bims-tremyl 2024-09-01 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2024‒09‒01
thirty-one papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Stearoyl-CoA desaturase inhibition is toxic to acute myeloid leukemia displaying high levels of the de novo fatty acid biosynthesis and desaturation.
Clinical relevance of NFYA splice variants in patients with acute myeloid leukaemia undergoing intensive chemotherapy.
RNA shielding of P65 is required to potentiate oncogenic inflammation in TET2 mutated clonal hematopoiesis.
Clinical and Therapeutic Implications of Clonal Hematopoiesis.
Evolution of transcriptomic profiles in relapsed inv(16) acute myeloid leukemia.
A phase 2 trial of mini-hyper-CVD, blinatumomab, and ponatinib in Philadelphia positive acute lymphoblastic leukemia.
Menin inhibitors in pediatric acute leukemia: a comprehensive review and recommendations to accelerate progress in collaboration with adult leukemia and the international community.
Clonal heterogeneity in STAG2m myeloid neoplasms: the Mayo Clinic experience.
Absence of PNH-clones in DDX41mutant-GPS aids in their distinction from acquired BM failure syndromes.
STING is crucial for the survival of RUNX1::RUNX1T1 leukemia cells.
Common Driver Mutations in AML: Biological Impact, Clinical Considerations, and Treatment Strategies.
Effects of donor-engrafted clonal hematopoiesis in allogeneic and autologous stem cell transplantation: a systematic review and meta-analysis.
TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cells.
Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.
CRISPR screen of venetoclax response-associated genes identifies transcription factor ZNF740 as a key functional regulator.
Triplet therapy with gilteritinib, venetoclax, and azacitidine for relapsed/refractory FLT3mut acute myeloid leukemia.
Modelling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs.
Genetic causes and cardiovascular consequences of clonal hematopoiesis in the UK Biobank.
Characteristics and outcomes of children, adolescent, and young adult patients with myelodysplastic neoplasms: A single-center retrospective analysis.
Hypomethylating agents are Effective in Treatment for Relapsed Myelofibrosis After Allogeneic Hematopoietic Cell Transplantation.
WT1 together with RUNX1::RUNX1T1 targets DUSP6 to dampen ERK activity in acute myeloid leukaemia.
HLA-lacking clones in aplastic anaemia: Adaptive or maladaptive?
A multidimensional analysis reveals distinct immune phenotypes and the composition of immune aggregates in pediatric acute myeloid leukemia.
Efficient megakaryopoiesis and platelet production require phospholipid remodeling and PUFA uptake through CD36.
Downregulation of UBA1 expression in myelodysplastic neoplasm.
Incidence, risk factors and therapy response of acute graft-versus-host disease after myeloablative hematopoietic stem cell transplantation with posttransplant cyclophosphamide.
Chromosome 9p trisomy increases stem cells clonogenic potential and fosters T-cell exhaustion in JAK2-mutant myeloproliferative neoplasms.
Mitochondrial serine catabolism safeguards maintenance of the hematopoietic stem cell pool in homeostasis and injury.
A potent and selective ENL degrader suppresses oncogenic gene expression and leukemia progression.
The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.
Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis.

Leukemia. 2024 Aug 26.

Stearoyl-CoA desaturase inhibition is toxic to acute myeloid leukemia displaying high levels of the de novo fatty acid biosynthesis and desaturation.

Vilma Dembitz, Hannah Lawson, Richard Burt, Sirisha Natani, Céline Philippe, Sophie C James, Samantha Atkinson, Jozef Durko, Lydia M Wang, Joana Campos, Aoife M S Magee, Keith Woodley, Michael J Austin, Ana Rio-Machin, Pedro Casado, Findlay Bewicke-Copley, Giovanny Rodriguez Blanco, Diego Pereira-Martins, Lieve Oudejans, Emeline Boet, Alex von Kriegsheim, Juerg Schwaller, Andrew J Finch, Bela Patel, Jean-Emmanuel Sarry, Jerome Tamburini, Jan Jacob Schuringa, Lori Hazlehurst, John A Copland Iii, Mariia Yuneva, Barrie Peck, Pedro Cutillas, Jude Fitzgibbon, Kevin Rouault-Pierre, Kamil Kranc, Paolo Gallipoli.

Identification of specific and therapeutically actionable vulnerabilities, ideally present across multiple mutational backgrounds, is needed to improve acute myeloid leukemia (AML) patients' outcomes. We identify stearoyl-CoA desaturase (SCD), the key enzyme in fatty acid (FA) desaturation, as prognostic of patients' outcomes and, using the clinical-grade inhibitor SSI-4, show that SCD inhibition (SCDi) is a therapeutic vulnerability across multiple AML models in vitro and in vivo. Multiomic analysis demonstrates that SCDi causes lipotoxicity, which induces AML cell death via pleiotropic effects. Sensitivity to SCDi correlates with AML dependency on FA desaturation regardless of mutational profile and is modulated by FA biosynthesis activity. Finally, we show that lipotoxicity increases chemotherapy-induced DNA damage and standard chemotherapy further sensitizes AML cells to SCDi. Our work supports developing FA desaturase inhibitors in AML while stressing the importance of identifying predictive biomarkers of response and biologically validated combination therapies to realize their full therapeutic potential.

DOI: https://doi.org/10.1038/s41375-024-02390-9
Br J Haematol. 2024 Aug 28.

Clinical relevance of NFYA splice variants in patients with acute myeloid leukaemia undergoing intensive chemotherapy.

Yi-Tsung Yang, Chi-Yuan Yao, Chein-Jun Kao, Po-Ju Chiu, Ming-En Lin, Hsin-An Hou, Chien-Chin Lin, Wen-Chien Chou, Hwei-Fang Tien.

  Aberrant alternative splicing (AS) contributes to leukemogenesis, but reports on the clinical and biological implications of aberrant AS in acute myeloid leukaemia (AML) remain limited. Here, we used RNA-seq to analyse AS in AML cells from 341 patients, comparing them to healthy CD34+ haematopoietic stem cells (HSCs). Our findings highlight distinct AS patterns in the nuclear transcription factor Y subunit alpha (NFYA) gene, with two main isoforms: NFYA-L (Long) and NFYA-S (Short), differing in exon 3 inclusion. Patients with lower NFYA-L but higher NFYA-S expression, termed NFYA-S predominance, displayed more favourable characteristics and better outcomes following intensive chemotherapy, regardless of age and European LeukemiaNet risk classification, compared to those with higher NFYA-L but lower NFYA-S expression, termed NFYA-L predominance. The prognostic effects were validated using The Cancer Genome Atlas cohort. Transcriptome analysis revealed upregulated cell cycle genes in NFYA-S predominant cases, resembling those of active HSCs, demonstrating relative chemosensitivity. Conversely, NFYA-L predominant cases, as observed in KMT2A-rearranged leukaemia, were associated with relative chemoresistance. NFYA-S overexpression in OCI-AML3 cells promoted cell proliferation, S-phase entry and increased cytarabine sensitivity, suggesting its clinical and therapeutic relevance in AML. Our study underscores NFYA AS as a potential prognostic biomarker in AML.

Keywords:  NFYA; RNA sequencing; acute myeloid leukaemia; alternative splicing; clinical significance

DOI:  https://doi.org/10.1111/bjh.19733
Cancer Discov. 2024 Aug 27.

RNA shielding of P65 is required to potentiate oncogenic inflammation in TET2 mutated clonal hematopoiesis.

Nana Adjoa Ben-Crentsil, Wazim Mohammed Ismail, Maria E Balasis, Hannah Newman, Ariel Quintana, Moritz Binder, Traci Kruer, Surendra Neupane, Meghan C Ferrall-Fairbanks, Jenna Fernandez, Terra L Lasho, Christy M Finke, Mohammed L Ibrahim, Kathy L McGraw, Michael Wysota, Amy L Aldrich, Christopher B Ryder, Christopher T Letson, Joshua Traina, Amy F McLemore, Nathalie Droin, Aditi Shastri, Seongseok Yun, Eric Solary, David A Sallman, Amer A Beg, Li Ma, Alexandre Gaspar-Maia, Mrinal M Patnaik, Eric Padron.

TET2 mutations (mTET2) are common genetic events in myeloid malignancies and clonal hematopoiesis (CH). These mutations arise in the founding clone and are implicated in many clinical sequelae associated with oncogenic feedforward inflammatory circuits. However, the direct downstream effector of mTET2 responsible for the potentiation of this inflammatory circuit is unknown. To address this, we performed scRNA and scATAC-seq in COVID-19 patients with and without TET2-mutated CH reasoning that the inflammation from COVID-19 may highlight critical downstream transcriptional targets of mTET2. Using this approach, we identified MALAT1, a therapeutically tractable lncRNA, as a central downstream effector of mTET2 that is both necessary and sufficient to induce the oncogenic pro-inflammatory features of mTET2 in vivo. We also elucidate the mechanism by which mTET2 upregulate MALAT1 and describe an interaction between MALAT1 and P65 which leads to RNA "shielding" from PP2A dephosphorylation thus preventing resolution of inflammatory signaling.

DOI: https://doi.org/10.1158/2159-8290.CD-24-0093
Annu Rev Genomics Hum Genet. 2024 Aug;25(1): 329-351

Clinical and Therapeutic Implications of Clonal Hematopoiesis.

Giulia Petrone, Isik Turker, Pradeep Natarajan, Kelly L Bolton.

  Clonal hematopoiesis (CH) is an age-related process whereby hematopoietic stem and progenitor cells (HSPCs) acquire mutations that lead to a proliferative advantage and clonal expansion. The most commonly mutated genes are epigenetic regulators, DNA damage response genes, and splicing factors, which are essential to maintain functional HSPCs and are frequently involved in the development of hematologic malignancies. Established risk factors for CH, including age, prior cytotoxic therapy, and smoking, increase the risk of acquiring CH and/or may increase CH fitness. CH has emerged as a novel risk factor in many age-related diseases, such as hematologic malignancies, cardiovascular disease, diabetes, and autoimmune disorders, among others. Future characterization of the mechanisms driving CH evolution will be critical to develop preventative and therapeutic approaches.

Keywords:  cardiovascular disease; cellular therapy; clonal hematopoiesis; hematologic malignancies; management of clonal hematopoiesis

DOI:  https://doi.org/10.1146/annurev-genom-120722-100409
Leuk Res. 2024 Aug 22. pii: S0145-2126(24)00134-6. [Epub ahead of print]145 107568

Evolution of transcriptomic profiles in relapsed inv(16) acute myeloid leukemia.

Serena Travaglini, Giorgia Silvestrini, Enrico Attardi, Maurizio Fanciulli, Stefano Scalera, Silvia Antonelli, Luca Maurillo, Raffaele Palmieri, Mariadomenica Divona, Ludovica Ciuffreda, Arianna Savi, Giovangiacinto Paterno, Tiziana Ottone, Caterina Barbieri, Jaroslaw P Maciejewski, Carmelo Gurnari, Gennaro Ciliberto, Maria Teresa Voso.

  Acute myeloid leukemia (AML) with inv(16) is typically associated with a favourable prognosis. However, up to 40 % of patients will eventually experience disease relapse. Herein, we dissected the genomic and transcriptomic profile of inv(16) AML to identify potential prognostic markers and therapeutic vulnerabilities. Sequencing data from 222 diagnostic samples, including 44 relapse/refractory patients, revealed a median of 1 concomitant additional mutation, cooperating with inv(16) in leukemogenesis. Notably, the mutational landscape at diagnosis did not differ significantly between patients experiencing primary induction failure or relapse when compared to the rest of the cohort, except for an increase in the mutational burden in the relapse/refractory group. RNA-Seq of unpaired diagnostic(n=7) and relapse(n=6) samples allowed the identification of oxidative phosphorylation (OXPHOS) as one of the most significantly downregulated pathways at relapse. Considering that OXPHOS could be targeted by Venetoclax/Azacitidine combination, we explored its biological effects on an inv(16) cell-line ME-1, but there was no additional advantage in terms of cell death over Azacitidine alone. To enhance Venetoclax efficacy, we tested in vitro effects of Metformin as a potential drug able to enhance chemosensitivity of AML cells by inhibiting the mitochondrial transfer. By challenging ME-1 with this combination, we observed a significant synergistic interaction at least similar to that of Venetoclax/Azacitidine. In conclusions, we identified a downregulated expression of oxidative phosphorylation (OXPHOS) at relapse in AML with inv(16), and explored the in vitro effects of metformin as a potential drug to enhance chemosensitivity in this setting.

Keywords:  Acute myeloid leukemia; Core binding factor; Metformin; OXPHOS; Venetoclax

DOI:  https://doi.org/10.1016/j.leukres.2024.107568
Am J Hematol. 2024 Aug 28.

A phase 2 trial of mini-hyper-CVD, blinatumomab, and ponatinib in Philadelphia positive acute lymphoblastic leukemia.

Wei-Ying Jen, Elias Jabbour, Nicholas J Short, Ghayas C Issa, Fadi G Haddad, Nitin Jain, Naveen Pemmaraju, Naval G Daver, Lucia Masarova, Gautam Borthakur, Kelly Chien, Rebecca Garris, Hagop M Kantarjian.

Twenty adults with newly diagnosed (ND) or relapsed/refractory (RR) Ph-positive acute lymphoblastic leukemia (ALL), or chronic myeloid leukemia in lymphoid blast phase (CML-LBP), were treated with mini-hyperCVD, ponatinib, and blinatumomab. Complete molecular response was achieved in 78% of ND patients, while CR/CRi was achieved in 100% of RR and CML-LBP. The 3-year overall survival rate was 76% (95% CI, 47%-90%).

DOI: https://doi.org/10.1002/ajh.27463
Leukemia. 2024 Aug 23.

Menin inhibitors in pediatric acute leukemia: a comprehensive review and recommendations to accelerate progress in collaboration with adult leukemia and the international community.

Branko Cuglievan, Hagop Kantarjian, Jeffrey E Rubnitz, Todd M Cooper, C Michel Zwaan, Jessica A Pollard, Courtney D DiNardo, Tapan M Kadia, Erin Guest, Nicholas J Short, David McCall, Naval Daver, Cesar Nunez, Fadi G Haddad, Miriam Garcia, Kapil N Bhalla, Abhishek Maiti, Samanta Catueno, Warren Fiskus, Bing Z Carter, Amber Gibson, Michael Roth, Sajad Khazal, Priti Tewari, Hussein A Abbas, Wallace Bourgeois, Michael Andreeff, Neerav N Shukla, Danh D Truong, Jeremy Connors, Joseph A Ludwig, Janine Stutterheim, Elisabeth Salzer, Kristian L Juul-Dam, Koji Sasaki, Kris M Mahadeo, Sarah K Tasian, Gautam Borthakur, Samantha Dickson, Nitin Jain, Elias Jabbour, Soheil Meshinchi, Guillermo Garcia-Manero, Farhad Ravandi, Eytan M Stein, E Anders Kolb, Ghayas C Issa.

Aberrant expression of HOX and MEIS1 family genes, as seen in KMT2A-rearranged, NUP98-rearranged, or NPM1-mutated leukemias leads to arrested differentiation and leukemia development. HOX family genes are essential gatekeepers of physiologic hematopoiesis, and their expression is regulated by the interaction between KMT2A and menin. Menin inhibitors block this interaction, downregulate the abnormal expression of MEIS1 and other transcription factors and thereby release the differentiation block. Menin inhibitors show significant clinical efficacy against KMT2A-rearranged and NPM1-mutated acute leukemias, with promising potential to address unmet needs in various pediatric leukemia subtypes. In this collaborative initiative, pediatric and adult hematologists/oncologists, and stem cell transplant physicians have united their expertise to explore the potential of menin inhibitors in pediatric leukemia treatment internationally. Our efforts aim to provide a comprehensive clinical overview of menin inhibitors, integrating preclinical evidence and insights from ongoing global clinical trials. Additionally, we propose future international, inclusive, and efficient clinical trial designs, integrating pediatric populations in adult trials, to ensure broad access to this promising therapy for all children and adolescents with menin-dependent leukemias.

DOI: https://doi.org/10.1038/s41375-024-02368-7
Ann Hematol. 2024 Aug 28.

Clonal heterogeneity in STAG2m myeloid neoplasms: the Mayo Clinic experience.

Bahga Katamesh, Ahmad Nanaa, Rong He, David Viswanatha, Patricia T Greipp, Kurt Bessonen, Phuong Nguyen, Dragan Jevremovic, Cecilia Arana Yi, James Foran, Kebede Begna, Naseema Gangat, Abhishek Mangaonkar, Antoine N Saliba, Mrinal M Patnaik, William J Hogan, Mark Litzow, Ayalew Tefferi, Mithun Vinod Shah, Hassan B Alkhateeb, Aref Al-Kali.

DOI: https://doi.org/10.1007/s00277-024-05971-x
Leuk Res. 2024 Aug 14. pii: S0145-2126(24)00127-9. [Epub ahead of print]145 107561

Absence of PNH-clones in DDX41mutant-GPS aids in their distinction from acquired BM failure syndromes.

Yael Kusne, Talha Badar, Terra Lasho, Alejandro Ferrer, Abhishek A Mangaonkar, Christy Finke, Ludovica Marando, James M Foran, Aref Al-Kali, Hassan B Alkhateeb, Timothy Chlon, Mrinal M Patnaik.



Keywords:  Acquired bone marrow failure; DDX41-GPS; GPI-deficient clones

DOI:  https://doi.org/10.1016/j.leukres.2024.107561
Leukemia. 2024 Aug 23.

STING is crucial for the survival of RUNX1::RUNX1T1 leukemia cells.

Yue Sun, Yushuang Wu, Guozheng Pang, Jingru Huang, Mengyao Sheng, Jiaying Xie, Pingyue Chen, Yin Wang, Dongrui Yin, Guangjie Zhao, Stefan K Bohlander, Jian Huang, Guo-Liang Xu, Hai Gao, Dan Zhou, Yuheng Shi.

Even though acute myeloid leukemia (AML) patients with a RUNX1::RUNX1T1 (AE) fusion have a relatively favorable prognosis, approximately 50% relapse within 2.5 years and develop resistance to subsequent chemotherapy [1]. It is therefore imperative to identify novel therapeutic targets for AE leukemia to improve outcomes. In this study, we unveil that targeting STING effectively suppresses the growth of AE leukemia cells. Both genetic and pharmacological inhibition of STING lead to the diminish of AE leukemia cells. Importantly, in a mouse primary AE leukemia model, STING deletion significantly attenuates leukemogenesis and prolongs the animals' lifespan. Blocking the downstream inflammatory pathway of STING yields similar effects to STING inhibition in AE leukemia cells, highlighting the pivotal role of STING-dependent inflammatory responses in sustaining the survival of AE leukemia cells. Moreover, through a genome-wide CRISPR screen, we identified fatty acid desaturase 2 (FADS2) as a non-canonical factor downstream of STING inhibition that mediates cell death. Inhibition of STING releases FADS2 activity, consequently inducing the synthesis of polyunsaturated fatty acids (PUFAs) and triggering lipid peroxidation-associated cell death [2]. Taken together, these findings reveal a critical function of STING in the survival of AE-positive AML cells and suggest STING to be a potential therapeutic target for clinical intervention in these patients.

DOI: https://doi.org/10.1038/s41375-024-02383-8
Cells. 2024 Aug 21. pii: 1392. [Epub ahead of print]13(16):

Common Driver Mutations in AML: Biological Impact, Clinical Considerations, and Treatment Strategies.

Tiffany Nong, Shefali Mehra, Justin Taylor.

  Next-generation sequencing of samples from patients with acute myeloid leukemia (AML) has revealed several driver gene mutations in adult AML. However, unlike other cancers, AML is defined by relatively few mutations per patient, with a median of 4-5 depending on subtype. In this review, we will discuss the most common driver genes found in patients with AML and focus on the most clinically relevant ones that impact treatment strategies. The most common driver gene mutations in AML occur in NPM1 and FLT3, accounting for ~30% each. There are now targeted therapies being tested or already approved for these driver genes. Menin inhibitors, a novel targeted therapy that blocks the function of the menin protein, are in clinical trials for NPM1 driver gene mutant AML after relapse. A number of FLT3 inhibitors are now approved for FLT3 driver gene mutant AML in combination with chemotherapy in the frontline and also as single agent in relapse. Although mutations in IDH1/2 and TP53 only occur in around 10-20% of patients with AML each, they can affect the treatment strategy due to their association with prognosis and availability of targeted agents. While the impact of other driver gene mutations in AML is recognized, there is a lack of data on the actionable impact of those mutations.

Keywords:  AML; FLT3; IDH; NPM1; TP53; driver mutations

DOI:  https://doi.org/10.3390/cells13161392
Bone Marrow Transplant. 2024 Aug 25.

Effects of donor-engrafted clonal hematopoiesis in allogeneic and autologous stem cell transplantation: a systematic review and meta-analysis.

Yiyu Xie, Vera Kazakova, Lachelle D Weeks, Jonathan M Gerber, Jesse Tai, Tian Y Zhang, Robert Lowsky, Xiaojin Wu, Chengwu Yang, Shyam A Patel.

Donor stem cell health may be critically important to the success of hematopoietic stem cell transplantation (HSCT). Herein, we performed this systematic review and meta-analysis including meta-regression to assess the impact of donor-engrafted clonal hematopoiesis (CH) in allogeneic HSCT (allo-HSCT) and impact of pre-transplant CH in autologous HSCT (auto-HSCT). We applied random-effects models to analyze 5 allo-HSCT studies with 3192 donor-recipient pairs and 9 auto-HSCT studies with 2854 patients. We found that donor-engrafted CH after allo-HSCT decreased the risk of disease relapse [Hazard Ratio (HR) = 0.79, 95% Confidence Interval (CI): (0.67, 0.93)], but did not affect overall survival (OS) [HR = 0.91, 95% CI: (0.75, 1.11)], progression-free survival (PFS) [HR = 0.94, 95% CI: (0.63, 1.41)], or non-relapse mortality [HR = 1.06, 95% CI: (0.81, 1.39)]. In contrast, pre-transplant CH in auto-HSCT recipients resulted in inferior OS [HR = 1.30, 95% CI: (1.16, 1.46)], inferior PFS [HR = 1.35, 95% CI: (1.18, 1.54)], and higher risk for therapy-related myeloid neoplasm [HR = 4.85, 95% CI: (2.39, 9.82)] when compared to auto-HSCT recipients without CH. This study sheds light onto the debate about prospective "CHIP screening" for stem cell donors and addresses the impact of CH as a transmissible phenomenon.

DOI: https://doi.org/10.1038/s41409-024-02403-2
Nat Commun. 2024 Aug 28. 15(1): 7360

TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cells.

Peter Truong, Sylvie Shen, Swapna Joshi, Md Imtiazul Islam, Ling Zhong, Mark J Raftery, Ali Afrasiabi, Hamid Alinejad-Rokny, Mary Nguyen, Xiaoheng Zou, Golam Sarower Bhuyan, Chowdhury H Sarowar, Elaheh S Ghodousi, Olivia Stonehouse, Sara Mohamed, Cara E Toscan, Patrick Connerty, Purvi M Kakadia, Stefan K Bohlander, Katharine A Michie, Jonas Larsson, Richard B Lock, Carl R Walkley, Julie A I Thoms, Christopher J Jolly, John E Pimanda.

Hypomethylating agents (HMAs) are frontline therapies for Myelodysplastic Neoplasms (MDS) and Acute Myeloid Leukemia (AML). However, acquired resistance and treatment failure are commonplace. To address this, we perform a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and identify TOPORS as a loss-of-function target that synergizes with HMAs, reducing leukemic burden and improving survival in xenograft models. We demonstrate that depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. The combination of HMAs with targeting of TOPORS does not impair healthy hematopoiesis. While inhibitors of TOPORS are unavailable, we show that inhibition of protein SUMOylation with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with inhibition of SUMOylation or TOPORS is a rational treatment option for High-Risk MDS (HR-MDS) or AML.

DOI: https://doi.org/10.1038/s41467-024-51646-6
Nat Cardiovasc Res. 2023 Sep;2(9): 805-818

Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.

Philipp J Rauch, Jayakrishnan Gopakumar, Alexander J Silver, Daniel Nachun, Herra Ahmad, Marie McConkey, Tetsushi Nakao, Marc Bosse, Thiago Rentz, Nora Vivanco Gonzalez, Noah F Greenwald, Erin F McCaffrey, Zumana Khair, Manu Gopakumar, Kameron B Rodrigues, Amy E Lin, Eti Sinha, Maia Fefer, Drew N Cohen, Amélie Vromman, Eugenia Shvartz, Galina Sukhova, Sean Bendall, Michael Angelo, Peter Libby, Benjamin L Ebert, Siddhartha Jaiswal.

Clonal hematopoiesis of indeterminate potential (CHIP) is defined by the presence of a cancer-associated somatic mutation in white blood cells in the absence of overt hematological malignancy. It arises most commonly from loss-of-function mutations in the epigenetic regulators DNMT3A and TET2. CHIP predisposes to both hematological malignancies and atherosclerotic cardiovascular disease in humans. Here we demonstrate that loss of Dnmt3a in myeloid cells increased murine atherosclerosis to a similar degree as previously seen with loss of Tet2. Loss of Dnmt3a enhanced inflammation in macrophages in vitro and generated a distinct adventitial macrophage population in vivo which merges a resident macrophage profile with an inflammatory cytokine signature. These changes surprisingly phenocopy the effect of loss of Tet2. Our results identify a common pathway promoting heightened innate immune cell activation with loss of either gene, providing a biological basis for the excess atherosclerotic disease burden in carriers of these two most prevalent CHIP mutations.

DOI: https://doi.org/10.1038/s44161-023-00326-7
Cell Death Dis. 2024 Aug 27. 15(8): 627

CRISPR screen of venetoclax response-associated genes identifies transcription factor ZNF740 as a key functional regulator.

Lixia Zhang, Xinyue Zhou, Sajesan Aryal, Virginia Veasey, Pengcheng Zhang, Fu Jun Li, Yu Luan, Ravi Bhatia, Yang Zhou, Rui Lu.

BCL-2 inhibitors such as venetoclax offer therapeutic promise in acute myeloid leukemia (AML) and other cancers, but drug resistance poses a significant challenge. It is crucial to understand the mechanisms that regulate venetoclax response. While correlative studies have identified numerous genes linked to venetoclax sensitivity, their direct impact on the drug response remains unclear. In this study, we targeted around 1400 genes upregulated in venetoclax-sensitive primary AML samples and carried out a CRISPR knockout screen to evaluate their direct effects on venetoclax response. Our screen identified the transcription factor ZNF740 as a critical regulator, with its expression consistently predicting venetoclax sensitivity across subtypes of the FAB classification. ZNF740 depletion leads to increased resistance to ventoclax, while its overexpression enhances sensitivity to the drug. Mechanistically, our integrative transcriptomic and genomic analysis identifies NOXA as a direct target of ZNF740, which negatively regulates MCL-1 protein stability. Loss of ZNF740 downregulates NOXA and increases the steady state protein levels of MCL-1 in AML cells. Restoring NOXA expression in ZNF740-depleted cells re-sensitizes AML cells to venetoclax treatment. Furthermore, we demonstrated that dual targeting of MCL-1 and BCL-2 effectively treats ZNF740-deficient AML in vivo. Together, our work systematically elucidates the causal relationship between venetoclax response signature genes and establishes ZNF740 as a novel transcription factor regulating venetoclax sensitivity.

DOI: https://doi.org/10.1038/s41419-024-06995-x
Leuk Res. 2024 Aug 22. pii: S0145-2126(24)00130-9. [Epub ahead of print]145 107564

Triplet therapy with gilteritinib, venetoclax, and azacitidine for relapsed/refractory FLT3mut acute myeloid leukemia.

Qiang Fu, Yunqi Wang, Hongtao Liu, Haitao Gao, Wei Sun, Qian Jiang, Hao Jiang, Kaiyan Liu, Xiaojun Huang, Feifei Tang.

  The FMS-related tyrosine kinase 3 (FLT3) inhibitor gilteritinib is standard therapy for relapsed/refractory (R/R) FLT3-mutated (FLT3mut) acute myeloid leukemia (AML) but the overall survival (OS) is only approximately 20 % and few patients achieve deep and/ or durable response. We retrospectively analyzed 29 R/R FLT3mut AML patients treated on triplet regimens (gilteritinib+ venetoclax［VEN] +azacitidine［AZA]). Nineteen patients (65.5 %) had received prior FLT3 inhibitor therapy. The modified composite complete remission (mCRc) rate was 62.1 % (n = 18; CR, 4/29,13.8 %; CRi, 6/29, 20.7 %; MLFS, 8/29, 27.6 %). Among 18 patients achieved mCRc, FLT3-PCR negativity was 94.4 % (n=17), and flow-cytometry negativity was 77.7 % (n=14). The mCRc rate was 70 % (n=7) in 10 patients without prior FLT3 TKI exposure and 57.8 % (n=11) in 19 patients with prior FLT3 TKI exposure (P=0.52). At the end of the first cycle, the median time to ANC > 0.5× 109/L was 38 days and platelet > 50× 109/L was 31 days among responders, but 60-day mortality was 0 %. The estimated 2-year OS was 60.9 % for all R/R FLT3mut patients. The 1-year OS was 80 % and 58.8 % in patients without and with prior FLT3 TKI exposure, respectively (P=0.79). The estimated 2-year OS was 62 % in 19 (65.5 %) patients who received allo-HSCT after triplet therapy and 37 % in 10 patients who did not receive allo-HSCT (P=0.03). In conclusion, triplet therapy with gilteritinib, VEN, and AZA is effective and safe and an excellent frontline option for R/R FLT3mut AML.

Keywords:  Acute myeloid leukemia; Azacitidine; Gilteritinib; Refractory; Relapsed; Venetoclax

DOI:  https://doi.org/10.1016/j.leukres.2024.107564
Br J Haematol. 2024 Aug 26.

Modelling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs.

Momoko Nakamura, Kazuhisa Chonabayashi, Megumi Narita, Yasuko Matsumura, Misato Nishikawa, Yotaro Ochi, Yasuhito Nannya, Masakatsu Hishizawa, Daichi Inoue, Ruud Delwel, Seishi Ogawa, Akifumi Takaori-Kondo, Yoshinori Yoshida.

  Structural variations involving enhancer hijacking induce aberrant oncogene expression and cause tumorigenesis. A rare translocation, t(3;8)(q26.2;q24), is associated with MECOM and MYC rearrangement, causing myeloid neoplasms with a dismal prognosis. The most recent World Health Organization classification recognises myeloid neoplasms with MECOM rearrangement as acute myeloid leukaemia (AML) with defining genetic abnormalities. Recently, the increasing use of induced pluripotent stem cell (iPSC) technology has helped elucidate the pathogenic processes of haematological malignancies. However, its utility for investigating enhancer hijacking in myeloid neoplasms remains unclear. In this study, we generated iPSC lines from patients with myelodysplastic syndromes (MDS) harbouring t(3;8)(q26.2;q24) and differentiated them into haematopoietic progenitor cells to model the pathophysiology of MDS with t(3;8)(q26.2;q24). Our iPSC model reproduced the primary patient's MECOM expression changes and histone H3 lysine 27 acetylation (H3K27ac) patterns in the MECOM promoter and MYC blood enhancer cluster (BENC). Furthermore, we revealed the apoptotic effects of the bromodomain and extra-terminal motif (BET) inhibitor on iPSC-derived MDS cells by suppressing activated MECOM. Our study demonstrates the usefulness of iPSC models for uncovering the precise mechanism of enhancer hijacking due to chromosomal structural changes and discovering potential therapeutic drug candidates for cancer treatment.

Keywords:  BET inhibitor; MECOM; enhancer hijacking; iPSC; myeloid neoplasm

DOI:  https://doi.org/10.1111/bjh.19720
Nat Cardiovasc Res. 2023 Jan;2(1): 13-15

Genetic causes and cardiovascular consequences of clonal hematopoiesis in the UK Biobank.

J Scott Beeler, Alexander G Bick, Kelly L Bolton.

DOI: https://doi.org/10.1038/s44161-022-00198-3
Leuk Res. 2024 Aug 20. pii: S0145-2126(24)00129-2. [Epub ahead of print]144 107563

Characteristics and outcomes of children, adolescent, and young adult patients with myelodysplastic neoplasms: A single-center retrospective analysis.

David McCall, Tareq Abuasab, Juan Jose Rodriguez-Sevilla, Shehab Fareed Mohamed, Anish Patnaik, Kirthi Devireddy, Naszrin Arani, Irtiza Sheikh, Raehannah Jamshidi, Amber Gibson, Michael Roth, Cesar Nuñez, Miriam Garcia, Kelly S Chien, Sanam Loghavi, Sherry A Pierce, Koji Sasaki, Ghayas Issa, Branko Cuglievan, Hagop Kantarjian, Guillermo Garcia-Manero.

  Myelodysplastic syndrome, or myelodysplastic neoplasms, are a rare finding in pediatric, adolescent, and young adult (AYA) patients. More literature is needed to highlight trends of survival or treatment resistance in subpopulations to improve treatment. Here we report a single center retrospective analysis of pediatric and AYA patients from 2000 to 2022 including molecular and cytogenetic data. Using the IPSS-R and IPSS-M, which have been reported exclusively in adults, and excluding patients with bone marrow failure syndromes, we analyzed 119 pediatric and AYA patients with myelodysplastic neoplasms. Therapy-related myelodysplastic neoplasms were present in 36 % of patients, and 31 % of patients developed acute myeloid leukemia. The 5-year overall survival (OS) rate for the entire cohort was 45 %. Contrary to young adults and older adults, mutations were not common in pediatrics. Those who underwent stem cell transplant (SCT)(at any time) had significantly longer median OS. Although SCT at any time improved OS in the de novo myelodysplastic neoplasm group, the choice of the initial treatment with intensive chemotherapy, hypomethylating agents, or SCT did not significantly alter OS. Median OS was shorter in the pediatric group (<18 years old) and longer for those with isolated deletion of 5q or TET2 mutation, but these were not significant findings. Median OS was significantly shorter in those with monosomy 7 or 7q deletion and those with therapy-related myelodysplastic neoplasms. These findings build on previously reported findings and encourage the use of SCT along with molecular and cytogenetic analysis.

Keywords:  Adolescent and young adult; Myelodysplastic neoplasms; Pediatrics; Stem cell transplantation

DOI:  https://doi.org/10.1016/j.leukres.2024.107563
Transplant Cell Ther. 2024 Aug 24. pii: S2666-6367(24)00606-7. [Epub ahead of print]

Hypomethylating agents are Effective in Treatment for Relapsed Myelofibrosis After Allogeneic Hematopoietic Cell Transplantation.

Dat Ngo, Jose Tinajero, Abdullah Ladha, Monzr M Al Malki, Salman Otoukesh, Idoroenyi Amanam, Haris Ali.

  BACKGROUND: Myelofibrosis (MF) is a myeloproliferative neoplasm with a relapse rate of 10-30% after allogeneic transplantation (alloHCT). Current recommendations to treat relapse include withdrawal of immunosuppression, donor lymphocyte infusion, and potentially a second alloHCT. Hypomethylating agents (HMA) have shown efficacy as salvage therapy by inducing an immune response and improving donor chimerism for myeloid neoplasm post-HCT. Data is limited on use of HMA for MF post-alloHCT relapse.OBJECTIVE: To determine the benefit of using HMA for MF patients relapsing after alloHCT.
STUDY DESIGN: We retrospectively analyzed 12 patients with MF post-alloHCT relapse who received HMA to determine response via restoration of donor chimerism and clearance of molecular mutation.
RESULTS: The median age was 61 years (range 41-72) with 92% classified as intermediate-2/high-risk by DIPSS and 83% as high/very high risk by MIPSS70+. The median time to relapse post-alloHCT was 282.5 days (range 96-2388) with median donor chimerism 57.82% (range 2.48-84) prior to starting HMA. After two cycles of HMA, 58% experienced restoration of donor chimerism. Molecular clearance of pre-HCT driver mutations occurred in 50% of patients at the most recent follow-up. New chronic GvHD occurred in 50% of patients with most being mild to moderate that resolved after treatment.
CONCLUSION: HMA was safe and effective in a high-risk population after post-alloHCT relapse and is an option for patients in the future.

Keywords:  Hematopoietic Cell Transplantation; Hypomethylating Agents; Myelofibrosis

DOI:  https://doi.org/10.1016/j.jtct.2024.08.013
Br J Haematol. 2024 Aug 27.

WT1 together with RUNX1::RUNX1T1 targets DUSP6 to dampen ERK activity in acute myeloid leukaemia.

Nan Xu, Feng-Ting Dao, Zong-Yan Shi, Kai Sun, Ya-Zhen Qin.

  Wilms' tumour 1 (WT1) can function as an oncogene or a tumour suppressor. Our previous clinical cohort studies showed that low WT1 expression at diagnosis independently predicted poor outcomes in acute myeloid leukaemia (AML) with RUNX1::RUNX1T1, whereas it had an opposite role in AML with non-favourable cytogenetic risk (RUNX1::RUNX1T1-deficient). The molecular mechanism by which RUNX1::RUNX1T1 affects the prognostic significance of WT1 in AML remains unknown. In the present study, first we validated the prognostic significance of WT1 expression in AML. Then by using the established transfected cell lines and xenograft tumour model, we found that WT1 suppresses proliferation and enhances effect of cytarabine in RUNX1::RUNX1T1(+) AML but has opposite functions in AML cells without RUNX1::RUNX1T1. Furthermore, as a transcription factor, WT1 physically interacts with RUNX1::RUNX1T1 and acts as a co-factor together with RUNX1::RUNX1T1 to activate the expression of its target gene DUSP6 to dampen extracellular signal-regulated kinase (ERK) activity. When RUNX1::RUNX1T1-deficient, WT1 can activate the mitogen-activated extracellular signal-regulated kinase/ERK axis but not through targeting DUSP6. These results provide a mechanism by which WT1 together with RUNX1::RUNX1T1 suppresses cell proliferation through WT1/DUSP6/ERK axis in AML. The current study provides an explanation for the controversial prognostic significance of WT1 expression in AML patients.

Keywords:  DUSP6; ERK; RUNX1::RUNX1T1; WT1; acute myeloid leukaemia

DOI:  https://doi.org/10.1111/bjh.19721
Br J Haematol. 2024 Aug 26.

HLA-lacking clones in aplastic anaemia: Adaptive or maladaptive?

Carmelo Gurnari, Alberto Cardoso Martins Lima, Simona Pagliuca.

  HLA loss represents the result of immune forces shaping bone marrow clonal dynamics in immune aplastic anaemia. Human leukocyte antigen (HLA)-deficient clones may rescue haematopoiesis by evading immune attacks, potentially guiding treatment strategies. Commentary on: Zaimoku et al. Haematopoietic regeneration by HLA-A*0206-deficient clones in severe aplastic anaemia without definitive immunosuppressive treatment. Br J Haematol 2024 (Online ahead of print). doi: 10.1111/bjh.19712.

Keywords:  aplastic anaemia; clonal haematopoiesis; haematopoietic stem cells; immune suppressive treatment

DOI:  https://doi.org/10.1111/bjh.19731
Leukemia. 2024 Aug 26.

A multidimensional analysis reveals distinct immune phenotypes and the composition of immune aggregates in pediatric acute myeloid leukemia.

Joost B Koedijk, Inge van der Werf, Livius Penter, Marijn A Vermeulen, Farnaz Barneh, Alicia Perzolli, Joyce I Meesters-Ensing, Dennis S Metselaar, Thanasis Margaritis, Marta Fiocco, Hester A de Groot-Kruseman, Rubina Moeniralam, Kristina Bang Christensen, Billie Porter, Kathleen Pfaff, Jacqueline S Garcia, Scott J Rodig, Catherine J Wu, Henrik Hasle, Stefan Nierkens, Mirjam E Belderbos, C Michel Zwaan, Olaf Heidenreich.

Because of the low mutational burden and consequently, fewer potential neoantigens, children with acute myeloid leukemia (AML) are thought to have a T cell-depleted or 'cold' tumor microenvironment and may have a low likelihood of response to T cell-directed immunotherapies. Understanding the composition, phenotype, and spatial organization of T cells and other microenvironmental populations in the pediatric AML bone marrow (BM) is essential for informing future immunotherapeutic trials about targetable immune-evasion mechanisms specific to pediatric AML. Here, we conducted a multidimensional analysis of the tumor immune microenvironment in pediatric AML and non-leukemic controls. We demonstrated that nearly one-third of pediatric AML cases has an immune-infiltrated BM, which is characterized by a decreased ratio of M2- to M1-like macrophages. Furthermore, we detected the presence of large T cell networks, both with and without colocalizing B cells, in the BM and dissected the cellular composition of T- and B cell-rich aggregates using spatial transcriptomics. These analyses revealed that these aggregates are hotspots of CD8+ T cells, memory B cells, plasma cells and/or plasmablasts, and M1-like macrophages. Collectively, our study provides a multidimensional characterization of the BM immune microenvironment in pediatric AML and indicates starting points for further investigations into immunomodulatory mechanisms in this devastating disease.

DOI: https://doi.org/10.1038/s41375-024-02381-w
Nat Cardiovasc Res. 2023 Aug;2(8): 746-763

Efficient megakaryopoiesis and platelet production require phospholipid remodeling and PUFA uptake through CD36.

Maria N Barrachina, Gerard Pernes, Isabelle C Becker, Isabelle Allaeys, Thomas I Hirsch, Dafna J Groeneveld, Abdullah O Khan, Daniela Freire, Karen Guo, Estelle Carminita, Pooranee K Morgan, Thomas J C Collins, Natalie A Mellett, Zimu Wei, Ibrahim Almazni, Joseph E Italiano, James Luyendyk, Peter J Meikle, Mark Puder, Neil V Morgan, Eric Boilard, Andrew J Murphy, Kellie R Machlus.

Lipids contribute to hematopoiesis and membrane properties and dynamics; however, little is known about the role of lipids in megakaryopoiesis. Here we show that megakaryocyte progenitors, megakaryocytes and platelets present a unique lipidome progressively enriched in polyunsaturated fatty acid (PUFA)-containing phospholipids. In vitro, inhibition of both exogenous fatty acid functionalization and uptake as well as de novo lipogenesis impaired megakaryocyte differentiation and proplatelet production. In vivo, mice on a high saturated fatty acid diet had significantly lower platelet counts, which was prevented by eating a PUFA-enriched diet. Fatty acid uptake was largely dependent on CD36, and its deletion in mice resulted in low platelets. Moreover, patients with a CD36 loss-of-function mutation exhibited thrombocytopenia and increased bleeding. Our results suggest that fatty acid uptake and regulation is essential for megakaryocyte maturation and platelet production and that changes in dietary fatty acids may be a viable target to modulate platelet counts.

DOI: https://doi.org/10.1038/s44161-023-00305-y
Leukemia. 2024 Aug 23.

Downregulation of UBA1 expression in myelodysplastic neoplasm.

Yue Wei, Hong Zheng, Ziyi Li, Pamela Pennington Lockyer, Faezeh Darbaniyan, Rashmi Kanagal-Shamanna, Hui Yang, Danielle Hammond, Guillermo Garcia-Manero.

DOI: https://doi.org/10.1038/s41375-024-02364-x
Bone Marrow Transplant. 2024 Aug 24.

Incidence, risk factors and therapy response of acute graft-versus-host disease after myeloablative hematopoietic stem cell transplantation with posttransplant cyclophosphamide.

P Asensi Cantó, I Gómez-Seguí, J Montoro, M Villalba Montaner, P Chorão, P Solves Alcaína, M Santiago Balsera, P Lloret Madrid, J Solís Ruiz, C Sopeña Pell-Ilderton, D Martínez Campuzano, P Granados Serrano, J Eiris Del Río, A Louro, P Rebollar, A Perla, R Benavente, J De la Rubia Comos, M A Sanz, A Balaguer, J Sanz.

Posttransplant cyclophosphamide, sirolimus and mycophenolate mofetil (PTCy/siro/MMF) constitutes an innovative and well-tolerated acute graft-versus-host disease (aGVHD) prophylaxis after allogeneic stem cell transplantation (allo-HSCT), but risk factors for aGVHD incidence and therapy failure in this setting are scarce. This study prospectively registered all consecutive adult patients with hematologic malignancies who received a myeloablative allo-HSCT using PTCy/siro/MMF prophylaxis at our institution between 2017 and 2023. A total of 385 patients were included, of whom 44%, 34% and 22% were transplanted from matched sibiling, matched unrelated and haploidentical donors, respectively. The 180-day cumulative incidence of aGVHD was 21% (95% confidence interval [CI] 17-25%) for grade II-IV and 11% (95% CI 8-14%) grade III-IV aGVHD. The use of haploidentical donors was associated with an increased risk of severe aGVHD. Among 75 patients receiving first-line systemic corticosteroids, 49% achieved a sustained complete response, while 23% and 24% developed steroid-dependent (SD-aGVHD) and steroid-refractory aGVHD (SR-aGVHD), respectively. SR-aGVHD was associated with worse salvage treatment response and overall survival compared to SD-aGVHD. The 1-year cumulative incidence of aGVHD-related mortality was 5.4% (95% CI, 3.3-8.1). Risk factors for aGVHD-related mortality included haploidentical donors, older donors, diagnosis of myeldysplastic neoplasms, and grade IV aGVHD. This study confirms a low incidence aGVHD with PTCy/siro/MMF prophylaxis. SR-aGVHD showed poorer response to salvage therapies and worse survival, while haploidentical donors and older donor age were negative predictors for aGVHD-related deaths.

DOI: https://doi.org/10.1038/s41409-024-02391-3
Leukemia. 2024 Aug 23.

Chromosome 9p trisomy increases stem cells clonogenic potential and fosters T-cell exhaustion in JAK2-mutant myeloproliferative neoplasms.

MYNERVA (Myeloid NEoplasms Research Venture AIRC)

JAK2V617F is the most recurrent genetic mutation in Philadelphia-negative chronic Myeloproliferative Neoplasms (MPNs). Since the JAK2 locus is located on Chromosome 9, we hypothesized that Chromosome 9 copy number abnormalities may be a disease modifier in JAK2V617F-mutant MPN patients. In this study, we identified a subset of MPN patients with partial or complete Chromosome 9 trisomy (+9p patients), who differ from JAK2V617F-homozygous MPN patients as they carry three JAK2 alleles as well as three copies of all neighboring gene loci, including CD274, encoding immunosuppressive Programmed death-ligand 1 (PD-L1) protein. Investigation of the clonal hierarchy revealed that the JAK2V617F occurs first, followed by +9p. Functionally, CD34+ cells from +9p MPN patients demonstrated increased clonogenicity, generating a greater number of primitive colonies, due to high OCT4 and NANOG expression, with knock-down of these genes leading to a genotype-specific decrease in colony numbers. Moreover, our analysis revealed increased PD-L1 surface expression in malignant monocytes from +9p patients, while analysis of the T cell compartment unveiled elevated levels of exhausted cytotoxic T cells. Overall, here we identify a distinct novel subgroup of MPN patients, who feature a synergistic interplay between +9p and JAK2V617F that shapes immune escape characteristics and increased stemness in CD34+ cells.

DOI: https://doi.org/10.1038/s41375-024-02373-w
Cell Stem Cell. 2024 Aug 21. pii: S1934-5909(24)00285-6. [Epub ahead of print]

Mitochondrial serine catabolism safeguards maintenance of the hematopoietic stem cell pool in homeostasis and injury.

Changhong Du, Chaonan Liu, Kuan Yu, Shuzhen Zhang, Zeyu Fu, Xinliang Chen, Weinian Liao, Jun Chen, Yimin Zhang, Xinmiao Wang, Mo Chen, Fang Chen, Mingqiang Shen, Cheng Wang, Shilei Chen, Song Wang, Junping Wang.

  Hematopoietic stem cells (HSCs) employ a very unique metabolic pattern to maintain themselves, while the spectrum of their metabolic adaptations remains incompletely understood. Here, we uncover a distinct and heterogeneous serine metabolism within HSCs and identify mouse HSCs as a serine auxotroph whose maintenance relies on exogenous serine and the ensuing mitochondrial serine catabolism driven by the hydroxymethyltransferase 2 (SHMT2)-methylene-tetrahydrofolate dehydrogenase 2 (MTHFD2) axis. Mitochondrial serine catabolism primarily feeds NAD(P)H generation to maintain redox balance and thereby diminishes ferroptosis susceptibility of HSCs. Dietary serine deficiency, or genetic or pharmacological inhibition of the SHMT2-MTHFD2 axis, increases ferroptosis susceptibility of HSCs, leading to impaired maintenance of the HSC pool. Moreover, exogenous serine protects HSCs from irradiation-induced myelosuppressive injury by fueling mitochondrial serine catabolism to mitigate ferroptosis. These findings reframe the canonical view of serine from a nonessential amino acid to an essential niche metabolite for HSC pool maintenance.

Keywords:  NADPH; SHMT2; ferroptosis; hematopoietic stem cell; heterogeneity; ionizing radiation; mitochondrial serine catabolism; myelosuppressive injury

DOI:  https://doi.org/10.1016/j.stem.2024.07.009
Sci Adv. 2024 Aug 30. 10(35): eado1432

A potent and selective ENL degrader suppresses oncogenic gene expression and leukemia progression.

Zhaoyu Xue, Lihuai Qin, Hongwen Xuan, Kaixiu Luo, Mengying Huang, Ling Xie, Yangzhou Su, Longxia Xu, Josiah Harsh, Brandon Dale, Xiaobing Shi, Xian Chen, H Ümit Kaniskan, Jian Jin, Hong Wen.

The histone acylation reader eleven-nineteen leukemia (ENL) plays a pivotal role in sustaining oncogenesis in acute leukemias, particularly in mixed-lineage leukemia-rearranged (MLL-r) leukemia. ENL relies on its reader domain to recognize histone lysine acylation promoting oncogenic gene expression and leukemia progression. Here, we report the development of MS41, a highly potent and selective von Hippel-Lindau-recruiting ENL degrader that effectively inhibits the growth of ENL-dependent leukemia cells. MS41-induced ENL degradation reduces the chromatin occupancy of ENL-associated transcription elongation machinery, resulting in the suppression of key oncogenic gene expression programs and the activation of differentiation genes. MS41 is well-tolerated in vivo and substantially suppresses leukemia progression in a xenograft mouse model of MLL-r leukemia. Notably, MS41 also induces the degradation of mutant ENL proteins identified in Wilms' tumors. Our findings emphasize the therapeutic potential of pharmacological ENL degradation for treating ENL-dependent cancers, making MS41 not only a valuable chemical probe but also potential anticancer therapeutic for further development.

DOI: https://doi.org/10.1126/sciadv.ado1432
Cell. 2024 Aug 20. pii: S0092-8674(24)00892-4. [Epub ahead of print]

The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.

Justin L Engel, Xiao Zhang, Mingming Wu, Yan Wang, Jose Espejo Valle-Inclán, Qing Hu, Kidist S Woldehawariat, Mathijs A Sanders, Agata Smogorzewska, Jin Chen, Isidro Cortés-Ciriano, Roger S Lo, Peter Ly.

  Chromothripsis describes the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei. Although micronuclei accumulate DNA double-strand breaks and replication defects throughout interphase, how chromosomes undergo shattering remains unresolved. Using CRISPR-Cas9 screens, we identify a non-canonical role of the Fanconi anemia (FA) pathway as a driver of chromothripsis. Inactivation of the FA pathway suppresses chromosome shattering during mitosis without impacting interphase-associated defects within micronuclei. Mono-ubiquitination of FANCI-FANCD2 by the FA core complex promotes its mitotic engagement with under-replicated micronuclear chromosomes. The structure-selective SLX4-XPF-ERCC1 endonuclease subsequently induces large-scale nucleolytic cleavage of persistent DNA replication intermediates, which stimulates POLD3-dependent mitotic DNA synthesis to prime shattered fragments for reassembly in the ensuing cell cycle. Notably, FA-pathway-induced chromothripsis generates complex genomic rearrangements and extrachromosomal DNA that confer acquired resistance to anti-cancer therapies. Our findings demonstrate how pathological activation of a central DNA repair mechanism paradoxically triggers cancer genome evolution through chromothripsis.

Keywords:  DNA repair; DNA replication; Fanconi anemia; chromothripsis; ecDNA; fragile sites; genome rearrangements; genomic instability; micronuclei; mitosis

DOI:  https://doi.org/10.1016/j.cell.2024.08.001
Cancer Res Commun. 2024 Aug 28.

Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis.

Mike Fernandez, Lei Yu, Qiong Jia, Xuesong Wang, Kevyn L Hart, Zhenyu Jia, Ren-Jang Lin, Lili Wang.

SF3B1 is the most recurrently mutated RNA splicing gene in cancer; However, the study of its pathogenic role has been hindered by a lack of disease-relevant cell line models. Here, we compared four genome engineering platforms to establish SF3B1 mutant cell lines: CRISPR-Cas9 editing, AAV HDR editing, base editing (ABEmax, ABE8e), and prime editing (PE2, PE3, PE5Max). We showed that prime editing via PE5max achieved the most efficient SF3B1 K700E editing across a wide range of cell lines. We further refined our approach by coupling prime editing with a fluorescent reporter that leverages a SF3B1 mutation-responsive synthetic intron to mark successfully edited cells. By applying this approach, called prime editing coupled intron-assisted selection (PRECIS), we introduced the K700E hotspot mutation into two chronic lymphocytic leukemia (CLL) cell lines, HG-3 and MEC-1. We demonstrated that our PRECIS-engineered cells faithfully recapitulate known mutant SF3B1 phenotypes including altered splicing, copy number variations, and cell growth defect. Moreover, we uncovered that SF3B1 mutation can cause the loss of Y chromosome in CLL. Our results showcase PRECIS as an efficient and generalizable method for engineering genetically faithful SF3B1 mutant models. Our approach provides new insights on the role of SF3B1 mutation in cancer and enables the generation of SF3B1 mutant cell lines in relevant cellular context.

DOI: https://doi.org/10.1158/2767-9764.CRC-24-0145