bims-tremyl 2024-06-09 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2024–06–09
38 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

BRD4 degraders may effectively counteract therapeutic resistance of leukemic stem cells in AML and ALL.
Clinical impact of mutated JAK2 allele burden reduction in polycythemia vera and essential thrombocythemia.
Missense mutations in Myc Box I influence nucleocytoplasmic transport to promote leukemogenesis.
Association between class III obesity and overall survival in previously untreated younger patients with acute myeloid leukemia enrolled on SWOG S1203.
Dose-dependent effects of Dnmt3a in an inducible murine model of KrasG12D-driven leukemia.
Impact of Cancer Therapy on Clonal Hematopoiesis Mutations and Subsequent Clinical Outcomes.
Iadademstat in combination with azacitidine in patients with newly diagnosed acute myeloid leukaemia (ALICE): an open-label, phase 2a dose-finding study.
Oral Decitabine/Cedazuridine Is an Effective Ambulatory Therapy for Patients With Myelofibrosis Refractory to JAK2 Inhibitor Therapy.
Reverse Phase Proteomic Array Profiling of Asparagine Synthetase Expression in Newly Diagnosed Acute Myeloid Leukemia.
Targeting anemia in myeloid neoplasms.
Early blast clearance during sequential conditioning prior to allogeneic stem cell transplantation in patients with acute myeloid leukaemia.
Safety and efficacy of fedratinib in patients with myelofibrosis previously treated with ruxolitinib: primary analysis of FREEDOM trial.
Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML.
Incidence and clinical correlates of NFE2 mutations in myeloid neoplasms.
Clonal hematopoiesis driven by mutated DNMT3A promotes inflammatory bone loss.
Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate.
Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis.
Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts.
Single-cell transcriptomics reveal synergistic and antagonistic effects of T21 and GATA1s on hematopoiesis.
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.
Myeloid Targeted Human MLL-ENL and MLL-AF9 Induces cdk9 and bcl2 Expression in Zebrafish Embryos.
How I Treat Low-risk Polycythemia Vera Patients who Require Cytoreduction.
A CD36-dependent non-canonical lipid metabolism program promotes immune escape and resistance to hypomethylating agent therapy in AML.
Immunotherapeutic targeting of surfaceome heterogeneity in AML.
MYCT1 controls environmental sensing in human haematopoietic stem cells.
Clonal evolution of hematopoietic stem cells after cancer chemotherapy.
CHIPing away at immunity: the role of clonal hematopoiesis of indeterminate potential in bacterial pneumonia.
DNA demethylating agents for chemoprevention of oncovirus-associated leukemogenesis.
Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers.
The ribotoxic stress response drives UV-mediated cell death.
Implementation of and Systems-Level Barriers to Guideline-Driven Germline Genetic Evaluation in the Care of Patients With Myelodysplastic Syndrome and Acute Myeloid Leukemia.
Silencing of the DNA damage repair regulator PPP1R15A sensitizes acute myeloid leukemia cells to chemotherapy.
CRISPR/Cas9-mediated gene disruption determines the roles of MITF and CITED2 in human mast cell differentiation.
RNA binding protein Lin28B promotes chronic myeloid leukemia blast crisis by transcriptionally upregulating miR-181d.
Clonal hematopoiesis of indeterminate potential as a prognostic factor: A systematic review and meta-analysis.
Asciminib is a novel inhibitor of ABL1 and ABL2 gene fusions in ALL but requires the ABL SH3 domain for efficacy.
IκBα controls dormancy in hematopoietic stem cells via retinoic acid during embryonic development.
A disease-associated gene desert directs macrophage inflammation through ETS2.

Am J Hematol. 2024 Jun 01.

BRD4 degraders may effectively counteract therapeutic resistance of leukemic stem cells in AML and ALL.

Karin Bauer, Alexander Hauswirth, Karoline V Gleixner, Georg Greiner, Johannes Thaler, Peter Bettelheim, Yüksel Filik, Elisabeth Koller, Gregor Hoermann, Philipp B Staber, Wolfgang R Sperr, Felix Keil, Peter Valent.

Acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) are life-threatening hematopoietic malignancies characterized by clonal expansion of leukemic blasts in the bone marrow and peripheral blood. The epigenetic reader BRD4 and its downstream effector MYC have recently been identified as potential drug targets in human AML and ALL. We compared anti-leukemic efficacies of the small-molecule BET inhibitor JQ1 and the recently developed BRD4 degraders dBET1 and dBET6 in AML and ALL cells. JQ1, dBET1, and dBET6 were found to suppress growth and viability in all AML and ALL cell lines examined as well as in primary patient-derived AML and ALL cells, including CD34+/CD38- and CD34+/CD38+ leukemic stem and progenitor cells, independent of the type (variant) of leukemia or molecular driver expressed in leukemic cells. Moreover, we found that dBET6 overcomes osteoblast-induced drug resistance in AML and ALL cells, regardless of the type of leukemia or the drug applied. Most promising cooperative or even synergistic drug combination effects were seen with dBET6 and the FLT3 ITD blocker gilteritinib in FLT3 ITD-mutated AML cells, and with dBET6 and the multi-kinase blocker ponatinib in BCR::ABL1+ ALL cells. Finally, all BRD4-targeting drugs suppressed interferon-gamma- and tumor necrosis factor-alpha-induced expression of the resistance-related checkpoint antigen PD-L1 in AML and ALL cells, including LSC. In all assays examined, the BRD4 degrader dBET6 was a superior anti-leukemic drug compared with dBET1 and JQ1. Together, BRD4 degraders may provide enhanced inhibition of multiple mechanisms of therapy resistance in AML and ALL.

DOI: https://doi.org/10.1002/ajh.27385
Am J Hematol. 2024 Jun 06.

Clinical impact of mutated JAK2 allele burden reduction in polycythemia vera and essential thrombocythemia.

Paola Guglielmelli, Barbara Mora, Francesca Gesullo, Francesco Mannelli, Giuseppe Gaetano Loscocco, Leonardo Signori, Chiara Pessina, Ilaria Colugnat, Raffaela Aquila, Manjola Balliu, Chiara Maccari, Simone Romagnoli, Chiara Paoli, Elena Nacca, Lorenzo Fagiolo, Margherita Maffioli, Tiziano Barbui, Francesco Passamonti, Alessandro M Vannucchi.

DOI: https://doi.org/10.1002/ajh.27400
Clin Cancer Res. 2024 Jun 07.

Missense mutations in Myc Box I influence nucleocytoplasmic transport 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.

PURPOSE: Somatic missense mutations in the phosphodegron domain of the MYC gene (MYC Box I or MBI) 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.
EXPERIMENTAL DESIGN: To investigate the effects of MBI MYC mutations on hematopoietic cells, we employed a multi-omic approach to systematically compare the cellular and molecular consequences of expressing oncogenic doses of wild type, threonine-58 and proline-59 mutant MYC proteins in hematopoietic cells, and we developed a knockin mouse harboring the germline MBI mutation p.T58N in the Myc< gene.
RESULTS: Both wild type and MBI mutant MYC proteins promote self-renewal programs and expand highly selected subpopulations of progenitor cells in the bone marrow. Compared to their wild type counterparts, mutant cells display decreased cell death and accelerated leukemogenesis in vivo, changes that are recapitulated in the transcriptomes of human AML bearing MYC mutations. The mutant phenotypes feature decreased stability and translation of mRNAs encoding proapoptotic and immune-regulatory genes, increased translation of RNA binding proteins and nuclear export machinery, and distinct nucleocytoplasmic RNAs profiles. MBI MYC mutant proteins also show a higher propensity to aggregate in perinuclear regions and the cytoplasm. Like the overexpression model, heterozygous p.T58N knockin mice displayed similar changes in subcellular MYC localization, progenitor expansion, transcriptional signatures, and develop hematopoietic tumors.
CONCLUSIONS: This study uncovers that MBI MYC mutations alter RNA nucleocytoplasmic transport mechanisms to contribute to the development of hematopoietic malignancies.

DOI: https://doi.org/10.1158/1078-0432.CCR-24-0926
Leukemia. 2024 Jun 03.

Association between class III obesity and overall survival in previously untreated younger patients with acute myeloid leukemia enrolled on SWOG S1203.

Michelle Y Zhang, Megan Othus, Kerry McMillen, Harry P Erba, Guillermo Garcia-Manero, John M Pagel, Mohamed L Sorror, Mary-Elizabeth M Percival.

There has been ongoing debate on the association between obesity and outcomes in acute myeloid leukemia (AML). Currently few studies have stratified outcomes by class I obesity, class II obesity, and class III obesity, and a more nuanced understanding is becoming increasingly important with the rising prevalence of obesity. We examined the association between body mass index (BMI) and outcomes in previously untreated AML in younger patients (age ≤60) enrolled in SWOG S1203 (n = 729). Class III obesity was associated with an increased rate of early death (p = 0.004) and worse overall survival (OS) in multivariate analysis (hazard ratio (HR) 2.48, 95% confidence interval (CI) 1.62-3.80 versus normal weight). Class III obesity was also associated with worse OS after allogeneic hematopoietic cell transplant (HR 2.37, 95% CI 1.24-4.54 versus normal weight). These findings highlight the unique risk of class III obesity in AML, and the importance of further investigation to better characterize this patient population.

DOI: https://doi.org/10.1038/s41375-024-02288-6
Exp Hematol. 2024 Jun 02. pii: S0301-472X(24)00107-3. [Epub ahead of print] 104248

Dose-dependent effects of Dnmt3a in an inducible murine model of KrasG12D-driven leukemia.

Jason H Rogers, Allison Rosen, Jaime M Reyes, Shamika Ketkar, Shannon E Conneely, Rohit Gupta, Luibin Yang, Matthew B Miller, Geraldo Medrano, Rogelio Aguilar, Nneka Uchenda, Margaret A Goodell, Rachel E Rau.

  DNMT3A mutations are frequently found in clonal hematopoiesis and a variety of hematologic malignancies including acute myeloid leukemia (AML). An assortment of mouse models have been engineered to explore the tumorigenic potential and malignant lineage bias due to loss of function of DNMT3A in consort with commonly co-mutated genes in myeloid malignancies such as Flt3, Nras, Kras, and c-Kit. We employed several tamoxifen-inducible Cre-ERT2 murine model systems to study the effects of constitutively active KrasG12D-driven myeloid leukemia (Kras) development together with heterozygous (3aHet) or homozygous Dnmt3a deletion (3aKO). Due to the rapid generation of diverse nonhematologic tumors appearing after tamoxifen induction, we employed a transplantation model. With pretransplant tamoxifen induction, most Kras mice died quickly of T-cell malignancies regardless of Dnmt3a status. Using post-transplant induction, we observed a dose-dependent effect of DNMT3A depletion that skewed the leukemic phenotype toward a myeloid lineage- 64% of 3aKO/Kras mice had exclusively myeloid disease compared with 36% of 3aHet/Kras, and only 13% of Kras mice. 3aKO combined with Kras led to increased disease burden, multi-organ infiltration, and faster disease progression. DOT1L inhibition exerted profound anti-leukemic effects in malignant 3aKO/Kras cells, but not malignant cells with Kras mutation alone, consistent with the known sensitivity of DNMT3A-mutant leukemia to DOT1L inhibition. RNAseq from malignant myeloid cells revealed that biallelic Dnmt3a deletion was associated with loss of cell cycle regulation, MYC activation, and TNF⍺ signaling. Overall, we have developed a robust model system for mechanistic and preclinical investigations of AML with DNMT3A and Ras pathway lesions.

Keywords:  Dnmt3a; Kras; hematologic malignancies; leukemia; murine transplant models

DOI:  https://doi.org/10.1016/j.exphem.2024.104248
Blood Adv. 2024 Jun 03. pii: bloodadvances.2024012929. [Epub ahead of print]

Impact of Cancer Therapy on Clonal Hematopoiesis Mutations and Subsequent Clinical Outcomes.

Kevin T Nead, Taebeom Kim, LiJin Joo, Tina McDowell, Justin Wong, Irenaeus Chi-Chung Chan, Elizabeth Brock, Jing Zhao, Ting Xu, Chad Tang, Chang-Lung Lee, Jun-Ichi Abe, Kelly L Bolton, Zhongxing Liao, Paul Scheet, Steven H Lin.

Exposure to cancer therapies is associated with an increased risk of clonal hematopoiesis (CH). The objective of our study was to investigate the genesis and evolution of CH following cancer therapy. In this prospective study, we undertook error-corrected duplex DNA sequencing in blood samples collected prior to and at two timepoints following chemoradiation in patients with esophageal or lung cancer recruited from 2013-2018. We applied a customized workflow to identify the earliest changes in CH mutation count and clone size and determine their association with clinical outcomes. Our study included 29 patients (87 samples). Their median age was 67 years, 76% (n = 22) were male; the median follow-up period was 3.9 years. The most mutated genes were DNMT3A, TET2, TP53, and ASXL1. We observed a two-fold increase in the number of mutations from before to after treatment in TP53, which differed from all other genes examined (P < .001). Among mutations detected before and after treatment, we observed an increased clone size in 38% and a decreased clone size in 5% of TP53 mutations (odds ratio = 3.7; 95% CI = 1.75-7.84; P < .001). Changes in mutation count and clone size were not observed in other genes. Individuals with an increase in the number of TP53 mutations following chemoradiation experienced shorter overall survival (hazard ratio = 7.07; 95% CI = 1.50-33.46; P = .014). In summary, we found an increase in the number and size of TP53 CH clones following chemoradiation that were associated with clinical outcomes.

DOI: https://doi.org/10.1182/bloodadvances.2024012929
Lancet Haematol. 2024 May 30. pii: S2352-3026(24)00132-7. [Epub ahead of print]

Iadademstat in combination with azacitidine in patients with newly diagnosed acute myeloid leukaemia (ALICE): an open-label, phase 2a dose-finding study.

Olga Salamero, Antonieta Molero, José Antonio Pérez-Simón, Montserrat Arnan, Rosa Coll, Sara Garcia-Avila, Evelyn Acuña-Cruz, Isabel Cano, Tim C P Somervaille, Sonia Gutierrez, María Isabel Arévalo, Jordi Xaus, Carlos Buesa, Ana Limón, Douglas V Faller, Francesc Bosch, Pau Montesinos.

BACKGROUND: Iadademstat is a potent, selective, oral inhibitor of both the enzymatic and scaffolding activities of the transcriptional repressor lysine-specific demethylase 1 (LSD1; also known as KDM1A) that showed promising early activity and safety in a phase 1 trial and strong preclinical synergy with azacitidine in acute myeloid leukaemia cell lines. Therefore, we aimed to investigate the combination of iadademstat and azacitidine for the treatment of adult patients with newly diagnosed acute myeloid leukaemia.
METHODS: The open-label, phase 2a, dose-finding ALICE study was conducted at six hospitals in Spain and enrolled patients aged 18 years or older with newly diagnosed acute myeloid leukaemia not eligible for intensive chemotherapy and an ECOG performance status of 0-2. In the dose escalation portion of the trial, patients received a starting dose of iadademstat at 90 μg/m2 per day (with de-escalation to 60 μg/m2 per day and escalation up to 140 μg/m2 per day) orally, for 5 days on, 2 days off weekly, with azacitidine 75 mg/m2 subcutaneously, for seven of 28 days. The primary objectives were safety (analysed in the safety analysis set; all patients who received at least one dose of study treatment) and establishing the recommended phase 2 dose; secondary objectives included response rates in the efficacy analysis set (all patients who had at least one efficacy assessment). This study is registered on EudraCT (EudraCT 2018-000482-36) and has been completed.
FINDINGS: Between Nov 12, 2018, and Sept 30, 2021, 36 patients with newly diagnosed acute myeloid leukaemia were enrolled; the median age was 76 (IQR 74-79) years, all patients were White, 18 (50%) were male, and 18 (50%) were female, and all had intermediate-risk or adverse-risk acute myeloid leukaemia. The median follow-up was 22 (IQR 16-31) months. The most frequent (≥10%) adverse events considered to be related to treatment were decreases in platelet (25 [69%]) and neutrophil (22 [61%]) counts (all grade 3-4) and anaemia (15 [42%]; of which ten [28%] were grade 3-4). Three patients had treatment-related serious adverse events (one fatal grade 5 intracranial haemorrhage, one grade 3 differentiation syndrome, and one grade 3 febrile neutropenia). Based on safety, pharmacokinetic and pharmacodynamic data, and efficacy, the recommended phase 2 dose of iadademstat was 90 μg/m2 per day with azacitidine. 22 (82%; 95% CI 62-94) of 27 patients in the efficacy analysis set had an objective response. 14 (52%) of 27 patients had complete remission or complete remission with incomplete haematological recovery; of these, ten of 11 evaluable for measurable residual disease achieved negativity. In the safety analysis set, 22 (61%) of 36 patients had an objective response.
INTERPRETATION: The combination of iadademstat and azacitidine has a manageable safety profile and shows promising responses in patients with newly diagnosed acute myeloid leukaemia, including those with high-risk prognostic factors.
FUNDING: Oryzon Genomics and Spain's Ministerio de Ciencia, Innovacion y Universidades (MICIU)-Agencia Estatal de Investigacion (AEI).

DOI: https://doi.org/10.1016/S2352-3026(24)00132-7
Clin Lymphoma Myeloma Leuk. 2024 May 14. pii: S2152-2650(24)00182-4. [Epub ahead of print]

Oral Decitabine/Cedazuridine Is an Effective Ambulatory Therapy for Patients With Myelofibrosis Refractory to JAK2 Inhibitor Therapy.

Shivani Handa, Ganesh Sivakumar, Andrew Srisuwananukorn, Amylou Dueck, Douglas Tremblay, John O Mascarenhas, Yelena Ginzburg, Marina Kremyanskaya, Ronald Hoffman.

   BACKGROUND: Outcomes are dismal for patients with myelofibrosis (MF) who are no longer responsive to JAK2 inhibitors (JAKi) and/or have increasing blast cell numbers. Although prior reports have suggested the benefits of intravenous decitabine (DAC) combined with ruxolitinib for patients with Myeloproliferative Neoplasm (MPN) accelerated/blast phase (AP/BP), decitabine-cedazuridine (DEC-C), an oral fixed-dose combination providing equivalent pharmacokinetic exposure, has not been evaluated in MF.
METHODS: We conducted a retrospective analysis of 14 patients with high-risk MF refractory to ruxolitinib or MPN-AP (10-19% blasts) treated with DEC-C +/- JAKi at Mount Sinai Hospital from 2021 to 2024.
RESULTS: The cohort was elderly (median age,76 years) and almost uniformly possessed high risk mutations with 13 of the 14 patients progressing on JAKi therapy. With a median follow-up of 9.4 months, the median overall survival (OS) was 29 months for the entire cohort. Median OS was 10.8 months for MPN-AP and was not reached for ruxolitinib refractory MF patients. All patients (n = 9) receiving > 4 cycles of DEC-C had clinical benefit exemplified by a reduction in blast cell numbers, spleen size, and lack of progression to MPN-BP (78%). Furthermore, 3/14 patients proceeded to allogeneic stem cell transplant. Myelosuppression was a common adverse event which was managed by reducing the number of days of administration of DEC-C from 5 to 3 per cycle.
CONCLUSIONS: This report demonstrates the feasibility, tolerability, and clinical benefit of an exclusively ambulatory regimen for high-risk, elderly patients with advanced MF which warrants further evaluation in a prospective clinical trial.

Keywords:  Chromatin-modifying agent; Hypomethylating agent; MPN-accelerated phase; Ruxolitinib-refractory; myeloproliferative neoplasms

DOI:  https://doi.org/10.1016/j.clml.2024.05.012
J Proteome Res. 2024 Jun 03.

Reverse Phase Proteomic Array Profiling of Asparagine Synthetase Expression in Newly Diagnosed Acute Myeloid Leukemia.

Nisha Narayanan, Jennifer Marvin-Peek, Mohamad K Abouelnaaj, Dhabya Majid, Bofei Wang, Brandon D Brown, Yihua Qiu, Steven M Kornblau, Hussein A Abbas.

  Asparaginase-based therapy is a cornerstone in acute lymphoblastic leukemia (ALL) treatment, capitalizing on the methylation status of the asparagine synthetase (ASNS) gene, which renders ALL cells reliant on extracellular asparagine. Contrastingly, ASNS expression in acute myeloid leukemia (AML) has not been thoroughly investigated, despite studies suggesting that AML with chromosome 7/7q deletions might have reduced ASNS levels. Here, we leverage reverse phase protein arrays to measure ASNS expression in 810 AML patients and assess its impact on outcomes. We find that AML with inv(16) has the lowest overall ASNS expression. While AML with deletion 7/7q had ASNS levels slightly lower than those of AML without deletion 7/7q, this observation was not significant. Low ASNS expression correlated with improved overall survival (46 versus 54 weeks, respectively, p = 0.011), whereas higher ASNS levels were associated with better response to venetoclax-based therapy. Protein correlation analysis demonstrated association between ASNS and proteins involved in methylation and DNA repair. In conclusion, while ASNS expression was not lower in patients with deletion 7/7q as initially predicted, ASNS levels were highly variable across AML patients. Further studies are needed to assess whether patients with low ASNS expression are susceptible to asparaginase-based therapy due to their inability to augment compensatory ASNS expression upon asparagine depletion.

Keywords:  acute myeloid leukemia (AML); asparagine synthetase (ASNS); chromosome 7/7q deletion; reverse phase proteomics array (RPPA); venetoclax

DOI:  https://doi.org/10.1021/acs.jproteome.4c00130
Am J Hematol. 2024 Jun 05.

Targeting anemia in myeloid neoplasms.

Naseema Gangat, Ayalew Tefferi.

Anemia-directed therapeutic approaches targeting the TGF-β-SMAD and HIF-PH pathways.

DOI: https://doi.org/10.1002/ajh.27408
Br J Haematol. 2024 Jun 04.

Early blast clearance during sequential conditioning prior to allogeneic stem cell transplantation in patients with acute myeloid leukaemia.

Julian Ronnacker, Marc-Andre Urbahn, Christian Reicherts, Lina Kolloch, Philipp Berning, Sarah Sandmann, Eva Eßeling, Simon Call, Matthias Floeth, Julia Marx, Jörn Albring, Jan-Henrik Mikesch, Christoph Schliemann, Georg Lenz, Matthias Stelljes.

  For patients with relapsed or refractory AML, sequential conditioning prior to allogeneic stem cell transplantation (alloSCT) is an established and potentially curative treatment option. Early response to treatment during conditioning indicates chemotherapy-responsive disease and may have prognostic value. We retrospectively evaluated blast clearance on day 5 after melphalan, administered 11 days prior to alloSCT as part of a sequential conditioning in 176 patients with active AML. Overall survival (OS) was 52% (95% confidence interval [CI] 45%-60%), and relapse-free survival (RFS) was 47% (95% CI 40%-55%) at 3 years. Patients who achieved early blast clearance did not show a significant improvement in OS and RFS (OS, hazard ratio [HR] HR 0.75, p 0.19; RFS, HR 0.71, p 0.09, respectively), but had a significantly lower non-relapse mortality rate (HR 0.46, p 0.017). HLA-mismatched donor, older age, adverse genetic risk and higher comorbidity scores were associated with inferior survival outcomes. A high initial blast count was only associated with inferior prognosis in patients receiving chemotherapy-only compared to total body irradiation containing conditioning therapy. These results indicate that for patients transplanted with active AML, sensitivity to chemotherapy might be of less importance, compared to other disease- and transplant-related factors.

Keywords:  acute myeloid leukaemia; allogeneic stem cell transplantation; melphalan

DOI:  https://doi.org/10.1111/bjh.19552
Leuk Lymphoma. 2024 Jun 05. 1-11

Safety and efficacy of fedratinib in patients with myelofibrosis previously treated with ruxolitinib: primary analysis of FREEDOM trial.

Vikas Gupta, Abdulraheem Yacoub, Ruben A Mesa, Claire N Harrison, Alessandro M Vannucchi, Jean-Jacques Kiladjian, Hans-Joachim Deeg, Salman Fazal, Lynda Foltz, Ryan J Mattison, Carole B Miller, Vinod Parameswaran, Patrick Brown, Christopher Hernandez, Jia Wang, Moshe Talpaz.

  The phase 3b FREEDOM trial (ClinicalTrials.gov: NCT03755518) evaluates efficacy/safety of fedratinib in intermediate- or high-risk myelofibrosis patients with platelet count ≥50 × 109/L, previously treated with ruxolitinib. The trial design included protocol specified strategies to mitigate the risk for gastrointestinal (GI) adverse events (AEs), thiamine supplementation, and encephalopathy surveillance. Due to COVID-19, accrual was cut short with 38 patients enrolled. In the efficacy evaluable population (n = 35), nine (25.7%; 95% confidence interval 12.5-43.3) patients achieved primary endpoint of ≥35% spleen volume reduction (SVR) at end of cycle (EOC) 6; and 22 (62.9%) patients showed best overall response of ≥35% SVR up to end of treatment. Sixteen (44.4%) patients showed ≥50% reduction in total symptom score at EOC6 (n = 36). Compared to previously reported JAKARTA-2 trial, rates of GI AEs were lower, and no patient developed encephalopathy. Overall, FREEDOM study showed clinically relevant spleen and symptom responses with fedratinib, and effective mitigation of GI AEs.

Keywords:  Fedratinib; adverse events; gastrointestinal mitigation strategies; myelofibrosis; myelofibrosis symptom assessment form (MSAF); spleen response

DOI:  https://doi.org/10.1080/10428194.2024.2346733
Nat Commun. 2024 Jun 04. 15(1): 4739

Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML.

Matteo Marchesini, Andrea Gherli, Elisa Simoncini, Lucas Moron Dalla Tor, Anna Montanaro, Natthakan Thongon, Federica Vento, Chiara Liverani, Elisa Cerretani, Anna D'Antuono, Luca Pagliaro, Raffaella Zamponi, Chiara Spadazzi, Elena Follini, Benedetta Cambò, Mariateresa Giaimo, Angela Falco, Gabriella Sammarelli, Giannalisa Todaro, Sabrina Bonomini, Valentina Adami, Silvano Piazza, Claudia Corbo, Bruno Lorusso, Federica Mezzasoma, Costanza Anna Maria Lagrasta, Maria Paola Martelli, Roberta La Starza, Antonio Cuneo, Franco Aversa, Cristina Mecucci, Federico Quaini, Simona Colla, Giovanni Roti.

The overexpression of the ecotropic viral integration site-1 gene (EVI1/MECOM) marks the most lethal acute myeloid leukemia (AML) subgroup carrying chromosome 3q26 abnormalities. By taking advantage of the intersectionality of high-throughput cell-based and gene expression screens selective and pan-histone deacetylase inhibitors (HDACis) emerge as potent repressors of EVI1. To understand the mechanism driving on-target anti-leukemia activity of this compound class, here we dissect the expression dynamics of the bone marrow leukemia cells of patients treated with HDACi and reconstitute the EVI1 chromatin-associated co-transcriptional complex merging on the role of proliferation-associated 2G4 (PA2G4) protein. PA2G4 overexpression rescues AML cells from the inhibitory effects of HDACis, while genetic and small molecule inhibition of PA2G4 abrogates EVI1 in 3q26 AML cells, including in patient-derived leukemia xenografts. This study positions PA2G4 at the crosstalk of the EVI1 leukemogenic signal for developing new therapeutics and urges the use of HDACis-based combination therapies in patients with 3q26 AML.

DOI: https://doi.org/10.1038/s41467-024-48953-3
Br J Haematol. 2024 Jun 06.

Incidence and clinical correlates of NFE2 mutations in myeloid neoplasms.

Iván Martín Castillo, Eva Villamón, Marisa Calabuig, Irene Pastor, Blanca Ferrer-Lores, Paula Amat, Eva Mas, Inma Castillo, Sara Blanco, Carlos Solano, Juan Carlos Hernández-Boluda, Mar Tormo.

DOI: https://doi.org/10.1111/bjh.19579
Cell. 2024 May 30. pii: S0092-8674(24)00492-6. [Epub ahead of print]

Clonal hematopoiesis driven by mutated DNMT3A promotes inflammatory bone loss.

Hui Wang, Kimon Divaris, Bohu Pan, Xiaofei Li, Jong-Hyung Lim, Gundappa Saha, Marko Barovic, Danai Giannakou, Jonathan M Korostoff, Yu Bing, Souvik Sen, Kevin Moss, Di Wu, James D Beck, Christie M Ballantyne, Pradeep Natarajan, Kari E North, Mihai G Netea, Triantafyllos Chavakis, George Hajishengallis.

  Clonal hematopoiesis of indeterminate potential (CHIP) arises from aging-associated acquired mutations in hematopoietic progenitors, which display clonal expansion and produce phenotypically altered leukocytes. We associated CHIP-DNMT3A mutations with a higher prevalence of periodontitis and gingival inflammation among 4,946 community-dwelling adults. To model DNMT3A-driven CHIP, we used mice with the heterozygous loss-of-function mutation R878H, equivalent to the human hotspot mutation R882H. Partial transplantation with Dnmt3aR878H/+ bone marrow (BM) cells resulted in clonal expansion of mutant cells into both myeloid and lymphoid lineages and an elevated abundance of osteoclast precursors in the BM and osteoclastogenic macrophages in the periphery. DNMT3A-driven clonal hematopoiesis in recipient mice promoted naturally occurring periodontitis and aggravated experimentally induced periodontitis and arthritis, associated with enhanced osteoclastogenesis, IL-17-dependent inflammation and neutrophil responses, and impaired regulatory T cell immunosuppressive activity. DNMT3A-driven clonal hematopoiesis and, subsequently, periodontitis were suppressed by rapamycin treatment. DNMT3A-driven CHIP represents a treatable state of maladaptive hematopoiesis promoting inflammatory bone loss.

Keywords:  DNMT3A; T cells; arthritis; bone marrow; clonal hematopoiesis of indeterminate potential; hematopoietic stem and progenitor cells; inflammation; neutrophils; osteoclastogenesis; periodontitis

DOI:  https://doi.org/10.1016/j.cell.2024.05.003
Nat Aging. 2024 Jun 04.

Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate.

Taralynn M Mack, Michael A Raddatz, Yash Pershad, Daniel C Nachun, Kent D Taylor, Xiuqing Guo, Alan R Shuldiner, Jeffrey R O'Connell, Eimear E Kenny, Ruth J F Loos, Susan Redline, Brian E Cade, Bruce M Psaty, Joshua C Bis, Jennifer A Brody, Edwin K Silverman, Jeong H Yun, Michael H Cho, Dawn L DeMeo, Daniel Levy, Andrew D Johnson, Rasika A Mathias, Lisa R Yanek, Susan R Heckbert, Nicholas L Smith, Kerri L Wiggins, Laura M Raffield, April P Carson, Jerome I Rotter, Stephen S Rich, Ani W Manichaikul, C Charles Gu, Yii-Der Ida Chen, Wen-Jane Lee, M Benjamin Shoemaker, Dan M Roden, Charles Kooperberg, Paul L Auer, Pinkal Desai, Thomas W Blackwell, Albert V Smith, Alexander P Reiner, Siddhartha Jaiswal, Joshua S Weinstock, Alexander G Bick.

Clonal hematopoiesis of indeterminate potential (CHIP), whereby somatic mutations in hematopoietic stem cells confer a selective advantage and drive clonal expansion, not only correlates with age but also confers increased risk of morbidity and mortality. Here, we leverage genetically predicted traits to identify factors that determine CHIP clonal expansion rate. We used the passenger-approximated clonal expansion rate method to quantify the clonal expansion rate for 4,370 individuals in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) cohort and calculated polygenic risk scores for DNA methylation aging, inflammation-related measures and circulating protein levels. Clonal expansion rate was significantly associated with both genetically predicted and measured epigenetic clocks. No associations were identified with inflammation-related lab values or diseases and CHIP expansion rate overall. A proteome-wide search identified predicted circulating levels of myeloid zinc finger 1 and anti-Müllerian hormone as associated with an increased CHIP clonal expansion rate and tissue inhibitor of metalloproteinase 1 and glycine N-methyltransferase as associated with decreased CHIP clonal expansion rate. Together, our findings identify epigenetic and proteomic patterns associated with the rate of hematopoietic clonal expansion.

DOI: https://doi.org/10.1038/s43587-024-00647-7
Exp Hematol. 2024 Jun 05. pii: S0301-472X(24)00106-1. [Epub ahead of print] 104247

Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis.

Rahul Chaudhary, Julianne N P Smith, Riya Tiwari, Bailey R Klein, Brittany A Cordova, Frederick Petroze, Brian Richardson, Alyssia V Broncano, Juyeun Lee, Prerana Bangalore Parthasarathy, Karina Inacio Ladislau De Carvalho, Scott J Cameron, Justin D Lathia, Wendy A Goodman, Mark J Cameron, Amar B Desai.

  Hematopoietic stem cells (HSCs) adapt to organismal blood production needs by balancing self-renewal and differentiation, adjusting to physiological demands and external stimuli. While sex differences have been implicated in differential hematopoietic function in males vs. females, the mediators responsible for these effects require further study. Here, we characterize hematopoiesis at steady state and during regeneration following hematopoietic stem cell transplantation (HST). RNA sequencing of lineage(-) bone marrow cells from C57/Bl6 mice revealed a broad transcriptional similarity between the sexes. However, we identified distinct sex differences in key biological pathways, with female cells showing reduced expression of signatures involved in inflammation and an enrichment of genes related to glycolysis, hypoxia, and cell cycle regulation, suggesting a more quiescent and less inflammatory profile compared to male cells. To determine the functional impacts of the observed transcriptomic differences, we performed sex-matched and mismatched transplantation studies of lineage(-) donor cells. During short-term 56-day HST recovery we found a male donor cell proliferative advantage, coinciding with elevated serum TNF-α, and a male recipient engraftment advantage, coinciding with increased serum CXCL12. Together, we show that sex-specific cell responses, marked by differing expression of pathways regulating metabolism, hypoxia, and inflammation, shapes normal and regenerative hematopoiesis, with implications for the clinical understanding of hematopoietic function.

Keywords:  hematopoiesis; hematopoietic stem cell transplantation; inflammation; sex differences; stem cells

DOI:  https://doi.org/10.1016/j.exphem.2024.104247
bioRxiv. 2024 May 23. pii: 2024.05.22.595241. [Epub ahead of print]

Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts.

Dennis J Yuan, John Zinno, Theo Botella, Dalia Dhingra, Shu Wang, Allegra Hawkins, Ariel Swett, Jesus Sotelo, Ramya Raviram, Clayton Hughes, Catherine Potenski, Akira Yokoyama, Nobuyuki Kakiuchi, Seishi Ogawa, Dan A Landau.

Somatic mosaicism is a hallmark of malignancy that is also pervasively observed in human physiological aging, with clonal expansions of cells harboring mutations in recurrently mutated driver genes. Bulk sequencing of tissue microdissection captures mutation frequencies, but cannot distinguish which mutations co-occur in the same clones to reconstruct clonal architectures, nor phenotypically profile clonal populations to delineate how driver mutations impact cellular behavior. To address these challenges, we developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure and observed a clonal landscape dominated by a large number of clones with a single driver event, but only rare clones with two driver mutations. NOTCH1 mutants dominate the clonal landscape and are linked to stunted epithelial differentiation, while TP53 mutants and double-driver mutants promote clonal expansion through both differentiation biases and increased cell cycling. Thus, joint single-cell highly multiplexed capture of somatic mutations and mRNA transcripts enables high resolution reconstruction of clonal architecture and associated phenotypes in solid tissue somatic mosaicism.

DOI: https://doi.org/10.1101/2024.05.22.595241
bioRxiv. 2024 May 25. pii: 2024.05.24.595827. [Epub ahead of print]

Single-cell transcriptomics reveal synergistic and antagonistic effects of T21 and GATA1s on hematopoiesis.

Kaoru Takasaki, Eric K Wafula, Sara S Kumar, David Smith, Alyssa L Gagne, Deborah L French, Christopher S Thom, Stella T Chou.

Trisomy 21 (T21), or Down syndrome (DS), is associated with baseline macrocytic erythrocytosis, thrombocytopenia, and neutrophilia, and transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). TAM and ML-DS blasts both arise from an aberrant megakaryocyte-erythroid progenitor and exclusively express GATA1s, the truncated isoform of GATA1 , while germline GATA1s mutations in a non-T21 context lead to congenital cytopenias without a leukemic predisposition. This suggests that T21 and GATA1s perturb hematopoiesis independently and synergistically, but this interaction has been challenging to study in part due to limited human cell and murine models. To dissect the developmental impacts of GATA1s on hematopoiesis in euploid and T21 cells, we performed a single-cell RNA-sequencing timecourse on hematopoietic progenitors (HPCs) derived from isogenic human induced pluripotent stem cells differing only by chromosome 21 and/or GATA1 status. These HPCs were surprisingly heterogeneous and displayed spontaneous lineage skew apparently dictated by T21 and/or GATA1s. In euploid cells, GATA1s nearly eliminated erythropoiesis, impaired MK maturation, and promoted an immature myelopoiesis, while in T21 cells, GATA1s appeared to compete with the enhanced erythropoiesis and suppressed megakaryopoiesis driven by T21 to give rise to immature erythrocytes, MKs, and myeloid cells. T21 and GATA1s both disrupted temporal regulation of lineage-specific transcriptional programs and specifically perturbed cell cycle genes. These findings in an isogenic system can thus be attributed specifically to T21 and GATA1s and suggest that these genetic changes together enhance HPC proliferation at the expense of maturation, consistent with a pro-leukemic phenotype.

DOI: https://doi.org/10.1101/2024.05.24.595827
Dev Cell. 2024 May 30. pii: S1534-5807(24)00327-7. [Epub ahead of print]

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

Brian T Do, Peggy P Hsu, Sidney Y Vermeulen, Zhishan Wang, Taghreed Hirz, Keene L Abbott, Najihah Aziz, Joseph M Replogle, Stefan Bjelosevic, Jonathan Paolino, Samantha A Nelson, Samuel Block, Alicia M Darnell, Raphael Ferreira, Hanyu Zhang, Jelena Milosevic, Daniel R Schmidt, Christopher Chidley, Isaac S Harris, Jonathan S Weissman, Yana Pikman, Kimberly Stegmaier, Sihem Cheloufi, Xiaofeng A Su, David B Sykes, Matthew G Vander Heiden.

  Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.

Keywords:  cancer; cell fate; cell state; dependencies; differentiation; epigenetics; hematopoiesis; metabolism; nucleotides; replication; replication stress

DOI:  https://doi.org/10.1016/j.devcel.2024.05.010
PLoS Genet. 2024 Jun 03. 20(6): e1011308

Myeloid Targeted Human MLL-ENL and MLL-AF9 Induces cdk9 and bcl2 Expression in Zebrafish Embryos.

Alex J Belt, Steven Grant, Robert M Tombes, Sarah C Rothschild.

Acute myeloid leukemia (AML) accounts for greater than twenty thousand new cases of leukemia annually in the United States. The average five-year survival rate is approximately 30%, pointing to the need for developing novel model systems for drug discovery. In particular, patients with chromosomal rearrangements in the mixed lineage leukemia (MLL) gene have higher relapse rates with poor outcomes. In this study we investigated the expression of human MLL-ENL and MLL-AF9 in the myeloid lineage of zebrafish embryos. We observed an expansion of MLL positive cells and determined these cells colocalized with the myeloid markers spi1b, mpx, and mpeg. In addition, expression of MLL-ENL and MLL-AF9 induced the expression of endogenous bcl2 and cdk9, genes that are often dysregulated in MLL-r-AML. Co-treatment of lyz: MLL-ENL or lyz:MLL-AF9 expressing embryos with the BCL2 inhibitor, Venetoclax, and the CDK9 inhibitor, Flavopiridol, significantly reduced the number of MLL positive cells compared to embryos treated with vehicle or either drug alone. In addition, cotreatment with Venetoclax and Flavopiridol significantly reduced the expression of endogenous mcl1a compared to vehicle, consist with AML. This new model of MLL-r-AML provides a novel tool to understand the molecular mechanisms underlying disease progression and a platform for drug discovery.

DOI: https://doi.org/10.1371/journal.pgen.1011308
Blood. 2024 Jun 07. pii: blood.2023022418. [Epub ahead of print]

How I Treat Low-risk Polycythemia Vera Patients who Require Cytoreduction.

Mary Frances McMullin, Claire N Harrison.

Polycythemia vera (PV) was first described by Vaquez in 1892. This is a chronic hematological malignancy which affects both older and young patients. Perhaps due to lack of a curative treatment and the perceived toxicities of prior therapies our focus in the past was to intensify treatment only for patients at higher risk of thrombosis. Recent triggers to challenge this approach include: a recognition that low-risk PV is not "no-risk", our ability to better recognize patients who would benefit from more intensive therapy from the perspective of thrombosis, and data showing that some treatments may reduce risk of transformation to myelofibrosis. Furthermore, there is emergent evidence that molecular monitoring may identify an improvement in disease state translating to improved overall survival. Here we describe clinical situations that would trigger the use of cytoreductive treatment for low-risk PV patients as well as our approach to choosing a specific cytoreductive agent and how to effectively monitor treatment.

DOI: https://doi.org/10.1182/blood.2023022418
Cell Rep Med. 2024 May 29. pii: S2666-3791(24)00284-2. [Epub ahead of print] 101592

A CD36-dependent non-canonical lipid metabolism program promotes immune escape and resistance to hypomethylating agent therapy in AML.

He-Zhou Guo, Rui-Xue Feng, Yan-Jie Zhang, Ye-Hua Yu, Wei Lu, Jia-Jia Liu, Shao-Xin Yang, Chong Zhao, Zhao-Li Zhang, Shan-He Yu, Hui Jin, Si-Xuan Qian, Jian-Yong Li, Jiang Zhu, Jun Shi.

Environmental lipids are essential for fueling tumor energetics, but whether these exogenous lipids transported into cancer cells facilitate immune escape remains unclear. Here, we find that CD36, a transporter for exogenous lipids, promotes acute myeloid leukemia (AML) immune evasion. We show that, separately from its established role in lipid oxidation, CD36 on AML cells senses oxidized low-density lipoprotein (OxLDL) to prime the TLR4-LYN-MYD88-nuclear factor κB (NF-κB) pathway, and exogenous palmitate transfer via CD36 further potentiates this innate immune pathway by supporting ZDHHC6-mediated MYD88 palmitoylation. Subsequently, NF-κB drives the expression of immunosuppressive genes that inhibit anti-tumor T cell responses. Notably, high-fat-diet or hypomethylating agent decitabine treatment boosts the immunosuppressive potential of AML cells by hijacking CD36-dependent innate immune signaling, leading to a dampened therapeutic effect. This work is of translational interest because lipid restriction by US Food and Drug Administration (FDA)-approved lipid-lowering statin drugs improves the efficacy of decitabine therapy by weakening leukemic CD36-mediated immunosuppression.

DOI: https://doi.org/10.1016/j.xcrm.2024.101592
Cell Rep. 2024 Jun 04. pii: S2211-1247(24)00588-6. [Epub ahead of print]43(6): 114260

Immunotherapeutic targeting of surfaceome heterogeneity in AML.

Marie-Eve Bordeleau, Éric Audemard, Arnaud Métois, Louis Theret, Véronique Lisi, Azer Farah, Jean-François Spinella, Jalila Chagraoui, Ossama Moujaber, Léo Aubert, Banafsheh Khakipoor, Laure Mallinger, Isabel Boivin, Nadine Mayotte, Azadeh Hajmirza, Éric Bonneil, François Béliveau, Sybille Pfammatter, Albert Feghaly, Geneviève Boucher, Patrick Gendron, Pierre Thibault, Frédéric Barabé, Sébastien Lemieux, Guillaume Richard-Carpentier, Josée Hébert, Vincent-Philippe Lavallée, Philippe P Roux, Guy Sauvageau.

  Immunotherapy remains underexploited in acute myeloid leukemia (AML) compared to other hematological malignancies. Currently, gemtuzumab ozogamicin is the only therapeutic antibody approved for this disease. Here, to identify potential targets for immunotherapeutic intervention, we analyze the surface proteome of 100 genetically diverse primary human AML specimens for the identification of cell surface proteins and conduct single-cell transcriptome analyses on a subset of these specimens to assess antigen expression at the sub-population level. Through this comprehensive effort, we successfully identify numerous antigens and markers preferentially expressed by primitive AML cells. Many identified antigens are targeted by therapeutic antibodies currently under clinical evaluation for various cancer types, highlighting the potential therapeutic value of the approach. Importantly, this initiative uncovers AML heterogeneity at the surfaceome level, identifies several antigens and potential primitive cell markers characterizing AML subgroups, and positions immunotherapy as a promising approach to target AML subgroup specificities.

Keywords:  AML antigens; CP: Cancer; acute myeloid leukemia; immunotherapy; leukemia stem cells; primary human AML specimens; single-cell RNA sequencing; surfaceome; therapeutic antibodies

DOI:  https://doi.org/10.1016/j.celrep.2024.114260
Nature. 2024 Jun 05.

MYCT1 controls environmental sensing in human haematopoietic stem cells.

Júlia Aguadé-Gorgorió, Yasaman Jami-Alahmadi, Vincenzo Calvanese, Maya Kardouh, Iman Fares, Haley Johnson, Valerie Rezek, Feiyang Ma, Mattias Magnusson, Yanling Wang, Juliana E Shin, Karina J Nance, Helen S Goodridge, Simone Liebscher, Katja Schenke-Layland, Gay M Crooks, James A Wohlschlegel, Hanna K A Mikkola.

The processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1-3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.

DOI: https://doi.org/10.1038/s41586-024-07478-x
bioRxiv. 2024 May 24. pii: 2024.05.23.595594. [Epub ahead of print]

Clonal evolution of hematopoietic stem cells after cancer chemotherapy.

Hidetaka Uryu, Koichi Saeki, Hiroshi Haeno, Chiraag Deepak Kapadia, Ken Furudate, Jyoti Nangalia, Michael Spencer Chapman, Li Zhao, Joanne I Hsu, Chong Zhao, Shujuan Chen, Tomoyuki Tanaka, Zongrui Li, Hui Yang, Courtney DiNardo, Naval Daver, Naveen Pemmaraju, Nitin Jain, Farhad Ravandi, Jianhua Zhang, Xingzhi Song, Erika Thompson, Hongli Tang, Latasha Little, Curtis Gumbs, Robert Z Orlowski, Muzaffar Qazilbash, Kapil Bhalla, Simona Colla, Hagop Kantarjian, Rashmi Kanagal Shamanna, Carlos Bueso- Ramos, Daisuke Nakada, P Andrew Futreal, Elizabeth Shpall, Margaret Goodell, Guillermo Garcia-Manero, Koichi Takahashi.

Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies 1 . The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D . Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D . Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.

DOI: https://doi.org/10.1101/2024.05.23.595594
J Clin Invest. 2024 Jun 03. pii: e181064. [Epub ahead of print]134(11):

CHIPing away at immunity: the role of clonal hematopoiesis of indeterminate potential in bacterial pneumonia.

Elsa N Bou Ghanem.

The occurrence of clonal hematopoiesis of indeterminate potential (CHIP), in which advantageous somatic mutations result in the clonal expansion of blood cells, increases with age, as do an increased risk of mortality and detrimental outcomes associated with CHIP. However, the role of CHIP in susceptibility to pulmonary infections, which also increase with age, is unclear. In this issue of the JCI, Quin and colleagues explored the role of CHIP in bacterial pneumonia. Using characterization of immune cells from human donors and mice lacking tet methylcytosine dioxygenase 2 (Tet2), the authors mechanistically link myeloid immune cell dysfunction to CHIP-mediated risk of bacterial pneumonia. The findings suggest that CHIP drives inflammaging and immune senescence, and provide Tet2 status in older adults as a potential prognostic tool for informing treatment options related to immune modulation.

DOI: https://doi.org/10.1172/JCI181064
Leukemia. 2024 Jun 05.

DNA demethylating agents for chemoprevention of oncovirus-associated leukemogenesis.

Yuta Yamamoto, Tatsuro Watanabe, Hiroshi Ureshino, Yuki Kurahashi, Yuki Fukuda-Kurahashi, Kazuharu Kamachi, Kazunori Kawasoe, Keisuke Kidoguchi, Satoshi Yamashita, Naoko Hattori, Toshikazu Ushijima, Shinya Kimura.

DOI: https://doi.org/10.1038/s41375-024-02299-3
Cancer Res. 2024 Jun 04.

Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers.

Patricia J Keller, Elizabeth J Adams, Rentian Wu, Alexandre Côté, Shilpi Arora, Nico Cantone, Rosana Meyer, Jennifer A Mertz, Victor Gehling, Jike Cui, Jacob I Stuckey, Avinash Khanna, Feng Zhao, Zehua Chen, Ziyang Yu, Richard Cummings, Mohammed Taimi, Nehal J Lakhani, Drew W Rasco, Martin Gutierrez, Linda Duska, Michael Devitt, Ronda Rippley, Julian Levell, Jennifer Truong, Jing Wang, Kaiming Sun, Patrick Trojer.

Recurrent somatic mutations in the BAF chromatin remodeling complex subunit ARID1A occur frequently in advanced urothelial carcinoma, endometrial cancers, and ovarian clear cell carcinoma, creating an alternative chromatin state that may be exploited therapeutically. The histone methyltransferase EZH2 has previously been identified as targetable vulnerability in the context of ARID1A mutations. Here, we describe the discovery of tulmimetostat, an orally available, clinical stage EZH2 inhibitor and elucidate its therapeutic potential for treating ARID1A mutant tumors. Tulmimetostat administration achieved efficacy in multiple ARID1A mutant bladder, ovarian, and endometrial tumor models and improved cisplatin response in chemotherapy-resistant models. Consistent with its comprehensive and durable level of target coverage, tulmimetostat demonstrated greater efficacy than other PRC2-targeted inhibitors at comparable or lower exposures in a bladder cancer xenograft mouse model. Tulmimetostat mediated extensive changes in gene expression in addition to a profound reduction in global H3K27me3 levels in tumors. Phase I clinical pharmacokinetic and pharmacodynamic data indicated that tulmimetostat exhibits durable exposure and profound target engagement. Importantly, a tulmimetostat controlled gene expression signature identified in whole blood from a cohort of 32 cancer patients correlated with tulmimetostat exposure, representing a pharmacodynamic marker for the assessment of target coverage for PRC2-targeted agents in the clinic. Collectively, this data suggests that tulmimetostat has the potential to achieve clinical benefit in solid tumors as a monotherapy but also in combination with chemotherapeutic agents and may be beneficial in various indications with recurrent ARID1A mutations.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0398
Cell. 2024 May 31. pii: S0092-8674(24)00527-0. [Epub ahead of print]

The ribotoxic stress response drives UV-mediated cell death.

Niladri K Sinha, Connor McKenney, Zhong Y Yeow, Jeffrey J Li, Ki Hong Nam, Tomer M Yaron-Barir, Jared L Johnson, Emily M Huntsman, Lewis C Cantley, Alban Ordureau, Sergi Regot, Rachel Green.

  While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.

Keywords:  DNA damage response; GCN2; UV radiation; ZAK; apoptosis; collisions; phosphoproteomics; ribosomes; ribotoxic stress; signaling

DOI:  https://doi.org/10.1016/j.cell.2024.05.018
JCO Precis Oncol. 2024 Jun;8 e2300518

Implementation of and Systems-Level Barriers to Guideline-Driven Germline Genetic Evaluation in the Care of Patients With Myelodysplastic Syndrome and Acute Myeloid Leukemia.

Lauren G Banaszak, Paloma L Cabral, Kelcy Smith-Simmer, Ayesha Hassan, Matthew Brunner, Michael Fallon, Kyle Shoger, Lauren Lovrien, Danielle Golner, Luke Zurbriggen, Ryan Mattison, Zhubin Gahvari, Aric Hall, Kalyan Nadiminti, Erica Reinig, Jane E Churpek.

PURPOSE: Knowledge of an inherited predisposition to myelodysplastic syndrome (MDS) and AML has important clinical implications for treatment decisions, surveillance, and care of at-risk relatives. National Comprehensive Cancer Network (NCCN) guidelines recently incorporated recommendations for germline genetic evaluation of patients with MDS/AML on the basis of personal and family history features, but the practicality of implementing these recommendations has not been studied.
METHODS: A hereditary hematology quality improvement (QI) committee was formed to implement these guidelines in a prospective cohort of patients diagnosed with MDS/AML. Referral for germline genetic testing was recommended for patients meeting NCCN guideline criteria. Referral patterns and genetic evaluation outcomes were compared with a historical cohort of patients with MDS/AML. Barriers to evaluation were identified.
RESULTS: Of the 90 patients with MDS/AML evaluated by the QI committee, 59 (66%) met criteria for germline evaluation. Implementation of the QI committee led to more referrals for germline evaluation in accordance with NCCN guidelines (31% v 14%, P = .03). However, the majority of those meeting criteria were never referred due to high medical acuity or being deceased or in hospice at the time of QI committee recommendations. Despite this, two (17%) of the 12 patients undergoing genetic testing were diagnosed with a hereditary myeloid malignancy syndrome.
CONCLUSION: Current NCCN guidelines resulted in two thirds of patients with MDS/AML meeting criteria for germline evaluation. A hereditary hematology-focused QI committee aided initial implementation and modestly improved NCCN guideline adherence. However, the high morbidity and mortality and prolonged inpatient stays associated with MDS/AML challenged traditional outpatient genetic counseling models. Further improvements in guideline adherence require innovating new models of genetic counseling and testing for this patient population.

DOI: https://doi.org/10.1200/PO.23.00518
Ann Hematol. 2024 Jun 06.

Silencing of the DNA damage repair regulator PPP1R15A sensitizes acute myeloid leukemia cells to chemotherapy.

Anthi Bouchla, Christina D Sotiropoulou, Christopher Esteb, Theodoros Loupis, Sotirios G Papageorgiou, Georgia G Deliconstantinos, Maria Pagoni, Eleftheria Hatzimichael, Maria Dellatola, Smaragdi Kalomoiri, Elisavet Apostolidou, Christos K Kontos, Thomas P Thomopoulos, Theodoros Karantanos, Vasiliki Pappa.

  Acute Myeloid Leukemia (AML) is a life-threatening disease whose induction treatment consists of combination chemotherapy with Idarubicin and Cytarabine for fit patients. Treatment failures are frequent, urging the need for novel treatments for this disease. The DNA Damage Response Mechanism (DDR) comprises numerous molecules and pathways intended to arrest the cell cycle until DNA damage is repaired or else drive the cell to apoptosis. AML-derived cell lines after treatment with Idarubicin and Cytarabine were used for studying the expression profile of 84 DDR genes, through PCR arrays. Utilizing de novo AML patient and control samples we studied the expression of PPP1R15A, CDKN1A, GADD45A, GADD45G, and EXO1. Next, we performed PPP1R15A silencing in AML cell lines in two separate experiments using siRNA and CRISPR-cas9, respectively. Our findings highlight that DDR regulators demonstrate increased expression in patients with high cytogenetic risk possibly reflecting increased genotoxic stress. Especially, PPP1R15A is mainly involved in the recovery of the cells from stress and it was the only DDR gene upregulated in AML patients. The PPP1R15A silencing resulted in decreased viability of Idarubicin and Cytarabine-treated cell lines, in contrast to untreated cells. These findings shed light on new strategies to enhance chemotherapy efficacy and demonstrate that PPP1R15A is an important DDR regulator in AML and its downregulation might be a safe and effective way to increase sensitivity to chemotherapy in this disease.

Keywords:  Acute myeloid leukemia; DNA damage response; GADD34; PPP1R15A; Resistance mechanisms

DOI:  https://doi.org/10.1007/s00277-024-05785-x
Blood Adv. 2024 Jun 05. pii: bloodadvances.2023012279. [Epub ahead of print]

CRISPR/Cas9-mediated gene disruption determines the roles of MITF and CITED2 in human mast cell differentiation.

Jiezhen Mo, Fredrik Wermeling, Gunnar P Nilsson, Joakim S Dahlin.

The differentiation of hematopoietic stem and progenitor cells into the various cell lineages is regulated by cell-intrinsic factors and the progenitors' microenvironment. Experiments in mice have allowed the identification of transcriptional modulators that control mast cell differentiation. However, a comprehensive approach that allows efficient disruption of individual transcriptional modulators in primary human hematopoietic progenitors coupled with a mast cell formation readout has not been described. Here, we report a simple electroporation- and ribonucleoprotein-based knockout system that allows the identification of genes that are required and dispensable for human mast cell differentiation. We show that the transcription factor MITF is upregulated in human mast cell progenitors and reveal that the loss of MITF results in the suppressed formation of mast cells. By contrast, CITED2, another transcriptional modulator that is upregulated along the mast cell differentiation trajectory, was dispensable for human mast cell differentiation. Taken together, we report a CRISPR/Cas9-based framework that serves to identify genes involved in regulating the formation of human mast cells, and the results uncover the role of two transcriptional modulators in controlling human mast cell differentiation.

DOI: https://doi.org/10.1182/bloodadvances.2023012279
Mol Cancer Res. 2024 Jun 07.

RNA binding protein Lin28B promotes chronic myeloid leukemia blast crisis by transcriptionally upregulating miR-181d.

Minran Zhou, Xiaolin Yin, Lu Zhang, Zelong Cui, Xinwen Jiang, Qingli Ji, Sai Ma, Chunyan Chen.

The blast crisis (BC) of chronic myeloid leukemia (CML) has poor efficacy against existing treatments and extremely short survival. However, the molecular mechanism of CML-chronic phase (CP) transformation to CML-BC is not yet fully understood. Here, we show that Lin28B, a RNA binding protein, acted as an activator enhancing the transformation to CML-BC by mediating excessive cell proliferation. The level of Lin28B expression was apparently elevated in CML-BC patients compared with newly diagnosed CML-CP patients. The overexpression of Lin28B promoted the proliferation of leukemia cells. Mechanistically, we identified Lin28B as a DNA binding protein by binding to the promoter region of miR-181d and upregulating its expression, which inhibited the expression of Programmed cell death 4 (PDCD4) by binding to the PDCD4 3'UTR region, thereby enhancing the proliferation of CML cells. Overall, the "Lin28B-miR-181d-PDCD4" regulatory axis promoted CML blast crisis. Implications: Our findings highlight the oncogenic role of Lin28B in CML blast crisis, acting as a DNA binding protein which transcriptionally upregulates miR-181d expression.

DOI: https://doi.org/10.1158/1541-7786.MCR-23-0928
Blood Adv. 2024 Jun 05. pii: bloodadvances.2024013228. [Epub ahead of print]

Clonal hematopoiesis of indeterminate potential as a prognostic factor: A systematic review and meta-analysis.

Jasmine Singh, Nancy Ying Li, Elham Ashrafi, Le Thi Phuong Thao, David J Curtis, Erica M Wood, Zoe McQuilten.

With advances in sequencing, individuals with clonal hematopoiesis of indeterminate potential (CHIP) are increasingly being identified, making it essential to understand its prognostic implications. We conducted a systematic review of studies comparing the risk of clinical outcomes in individuals with and without CHIP. We searched MEDLINE and EMBASE, and included original research reporting an outcome risk measure in individuals with CHIP, adjusted for the effect of age. From 3305 studies screened, we included 88 studies of 45 to 470960 participants. Most studies had low to moderate risk of bias in all domains of the QUIPS tool. Random effects meta-analyses were performed for outcomes reported in at least 3 studies. CHIP conferred increased risk of all-cause mortality (hazard ratio [HR] 1.34 [95% CI 1.19-1.50]), cancer-mortality (HR 1.46 [1.13-1.88]), composite cardiovascular events (HR 1.40 [1.19-1.65]), coronary heart disease (HR = 1.76 [1.27-2.44]), stroke (HR 1.16 [1.05-1.28]), heart failure (HR 1.27 [1.15-1.41]), hematologic malignancy (HR 4.28 [2.29-7.98]), lung cancer (HR 1.40 [1.27-1.54]), renal impairment (HR 1.25 [1.18-1.33]) and severe COVID19 (odds ratio [OR] 1.46 [1.18-1.80]). CHIP was not associated with cardiovascular mortality (HR 1.09 [0.97-1.22]), except in subgroup analysis restricted to larger clones (HR 1.31 [1.12-1.54]). Isolated DNMT3A mutations did not increase risk of myeloid malignancy, all-cause mortality or renal impairment. Reasons for heterogeneity between studies included differences in definitions and measurement of CHIP and outcomes, and populations studied. In summary, CHIP is associated with diverse clinical outcomes, with clone size, specific gene and inherent patient characteristics important mediators of risk.

DOI: https://doi.org/10.1182/bloodadvances.2024013228
Blood. 2024 Jun 07. pii: blood.2024024776. [Epub ahead of print]

Asciminib is a novel inhibitor of ABL1 and ABL2 gene fusions in ALL but requires the ABL SH3 domain for efficacy.

Laura N Eadie, Elias Lagonik, Elyse C Page, Caitlin E Schutz, Susan L Heatley, Barbara J McClure, Michelle Olivia Forgione, David T Yeung, Timothy P Hughes, Deborah L White.

High-risk Ph-like ALL includes genomic rearrangement of the ABL1 and ABL2 genes (collectively ABL-rearranged, ABLr), and novel treatments are required. For the first time, we demonstrate asciminib efficacy in ABLr ALL, but only when the ABL SH3 domain is present.

DOI: https://doi.org/10.1182/blood.2024024776
Nat Commun. 2024 Jun 01. 15(1): 4673

IκBα controls dormancy in hematopoietic stem cells via retinoic acid during embryonic development.

Roshana Thambyrajah, Maria Maqueda, Muhammad Zaki Fadlullah, Martin Proffitt, Wen Hao Neo, Yolanda Guillén, Marta Casado-Pelaez, Patricia Herrero-Molinero, Carla Brujas, Noemi Castelluccio, Jessica González, Arnau Iglesias, Laura Marruecos, Cristina Ruiz-Herguido, Manel Esteller, Elisabetta Mereu, Georges Lacaud, Lluis Espinosa, Anna Bigas.

Recent findings suggest that Hematopoietic Stem Cells (HSC) and progenitors arise simultaneously and independently of each other already in the embryonic aorta-gonad mesonephros region, but it is still unknown how their different features are established. Here, we uncover IκBα (Nfkbia, the inhibitor of NF-κB) as a critical regulator of HSC proliferation throughout development. IκBα balances retinoic acid signaling levels together with the epigenetic silencer, PRC2, specifically in HSCs. Loss of IκBα decreases proliferation of HSC and induces a dormancy related gene expression signature instead. Also, IκBα deficient HSCs respond with superior activation to in vitro culture and in serial transplantation. At the molecular level, chromatin regions harboring binding motifs for retinoic acid signaling are hypo-methylated for the PRC2 dependent H3K27me3 mark in IκBα deficient HSCs. Overall, we show that the proliferation index in the developing HSCs is regulated by a IκBα-PRC2 axis, which controls retinoic acid signaling.

DOI: https://doi.org/10.1038/s41467-024-48854-5
Nature. 2024 Jun 05.

A disease-associated gene desert directs macrophage inflammation through ETS2.

C T Stankey, C Bourges, L M Haag, T Turner-Stokes, A P Piedade, C Palmer-Jones, I Papa, M Silva Dos Santos, Q Zhang, A J Cameron, A Legrini, T Zhang, C S Wood, F N New, L O Randzavola, L Speidel, A C Brown, A Hall, F Saffioti, E C Parkes, W Edwards, H Direskeneli, P C Grayson, L Jiang, P A Merkel, G Saruhan-Direskeneli, A H Sawalha, E Tombetti, A Quaglia, D Thorburn, J C Knight, A P Rochford, C D Murray, P Divakar, M Green, E Nye, J I MacRae, N B Jamieson, P Skoglund, M Z Cader, C Wallace, D C Thomas, J C Lee.

Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22-which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu's arteritis3-6-we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.

DOI: https://doi.org/10.1038/s41586-024-07501-1