduces differentiation of AML induced by LDAC. These findings provide insights into the limited occurrence of terminal differentiation observed in AML patients, and suggest a potential explanation for this observation.

Keywords:  acute myeloid leukemia; bone marrow stromal cells; cell cycle; cytarabine; differentiation

DOI:  https://doi.org/10.3389/fphar.2023.1258151
medRxiv. 2023 Nov 03. pii: 2023.11.01.23297696. [Epub ahead of print]

Acute myeloid leukemia with mixed phenotype is characterized by stemness transcriptomic signatures and limited lineage plasticity.

Pallavi Galera, Deepika Dilip, Andriy Derkach, Alexander Chan, Yanming Zhang, Sonali Persuad, Tanmay Mishera, Ying Liu, Christopher Famulare, Qi Gao, Douglas A Mata, Maria Arcila, Mark B Geyer, Eytan Stein, Ahmet Dogan, Ross L Levine, Mikhail Roshal, Jacob Glass, Wenbin Xiao.

Mixed phenotype (MP) in acute leukemias poses unique classification and management dilemmas and can be seen in entities other than de novo mixed phenotype acute leukemia (MPAL). Although WHO classification empirically recommends excluding AML with myelodysplasia related changes (AML-MRC) and therapy related AML (t-AML) with mixed phenotype (AML-MP) from MPAL, there is lack of studies investigating the clinical, genetic, and biologic features of AML-MP. We report the first cohort of AML-MRC and t-AML with MP integrating their clinical, immunophenotypic, genomic and transcriptomic features with comparison to MPAL and AML-MRC/t-AML without MP. Both AML cohorts with and without MP shared similar clinical features including adverse outcomes but were different from MPAL. The genomic landscape of AML-MP overlaps with AML without MP but differs from MPAL. AML-MP harbors more frequent RUNX1 mutations than AML without MP and MPAL. RUNX1 mutations did not impact the survival of patients with MPAL. Unsupervised hierarchal clustering based on immunophenotype identified biologically distinct clusters with phenotype/genotype correlation and outcome differences. Furthermore, transcriptomic analysis showed an enrichment for stemness signature in AML-MP and AML without MP as compared to MPAL. Lastly, MPAL but not AML-MP often switched to lymphoid only immunophenotype after treatment. Expression of transcription factors critical for lymphoid differentiation were upregulated only in MPAL, but not in AML-MP. Our study for the first time demonstrates that AML-MP clinically and biologically resembles its AML counterpart without MP and differs from MPAL, supporting the recommendation to exclude these patients from the diagnosis of MPAL. Future studies are needed to elucidate the molecular mechanism of mixed phenotype in AML.Key points: AML-MP clinically and biologically resembles AML but differs from MPAL. AML-MP shows RUNX1 mutations, stemness signatures and limited lymphoid lineage plasticity.

DOI: https://doi.org/10.1101/2023.11.01.23297696
Cancer Res. 2023 Nov 15.

R-loop accumulation in spliceosome mutant leukemias confers sensitivity to PARP1 inhibition by triggering transcription-replication conflicts.

Zhiyan Silvia Liu, Sayantani Sinha, Maxwell Bannister, Axia Song, Erica Arriaga-Gomez, Alexander J McKeeken, Elizabeth A Bonner, Benjamin K Hanson, Martina Sarchi, Kouhei Takashima, Dawei Zong, Victor M Corral, Evan Nguyen, Jennifer Yoo, Wannasiri Chiraphapphaiboon, Cassandra Leibson, Matthew C McMahon, Sumit Rai, Elizabeth M Swisher, Zohar Sachs, Srinivas Chatla, Derek L Stirewalt, H Joachim Deeg, Tomasz Skorski, Eirini P Papapetrou, Matthew J Walter, Timothy A Graubert, Sergei Doulatov, Stanley C Lee, Hai Dang Nguyen.

RNA splicing factor (SF) gene mutations are commonly observed in patients with myeloid malignancies. Here we showed that SRSF2- and U2AF1-mutant leukemias are preferentially sensitive to PARP inhibitors (PARPi) despite being proficient in homologous recombination repair. Instead, SF-mutant leukemias exhibited R-loop accumulation that elicited an R-loop associated PARP1 response, rendering cells dependent on PARP1 activity for survival. Consequently, PARPi induced DNA damage and cell death in SF-mutant leukemias in an R-loop dependent manner. PARPi further increased aberrant R-loop levels, causing higher transcription-replication collisions and triggering ATR activation in SF-mutant leukemias. Ultimately, PARPi-induced DNA damage and cell death in SF-mutant leukemias could be enhanced by ATR inhibition. Finally, the level of PARP1 activity at R loops correlated with PARPi sensitivity, suggesting that R-loop associated PARP1 activity could be predictive of PARPi sensitivity in patients harboring SF gene mutations. This study highlights the potential of targeting different R-loop response pathways caused by spliceosome gene mutations as a therapeutic strategy for treating cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3239
bioRxiv. 2023 Oct 23. pii: 2023.10.22.563493. [Epub ahead of print]

Missense mutations in Myc Box I influence MYC cellular localization, mRNA partitioning and turnover to promote leukemogenesis.

Nancy Bj Arthur, Keegan A Christensen, Kathleen Mannino, Marianna B Ruzinova, Ashutosh Kumar, Agata Gruszczynska, Ryan B Day, Petra Erdmann-Gilmore, Yiling Mi, Robert Sprung, Conner R York, R Reid Townsend, David H Spencer, Stephen M Sykes, Francesca Ferraro.

Somatic missense mutations in the phosphodegron domain of the MYC gene ( M YC Box I) are detected in the dominant clones of a subset of acute myeloid leukemia (AML) patients, but the mechanisms by which they contribute to AML are unknown. To unveil unique proprieties of MBI MYC mutant proteins, we systematically compared the cellular and molecular consequences of expressing similar oncogenic levels of wild type and MBI mutant MYC. We found that MBI MYC mutants can accelerate leukemia by driving unique transcriptional signatures in highly selected, myeloid progenitor subpopulations. Although these mutations increase MYC stability, they overall dampen MYC chromatin localization and lead to a cytoplasmic accumulation of the mutant proteins. This phenotype is coupled with increased translation of RNA binding proteins and nuclear export machinery, which results in altered RNA partitioning and accelerated decay of select transcripts encoding proapoptotic and proinflammatory genes. Heterozygous knockin mice harboring the germline MBI mutation Myc p.T73N exhibit cytoplasmic MYC localization, myeloid progenitors' expansion with similar transcriptional signatures to the overexpression model, and eventually develop hematological malignancies. This study uncovers that MBI MYC mutations alter MYC localization and disrupt mRNA subcellular distribution and turnover of select transcripts to accelerate tumor initiation and growth.

DOI: https://doi.org/10.1101/2023.10.22.563493
bioRxiv. 2023 Oct 23. pii: 2023.10.21.563437. [Epub ahead of print]

Acid Ceramidase Inhibitor LCL-805 Antagonizes Akt Signaling and Promotes Iron-Dependent Cell Death in Acute Myeloid Leukemia.

Johnson Ung, Su-Fern Tan, Todd E Fox, Jeremy Jp Shaw, Maansi Taori, Bethany J Horton, Upendarrao Golla, Arati Sharma, Zdzislaw M Szulc, Hong-Gang Wang, Charles E Chalfant, Myles C Cabot, David F Claxton, Thomas P Loughran, David J Feith.

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy requiring urgent treatment advancements. Ceramide is a cell death-promoting signaling lipid that plays a central role in therapy-induced cell death. Acid ceramidase (AC), a ceramide-depleting enzyme, is overexpressed in AML and promotes leukemic survival and drug resistance. The ceramidase inhibitor B-13 and next-generation lysosomal-localizing derivatives termed dimethylglycine (DMG)-B-13 prodrugs have been developed but remain untested in AML. Here, we report the in vitro anti-leukemic efficacy and mechanism of DMG-B-13 prodrug, LCL-805, across AML cell lines and primary patient samples. LCL-805 inhibited AC enzymatic activity, increased total ceramides, and reduced sphingosine levels. A median EC50 value of 11.7 μM was achieved for LCL-805 in cell viability assays across 32 human AML cell lines. As a single agent tested across a panel of 71 primary AML patient samples, a median EC50 value of 15.8 μM was achieved. Exogenous ceramide supplementation with C6-ceramide nanoliposomes, which is entering phase I/II clinical trial for relapsed/refractory AML, significantly enhanced LCL-805 killing. Mechanistically, LCL-805 antagonized Akt signaling and led to iron-dependent cell death distinct from canonical ferroptosis. These findings elucidated key factors involved in LCL-805 cytotoxicity and demonstrated the potency of combining AC inhibition with exogenous ceramide.

DOI: https://doi.org/10.1101/2023.10.21.563437
BMC Med Genomics. 2023 Nov 16. 16(1): 290

Mutation spectrum, expression profiling, and prognosis evaluation of Fanconi anemia signaling pathway genes for 4259 patients with myelodysplastic syndromes or acute myeloid leukemia.

Lixian Chang, Li Zhang, Beibei Zhao, Xuelian Cheng, Yang Wan, Ranran Zhang, Weiping Yuan, Xingjie Gao, Xiaofan Zhu.

  BACKGROUND: Individuals diagnosed with Fanconi anemia (FA), an uncommon disorder characterized by chromosomal instability affecting the FA signaling pathway, exhibit heightened vulnerability to the onset of myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML).METHODS: Herein, we employed diverse bioinformatics and statistical analyses to investigate the potential associations between the expression/mutation patterns of FA pathway genes and MDS/AML.
RESULTS: The study included 4295 samples, comprising 3235 AML and 1024 MDS from our and nine other online cohorts. We investigated the distinct proportion of race, age, French-American-British, and gender factors. Compared to the FA wild-type group, we observed a decrease in the expression of FNACD2, FANCI, and RAD51C in the FA mutation group. The FA mutation group exhibited a more favorable clinical overall survival prognosis. We developed a random forest classifier and a decision tree based on FA gene expression for cytogenetic risk assessment. Furthermore, we created an FA-related Nomogram to predict survival rates in AML patients.
CONCLUSIONS: This investigation facilitates a deeper understanding of the functional links between FA and MDS/AML.

Keywords:  AML; Expression; Fanconi anemia pathway; MDS; Mutation

DOI:  https://doi.org/10.1186/s12920-023-01730-5
Blood Adv. 2023 Nov 15. pii: bloodadvances.2023011076. [Epub ahead of print]

Deep Learning Predicts Therapy-Relevant Genetics in Acute Myeloid Leukemia from Pappenheim-stained Bone Marrow Smears.

Jacqueline Kockwelp, Sebastian Thiele, Jannis Bartsch, Lars Haalck, Jörg Gromoll, Stefan Schlatt, Rita Exeler, Annalen Bleckmann, Georg Lenz, Sebastian Wolf, Björn Steffen, Wolfgang E Berdel, Christoph Schliemann, Benjamin Risse, Linus Angenendt.

The detection of genetic aberrations is crucial for early therapy decisions in acute myeloid leukemia (AML) and is recommended for all patients. Since genetic testing is expensive and time-consuming, a need remains for cost-effective, fast, and broadly accessible tests to predict these aberrations in this aggressive malignancy. Here, we developed a novel fully automated end-to-end deep learning pipeline to predict genetic aberrations directly from single-cell images from scans of conventionally stained bone marrow smears already on the day of diagnosis. We used this pipeline to compile a multi-terabyte dataset of over 2,000,000 single-cell images from diagnostic samples of 408 AML patients. These images were then used to train convolutional neural networks for the prediction of various therapy-relevant genetic alterations. We show that the models from our pipeline can significantly predict these subgroups with high AUROCs. Potential genotype-phenotype links were visualized with two different strategies. Our pipeline holds the potential to be used as a fast and inexpensive automated tool to screen AML patients for therapy-relevant genetic aberrations directly from routine, conventionally stained bone marrow smears already on the day of diagnosis. It also creates a foundation to develop similar approaches for other bone marrow disorders in the future.

DOI: https://doi.org/10.1182/bloodadvances.2023011076
Blood. 2023 Nov 14. pii: blood.2023022345. [Epub ahead of print]

Outcomes and Characteristics of Non-Melanoma Skin Cancers in Patients with Myeloproliferative Neoplasms on Ruxolitinib.

Alexandros Rampotas, Luke Carter-Brzezinski, Tim C Somervaille, James Forryan, Fotios P Panitsas, Claire N Harrison, Ruth Witherall, Andrew J Innes, Louise Wallis, Nauman M Butt, Bethan Psaila, Adam J Mead, Matthew Carter, Anna L Godfrey, Heather Laing, Mamta Garg, Sebastian Francis, Joanne Ewing, Chun Huat Teh, Hannah B Cowan, Peter Dyer, Conal McConville, Frances Wadelin, Sahra Ali, Andrew McGregor, Elizabeth Kulakov, Donal P McLornan, Jonathan Lambert.

Non-melanoma skin cancers in ruxolitinib-treated MPN patients behave aggressively, with adverse features and high recurrence. In our cohort, mortality from metastatic NMSC exceeded that from myelofibrosis . Vigilant skin assessment, counselling on NMSC risks, and prospective ruxolitinib-NMSC studies are crucial.

DOI: https://doi.org/10.1182/blood.2023022345
bioRxiv. 2023 Oct 25. pii: 2023.10.23.563660. [Epub ahead of print]

A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies.

Brian Freie, Patrick A Carroll, Barbara J Varnum-Finney, Vijay Ramani, Irwin Bernstein, Robert N Eisenman.

Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently contain point mutations in the MYC phospho-degron, including at threonine-58 (T58), where phosphorylation permits binding by the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60% of adult homozygous T58A mice. We find that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and upregulate a subset of Myc target genes important in maintaining stem/progenitor cell balance. Genomic occupancy by MYC-T58A was increased at all promoters, compared to WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation in Myc is sufficient to produce a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.

DOI: https://doi.org/10.1101/2023.10.23.563660
Cell Rep Med. 2023 Nov 02. pii: S2666-3791(23)00480-9. [Epub ahead of print] 101286

A combinatorial therapeutic approach to enhance FLT3-ITD AML treatment.

Jun Long, Xinjie Chen, Yan Shen, Yichen Lei, Lili Mu, Zhen Wang, Rufang Xiang, Wenhui Gao, Lining Wang, Ling Wang, Jieling Jiang, Wenjun Zhang, Huina Lu, Yan Dong, Yi Ding, Honghu Zhu, Dengli Hong, Yi Eve Sun, Jiong Hu, Aibin Liang.

  Internal tandem duplication mutations of the FMS-like tyrosine kinase-3 (FLT3-ITDs) occur in 25%-30% of patients with acute myeloid leukemia (AML) and are associated with dismal prognosis. Although FLT3 inhibitors have demonstrated initial clinical efficacy, the overall outcome of patients with FLT3-ITD AML remains poor, highlighting the urgency to develop more effective treatment strategies. In this study, we reveal that FLT3 inhibitors reduced protein stability of the anti-cancer protein p53, resulting in drug resistance. Blocking p53 degradation with proteasome inhibitors restores intracellular p53 protein levels and, in combination with FLT3-ITD inhibitors, shows superior therapeutic effects against FLT3-ITD AML in cells, mouse models, and patients. These data suggest that this combinatorial therapeutic approach may represent a promising strategy to target FLT3-ITD AML.

Keywords:  FLT3 inhibitor; FLT3-ITD; MYC; USP10; acute myeloid leukemia; p53; proteasome inhibitor; ubiquitination

DOI:  https://doi.org/10.1016/j.xcrm.2023.101286
Br J Haematol. 2023 Nov 13.

Proof of concept of triple COMBI therapy to prohibit MPN progression to AML.

Hans Carl Hasselbalch, Vibe Skov, Lasse Kjaer, Morten Kranker Larsen.

  Patients with accelerated or blast phase myeloproliferative neoplasms have a dismal prognosis. The report by de Castro et al. provides important information on the rationale and prospect for a novel therapeutic approach combining interferon-alpha2 with 5-azacytidine and a JAK1-2 inhibitor (ruxolitinib) to be explored in well-designed clinical trials. Commentary on: Castro et al. Ratio of stemness to interferon signalling as a biomarker and therapeutic target of myeloproliferative neoplasm progression to acute myeloid leukaemia. Br J Haematol 2023 (Online ahead of print). doi: 10.1111/bjh.19107.

Keywords:  AML; prohibit MPN progression; triple COMBI therapy

DOI:  https://doi.org/10.1111/bjh.19173
Leukemia. 2023 Nov 17.

Monitoring clone dynamics and reversibility in clonal haematopoiesis and myelodysplastic neoplasm associated with PARP inhibitor therapy-a role for early monitoring and intervention.

Ellen Nuttall Musson, Rowan E Miller, Marc R Mansour, Michelle Lockley, Jonathan A Ledermann, Elspeth M Payne.

DOI: https://doi.org/10.1038/s41375-023-02040-6
Cancer Prev Res (Phila). 2023 Nov 13.

High-fat diet promotes Acute Promyelocytic Leukemia through PPARδ-enhanced self-renewal of preleukemic progenitors.

Luca Mazzarella, Paolo Falvo, Marta Adinolfi, Giulia Tini, Elena Gatti, Rossana Piccioni, Emanuele Bonetti, Elena Gavilán, Debora Valli, Alicja Gruszka, Margherita Bodini, Barbara Gallo, Stefania Orecchioni, Giulia de Michele, Enrica Migliaccio, Bruno A Duso, Sophie Roerink, Mike Stratton, Francesco Bertolini, Myriam Alcalay, Gaetano Ivan Dellino, Pier Giuseppe Pelicci.

Risk and outcome of Acute Promyelocytic Leukemia (APL) are particularly worsened in obese-overweight individuals, but the underlying molecular mechanism is unknown. In established mouse APL models (Ctsg-PML::RARA), we confirmed that obesity induced by High-Fat Diet (HFD) enhances leukemogenesis by increasing penetrance and shortening latency, providing an ideal model to investigate obesity-induced molecular events in the preleukemic phase. Surprisingly, despite increasing DNA damage in hematopoietic stem cells (HSCs), HFD only minimally increased mutational load, with no relevant impact on known cancer-driving genes . HFD expanded and enhanced self-renewal of hematopoietic progenitor cells (HPC), with concomitant reduction in long-term HSCs. Importantly, Linoleic Acid, abundant in HFD, fully recapitulates the effect of HFD on the self-renewal of PML::RARA HPCs through activation of peroxisome proliferator-activated receptor delta (PPARδ), a central regulator of fatty acid metabolism. Our findings inform dietary/pharmacological interventions to counteract obesity-associated cancers and suggest that nongenetic factors play a key role.

DOI: https://doi.org/10.1158/1940-6207.CAPR-23-0246
Cancer Cell. 2023 Nov 08. pii: S1535-6108(23)00364-1. [Epub ahead of print]

A longitudinal single-cell atlas of treatment response in pediatric AML.

Sander Lambo, Diane L Trinh, Rhonda E Ries, Dan Jin, Audi Setiadi, Michelle Ng, Veronique G Leblanc, Michael R Loken, Lisa E Brodersen, Fangyan Dai, Laura M Pardo, Xiaotu Ma, Suzanne M Vercauteren, Soheil Meshinchi, Marco A Marra.

  Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. We used single-cell RNA sequencing and single-cell ATAC sequencing to profile 28 patients representing different pAML subtypes at diagnosis, remission and relapse. At diagnosis, cellular composition differed between genetic subgroups. Upon relapse, cellular hierarchies transitioned toward a more primitive state regardless of subtype. Primitive cells in the relapsed tumor were distinct compared to cells at diagnosis, with under-representation of myeloid transcriptional programs and over-representation of other lineage programs. In some patients, this was accompanied by the appearance of a B-lymphoid-like hierarchy. Our data thus reveal the emergence of apparent subtype-specific plasticity upon treatment and inform on potentially targetable processes.

Keywords:  acute myeloid leukemia; hematopoiesis; heterogeneity; leukemia; pediatric cancer; single-cell ATAC-seq; single-cell RNA-seq; therapy resistance; transcriptional regulation

DOI:  https://doi.org/10.1016/j.ccell.2023.10.008
Res Sq. 2023 Oct 30. pii: rs.3.rs-3487715. [Epub ahead of print]

Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia.

Kai Tan, Jason Xu, Changya Chen, Tiffaney Vincent, Petri Pölönen, Jianzhong Hu, Satoshi Yoshimura, Wenbao Yu, Jonathan Sussman, Chia-Hui Chen, Elizabeth Li, Caroline Diorio, Rawan Shraim, Haley Newman, Lahari Uppuluri, Alexander Li, Gregory Chen, Shovik Bandyopadhyay, David Wu, Yang-Yang Ding, Jessica Xu, Tristan Lim, Miles Hsu, Anusha Thadi, Kyung Jin Ahn, Chi-Yun Wu, Jacqueline Peng, Yusha Sun, Alice Wang, Rushabh Mehta, David Frank, Lauren Meyer, Mignon Loh, Elizabeth Raetz, Zhiguo Chen, Brent Wood, Meenakshi Devidas, Kimberly Dunsmore, Stuart Winter, Ti-Cheng Chang, Gang Wu, Stanley Pounds, Nancy Zhang, William Carroll, Stephen Hunger, Kathrin Bernt, Jun Yang, Charles Mullighan, David Teachey.

Refractoriness to initial chemotherapy and relapse after remission are the main obstacles to cure in T-cell Acute Lymphoblastic Leukemia (T-ALL). Biomarker guided risk stratification and targeted therapy have the potential to improve outcomes in high-risk T-ALL; however, cellular and genetic factors contributing to treatment resistance remain unknown. Previous bulk genomic studies in T-ALL have implicated tumor heterogeneity as an unexplored mechanism for treatment failure. To link tumor subpopulations with clinical outcome, we created an atlas of healthy pediatric hematopoiesis and applied single-cell multiomic (CITE-seq/snATAC-seq) analysis to a cohort of 40 cases of T-ALL treated on the Children's Oncology Group AALL0434 clinical trial. The cohort was carefully selected to capture the immunophenotypic diversity of T-ALL, with early T-cell precursor (ETP) and Near/Non-ETP subtypes represented, as well as enriched with both relapsed and treatment refractory cases. Integrated analyses of T-ALL blasts and normal T-cell precursors identified a bone-marrow progenitor-like (BMP-like) leukemia sub-population associated with treatment failure and poor overall survival. The single-cell-derived molecular signature of BMP-like blasts predicted poor outcome across multiple subtypes of T-ALL within two independent patient cohorts using bulk RNA-sequencing data from over 1300 patients. We defined the mutational landscape of BMP-like T-ALL, finding that NOTCH1 mutations additively drive T-ALL blasts away from the BMP-like state. We transcriptionally matched BMP-like blasts to early thymic seeding progenitors that have low NR3C1 expression and high stem cell gene expression, corresponding to a corticosteroid and conventional cytotoxic resistant phenotype we observed in ex vivo drug screening. To identify novel targets for BMP-like blasts, we performed in silico and in vitro drug screening against the BMP-like signature and prioritized BMP-like overexpressed cell-surface (CD44, ITGA4, LGALS1) and intracellular proteins (BCL-2, MCL-1, BTK, NF-κB) as candidates for precision targeted therapy. We established patient derived xenograft models of BMP-high and BMP-low leukemias, which revealed vulnerability of BMP-like blasts to apoptosis-inducing agents, TEC-kinase inhibitors, and proteasome inhibitors. Our study establishes the first multi-omic signatures for rapid risk-stratification and targeted treatment of high-risk T-ALL.

DOI: https://doi.org/10.21203/rs.3.rs-3487715/v1
Eur Heart J. 2023 Nov 11. pii: ehad670. [Epub ahead of print]

Clonal haematopoiesis of indeterminate potential predicts incident cardiac arrhythmias.

Art Schuermans, Caitlyn Vlasschaert, Victor Nauffal, So Mi Jemma Cho, Md Mesbah Uddin, Tetsushi Nakao, Abhishek Niroula, Marcus D R Klarqvist, Lachelle D Weeks, Amy E Lin, Seyedmohammad Saadatagah, Kim Lannery, Megan Wong, Whitney Hornsby, Steven A Lubitz, Christie Ballantyne, Siddhartha Jaiswal, Peter Libby, Benjamin L Ebert, Alexander G Bick, Patrick T Ellinor, Pradeep Natarajan, Michael C Honigberg.

  BACKGROUND AND AIMS: Clonal haematopoiesis of indeterminate potential (CHIP), the age-related expansion of blood cells with preleukemic mutations, is associated with atherosclerotic cardiovascular disease and heart failure. This study aimed to test the association of CHIP with new-onset arrhythmias.METHODS: UK Biobank participants without prevalent arrhythmias were included. Co-primary study outcomes were supraventricular arrhythmias, bradyarrhythmias, and ventricular arrhythmias. Secondary outcomes were cardiac arrest, atrial fibrillation, and any arrhythmia. Associations of any CHIP [variant allele fraction (VAF) ≥ 2%], large CHIP (VAF ≥10%), and gene-specific CHIP subtypes with incident arrhythmias were evaluated using multivariable-adjusted Cox regression. Associations of CHIP with myocardial interstitial fibrosis [T1 measured using cardiac magnetic resonance (CMR)] were also tested.
RESULTS: This study included 410 702 participants [CHIP: n = 13 892 (3.4%); large CHIP: n = 9191 (2.2%)]. Any and large CHIP were associated with multi-variable-adjusted hazard ratios of 1.11 [95% confidence interval (CI) 1.04-1.18; P = .001] and 1.13 (95% CI 1.05-1.22; P = .001) for supraventricular arrhythmias, 1.09 (95% CI 1.01-1.19; P = .031) and 1.13 (95% CI 1.03-1.25; P = .011) for bradyarrhythmias, and 1.16 (95% CI, 1.00-1.34; P = .049) and 1.22 (95% CI 1.03-1.45; P = .021) for ventricular arrhythmias, respectively. Associations were independent of coronary artery disease and heart failure. Associations were also heterogeneous across arrhythmia subtypes and strongest for cardiac arrest. Gene-specific analyses revealed an increased risk of arrhythmias across driver genes other than DNMT3A. Large CHIP was associated with 1.31-fold odds (95% CI 1.07-1.59; P = .009) of being in the top quintile of myocardial fibrosis by CMR.
CONCLUSIONS: CHIP may represent a novel risk factor for incident arrhythmias, indicating a potential target for modulation towards arrhythmia prevention and treatment.

Keywords:  Aging; Arrhythmia; Atrial fibrillation; Cardiac arrest; Genomics; Prevention

DOI:  https://doi.org/10.1093/eurheartj/ehad670
Blood Adv. 2023 Nov 13. pii: bloodadvances.2023012110. [Epub ahead of print]

JAK2V617F and ischemic stroke: CHIP or CMD-NBV?

Giovanni Barosi, Vittorio Rosti, Robert Peter Gale.

DOI: https://doi.org/10.1182/bloodadvances.2023012110
Nat Commun. 2023 Nov 13. 14(1): 7332

A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics.

Hyeong-Min Lee, William C Wright, Min Pan, Jonathan Low, Duane Currier, Jie Fang, Shivendra Singh, Stephanie Nance, Ian Delahunty, Yuna Kim, Richard H Chapple, Yinwen Zhang, Xueying Liu, Jacob A Steele, Jun Qi, Shondra M Pruett-Miller, John Easton, Taosheng Chen, Jun Yang, Adam D Durbin, Paul Geeleher.

Combination chemotherapy is crucial for successfully treating cancer. However, the enormous number of possible drug combinations means discovering safe and effective combinations remains a significant challenge. To improve this process, we conduct large-scale targeted CRISPR knockout screens in drug-treated cells, creating a genetic map of druggable genes that sensitize cells to commonly used chemotherapeutics. We prioritize neuroblastoma, the most common extracranial pediatric solid tumor, where ~50% of high-risk patients do not survive. Our screen examines all druggable gene knockouts in 18 cell lines (10 neuroblastoma, 8 others) treated with 8 widely used drugs, resulting in 94,320 unique combination-cell line perturbations, which is comparable to the largest existing drug combination screens. Using dense drug-drug rescreening, we find that the top CRISPR-nominated drug combinations are more synergistic than standard-of-care combinations, suggesting existing combinations could be improved. As proof of principle, we discover that inhibition of PRKDC, a component of the non-homologous end-joining pathway, sensitizes high-risk neuroblastoma cells to the standard-of-care drug doxorubicin in vitro and in vivo using patient-derived xenograft (PDX) models. Our findings provide a valuable resource and demonstrate the feasibility of using targeted CRISPR knockout to discover combinations with common chemotherapeutics, a methodology with application across all cancers.

DOI: https://doi.org/10.1038/s41467-023-43134-0
Blood. 2023 Nov 16. 142(20): 1674-1676

Sphingolipids and HSC fitness: enigma no more.

Stephanie Z Xie.

DOI: https://doi.org/10.1182/blood.2023022497
bioRxiv. 2023 Oct 26. pii: 2023.10.23.563619. [Epub ahead of print]

Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms.

Sarah Kelliher, Sara Gamba, Luisa Weiss, Zhu Shen, Marina Marchetti, Francesca Schieppati, Caitriona Scaife, Stephen Madden, Kathleen Bennett, Anne Fortune, Su Maung, Michael Fay, Fionnuala Ní Áinle, Patricia Maguire, Anna Falanga, Barry Kevane, Anandi Krishnan.

Patients with chronic Myeloproliferative Neoplasms (MPN) including polycythemia vera (PV) and essential thrombocythemia (ET) exhibit unique clinical features, such as a tendency toward thrombosis and hemorrhage, and risk of disease progression to secondary bone marrow fibrosis and/or acute leukemia. Although an increase in blood cell lineage counts (quantitative features) contribute to these morbid sequelae, the significant qualitative abnormalities of myeloid cells that contribute to vascular risk are not well understood. Here, we address this critical knowledge gap via a comprehensive and untargeted profiling of the platelet proteome in a large (n= 140) cohort of patients (from two independent sites) with an established diagnosis of PV and ET (and complement prior work on the MPN platelet transcriptome from a third site). We discover distinct MPN platelet protein expression and confirm key molecular impairments associated with proteostasis and thrombosis mechanisms of potential relevance to MPN pathology. Specifically, we validate expression of high-priority candidate markers from the platelet transcriptome at the platelet proteome ( e.g., calreticulin (CALR), Fc gamma receptor (FcγRIIA ) and galectin-1 (LGALS1 ) pointing to their likely significance in the proinflammatory, prothrombotic and profibrotic phenotypes in patients with MPN. Together, our proteo-transcriptomic study identifies the peripherally-derived platelet molecular profile as a potential window into MPN pathophysiology and demonstrates the value of integrative multi-omic approaches in gaining a better understanding of the complex molecular dynamics of disease.Highlights: MPN patient platelet proteome identifies key pathobiological mediators of thrombosis and proteostasis. The MPN platelet proteomic profile validates our prior findings from the platelet transcriptome.

DOI: https://doi.org/10.1101/2023.10.23.563619
bioRxiv. 2023 Oct 29. pii: 2023.10.28.564559. [Epub ahead of print]

Haematopoietic stem cell numbers are not solely determined by niche availability.

Shoichiro Takeishi, Tony Marchand, Wade R Koba, Daniel K Borger, Chunliang Xu, Chandan Guha, Aviv Bergman, Paul S Frenette, Kira Gritsman, Ulrich Steidl.

Haematopoietic stem cells (HSCs) reside in specialized microenvironments, also referred to as niches, and it has been widely believed that HSC numbers are determined by the niche size alone 1-5 . However, the vast excess of the number of niche cells over that of HSCs raises questions about this model. We initially established a mathematical model of niche availability and occupancy, which predicted that HSC numbers are restricted at both systemic and local levels. To address this question experimentally, we developed a femoral bone transplantation system, enabling us to increase the number of available HSC niches. We found that the addition of niches does not alter total HSC numbers in the body, regardless of whether the endogenous (host) niche is intact or defective, suggesting that HSC numbers are limited at the systemic level. Additionally, HSC numbers in transplanted wild-type femurs did not increase beyond physiological levels when HSCs were mobilized from defective endogenous niches to the periphery, indicating that HSC numbers are also constrained at the local level. Our study demonstrates that HSC numbers are not solely determined by niche availability, thereby rewriting the long-standing model for the regulation of HSC numbers.

DOI: https://doi.org/10.1101/2023.10.28.564559