bims-tremyl 2025-11-30 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2025–11–30
forty papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Combinatorial inhibition of LSD1 and Menin induces therapeutic differentiation in AML.
Optimizing lower intensity triplet therapy in acute myeloid leukemia: a practical guide.
Co-targeting menin and LSD1 dismantles oncogenic programs and restores differentiation in MLL-rearranged AML.
Pitavastatin counteracts venetoclax resistance mechanisms in acute myeloid leukemia by depleting geranylgeranyl pyrophosphate.
Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss.
Prognostic impact of age and MDS-associated mutations in NPM1 -mutated AML.
Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia.
Lymphotoxin alpha eradicates acute myeloid leukemia and simultaneously promotes healthy hematopoiesis in mice.
A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML.
Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1.
Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling.
Human plasma proteomic profile of clonal hematopoiesis.
Balancing Activation and Repression: CoREST-p300 Antagonism Controls Retinoic Acid-Driven Differentiation in AML.
Post-transplant MRD Monitoring by TP53 Duplex Sequencing with APR-246 + Azacitidine Maintenance Predicts Outcomes.
Measurable residual mutated NPM1 before allogeneic transplant for acute myeloid leukemia.
Clonal hematopoiesis may precede the diagnosis of aplastic anemia by several years.
A phase 1/2 study of DS-1594 menin inhibitor in relapsed/refractory acute leukemias.
Influence of Oxidation Resistance 1 on disease progression in chronic myeloid leukemia.
A Unifying Mechanism for Shared Splicing Aberrations in Splicing Factor Mutant Cancers.
TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity.
Somatic genetic rescue in ZCCHC8-associated telomere biology disorders.
Reversing lysosomal dysfunction restores youthful state in aged hematopoietic stem cells.
Harnessing the E3 ligase SPOP for targeted degradation of the NUP98::KDM5A fusion oncoprotein.
Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS.
Comorbidities and mutations including single- and multihit TET2 mutations in relation to outcome in chronic myelomonocytic leukaemia-A population-based study.
Mitofusin agonists enhances long-term engraftment and potency of HSC cultures in vivo.
NLRP3-induced systemic inflammation controls the development of JAK2V617F mutant myeloproliferative neoplasms.
European LeukemiaNet criteria for safety and efficacy evaluation of new drugs for myelofibrosis.
Predictive Capacity of Peri-Transplant Measurable Residual Disease Thresholds in NPM1-Mutant Acute Myeloid Leukemia.
The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes.
A Rapid Gene Expression Profiler Classifies AML Tumor Responsiveness to Standard Therapies.
Predicting secondary myeloid neoplasms in acquired aplastic anemia using machine learning models.
Single-cell spatial mapping reveals dynamic bone marrow microarchitectural alterations and enhances clinical diagnostics in MDS.
Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses.
Dynamic BH3 profiling predicts clinical outcomes in acute myeloid leukemia.
PRDM15 regulates differentiation and proliferation of hematopoietic stem cells.
Inhibition of farnesyltransferase activity diminishes hematopoietic stem cell ex vivo expansion ability.
CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias.
Space-associated stem cell hallmarks of aging and resilience in astronauts.
FTO depletion does not alter m6A stoichiometry in AML mRNA: a reassessment using direct RNA nanopore sequencing.

bioRxiv. 2025 Nov 11. pii: 2025.11.09.687496. [Epub ahead of print]

Combinatorial inhibition of LSD1 and Menin induces therapeutic differentiation in AML.

María F Carrera Rodríguez, Joshua Rico, Manaswini Vijayaraghavan, Fangxue Yan, Austin King, Ricardo Petroni, Nicolae Adrian Leu, Haley Goodrow, Kathrin Bernt, Gerald McGeehan, M Andrés Blanco.

Acute myeloid leukemia (AML) is characterized by differentiation arrest and uncontrolled proliferation. Differentiation therapy aims to treat AML by de-repressing latent myeloid maturation programs to induce cell cycle arrest and subsequent cell death. This approach is curative in the promyelocytic AML subtype, but has met with limited success in other subtypes. Genes such as LSD1 have emerged as intriguing non-APL AML differentiation therapy targets, but results as monoagents in clinical trials have been mixed. Here, we performed differentiation-specific CRISPR screens to identify targets whose inhibition synergizes with LSD1 inhibition to induce terminal differentiation of non-APL AML cells. Intriguingly, the MLL co-factor Menin scored as the top hit. Using cell lines, primary patient samples, and mouse AML models, we find that dual inhibition of LSD1 and Menin is a highly promising approach for differentiation therapy. Mechanistically, we determine that inhibition of Menin downregulates drivers of proliferation and stemness such as MEIS1, and inhibition of LSD1 induces inflammatory and interferon-related pro-myeloid differentiation expression programs. Surprisingly, we find that this combination is effective in selected AML models without mutations in MLL or NPM1, thus nominating dual inhibition of LSD1 and Menin as an attractive therapeutic approach for a mutationally diverse set of non-APL AMLs.
Highlights: Inhibition of LSD1 and Menin synergizes to induce differentiation of MLL-r and MLL-WT AMLs.Inhibition of Menin downregulates drivers of proliferation and stemness.Inhibition of LSD1 induces differentiation-associated inflammatory and interferon responses.LSD1 and Menin occupy different areas of the genome.

DOI: https://doi.org/10.1101/2025.11.09.687496
Blood Cancer J. 2025 Nov 25.

Optimizing lower intensity triplet therapy in acute myeloid leukemia: a practical guide.

Wei-Ying Jen, Curtis A Lachowiez, Jennifer Marvin-Peek, Jessica K Altman, Musa Yilmaz, Jacqueline S Garcia, Yasmin Abaza, Nicholas J Short, Joshua F Zeidner, Naval G Daver, Andrew H Wei, Ghayas C Issa, Courtney D DiNardo.

Venetoclax-based doublets with azacitidine or low dose cytarabine are the standard of care for the treatment of acute myeloid leukemia (AML) in older patients or those unfit for intensive chemotherapy. However, some patients do not attain complete remission, and over time, most patients relapse. Frontline triplet therapy incorporating a targeted therapy (FLT3, IDH or menin inhibitor) is an emerging treatment concept under investigation for this population. Initial triplet regimens have yielded encouraging composite complete remission and measurable residual disease negativity rates, enabling the transition to allogeneic stem cell transplantation for eligible patients. While effective, triplets are associated with myelosuppression and cytopenia-related toxicities, which can affect treatment tolerability and quality of life. In this review, we summarize the available evidence for triplet therapy in AML and offer our recommendations on the practical application of triplets in clinical practice, with particular focus on adjustments to dosing schedules in induction and continuation cycles. We also outline drug-specific adverse effects and interactions based on emerging clinical data to help guide the clinician, given the increasing use of novel combination therapies.

DOI: https://doi.org/10.1038/s41408-025-01429-z
bioRxiv. 2025 Oct 15. pii: 2025.10.13.681683. [Epub ahead of print]

Co-targeting menin and LSD1 dismantles oncogenic programs and restores differentiation in MLL-rearranged AML.

Mina M Tayari, Helena Gomes Dos Santos, Felipe Beckedorff, Tulasigeri Totiger, Adnan Mookhtiar, Anna Lesley Kingham, Guilherme Miura Lavezzo, Gloria Mas Martin, Hsuan-Ting Huang, Efe Karaca, Daniel Bilbao, Justin Taylor, Ramin Shiekhattar, Justin M Watts.

Acute myeloid leukemia (AML) harboring MLL ( MLL1, KMT2A ) rearrangement ( MLL-r ) remains a lethal subtype with limited durable responses to single-agent menin inhibition. To define rational combination strategies, we performed a high-throughput screen of >900 epigenetic modulators in combination with menin inhibition in MLL-r AML models. This uncovered consistent synergy between menin and lysine-specific demethylase 1 (LSD1) inhibition, including with the clinical agent iadademstat. Mechanistically, LSD1 was found to interact with LEDGF/p75 (PSIP1), a chromatin-anchoring cofactor of the menin-MLL complex at H3K36me3 marked euchromatin. Chromatin profiling revealed extensive co-occupancy of LSD1 and menin-MLL components at leukemogenic loci in MLL-r AML cells. Dual inhibition of menin and LSD1 dismantled this chromatin complex, evicted H3K36me3 from LEDGF-bound sites, and reprogrammed transcription toward myeloid differentiation. Combined menin and LSD1 blockade repressed canonical MLL targets, including HOXA9, MYC, FLT3, PBX3 , and CDK6 , while restoring H3K36me3 and H3K4me3 and activating differentiation-associated genes. In vivo, the combination produced potent antileukemic effects in both MOLM-13 and MLL-r patient-derived xenografts, markedly reducing leukemic burden and extending survival without overt toxicity. These findings identify LSD1 as a critical cofactor of the menin-MLL-LEDGF axis and establish concurrent menin and LSD1 inhibition as a mechanistically informed combinatorial therapeutic approach in MLL-r AML.

DOI: https://doi.org/10.1101/2025.10.13.681683
bioRxiv. 2025 Nov 05. pii: 2025.10.27.684888. [Epub ahead of print]

Pitavastatin counteracts venetoclax resistance mechanisms in acute myeloid leukemia by depleting geranylgeranyl pyrophosphate.

Roberta Buono, Dennis Juarez, Madhuri Paul, Sarah J Skuli, Ian B Wong, Ishita Tarnekar, Zhili Ying, Izabelle Le, Gerald Wertheim, A'ishah Bakayoko, Marisa Kruidenier, Said M Sebti, Marina Konopleva, Angela G Fleischman, Cholsoon Jang, Martin Carroll, David A Fruman.

The BCL2 inhibitor venetoclax has therapeutic activity in several hematological malignancies. In acute myeloid leukemia (AML), venetoclax combined with hypomethylating agents is the standard of care for patients unfit for intensive chemotherapy, but intrinsic and acquired resistance are common. Loss of p53 function is strongly associated with venetoclax resistance, and adding venetoclax to 5-azacitidine provides no overall survival benefit in TP53 -mutant AML. Other frequent mechanisms of venetoclax resistance in AML include FLT3 mutations, MCL-1 upregulation, and altered mitochondrial metabolism. Unfortunately, it has been challenging to develop agents that target these mechanisms directly and combinatorially. Here we report that pitavastatin, an inhibitor of HMG-CoA-reductase, promotes apoptosis and overcomes several venetoclax resistance mechanisms in human AML cells. At clinically achievable concentrations, pitavastatin treatment has potent cytotoxic activity in cells with mutations in TP53 or FLT3 . The apoptotic mechanism involves p53-independent PUMA upregulation and reduced MCL-1 expression. Pitavastatin also suppresses mitochondrial gene expression and oxidative metabolism. The pro-apoptotic actions of pitavastatin depend on depletion of geranylgeranyl pyrophosphate (GGPP) and can be recapitulated by inhibiting GGPP synthase or geranylgeranyltransferase-1 enzymes. These results provide a mechanistic rationale for adding pitavastatin to AML regimens to prevent or overcome venetoclax resistance.

DOI: https://doi.org/10.1101/2025.10.27.684888
bioRxiv. 2025 Oct 07. pii: 2025.10.06.680457. [Epub ahead of print]

Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss.

Samuli Eldfors, Sumit Rai, Vineet Sharma, Tareq Hossan, Claudia Cabrera Pastrana, Amy Bertino, Angelique Gilbert, Kimmo Porkka, Matthew Walter, Timothy A Graubert.

SRSF2 mutations occur in up to 25% of acute myeloid leukemia (AML) and 17% of myelodysplastic syndrome (MDS) cases and are associated with poor prognosis, yet no mutation-directed therapy exists. Here, we aimed to identify therapeutically targetable vulnerabilities in MDS/AML with SRSF2 mutations. Ex vivo drug-sensitivity testing of bone marrow cells from AML patients and healthy donors showed that SRSF2 -mutant cells are sensitive to inhibitors of CHK1, and WEE1 DNA damage response (DDR) kinases. To test causality, we engineered isogenic K562 cell line clones expressing SRSF2 P95H/L/R mutations. RNA sequencing confirmed splicing aberrations characteristic of MDS/AML in these clones. We found that SRSF2 P95H/L/R sensitize leukemia cells to ATR-CHK1-WEE1 inhibition. Bone marrow progenitors from Srsf2 P95H and U2AF1 S34F knock-in mice showed heightened sensitivity to CHK1 inhibition, corroborating the human data. In contrast, RUNX1 mutations were linked to resistance against CHK1 and WEE1 inhibition in SRSF2 -mutant AML samples. Runx1 loss also caused resistance to CHK1 inhibitors in knock-in mouse progenitors harboring Srsf2 P95H or U2AF1 S34F , indicating that RUNX1 loss is a mechanism of resistance. In conclusion, SRSF2 and U2AF1 mutations are biomarkers of sensitivity to ATR-CHK1 pathway inhibitors, while RUNX1 mutations cause resistance. These biomarkers can support patient stratification in MDS/AML.

DOI: https://doi.org/10.1101/2025.10.06.680457
medRxiv. 2025 Nov 06. pii: 2025.11.03.25339099. [Epub ahead of print]

Prognostic impact of age and MDS-associated mutations in NPM1 -mutated AML.

Vivian M Liu, Megan Othus, Jasmine Naru, Rhonda E Ries, Era L Pogosova-Agadjanyan, Frederick R Appelbaum, Thomas R Chauncey, Eliana Dietrich, Harry P Erba, John E Godwin, Matthew P Fitzgibbon, Min Fang, Stanley C Lee, Anna Moseley, Mary-Elizabeth Percival, Guangrong Qin, Jerald P Radich, Suravi Raychaudhuri, Cheryl L Willman, Soheil Meshinchi, Derek L Stirewalt.

Nucleophosmin-1 ( NPM1 ) mutations define a major molecular subtype of acute myeloid leukemia (AML) and is generally associated with favorable prognosis. However, the impact of myelodysplasia-associated mutations (MDSm+) on patient outcomes within this subgroup remains uncertain. We retrospectively analyzed 271 NPM1 -mutated AML patients from three independent cohorts (SWOG, Fred Hutch, and Beat AML) to assess the prognostic significance of MDSm+ and its interaction with age. MDSm+ occurred in 17% of cases, most commonly involving SRSF2 and SF3B1 . Although MDSm+ was associated with inferior overall survival compared to MDSm-in ELN2022 favorable-risk patients (HR 2.0, p =0.008), this effect was largely driven by worse outcomes in older patients ( ≥ 65 years) as older ELN22 favorable-risk patients had poor OS regardless of presence of MDSm+ compared to younger patients. After stratification of patients by age, there was not a significant difference between MDSm+ and MDSm-in either younger patients (HR 0.99, p=0.98) or older patients (HR 1.42, p =0.33). These findings indicate that MDSm+ in NPM1 + AML is not independently associated with adverse risk after adjusting for age and highlight the need for age-adjusted AML risk models.

DOI: https://doi.org/10.1101/2025.11.03.25339099
bioRxiv. 2025 Oct 15. pii: 2025.10.14.682328. [Epub ahead of print]

Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia.

Darren Lee, Yazan Abu-Shihab, Kate Plas, Deedra Nicolet, Krzysztof Mrozek, Mark J Routbort, Keyur P Patel, Christopher J Walker, Jill Buss, Andrew R Stiff, Andrea Laganson, Courtney D DiNardo, Naval G Daver, Tapan M Kadia, Farhad Ravandi, Andrew J Carroll, Jonathan E Kolitz, Bayard L Powell, William G Blum, Maria R Baer, Guido Marcucci, Geoffrey L Uy, Wendy Stock, Richard M Stone, L Jeffrey Medeiros, John C Byrd, James S Blachly, Robert L Bowman, Jeffrey W Tyner, Sanam Loghavi, Ann-Kathrin Eisfeld, Linde A Miles.

Mutations in the RAS/MAPK signaling pathway are recurrent in acute myeloid leukemia (AML), primarily involving NRAS and KRAS. In contrast, mutations in the gene encoding an effector protein, BRAF, occur at relatively lower frequencies in AML and are associated with poor outcomes. To date, no comprehensive analysis has assessed the clinical and molecular characteristics of BRAF-mutated AML. In this study, we report the identification of canonical and non-canonical BRAF mutations in ~1% of 5,779 consecutive clinically and molecularly fully-annotated AML patients treated at two major United States Cancer Centers (50/5779 AML patients: 21 newly diagnosed AML; 9 relapsed/refractory; 20 newly diagnosed secondary AML). We performed single-cell multiomic analysis on a subset of AML samples. BRAF mutations were enriched in myelodysplasia-related AML (AML-MR), and most mutations were located outside the V600 hotspot. Single-cell multiomic profiling delineated BRAF mutation class-specific patterns of co-mutations, clonality, and immunophenotypes. Notably, BRAF mutations and other signaling co-mutation(s) could be found in the same cell, a finding that significantly diverges from prior studies of RAS-mutant AML. In this cohort, BRAF-mutant AML patients had poor overall survival with currently available treatments, including venetoclax-based regimens. Drug sensitivity data suggest possible avenues for targeted treatment of BRAF-mutated AML.

DOI: https://doi.org/10.1101/2025.10.14.682328
Sci Transl Med. 2025 Nov 26. 17(826): eadu3313

Lymphotoxin alpha eradicates acute myeloid leukemia and simultaneously promotes healthy hematopoiesis in mice.

Ulrike Höckendorf, Sayantanee Dutta, Arnold Kloos, Marah Runtsch, Carina Zötsch, Sebastian Vosberg, Yongjie Wang, Sophie Kienreich, Bettina Flasch, Grazia Malovan, Vanessa Jäger, Stefanie Stanzer, Stefanie Prein, Timo O Odinius, Celina V Wagner, Lars Buschhorn, Veronika Dill, Bianca Perfler, Torsten Haferlach, Konstanze Döhner, Katharina S Götze, Jürgen Ruland, Florian Bassermann, Adam Wahida, Mathias Heikenwälder, Caterina Branca, Johannes Schmöllerl, Johannes Zuber, Ann-Cathrin Burk, Robert Zeiser, Heinz Sill, Ashok Kumar Jayavelu, Armin Zebisch, Michael Heuser, Michael A Dengler, Philipp J Jost.

Acute myeloid leukemia (AML) is characterized by frequent relapse, which is driven by resistant leukemic stem or progenitor cells (LSCs). Here, we reported on a tumor-suppressive mechanism that can be harnessed to simultaneously clear LSCs and promote healthy hematopoiesis. Genetic deletion of the tumor necrosis factor (TNF) superfamily member lymphotoxin alpha (Lta) blocked cell death and accelerated leukemogenesis in murine AML models. Accordingly, exposure of leukemic cells to exogenous recombinant lymphotoxin alpha (LTα3) induced myeloid differentiation and, in part, cell death in AML progenitors. In syngeneic and patient-derived xenograft mouse models, exposure to recombinant LTα3 resulted in deep and durable remissions. LTα3 repressed leukemia by depleting tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) through activation of TNF receptors TNFR1 and TNFR2. In contrast with conventional therapies, LTα3 exerted only minimal toxicity on the healthy hematopoiesis but instead promoted hematopoietic progenitors. Leveraging this endogenous tumor-suppressive mechanism may decouple treatment efficacy on malignant cells from undesired bone marrow suppression.

DOI: https://doi.org/10.1126/scitranslmed.adu3313
Res Sq. 2025 Oct 29. pii: rs.3.rs-7763372. [Epub ahead of print]

A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML.

Theodoros Karantanos, Nour Naji, Taha Ahmedna, J Peske, Xinghan Zeng, Brandy Perkins, Zanshé Thompson, Tushar Nichakawade, Bum Lee, Evangeline Watson, Theodora Chatzilygeroudi, Li Luo, Bogdan Paun, Melanie Klausner, Yuju An, Teodora Supeanu, Ivana Gojo, Gabriel Ghiaur, Amy DeZern, Mark Levis, Linda Resar, Richard John Jones, Styliani Karanika, Suman Paul.

Patients with myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) with high-risk features including TP53 mutations have poor outcomes due to lack of effective therapies. The atypical chemokine surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in MDS and secondary AML (sAML) compared to healthy hematopoietic cells and we recently found that TP53 -mutated MDS/AML and AML with erythroid features express the highest levels of this receptor across MDS/AML subtypes. To illustrate the therapeutic potential of CCRL2 as a therapeutic target, we developed an anti-CCRL2 antibody-drug conjugate (ADC) by conjugating an anti-CCRL2 antibody with the cytotoxic drug pyrrolobenzodiazepine (PBD), which causes DNA double-strand breaks leading to cancer cell death. The anti-CCRL2 ADC demonstrated strong CCRL2-selective cytotoxicity against cell lines derived from MDS/AML patients with TP53 mutations and erythroid features, surpassing the cytotoxic effects observed with gemtuzumab and PBD-conjugated anti-CD33 and anti-CD123 ADCs. It also induced apoptosis and suppressed the clonogenicity of primary MDS/AML bone marrow samples without affecting the survival, differentiation and clonogenicity of healthy hematopoietic stem and progenitor cells. This agent also suppressed the leukemic growth of TP53- mutated MDS/AML cell line xenografts, improving mice survival and decreasing the leukemic burden in patient-derived TP53 -mutated MDS/AML xenografts. In conclusion, our study introduces CCRL2 as a potential new therapeutic target in high-risk MDS/AML.

DOI: https://doi.org/10.21203/rs.3.rs-7763372/v1
J Clin Invest. 2025 Nov 25. pii: e181943. [Epub ahead of print]

Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1.

Hayle Kincross, Ya-Chi Angela Mo, Xuan Wang, Linda Chang, Gerben Duns, Franziska Mey, Jihong Jiang, Zurui Zhu, Naomi Isak, Harwood Kwan, Tammy Ty Lau, T Roderick Docking, Pranav Garg, Jessica Tran, Shane Colborne, Se-Wing Grace Cheng, Shujun Huang, Nadia Gharaee, Elijah Willie, Jeremy Dk Parker, Joshua Bridgers, Davis Wood, Ramon I Klein Geltink, Gregg B Morin, Aly Karsan.

  Acute myeloid leukemia (AML) is an aggressive cancer with very poor outcomes. To identify additional drivers of leukemogenesis, we analyzed sequencing data from 1,727 unique individual AML patients, which revealed mutations in ubiquitin ligase family genes in 11.2% of adult AML samples with mutual exclusivity. The SKP1/CUL1/F-box (SCF) E3 ubiquitin ligase complex gene, FBXO11, was the most significantly downregulated gene of the SCF complex in AML. We found that FBXO11 interacts with and catalyzes K63-linked ubiquitination of LONP1 in the cytosol, to promote LONP1 entry into mitochondria. We show that depletion of FBXO11 or LONP1 reduces mitochondrial respiration through impaired LONP1 chaperone activity to assemble electron transport chain Complex IV. Reduced mitochondrial respiration secondary to FBXO11 or LONP1 depletion imparted myeloid-biased stem cell properties in primary CD34+ hematopoietic stem and progenitor cells (HSPC) in vitro. In a human xenograft model, depletion of FBXO11 cooperated with AML1-ETO and mutant KRASG12D to generate serially transplantable AML. Our findings suggest that reduced FBXO11 cooperates to initiate AML by priming HSPC for myeloid-biased self-renewal through attenuation of LONP1-mediated regulation of mitochondrial respiration.

Keywords:  Hematology; Hematopoietic stem cells; Leukemias; Mitochondria; Stem cells

DOI:  https://doi.org/10.1172/JCI181943
bioRxiv. 2025 Nov 14. pii: 2025.11.13.688312. [Epub ahead of print]

Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling.

Benjamin J Huang, Jeevitha D'Souza, Alexa Rane Batingana, Max D Harris, Xinyue Wang, Eugene Hwang, Anica M Wandler, Michael R Burgess, Qing Li, Soheil Meshinchi, Gideon Bollag, Kevin Shannon.

Adult and pediatric acute myeloid leukemias (AMLs) harbor distinct mutational profiles, including a higher incidence of RAS and other signaling mutations in young patients. Here we show that the BET inhibitor PLX51107 potently suppresses the growth of NRAS -mutant AML cell lines, and that these activities are enhanced by co-treatment with the MEK inhibitor PD0325901. Controlled preclinical trials in primary mouse Nras -mutant AMLs revealed single agent efficacy of PLX51107 that was enhanced by PD0325901. Leukemias that relapsed during treatment developed intrinsic drug resistance characterized by transition to a more primitive state, up-regulation of Myc target genes, and down-regulation of Ras-associated transcriptional programs. AMLs that relapsed after frontline chemotherapy showed similar transcriptional remodeling. These studies demonstrate transcriptional plasticity in primary AMLs that relapse following in vivo treatment with either targeted agents or chemotherapy, and support evaluating BET inhibition in leukemias with monocytic differentiation and RAS mutations.

DOI: https://doi.org/10.1101/2025.11.13.688312
Nat Commun. 2025 Nov 27.

Human plasma proteomic profile of clonal hematopoiesis.

NHLBI Trans-Omics for Precision Medicine

Plasma proteomic profiles associated with subclinical somatic mutations in blood cells may offer insights into downstream clinical consequences. Here we explore these patterns in clonal hematopoiesis of indeterminate potential (CHIP), which is linked to several cancer and non-cancer outcomes, including coronary artery disease (CAD). Among 61,833 participants (3881 with CHIP) from TOPMed and UK Biobank (UKB) with blood-based DNA sequencing and proteomic measurements (1,148 proteins by SomaScan in TOPMed and 2917 proteins by Olink in UKB), we identify 32 and 345 proteins from TOPMed and UKB, respectively, associated with CHIP and most prevalent driver genes (DNMT3A, TET2, and ASXL1). These associations show substantial heterogeneity by driver genes, sex, and race, and were enriched for immune response and inflammation pathways. Mendelian randomization in humans, coupled with ELISA in hematopoietic Tet2-/- vs wild-type mice validation, disentangle causal proteomic perturbations from TET2 CHIP. Lastly, we identify plasma proteins shared between CHIP and CAD.

DOI: https://doi.org/10.1038/s41467-025-66755-z
bioRxiv. 2025 Oct 15. pii: 2025.10.13.682235. [Epub ahead of print]

Balancing Activation and Repression: CoREST-p300 Antagonism Controls Retinoic Acid-Driven Differentiation in AML.

Mina M Tayari, Helena Gomes Dos Santos, Sadat Dokaneheifard, Samuel D Whedon, Monica Valencia, Harikumar Arigela, Felipe Beckedorff, Justin M Watts, Philip A Cole, Ramin Shiekhattar.

  The histone demethylase KDM1A (LSD1), a component of the CoREST corepressor complex, is highly expressed in hematologic malignancies and regulates hematopoietic differentiation. Despite its essential developmental role, LSD1 inhibition has emerged as a promising strategy to enhance retinoic acid (RA)-responsive gene expression in subsets of acute myeloid leukemia (AML). Here, we show that LSD1 physically interacts with RAR/RXR heterodimers at specific genomic loci, restricting chromatin accessibility and transcriptional activation of differentiation programs. Single-agent inhibition of LSD1 or HDACs promotes only partial differentiation. In contrast, Corin, a dual LSD1/CoREST inhibitor, synergizes with all-trans retinoic acid (ATRA) to induce robust myeloid differentiation and apoptosis. Corin treatment alone does not significantly increase H3K4me3 levels; however, in combination with ATRA, it disrupts CoREST-RAR/RXR complexes and facilitates the recruitment of the coactivator p300. Together, they shift chromatin to an active state, enhancing H3K4me3 via increased transcriptional engagement and coactivator recruitment. Our findings identify the functional antagonism between CoREST and p300 as a regulatory axis of RA signaling in AML. Targeting this mechanism with Corin and ATRA re-sensitizes non-APL AML cells to RA-induced differentiation, suggesting a broader therapeutic approach for overcoming resistance in ATRA-refractory leukemias.

Keywords:  HDAC; LSD1; acute myeloid leukemia (AML); differentiation therapy; enhancer; epigenetic regulation; histone modification; p300

DOI:  https://doi.org/10.1101/2025.10.13.682235
Blood Adv. 2025 Nov 25. pii: bloodadvances.2025017742. [Epub ahead of print]

Post-transplant MRD Monitoring by TP53 Duplex Sequencing with APR-246 + Azacitidine Maintenance Predicts Outcomes.

David A Sallman, Amy F McLemore, Rami S Komrokji, Hany Elmariah, Andrew T Kuykendall, Nelli Bejanyan, Onyee Chan, Rawan Faramand, Joseph A Pidala, Sean J Yoder, Lia E Perez, Taiga Nishihori, Eric Padron, Hugo Fernandez, Jeffrey E Lancet, Asmita Mishra.

Outcomes are poor for TP53 mutant myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) patients who undergo allo-HSCT. Notably, minimal data exist on the impact of TP53 MRD monitoring post allo-HSCT. Thus, we completed duplex TP53 MRD sequencing for all patients on our prospective eprenetapopt (APR-246) + azacitidine maintenance study (n=14). Bone marrow aspirates were obtained prior to allo-HSCT, prior to the start of investigational therapy (day +30 to day +100) and after cycle 3 and cycle 12 of therapy. To assess low allele frequency mutations in TP53, a custom-targeted sequencing panel was used with duplex sequencing, targeting 30,000-70,000X duplex coverage to detect variants at a frequency as low as .005%. For all analyses, TP53 MRD negativity cutoff was 0.01%. All study patients had significant TP53 positivity prior to allo-HSCT and 57% post-HSCT. MRD evaluation after end of maintenance (12 cycles) was the strongest predictor of outcomes. Specifically, MRD negativity after cycle 12 strongly predicted OS (33.9 vs 20.4 months; P=.005) and EFS (33.9 vs 10.1 months; P=.004) with a trend for RFS (32.6 vs 13.5 months; P=.06). TP53 MRD was strongly predictive of outcomes, supporting incorporation of this assay in future novel strategies.

DOI: https://doi.org/10.1182/bloodadvances.2025017742
Bone Marrow Transplant. 2025 Nov 24.

Measurable residual mutated NPM1 before allogeneic transplant for acute myeloid leukemia.

Rasha W Al-Ali, Gege Gui, Niveditha Ravindra, Georgia Andrew, Devdeep Mukherjee, Zoë C Wong, Ying Huang, Jason Gerhold, Matt Holman, Austin Jacobsen, Julian D'Angelo, Jeffrey Miller, Karina Elias, Jeffery J Auletta, Firas El Chaer, Steven M Devine, Antonio Martin Jimenez Jimenez, Marcos J G De Lima, Mark R Litzow, Partow Kebriaei, Wael Saber, Stephen R Spellman, Scott L Zeger, Kristin M Page, Jerald P Radich, R Coleman Lindsley, Laura W Dillon, Christopher S Hourigan.

DOI: https://doi.org/10.1038/s41409-025-02757-1
Blood Adv. 2025 Nov 26. pii: bloodadvances.2024015776. [Epub ahead of print]

Clonal hematopoiesis may precede the diagnosis of aplastic anemia by several years.

Qian Wei Liu, Fang Fang, Huiwen Xue, Tove Wästerlid, Karin E Smedby, Xinyuan Liu.

Aplastic anemia (AA) is a bone marrow failure syndrome resulting from the immune destruction of hematopoietic stem cells. Clonal hematopoiesis (CH) is characterized by expansion of progenitor hematopoietic stem cells that harbor leukemogenic driver mutations. It has previously been shown that individuals with AA have a high prevalence of CH. However, the association between CH and AA remains unknown. We conducted a prospective, matched cohort study within the UK Biobank during 2006-2022. Individuals with CH were ascertained based on whole exome sequencing data. For each individual with CH, we randomly selected ten CH-free individuals, matched by sex, birth year, and ethnicity from the study population. We calculated hazard ratios (HRs) and 95% confidence intervals (CIs) of AA associated with CH by Cox regression model. We also studied the association by different mutations of CH. We identified 14,471 individuals with CH, and 144,323 matched individuals free of CH. Individuals with CH had a higher risk of AA (HR 2.72, 95% CI: 2.16-3.43), compared to reference group. The risk increase was greater for individuals with CH mutations in SRSF2 (HR 19.35, 95% CI: 11.07-33.80), TET2 (HR 4.45, 95% CI: 3.14-6.29), ASXL1 (HR 2.06, 95% CI: 1.06-4.00), or DNMT3A (HR 1.88, 95% CI: 1.31-2.70). In conclusion, CH may precede the diagnosis of AA, particularly in those with SRSF2, TET2, ASXL1, and DNMT3A mutations. Further studies are needed to understand the nature of this association and potential shared pathogenic mechanisms between CH and AA.

DOI: https://doi.org/10.1182/bloodadvances.2024015776
J Hematol Oncol. 2025 Nov 27. 18(1): 108

A phase 1/2 study of DS-1594 menin inhibitor in relapsed/refractory acute leukemias.

Jayastu Senapati, Marina Konopleva, Ghayas C Issa, Elias Jabbour, Tapan Kadia, Courtney DiNardo, Gautam Borthakur, Naveen Pemmaraju, Nicholas J Short, Musa Yilmaz, Indraneel Deshmukh, Joie Alvarez, Sanam Loghavi, Guilin Tang, Hussein A Abbas, Michael Andreeff, Kapil Bhalla, Narasimha M Midde, Nabil Said, Amy Noyalis, Derek E Mires, Jing Ning, Lianchun Xiao, Farhad Ravandi, Guillermo Garcia-Manero, Hagop M Kantarjian, Naval G Daver.

  Several menin inhibitors are in development targeting menin dependent leukemias, however available preclinical results show variable level of activity. We report the phase 1 portion (to establish a recommended phase 2 dose [RP2D]) and pharmacokinetic analysis of a phase 1/2 first-in-human clinical trial of DS-1594b menin inhibitor. Eligible patients included adults (≥ 18 years of age) with relapsed/refractory (R/R) acute myeloid leukemia (AML) or acute lymphoblastic leukemia (ALL) including but not restricted to those with KMT2A-rearrangement (r) or NPM1 mutation. Seventeen patients at a median of age 56 years (range, 19-82 years) were treated, 15 (88%) had R/R AML, and 2 (12%) had R/R B-ALL; 9 (53%) had a KMT2A-r but none had an NPM1 mutation. The median prior lines of therapy was 3 (range 1-8) and 5 patients (29%) had received prior menin inhibitors. Five dose escalation cohorts were evaluated; no RP2D was established, and the trial was stopped at phase 1 due to a decision by supporting company due to lack of efficacy at studied dose levels and portfolio realignment. Differentiation syndrome (DS) was seen in 5 patients (29%); 2 in cohort 1 (70 mg twice daily, n = 4) 1 each had grade 1 and grade 4 DS, 3 patients in cohort 2 (50 mg twice daily/100 mg daily, n = 4) of whom 2 had grade 2 and 1 patient had grade 3 DS (considered as dose limiting toxicity). No DS was noted at cohort 3 (20 mg/day), and in subsequent dose-escalation cohorts (cohorts 4 and 5) a lead-in ramp-up dosing starting at 20 mg/day was instituted to improve tolerability. Other relevant treatment emergent adverse events of grade ≥ 3 included infections; pneumonia and febrile neutropenia in 7 patients each (41%), and sepsis in 6 patients (35%). No study drug related deaths were noted. No patient achieved a response, however 4 patients (23%) had > 25% bone marrow blast reduction. Pharmacokinetic analysis showed DS-1594b reached maximum concentration approximately in 2 h with total exposure increasing with escalating doses and reached stead-state by Cycle 1 Day 8. DS-1594b showed limited efficacy at the doses tested but appeared safe with a lead-in dosing approach.

Keywords:  Acute myeloid leukemia; Differentiation syndrome; KMT2A; Menin inhibitor; NPM1

DOI:  https://doi.org/10.1186/s13045-025-01757-4
JCI Insight. 2025 Nov 25. pii: e190833. [Epub ahead of print]

Influence of Oxidation Resistance 1 on disease progression in chronic myeloid leukemia.

Weiqi Huang, Bin Liu, Liping Hu, Chi-Hao Luan, Priyam Patel, Elizabeth T Bartom, Elizabeth A Eklund.

  Survival in chronic myeloid leukemia (CML) was dramatically improved by development of tyrosine kinase inhibitors (TKIs) directed to the BCR::ABL1 oncogene. Unfortunately, ~30% of CML patients develop TKI-resistance during prolonged treatment, with enhanced blast crisis risk. Oxidation Resistance 1 (Oxr1) regulates anti-oxidant pathways that detoxify reactive oxygen species (ROS) generated by the phagocyte-NADPH oxidase. In the current studies, we found that Oxr1 expression increased in hematopoietic stem and progenitor cells (HSPCs) from CML mice versus controls; decreased during TKI-induced remission; and rose during chronic phase relapse. Oxr1 has long and short isoforms, and we found increased short, but decreased long, Oxr1 in mice or humans during CML relapse. We determined long Oxr1 prevents ROS accumulation in CML marrow, but short Oxr1 is a dominant negative. Previously, we found exaggerated and sustained emergency granulopoiesis in CML mice, with repeated episodes facilitating relapse during TKI-remission. In the current studies, we found knocking-down Oxr1 in murine marrow further accelerates CML progression during this physiologic stress. We found increased DNA-damage in HSPCs from these mice, including a BCR::ABL1 kinase-domain mutation found in TKI-resistant human CML. These studies suggest long Oxr1 detoxifies ROS to decrease mutagenesis in CML, but aberrant short Oxr1 expression enhances progression.

Keywords:  Hematology; Innate immunity; Leukemias; Oncology

DOI:  https://doi.org/10.1172/jci.insight.190833
bioRxiv. 2025 Oct 09. pii: 2025.10.08.679601. [Epub ahead of print]

A Unifying Mechanism for Shared Splicing Aberrations in Splicing Factor Mutant Cancers.

Prajwal C Boddu, Rahul Roy, Stephen Hutter, Francis Baumgartner, Wenxue Li, Gabriele Todisco, Francesca Ficara, Matteo Giovanni Della Porta, Yansheng Liu, Torsten Haferlach, Manoj M Pillai.

Cancer-associated splicing factor (SF) mutations in SF3B1 , U2AF1 , and SRSF2 induce distinct changes in alternative splicing (AS). Yet these mutations are strikingly mutually exclusive, pointing to a convergent downstream mechanism. We hypothesized this would be reflected in the AS transcriptome. By analyzing transcriptomes of 395 patients with clonal myeloid disorders and 64 healthy donors, we found most AS alterations to be mutation-specific. However, a robust subset, enriched in the retained intron (RI) program, was shared across mutants. These RI events were bidirectional but highly concordant, and mirrored the effects of SRSF1 loss. SF-mutant states induced hypophosphorylation of RS domains in SRSF1, reducing its function. This arose from an altered AMPKα-AKT balance impairing the AKT-SRPK1-SRSF1 axis. A common upstream trigger was activation of DNA damage response (DDR) by transcriptional R-loops, which increased AMPKα signaling and reduced AKT activity. Pharmacologic DDR activation recapitulated reduced AKT/SRPK1 activity and SRSF1 hypophosphorylation, while relieving DDR restored SRSF1 phosphorylation and corrected RI defects. Thus, beyond cis-acting, mutation-specific changes, SF-mutant cancers share a trans-acting, stress-driven AS signature wherein DDR signaling rewires SRSF1 activity impacting AS. Our results link replication stress, kinase signaling, and RNA processing across genetically diverse clonal states, highlighting potential therapeutic approaches at these nodes.
Highlights: While most splicing changes differ by splicing factor (SF) mutation, certain retained introns are common across subtypes.Changes in RI are bidirectional, concordant across mutant groups, and mirrors SRSF1 loss.SF mutations activate DDR, triggering an AMPKα/AKT imbalance that culminates in SRSF1 hypophosphorylation.Relieving R-loop induced DDR restores SRSF1 phosphorylation and reverses RI.

DOI: https://doi.org/10.1101/2025.10.08.679601
bioRxiv. 2025 Nov 13. pii: 2025.11.07.687000. [Epub ahead of print]

TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity.

Jacob Du, Uthpala N Wijayaratna, Xinyue Wang, Jeffrey P Fung, Belinda Huang, Farzin Farzaneh, Donald B Kohn, Alexis J Combes, Karin M L Gaensler.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and is associated with poor outcomes due to frequent relapse after remission induction. While hematopoietic stem cell transplantation (HSCT) can improve survival, many individuals, especially older patients, are ineligible. Prior immunotherapies have not reliably induced effective anti-leukemic immunity and have been associated with severe and unpredictable toxicities. Thus, there is a need for safe and effective therapies that reduce relapse and increase overall survival (OS). We have developed a universally applicable, patient-specific, lentivirally engineered autologous AML cell vaccine, TriLeukeVax (TLV), designed to stimulate leukemia-specific cytolytic immune responses in AML patients in remission. To generate TLV, AML cells are engineered to express the highly synergistic combination of the co-stimulatory protein CD80 and the IL-15/IL-15-receptor alpha (IL-15Rα) heterodimer. Prior proof-of-concept (POC) studies demonstrated eradication of disease in >80% of leukemic mice with serial administration of TLV. In the current studies, TLV was generated from 59/60 cryopreserved, diagnostic bone marrow-derived patient AML samples. Ex vivo priming of post-remission patient T-cells by ex vivo co-culture with autologous TLV stimulated robust proliferative and cytotoxic responses. In secondary co-cultures, T-cells previously primed by initial co-culture with TLV, showed greater clonal expansion and leukemia-specific cytolytic activity towards de novo autologous AML blasts than did control, unprimed T-cells. The enhanced anti-leukemic activity of TLV-primed T-cells against de novo AML confirms the potential for vaccine administration to effectively target minimal residual disease (MRD) persisting after chemotherapy and reduce relapse.
Key Points: TriLeukeVax induces proliferation, activation, and effective anti-leukemic cytolytic responses in remission T-cells.Primed T-cells show polyclonal expansion and transcription profiles associated with proliferation, memory, and cytotoxicity.
Abstract Figure:

DOI: https://doi.org/10.1101/2025.11.07.687000
Blood. 2025 Nov 25. pii: blood.2025031248. [Epub ahead of print]

Somatic genetic rescue in ZCCHC8-associated telomere biology disorders.

Sophie De Tocqueville, Flavia Donaires, Nicholas F DeCleene, Ibrahima Ba, Mina Nouri, Laëtitia Kermasson, Malika Chelbi, Emmanuel Bergot, Thierry M Leblanc, Raphael Borie, Quentin Philippot, Elise Antone, Grégoire Prevot, Elodie Blanchard, Boris Keren, Elodie Lainey, Marilia Bazzo Catto, Barbara A Santana, Settara C Chandrasekharappa, Frank X Donovan, Luiz Fernando Bazzo Catto, Isabelle Callebaut, Neal S Young, Carine Halfon-Domenech, Rodrigo T Calado, Alison A Bertuch, Fernanda Gutierrez-Rodrigues, Caroline Kannengiesser, Patrick Revy.

Here we show that somatic genetic rescue is frequent in telomere biology disorders (TBDs) caused by germline ZCCHC8 variants. Our results highlight the critical intrinsic role of ZCCHC8 in human hematopoiesis and a potential mechanism for disease modification in TBDs.

DOI: https://doi.org/10.1182/blood.2025031248
Cell Stem Cell. 2025 Nov 24. pii: S1934-5909(25)00405-9. [Epub ahead of print]

Reversing lysosomal dysfunction restores youthful state in aged hematopoietic stem cells.

Tasleem Arif, Jiajing Qiu, Hossein Khademian, Anusree Lohithakshan, Anagha Menon, Vijay Menon, Mary Slavinsky, Maxime Batignes, Miao Lin, Robert Sebra, Kristin G Beaumont, Deanna L Benson, Nikolaos Tzavaras, Mickaël M Ménager, Saghi Ghaffari.

  Aging impairs hematopoietic stem cells (HSCs), driving clonal hematopoiesis, myeloid malignancies, and immune decline. The role of lysosomes in HSC aging-beyond their passive mediation of autophagy-is unclear. We show that lysosomes in aged HSCs are hyperacidic, depleted, damaged, and aberrantly activated. Single-cell transcriptomics and functional analyses reveal that suppression of hyperactivated lysosomes using a vacuolar ATPase (v-ATPase) inhibitor restores lysosomal integrity and metabolic and epigenetic homeostasis in old HSCs. This intervention reduces inflammatory and interferon-driven programs by improving lysosomal processing of mitochondrial DNA and attenuating cyclic GMP-AMP synthase-stimulator of interferon gene (cGAS-STING) signaling. Strikingly, ex vivo lysosomal inhibition boosts old HSCs' in vivo repopulation capacity by over eightfold and improves their self-renewal. Thus, lysosomal dysfunction emerges as a key driver of HSC aging. Targeting hyperactivated lysosomes reinstates a youthful state in old HSCs, offering a promising strategy to restore hematopoietic function in the elderly.

Keywords:  MMP; aging; cGas-STING; hematopoietic stem cell; inflammation; interferon; lysosomes; mitochondria; mtDNA; quiescence

DOI:  https://doi.org/10.1016/j.stem.2025.10.012
Cell Rep. 2025 Nov 25. pii: S2211-1247(25)01374-9. [Epub ahead of print]44(12): 116602

Harnessing the E3 ligase SPOP for targeted degradation of the NUP98::KDM5A fusion oncoprotein.

Ecem Kirkiz, Gabriel Kaufmann, Simone Bergqvist, Pablo Fernández-Pernas, Thomas Eder, Laura Quell, Melanie Allram, Gabriele Manhart, Wencke Walter, Torsten Haferlach, Florian Grebien.

  Nucleoporin 98-rearranged (NUP98-r) acute myeloid leukemia (AML) is associated with poor outcomes and remains a major therapeutic challenge due to the absence of strategies that directly eliminate NUP98 fusion oncoproteins. Targeted degradation of cancer-driving oncofusions is an attractive approach, but the molecular mechanisms controlling NUP98 oncofusion stability are unknown. Using a CRISPR-Cas9 screen, we identify the E3 ligase Speckle-type POZ protein (SPOP) as a direct regulator of NUP98 fusion oncoprotein stability and a novel tumor suppressor in NUP98-r AML. Loss of SPOP increases NUP98 oncofusion levels and promotes leukemia cell proliferation. Exploiting this specificity, we demonstrate that induced proximity of SPOP and NUP98::lysine-specific demethylase 5A (KDM5A) through a biological proteolysis-targeting chimera (bioPROTAC) induces full clearance of the fusion oncoprotein, driving terminal differentiation and apoptosis of NUP98-r leukemia cells in vitro and in vivo. This study identifies SPOP as a direct regulator of NUP98 oncofusion stability and outlines a strategy to redirect the ubiquitin-proteasome system against oncogenic fusions.

Keywords:  AML; CP: cancer; NUP98; PROTAC; SPOP; condensate; fusion protein; targeted protein degradation

DOI:  https://doi.org/10.1016/j.celrep.2025.116602
bioRxiv. 2025 Nov 14. pii: 2025.11.13.688350. [Epub ahead of print]

Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS.

Nurefsan E Sariipek, Ksenia R Safina, Wesley S Lu, Shuqiang Li, J Thomas Janes, McKayla Van Orden, Kenneth J Livak, Haynes Heaton, Vincent T Ho, John Koreth, Marlise R Luskin, Gabriel K Griffin, Jacqueline S Garcia, R Coleman Lindsley, Corey Cutler, Robert J Soiffer, Jerome Ritz, Catherine J Wu, Joseph H Antin, Andrew A Lane, Mahasweta Gooptu, Peter van Galen.

Hematopoietic stem cell transplantation (HSCT) offers the best curative option for acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), yet relapse remains common. Current relapse detection methods are often too late for effective intervention. To identify earlier predictors and therapeutic targets, we performed longitudinal single-cell RNA and T cell receptor (TCR) sequencing of bone marrow from 33 AML/MDS patients during post-transplant immune reconstitution, comparing those who relapsed to those who remained in remission. Persistence of recipient hematopoietic stem and progenitor cells (HSPCs) in the marrow was associated with relapse months later. These residual recipient HSPCs harbored copy number variations (CNVs), supporting their leukemic origin, and overexpressed PRAME and CALCRL compared to coexisting donor HSPCs. Further, in a subset of TP53 -mutant disease, low TCR diversity with skewing toward dominant clonotypes foreshadowed relapse. These findings lay the groundwork for improved relapse prediction and nominate therapeutic targets for early post-transplant intervention.

DOI: https://doi.org/10.1101/2025.11.13.688350
Br J Haematol. 2025 Nov 25.

Comorbidities and mutations including single- and multihit TET2 mutations in relation to outcome in chronic myelomonocytic leukaemia-A population-based study.

Matilda Kjellander Kynning, Ebba Westerberg, Linda Forsell, Maria Creignou, Daniel Moreno Berggren, Bianca Tesi, Elsa Bernard, Elli Papaemmanuil, Yasuhito Nannya, Lucia Cavelier Franco, Davide Valentini, Eva Hellström Lindberg, Seishi Ogawa, Elisabeth Ejerblad, Johanna Ungerstedt.

  To explore the relation between disease characteristics, comorbidities, mutations and overall survival (OS) in chronic myelomonocytic leukaemia (CMML), we collected data from a population-based cohort of 149 consecutive patients. TET2 mutation (TET2MT) was associated with higher haemoglobin, less leucocytosis and longer OS compared to no TET2MT (TET2WT), despite patients being significantly older. Patients with multihit TET2MT had the most favourable outcome (HR 0.55, CI 0.35-0.88, p < 0.05). Multihit TET2MT was associated with lower lactate dehydrogenase and less monocytosis, indicating multihit TET2MT as a separate disease entity. Autoimmune disease (AID) was present in 33.6% of patients, with no association to any mutations. In multivariable analysis, the number of TET2MT was demonstrated to be an independent factor associated with improved OS, and RUNX1MT, myeloproliferative CMML (CMML-MP), ECOG >0 and transfusion dependence remained significant adverse factors. Internal validation including cross-validation and correction for optimism consistently demonstrated that a prognostic model containing the number of TET2MT, RUNX1, CMML-MP, ECOG >0 and transfusion dependence showed better calibration, discrimination and overall performance than CPSS-Mol in predicting OS. Importantly, the addition of TET2 mutation status to CPSS-Mol also improved the CPSS-Mol score performance. Taken together, TET2MT status, especially multihit TET2MT, defines a specific CMML phenotype and should be considered in future prognostic scores.

Keywords:   TET2 ; autoimmune disease; comorbidities; thrombosis

DOI:  https://doi.org/10.1111/bjh.70264
bioRxiv. 2025 Oct 27. pii: 2025.10.27.684807. [Epub ahead of print]

Mitofusin agonists enhances long-term engraftment and potency of HSC cultures in vivo.

Alyssa Biondo, Gabriela Candelaria, Daniel Jin, Emily Lin, Daniel McLaughlin, Zhaolun Liang, Katherine Leong, Christopher D Hillyer, Hans-Willem Snoeck, Larry L Luchsinger.

Umbilical cord blood (CBU) is a valuable source of hematopoietic stem cells (HSCs) due to its superior donor compatibility and lower incidence of graft-versus-host disease. However, its limited HSC content restricts its use in adult transplantation, necessitating new targets for ex vivo expansion and improved HSC potency. Mitofusin 2 (MFN2), a mitochondrial membrane fusion protein, is necessary for preserving HSC function and agonists of mitofusin activity have been characterized. We report that ex vivo culture of CBU HSCs with mitofusin agonists (MAs) enhances long-term repopulating activity by over five-fold in both primary and secondary transplantation assays without changes of total nucleated cells or phenotypic HSCs. Mechanistically, MA-treated HSCs show suppressed protein synthesis, increased autophagic flux, and elevated lysosomal acidification. Transcriptomic analysis implicates downregulation of MTOR signaling, and immunoprecipitation studies confirm a direct interaction between MFN2 and MTOR. These data support a model in which fusion-competent MFN2 sequesters MTOR, promoting a catabolic state that preserves HSC potency. Our findings suggest a novel MFN2-MTOR regulatory axis that enhances the functional expansion of human HSCs for potential therapeutic application.

DOI: https://doi.org/10.1101/2025.10.27.684807
Nat Commun. 2025 Nov 26. 16(1): 10591

NLRP3-induced systemic inflammation controls the development of JAK2V617F mutant myeloproliferative neoplasms.

Ruth-Miriam Koerber, Calvin Krollmann, Kevin Cieslak, Elisabeth Tregel, Maria L Saenz, Tim H Brümmendorf, Steffen Koschmieder, Martin Griesshammer, Ines Gütgemann, Conny K Baldauf, Thomas Fischer, Peter Brossart, Carl Christian Kolbe, Eicke Latz, Dominik Wolf, Lino L Teichmann.

The development of Philadelphia chromosome-negative classical myeloproliferative neoplasms (MPN) involves an inflammatory process that facilitates outgrowth of the malignant clone and correlates with clinical outcome measures. This raises the question to which extent inflammatory circuits in MPN depend on activation of innate immune sensors. Here, we investigate whether NLRP3, which precipitates inflammasome assembly upon detection of cellular stress, drives murine JAK2V617F mutant MPN. Deletion of Nlrp3 within the hematopoietic compartment completely prevents increased IL-1β and IL-18 release in MPN. NLRP3 in JAK2V617F hematopoietic cells, but not in JAK2 wild type radioresistant cells, promotes excessive platelet production via stimulation of the direct thrombopoiesis differentiation pathway, as well as granulocytosis. It also promotes expansion of the hematopoietic stem and progenitor cell compartment despite inducing pyroptosis at the same time. Importantly, NLRP3 inflammasome activation enhances bone marrow fibrosis and splenomegaly. Pharmacological blockade of NLRP3 in fully established disease leads to regression of thrombocytosis, splenomegaly and bone marrow fibrosis. These findings suggest that NLRP3 is critical for MPN development and its inhibition represents a new therapeutic intervention for MPN patients.

DOI: https://doi.org/10.1038/s41467-025-65673-4
Blood Cancer J. 2025 Nov 24. 15(1): 207

European LeukemiaNet criteria for safety and efficacy evaluation of new drugs for myelofibrosis.

Monia Marchetti, Alessandro Maria Vannucchi, John O Mascarenhas, Alberto Alvarez-Larran, Prithviraj Bose, Robert Peter Gale, Claire Harrison, Rűdiger Hehlmann, Jean-Jacques Kiladjian, Steffen Koschmieder, Ruben Mesa, Francesco Passamonti, Alessandro Rambaldi, Ayalew Tefferi, Tiziano Barbui.

Most myelofibrosis (MF) drug approvals by Health Authorities are based on 1 or 2 outcome measures such as spleen volume reduction and/or improved quality of life. This 1-2 dimensional approach fails to capture the clinical complexity of MF. A European LeukemiaNet (ELN) task force developed a composite endpoint that allows multiple outcomes to be simultaneously measured. The panel used the Desirability Of Outcome Ranking (DOOR) method to assign 25 outcomes into 4 quartiles based on a multi-dimensional desirability score and build a 5-layer composite outcome named Desirability of Myelofibrosis Outcomes (DEMYO). Outcome operational definitions were tested by Delphi consensus, and correlations with survival were validated by a literature review. The outcomes assigned to the first two quartiles were negatively correlated with leukemia-free survival and survival. DEMYO comprehensively captures relevant MF clinical features and meaningful endpoints. Despite DEMYO requiring validation based on available trial data, it is expected to improve the quality of Health Authority approvals for new drugs for MF.

DOI: https://doi.org/10.1038/s41408-025-01381-y
Blood Adv. 2025 Nov 25. pii: bloodadvances.2025017908. [Epub ahead of print]

Predictive Capacity of Peri-Transplant Measurable Residual Disease Thresholds in NPM1-Mutant Acute Myeloid Leukemia.

Jan Schröder, Friederike Schwartz, Judith Metzdorf, Nick Barensteiner, Lucas Mix, Lisa-Marie Necke, Adrian Fehn, Andreas Riedel, Liv Jentzsch, Philipp Faustmann, Wichard Vogel, Wolfgang Andreas Bethge, Thomas Schroeder, Claudia Lengerke.

Minimal residual disease (MRD) monitoring for mutated NPM1 is increasingly used to guide treatment decisions in patients with acute myeloid leukemia (AML) carrying this mutation. NPM1-MRD positivity after induction was shown to identify patients who benefit from allogeneic hematopoietic cell transplantation (alloHCT), and NPM1-MRD monitoring after alloHCT can detect early relapse enabling the prompt initiation of salvage therapy. However, recommendations for clinical decision making based on peri-transplant NPM1-MRD levels are missing. In this study, we retrospectively analyze 172 patients with NPM1-mutant AML treated at two German centers to explore the predictive values of NPM1-MRD measured pre- and post-alloHCT. We found that pre-transplant MRD negativity was a strong predictor of favorable long-term overall survival (OS). In contrast, patients with positive and negative NPM1-MRD status at day 30 post-HCT showed comparable OS. Finally, statistically derived NPM1-MRD thresholds effectively stratified MRD-high and MRD-low patient groups with differential outcome with two peri-transplant MRD risk scores obtained by longitudinal integration. Firstly, a combined pre-HCT/+d30 post-HCT score to guide early reduction of immunosuppression (C-index, 0.737), and secondly, a combined pre-HCT+d30+d100 score to guide later interventions post-HCT (C-index, 0.841; stratified 2-year OS groups 100%, 90.1%, 57.1% and 25.7%; p<0.0001). This approach predicted OS better than age, FLT3-ITD status, or morphological remission status. We propose that in the peri-transplant setting, NPM1-MRD thresholds are superior to conventional MRD analysis based on binary or log-step change data.

DOI: https://doi.org/10.1182/bloodadvances.2025017908
Nat Commun. 2025 Nov 25. 16(1): 10592

The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes.

Henrik Lilljebjörn, Pablo Peña-Martínez, Hanna Thorsson, Rasmus Henningsson, Marianne Rissler, Niklas Landberg, Noelia Puente-Moncada, Sofia von Palffy, Vendela Rissler, Petr Stanek, Jonathan Desponds, Xiangfu Zhong, Gunnar Juliusson, Vladimir Lazarevic, Sören Lehmann, Magnus Fontes, Helena Ågerstam, Carl Sandén, Christina Orsmark-Pietras, Thoas Fioretos.

Acute myeloid leukemia is a genetically and cellularly heterogeneous disease. We characterize 120 AMLs using genomic and transcriptomic analyses, including single-cell RNA sequencing. Our results reveal an extensive cellular heterogeneity that distorts the bulk transcriptomic profiles. Selective examination of the transcriptional signatures of >90,000 immature AML cells identifies four main clusters, thereby extending current genomic classification of AML. Notably, NPM1-mutated AML can be stratified into two clinically relevant classes, with NPM1class I associated with downregulation of MHC class II and excellent survival following hematopoietic stem cell transplantation. NPM1class II is instead associated with resistance to allogeneic T cells in an ex vivo co-culture assay, and importantly, dismal survival following hematopoietic stem cell transplantation. These findings provide insights into the cellular state space of AML, define diagnostic entities, and highlight potential therapeutic intervention points.

DOI: https://doi.org/10.1038/s41467-025-66546-6
bioRxiv. 2025 Oct 09. pii: 2025.10.08.681215. [Epub ahead of print]

A Rapid Gene Expression Profiler Classifies AML Tumor Responsiveness to Standard Therapies.

Stephen E Kurtz, Christopher A Eide, Andy Kaempf, Nicola Long, Alexandria Miller, Daniel Bottomly, Shannon K McWeeney, Curtis Lachowiez, Sudharshan Anand, Stanley W K Ng, Jean C Y Wang, John E Dick, Jeffrey W Tyner.

The emergence of transcriptional signatures that define cell types and pathways has made it possible to guide cancer therapy selection through gene expression profiling. We developed a rapid qPCR-based platform to profile cell state, stemness, and BCL2 family gene expression as a companion diagnostic test for acute myeloid leukemia (AML). We validated the stability and utility of the signatures across multiple measurement platforms and using patient samples from two centers. Integrating these signatures with clinical features enables an expedient means to predict the likelihood of patient responses to two standard-of-care therapies: intensive chemotherapy and hypomethylating agent plus venetoclax (HMA+Ven). For patients treated with HMA+Ven, expression levels of the promonocyte-like signature and BCL2 add predictive value for response and overall survival in multivariable models that include genetic features. The incorporation of the rapid profiler into the prospective evaluation of newly diagnosed AML patients may enhance treatment stratification and improve outcomes.

DOI: https://doi.org/10.1101/2025.10.08.681215
Blood Neoplasia. 2025 Nov;2(4): 100163

Predicting secondary myeloid neoplasms in acquired aplastic anemia using machine learning models.

Ahmet Celal Toprak, Mutlu Mete, Julia J Shi, Daria V Babushok, Carmelo Gurnari, Jaroslaw P Maciejewski, Zoe Bass, Zehra Tombul, Carlos I A Santos, Munevver N Duran, Hussein Awada, Ibrahim Ibrahim, Alper Olcal, Yusuf Ozcan, Leslie Guerrero, Julio Alvarenga Thiebaud, Taha Bat.

Patients with acquired aplastic anemia (AA) treated with immunosuppressive therapy (IST) face up to a 20% long-term risk of developing secondary myeloid neoplasms (sMNs), including acute myeloid leukemia and myelodysplastic syndromes. Although hematopoietic stem cell transplantation (HSCT) is curative and prevents sMNs, older patients and those lacking suitable donors have historically received IST as first-line therapy. Recent improvements in HSCT outcomes have expanded transplant eligibility, highlighting the need for tools to better identify patients at high risk for sMN. Validated predictive models could help guide early HSCT consideration or tailor surveillance strategies. We developed 2 binary machine learning models to predict sMN development in patients with acquired AA at clinically relevant time points: diagnosis (model 1) and 6 months after IST response (model 2). We analyzed data from 275 adult patients with AA treated at University of Texas Southwestern, Cleveland Clinic, and the Hospital of the University of Pennsylvania between 1975 and 2023. Seventy-nine clinical variables were collected, including demographics, somatic mutations, and treatment response. Neural networks were trained with leave-1-out crossvalidation. Both models achieved strong performance (area under the curve, 0.82; sensitivity, 0.82, specificity, 0.73). Shared key predictors included DNMT3A mutation, CUX1 mutation, total mutation count, and age. TET2 mutation was specific to model 1; paroxysmal nocturnal hemoglobinuria clone presence was unique to model 2. High-risk classification was significantly associated with worse overall survival (P < .0001). These findings support the feasibility of machine learning-based sMN risk prediction in AA. With training on larger data sets and external validation, these models may support individualized decision-making around HSCT and post-IST surveillance.

DOI: https://doi.org/10.1016/j.bneo.2025.100163
bioRxiv. 2025 Oct 08. pii: 2025.10.02.680138. [Epub ahead of print]

Single-cell spatial mapping reveals dynamic bone marrow microarchitectural alterations and enhances clinical diagnostics in MDS.

Ryan Nachman, Aleksandra Kopacz, Caitlin Unkenholz, Jian Chai, Arvin Ruiz, Itzel Valencia, Jeanne Jiang, Fabio Socciarelli, Jiwoon Park, Christopher Mason, Ling Zhang, David Sallman, Gail J Roboz, Pinkal Desai, Justin Kaner, Joshua Fein, Monica Guzman, Neal Lindeman, Amy Chadburn, Madhu Ouseph, Paul Simonson, Julia Geyer, Giorgio Inghirami, Shahin Rafii, David Redmond, Sanjay Patel.

Myelodysplastic neoplasms (MDS) are genetically diverse hematopoietic cancers characterized by ineffective blood cell production, peripheral cytopenias, and an increased risk of acute myeloid leukemia. Diagnosis traditionally requires subjective histomorphologic assessment of a bone marrow biopsy sample. The potential biological and/or clinical relevance of subtle microarchitectural changes, unrecognizable using conventional methods, remains unknown. Here, we applied a recently developed AI-driven, whole slide imaging-based single-cell spatial proteomic profiling method to 77 annotated MDS and precursor state bone marrow tissue samples, including longitudinal cases. Compared to age-matched controls, MDS tissues showed significant changes in progenitor cell frequencies, morphologies of erythroid precursors and megakaryocytes, HSPC displacement from vasculature, abnormal progenitor cell clustering, and disrupted erythroid islands. Some alterations correlated more closely with specific mutations (e.g., SF3B1, TP53 ) than clinical risk scores (IPSS-M). Using all extracted tissue features, we developed a composite spatially informed "MDS severity score", which aligned with clinical and genetic parameters across serial samples. This work uncovers previously unrecognized, genotype-linked microarchitectural alterations in MDS, the measurement of which may enhance existing diagnostic and disease monitoring strategies.

DOI: https://doi.org/10.1101/2025.10.02.680138
bioRxiv. 2025 Nov 09. pii: 2025.11.07.687077. [Epub ahead of print]

Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses.

Matthew W Hagen, Nicollette J Setiawan, Rachel Wellington, Kelsey A Woodruff, Carli Newman, Taylor M Billings, Mary N Nazzaro, Brandon Hadland, Christina M Termini.

Syndecan-2 is a heparan sulfate proteoglycan highly enriched on murine bone marrow hematopoietic stem cells (HSCs) compared to terminally differentiated hematopoietic cells. Syndecan-2 binds growth factors via its heparan sulfate glycosaminoglycan chains to coordinate cell signaling. Knockdown of syndecan-2 reduces HSC self-renewal ability and promotes cell cycling via Cdkn1c . In this study, we analyzed the function of syndecan-2 expressed by bone marrow niche cells in hematopoiesis and HSC self-renewal. We determined that syndecan-2 is highly expressed by bone marrow mesenchymal stromal cells and moderately expressed by endothelial cells. To test the function of niche-expressed syndecan-2 in hematopoiesis, we generated transgenic mice depleted of Sdc2 in Lepr- targeted mesenchymal stromal cells ( Sdc2 ΔMSC mice) or Cdh5 -targeted endothelial cells ( Sdc2 ΔEC mice). Loss of syndecan-2 from endothelial or mesenchymal stromal cells did not change bone marrow HSC frequencies or numbers. However, depletion of syndecan-2 from Lepr -targeted mesenchymal stromal cells, but not Cdh5 -targeted endothelial cells, diminishes HSC self-renewal ability analyzed by competitive transplants into lethally irradiated mice. Ex vivo studies further show that HSCs co-cultured with HS-5 stromal cells depleted of SDC2 exhaust more rapidly than HSCs cultured with control HS-5 cells. Single-cell RNA sequencing analyses reveal that the depletion of Sdc2 from mesenchymal stromal cells significantly remodels the HSC transcriptome by enriching for pathways associated with excessive growth factor signaling. Together, our findings suggest that HSC self-renewal is supported by cell-extrinsic mechanisms enacted by syndecan-2 from the MSC niche, highlighting the importance of the niche proteoglycome in HSC functions.
KEY POINTS: The heparan sulfate proteoglycan syndecan-2 expressed by mesenchymal stromal cells but not endothelial cells regulates HSC self-renewal Depletion of syndecan-2 from Lepr -targeted mesenchymal stromal cells remodels the hematopoietic stem cell transcriptional landscape.

DOI: https://doi.org/10.1101/2025.11.07.687077
bioRxiv. 2025 Oct 15. pii: 2025.10.14.682414. [Epub ahead of print]

Dynamic BH3 profiling predicts clinical outcomes in acute myeloid leukemia.

Emma-Jayne Minihane, Leah Krotee, Jason Wu, Lindsey Thornton, Geoffrey Fell, Sonja Herter, Jeremy Ryan, Amulya Jakkani, Kate Marinchev, Andrew A Lane, Marlise R Luskin, Eric S Winer, Evan C Chen, Shai Shimony, Martha Wadleigh, Rahul Vedula, Virginia O Volpe, Christopher Reilly, Ilene Galinsky, Daniel J DeAngelo, Richard M Stone, Donna S Neuberg, Anthony Letai, Jacqueline S Garcia.

Predictive biomarkers can potentially meet the need for improved drug assignment in acute myeloid leukemia (AML). Fewer than half of AML patients have actionable mutations: consequently, targeted therapy achieves remission in only a fraction of those who have them. Dynamic BH3 Profiling (DBP), a functional assay, can measure changes in ex vivo drug-induced apoptotic priming in multiple cancers. To assess the feasibility and predictive capacity of DBP in AML, we prospectively tested DBP using a fixed-drug panel in myeloblasts from 92 patients. We generated a database combining genetic and functional annotation. Established AML clinical and genetic prognostic characteristics were associated with drug-induced apoptotic priming. We observed distinct inter patient sensitivities to single drugs or combinations with the BCL2-inhibitor venetoclax, and intra patient apoptotic priming differences based on CD123-expression within distinct cell subpopulations. DBP further predicted the likelihood of remission to chemotherapy and targeted agents, supporting its use to identify optimal personalized therapy.
Statement of significance: Dynamic BH3 profiling provides patient-specific drug vulnerability data in real-time to inform prognosis and therapy selection.
Key takeaways: Dynamic BH3 profiling can be performed on bone marrow and leukemic blood from AML patients in 48 hours.Known clinical prognostic factors associate with drug-induced apoptotic priming in AML.Drug-induced apoptotic priming identifies drug vulnerabilities in individual patients and predicts clinical response to chemotherapy and small molecule inhibitors.

DOI: https://doi.org/10.1101/2025.10.14.682414
Res Sq. 2025 Nov 03. pii: rs.3.rs-7956606. [Epub ahead of print]

PRDM15 regulates differentiation and proliferation of hematopoietic stem cells.

Ernesto Guccione, Nesteene Param, Alex Rialdi, Nayeli Guiterrez Trejo, Max Fortescue-Poole, Ke Wang, Habiba Zorgati, Daniel Lozano-Ojalvo, Magan Schwarz, Francesco Cantatore, Frank Fonseca, Kensey Portman, Kevin Mohammed, David Dominguez-Sola, Slim Mzoughi, Elvin Wagenblast.

Hematopoietic stem cells (HSCs) sustain lifelong hematopoiesis through a tightly regulated balance of self-renewal, proliferation and differentiation, particularly under stress conditions.Here, we identify PRDM15, a transcription factor with well described roles in early embryonic development, as a crucial regulator of hematopoiesis during stress responses. While PRDM15 deletion is tolerated at steady state in adult hematopoiesis, its absence severely impairs bone marrow reconstitution following transplantation, causing sustained reduction in bone marrow cellularity and differentiation blocks. Notably, PRDM15-deleted bone marrow exhibited an accumulation of stem and progenitor cells, indicating a block in lineage differentiation. Furthermore, in competitive transplantation assays, PRDM15-deficient cells were unable to compete with wild-type counterparts, demonstrating a profound loss of fitness.Transcriptomic and epigenomic analyses reveal PRDM15 as a critical regulator of differentiation and proliferation of HSCs. Mechanistically, PRDM15 directly regulates the expression of several key genes involved in proliferation and differentiation pathways, including the transcription factor Cux1 . Cux1 overexpression partially rescues colony-forming ability of PRDM15-deficient HSCs.These findings establish PRDM15 as a pivotal stress-responsive regulator of HSC differentiation and survival, with implications for therapeutic modulation of hematopoiesis.

DOI: https://doi.org/10.21203/rs.3.rs-7956606/v1
bioRxiv. 2025 Oct 31. pii: 2025.10.30.685582. [Epub ahead of print]

Inhibition of farnesyltransferase activity diminishes hematopoietic stem cell ex vivo expansion ability.

Carli Newman, Isabella M Alves, Matthew W Hagen, Rachel Wellington, Brandon Hadland, Anita M Quintana, Christina Marie Termini.

The rationale underlying this work is that elucidating the contribution of farnesyltransferase activity to hematopoietic stem cell expansion ex vivo will provide knowledge needed to better support hematopoietic stem cell expansion techniques for clinical applications that rely on this approach, like hematopoietic cell transplants and gene therapy. We discovered that pharmacological inhibition of farnesyltransferase activity with lonafarnib substantially diminished the ex vivo expansion potential of human and mouse hematopoietic stem cells, highlighting that hematopoietic stem cells rely on isoprenoids for their ex vivo maintenance.

DOI: https://doi.org/10.1101/2025.10.30.685582
Res Sq. 2025 Oct 21. pii: rs.3.rs-7746241. [Epub ahead of print]

CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias.

Ash Alizadeh, Mark Hamilton, Nick Phillips, Troy Noordenbos, Jan Boegeholz, Takeshi Sugio, Brian Sworder, Stefan Alig, Zinaida Good, Joseph Schroers-Martin, John Tamaresis, Mohammad Esfahani, Ying Lu, Mari Olsen, Chih Long Liu, Zachary Ehlinger, Moksha Desai, Lori Muffly, Robert Negrin, Sally Arai, Laura Johnston, Robert Lowsky, Everett Meyer, Andrew Rezvani, Judith Shizuru, Wen-Kai Weng, Parveen Shiraz, Surbhi Sidana, Sushma Bharawaj, Melody Smith, Saurabh Dahiya, Bita Sahaf, Matthew Frank, Crystal Mackall, Maximilian Diehn, David Kurtz, David Miklos.

CD19-directed chimeric antigen receptor T-cell therapy (CAR19) improves survival in patients with relapsed/refractory large B-cell lymphoma (rrLBCL) compared to immunochemotherapy with intent for autologous hematopoietic cell transplantation (HCT). However, major toxicities of CAR19 therapy include prolonged cytopenias, infection, and secondary hematologic malignancies. To investigate the mechanisms underlying these toxicities we studied a cohort of lymphoma patients receiving CAR19. CAR19-treated patients exhibited impaired immune reconstitution and increased infection compared to propensity-matched HCT-treated controls. Bone marrow analysis revealed prolonged post-CAR cytopenias is associated with clonal cytopenias of undetermined significance (CCUS) and is characterized by interferon-mediated inflammation. Despite durable lymphoma remissions, clonal hematopoiesis (CH) commonly expanded following CAR19 infusion and was associated with impaired immune reconstitution and the development of treatment related myeloid malignancy (tMN). The molecular composition and clinical outcomes of post-CAR tMN were comparable to those of post-HCT tMN. Single-cell DNA analysis revealed that most post-CAR CH clones harbored a single independent mutation and that CAR integration into T cells with CH mutations may drive persistence. These findings broadly implicate CH mutation burden and CH expansion in the development of post-CAR cytopenias and malignancies as well as mechanistically suggest these expansions occur in a background of marrow inflammation. Together, our results provide insight into the origins of key CAR19-associated toxicities, including infection and tMN.

DOI: https://doi.org/10.21203/rs.3.rs-7746241/v1
Cell Stem Cell. 2025 Nov 24. pii: S1934-5909(25)00408-4. [Epub ahead of print]

Space-associated stem cell hallmarks of aging and resilience in astronauts.

Jessica Pham, Shuvro P Nandi, Larisa Balaian, Claire Engstrom, Patrick Chang, Karla Mack, Inge van der Werf, Emma Klacking, Jenna Sneifer, Neha Katragadda, Kendale Wirtjes, Antonio Ruiz, Daisy Chilin-Fuentes, Elsa Molina, Pinar Mesci, Jana Stoudemire, Sheldon R Morris, Thomas Whisenant, Ludmil B Alexandrov, Catriona H M Jamieson.

  Previous reports revealed immune dysfunction, chromosomal abnormalities, cytokine deregulation, and telomere alterations after prolonged spaceflight. However, the stress of space on hematopoietic stem and progenitor cells (HSPCs) and the resilience properties maintaining lifelong hematopoiesis and immunity were not studied. We performed HSPC functionally organized multi-omics aging and resilience (HSPC-FOMA-R) analyses in 9 astronauts before, during, and after three short-duration International Space Station (ISS) missions. Whole-genome sequencing (with telomere length analysis and mitochondrial and clonal mutational profiling), whole-transcriptome sequencing (with RNA editing and retrotransposon analyses), single-cell RNA sequencing, cytokine arrays, and fluorescence-activated cell sorting (FACS) analyses assessed HSPC and immune subpopulation survival dynamics. We show that spaceflight is associated with partially reversible changes in HSPC survival and self-renewal, adenosine deaminase associated with RNA1 (ADAR1), telomere maintenance, mobilization, cell cycle, and "fight or flight" gene expression. Combined with clonal hematopoietic mutations, apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC3C) activation, and retrotransposon deregulation, HSPC-FOMA-R analyses are needed before extended missions.

Keywords:  ADAR1; APOBEC3C; astronauts; clonal mutations; hematopoietic stem and progenitor cells; mitochondria; resilience; retrotransposons; spaceflight; telomere

DOI:  https://doi.org/10.1016/j.stem.2025.11.001
bioRxiv. 2025 Oct 23. pii: 2025.10.22.681652. [Epub ahead of print]

FTO depletion does not alter m6A stoichiometry in AML mRNA: a reassessment using direct RNA nanopore sequencing.

Luke S Nicholson, Catarina Guimarães-Teixeira, Jianheng Fox Liu, Hui Xian Poh, Samie R Jaffrey.

The RNA demethylase FTO has been proposed to promote acute myeloid leukemia (AML) by demethylating N 6-methyladenosine (m6A) from oncogenic transcripts, especially MYC. However, the evidence that supports the idea that FTO demethylates m6A in AML relies on methods that are non-quantitative and unable to reveal m6A stoichiometry changes before or after FTO depletion. To directly test whether FTO regulates m6A in mRNA, we employed Oxford Nanopore direct RNA sequencing to map and quantify m6A at single-nucleotide resolution. We find that the stoichiometry of m6A sites throughout the transcriptome and especially at MYC-specific sites are unaffected despite depletion of FTO activity by knockout, knockdown, or pharmacologic inhibition. This pattern was seen in AML cell lines MONOMAC-6 and MOLM-13, as well as in the non-AML cell line HEK293T. We also find that the anti-leukemia effect of the small-molecule FTO inhibitor FB23-2 is not due to FTO inhibition since it remains cytotoxic to FTO-deficient cells. Instead of regulating m6A, we find that FTO depletion markedly increases N 6,2'-O-dimethyladenosine (m6Am) in snRNAs, consistent with m6Am in snRNA being a target of FTO. Overall, our findings do not support an 'm6A eraser' role for FTO in AML cell lines under the conditions tested, and they suggest that the reported demethylation functions of FTO on m6A should be reinvestigated using quantitative m6A mapping methods.

DOI: https://doi.org/10.1101/2025.10.22.681652