bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2024–09–22
twenty-one papers selected by
William Grey, University of York
  1. CCR2 cooperativity promotes hematopoietic stem cell homing to the bone marrow.
  2. Proteomics reveals dynamic metabolic changes in human hematopoietic stem progenitor cells from fetal to adulthood.
  3. Epigenetic modifications in hematopoietic ecosystem: a key tuner from homeostasis to acute myeloid leukemia.
  4. Lipoprotein metabolism mediates hematopoietic stem cell responses under acute anemic conditions.
  5. A developmental route to hematopoietic stem cells.
  6. Selective degradation of mutant FMS-like tyrosine kinase-3 requires BIM-dependent depletion of heat shock proteins.
  7. UM171 enhances fitness and engraftment of gene modified hematopoietic stem cells from sickle cells disease patients.
  8. Auto-expansion of in vivo HDAd-transduced hematopoietic stem cells by constitutive expression of tHMGA2.
  9. Expansion effect of romiplostim on hematopoietic stem and progenitor cells versus thrombopoietin and eltrombopag.
  10. Proteasome inhibition enhances the anti-leukemic efficacy of chimeric antigen receptor (CAR) expressing NK cells against acute myeloid leukemia.
  11. Pharmacological restriction of genomic binding sites redirects PU.1 pioneer transcription factor activity.
  12. Inhibition of JAK/STAT3 Expression by Acute Myeloid Leukemia-Targeted Nanoliposome for Chemotherapy Enhancement.
  13. Multiomic single cell sequencing identifies stemlike nature of mixed phenotype acute leukemia.
  14. Long-lived lung megakaryocytes contribute to platelet recovery in thrombocytopenia models.
  15. Phosphoproteomics predict response to midostaurin plus chemotherapy in independent cohorts of FLT3-mutated acute myeloid leukaemia.
  16. Knowledge graphs facilitate prediction of drug response for acute myeloid leukemia.
  17. Hematopoietic stem cell gene therapy to halt neurodegeneration.
  18. Targeted protein relocalization via protein transport coupling.
  19. Therapy-related AML: long-term outcome in a large cohort of AML-patients with intensive and non-intensive therapy.
  20. CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics.
  21. Changes in Hematopoietic Stem Cell Numbers Following Acute Exercise in Non-Athlete Marathon Runners.
  1. Sci Adv. 2024 Sep 20. 10(38): eadq1476
    CCR2 cooperativity promotes hematopoietic stem cell homing to the bone marrow.
    Stephanie N Hurwitz, Danielle R Kobulsky, Seul K Jung, Jennifer J Chia, Jason M Butler, Peter Kurre.
      Cross-talk between hematopoietic stem and progenitor cells (HSPCs) and bone marrow (BM) cells is critical for homing and sustained engraftment after transplantation. In particular, molecular and physical adaptation of sinusoidal endothelial cells (ECs) promote HSPC BM occupancy; however, signals that govern these events are not well understood. Extracellular vesicles (EVs) are mediators of cell-cell communication crucial in shaping tissue microenvironments. Here, we demonstrate that integrin α4β7 on murine HSPC EVs targets uptake into ECs. In BM ECs, HSPC EVs induce up-regulation of C-C motif chemokine receptor 2 (CCR2) ligands that synergize with CXCL12-CXCR4 signaling to promote BM homing. In nonirradiated murine models, marrow preconditioning with HSPC EVs or recombinant CCR2 ligands improves homing and early graft occupancy after transplantation. These findings identify a role for HSPC EVs in remodeling ECs, newly define CCR2-dependent graft homing, and inform novel translational conditioning strategies to improve HSPC transplantation.
    DOI:  https://doi.org/10.1126/sciadv.adq1476
  2. Stem Cell Res Ther. 2024 Sep 15. 15(1): 303
    Proteomics reveals dynamic metabolic changes in human hematopoietic stem progenitor cells from fetal to adulthood.
    Mingfang Xiong, Yanyu Xiu, Juan Long, Xiao Zhao, Qianqian Wang, Haoyu Yang, Hang Yu, Lihong Bian, Yan Ju, Hongyu Yin, Qingxiang Hou, Fei Liang, Nan Liu, Fudong Chen, Ruiwen Fan, Yuying Sun, Yang Zeng.
       BACKGROUND: Hematopoietic stem progenitor cells (HSPCs) undergo phenotypical and functional changes during their emergence and development. Although the molecular programs governing the development of human hematopoietic stem cells (HSCs) have been investigated broadly, the relationships between dynamic metabolic alterations and their functions remain poorly characterized.
    METHODS: In this study, we comprehensively described the proteomics of HSPCs in the human fetal liver (FL), umbilical cord blood (UCB), and adult bone marrow (aBM). The metabolic state of human HSPCs was assessed via a Seahorse assay, RT‒PCR, and flow cytometry-based metabolic-related analysis. To investigate whether perturbing glutathione metabolism affects reactive oxygen species (ROS) production, the metabolic state, and the expansion of human HSPCs, HSPCs were treated with buthionine sulfoximine (BSO), an inhibitor of glutathione synthetase, and N-acetyl-L-cysteine (NAC).
    RESULTS: We investigated the metabolomic landscape of human HSPCs from the fetal, perinatal, and adult developmental stages by in-depth quantitative proteomics and predicted a metabolic switch from the oxidative state to the glycolytic state during human HSPC development. Seahorse assays, mitochondrial activity, ROS level, glucose uptake, and protein synthesis rate analysis supported our findings. In addition, immune-related pathways and antigen presentation were upregulated in UCB or aBM HSPCs, indicating their functional maturation upon development. Glutathione-related metabolic perturbations resulted in distinct responses in human HSPCs and progenitors. Furthermore, the molecular and immunophenotypic differences between human HSPCs at different developmental stages were revealed at the protein level for the first time.
    CONCLUSION: The metabolic landscape of human HSPCs at three developmental stages (FL, UCB, and aBM), combined with proteomics and functional validations, substantially extends our understanding of HSC metabolic regulation. These findings provide valuable resources for understanding human HSC function and development during fetal and adult life.
    Keywords:  Adult bone marrow (aBM); Fetal liver (FL); Glutathione (GSH); Hematopoietic stem progenitor cells (HSPCs); Metabolic remodelling; Proteomics; Umbilical cord blood (UCB)
    DOI:  https://doi.org/10.1186/s13287-024-03930-x
  3. Blood Sci. 2024 Oct;6(4): e00206
    Epigenetic modifications in hematopoietic ecosystem: a key tuner from homeostasis to acute myeloid leukemia.
    Shuxin Yao, Rongxia Guo, Wen Tian, Yanbing Zheng, Jin Hu, Guoqiang Han, Rong Yin, Fuling Zhou, Haojian Zhang.
      Hematopoietic stem cells (HSCs) maintain homeostasis in the hematopoietic ecosystem, which is tightly regulated at multiple layers. Acute myeloid leukemia (AML) is a severe hematologic malignancy driven by genetic and epigenetic changes that lead to the transformation of leukemia stem cells (LSCs). Since somatic mutations in DNA methylation-related genes frequently occur in AML, DNA methylation is widely altered and functions as a starting engine for initiating AML. Additionally, RNA modifications, especially N6-methyladenosine (m6A), also play an important role in the generation and maintenance of the hematopoietic ecosystem, and AML development requires reprogramming of m6A modifications to facilitate cells with hallmarks of cancer. Given the complex pathogenesis and poor prognosis of AML, it is important to fully understand its pathogenesis. Here, we mainly focus on DNA methylation and RNA m6A modification in hematopoiesis and AML and summarize recent advances in this field.
    Keywords:  Acute myeloid leukemia; DNA methylation; Hematopoiesis; Hematopoietic stem cells; Leukemia stem cells; RNA modification
    DOI:  https://doi.org/10.1097/BS9.0000000000000206
  4. Nat Commun. 2024 Sep 16. 15(1): 8131
    Lipoprotein metabolism mediates hematopoietic stem cell responses under acute anemic conditions.
    Kiyoka Saito, Mark van der Garde, Terumasa Umemoto, Natsumi Miharada, Julia Sjöberg, Valgardur Sigurdsson, Haruki Shirozu, Shunsuke Kamei, Visnja Radulovic, Mitsuyoshi Suzuki, Satoshi Nakano, Stefan Lang, Jenny Hansson, Martin L Olsson, Takashi Minami, Gunnar Gouras, Johan Flygare, Kenichi Miharada.
      Hematopoietic stem cells (HSCs) react to various stress conditions. However, it is unclear whether and how HSCs respond to severe anemia. Here, we demonstrate that upon induction of acute anemia, HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia, lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs, transcription levels of lipid metabolism-related genes, such as very low-density lipoprotein receptor (Vldlr), are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential, whereas HSCs in Apoe knockout mice do not respond to anemia induction. VldlrhighHSCs show higher erythroid potential, which is enhanced after acute anemia induction. VldlrhighHSCs are epigenetically distinct because of their low chromatin accessibility, and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays an important role in HSC regulation under severe anemic conditions.
    DOI:  https://doi.org/10.1038/s41467-024-52509-w
  5. Nat Biotechnol. 2024 Sep 18.
    A developmental route to hematopoietic stem cells.
    Adam C Wilkinson, Marella F T R de Bruijn.
      
    DOI:  https://doi.org/10.1038/s41587-024-02398-7
  6. Leukemia. 2024 Sep 17.
    Selective degradation of mutant FMS-like tyrosine kinase-3 requires BIM-dependent depletion of heat shock proteins.
    Melisa Halilovic, Mohamed Abdelsalam, Joanna Zabkiewicz, Michelle Lazenby, Caroline Alvares, Matthias Schmidt, Walburgis Brenner, Sara Najafi, Ina Oehme, Christoph Hieber, Yanira Zeyn, Matthias Bros, Wolfgang Sippl, Oliver H Krämer.
      Internal tandem duplications in the FMS-like tyrosine kinase-3 (FLT3-ITD) are common mutations in acute myeloid leukemia (AML). Proteolysis-targeting chimeras (PROTACs) that induce proteasomal degradation of mutated FLT3 emerge as innovative pharmacological approach. Molecular mechanisms that control targeted proteolysis beyond the ubiquitin-proteasome-system are undefined and PROTACs are the only known type of FLT3 degraders. We report that the von-Hippel-Lindau ubiquitin-ligase based FLT3 PROTAC MA49 (melotinib-49) and the FLT3 hydrophobic tagging molecule MA50 (halotinib-50) reduce endoplasmic reticulum-associated, oncogenic FLT3-ITD but spare FLT3. Nanomolar doses of MA49 and MA50 induce apoptosis of human leukemic cell lines and primary AML blasts with FLT3-ITD (p < 0.05-0.0001), but not of primary hematopoietic stem cells and differentiated immune cells, FLT3 wild-type cells, retinal cells, and c-KIT-dependent cells. In vivo activity of MA49 against FLT3-ITD-positive leukemia cells is verified in a Danio rerio model. The degrader-induced loss of FLT3-ITD involves the pro-apoptotic BH3-only protein BIM and a previously unidentified degrader-induced depletion of protein-folding chaperones. The expression levels of HSP90 and HSP110 correlate with reduced AML patient survival (p < 0.1) and HSP90, HSP110, and BIM are linked to the expression of FLT3 in primary AML cells (p < 0.01). HSP90 suppresses degrader-induced FLT3-ITD elimination and thereby establishes a mechanistically defined feed-back circuit.
    DOI:  https://doi.org/10.1038/s41375-024-02405-5
  7. Blood Adv. 2024 Sep 18. pii: bloodadvances.2024013932. [Epub ahead of print]
    UM171 enhances fitness and engraftment of gene modified hematopoietic stem cells from sickle cells disease patients.
    Boya Liu, Denise Klatt, Yu Zhou, John P Manis, Guy Sauvageau, Danilo Pellin, Christian Brendel, David A Williams.
      Hematopoietic stem cell transplantation with lentiviral vector (LVV) transduced autologous cells has proven an effective therapeutic strategy for sickle cell disease (SCD). However, ex vivo culture or proliferative stress associated with in vivo reconstitution may amplify any underlying genetic risk of leukemia. We aimed to minimize culture-induced stress and reduce genomic damage during ex vivo culture, enhance stem cell fitness and reconstitution of SCD CD34+ cells transduced with BCL11A shmiR-encoding LVV currently in clinical trials (NCT NCT03282656). UM171, a pyrimidoindole derivative can expand normal hematopoietic stem cells (HSCs) during in vitro culture and has been shown to be safe and effective in clinical trials using umbilical cord blood (NCT02668315). We examined the effect of UM171 during ex vivo LVV transduction of SCD HSCs. Culture of SCD CD34+ HSCs with UM171 during transduction reduced DNA damage and reactive oxygen species (ROS), decreased apoptosis, and was associated with increased numbers of immunophenotypically defined long-term HSCs. UM171 increased the engraftment of LVV transduced human HSCs in immunodeficient mice and barcode tracing revealed increased clonal diversity of engrafting cells. In competitive transplantation assays, analysis of BM showed that cells transduced in the presence of UM171 consistently outcompeted those transduced under control conditions. In summary, exposure of SCD peripheral blood CD34+ cells to UM171 during LVV transduction enhances stem cell fitness. These findings suggest manufacturing of genetically modified HSCs in the presence of UM171 may improve efficacy, safety and sustainability of gene therapy utilizing ex vivo approaches.
    DOI:  https://doi.org/10.1182/bloodadvances.2024013932
  8. Mol Ther Methods Clin Dev. 2024 Sep 12. 32(3): 101319
    Auto-expansion of in vivo HDAd-transduced hematopoietic stem cells by constitutive expression of tHMGA2.
    Hongjie Wang, Aphrodite Georgakopoulou, Evangelos Nizamis, Ka Wai Mok, Raïssa Eluère, Robert A Policastro, Paul N Valdmanis, André Lieber.
      We developed an in vivo hematopoietic stem cell (HSC) gene therapy approach that does not require cell transplantation. To achieve therapeutically relevant numbers of corrected cells, we constructed HSC-tropic HDAd5/35++ vectors expressing a 3' UTR truncated HMGA2 gene and a GFP reporter gene. A SB100x transposase vector mediated random integration of the tHMGA2/GFP transgene cassette. HSCs in mice were mobilized by subcutaneous injections of G-CSF and AMD3100/Plerixafor and intravenously injected with the integrating tHMGA2/GFP vector. This resulted in a slow but progressive, competitive expansion of GFP+ PBMCs, reaching about 50% by week 44 with further expansion in secondary recipients. Expansion occurred at the level of HSCs as well as at the levels of myeloid, lymphoid, and erythroid progenitors within the bone marrow and spleen. Importantly, based on genome-wide integration site analyses, expansion was polyclonal, without any signs of clonal dominance. Whole-exome sequencing did not show significant differences in the genomic instability indices between tHGMGA2/GFP mice and untreated control mice. Auto-expansion by tHMGA2 was validated in humanized mice. This is the first demonstration that simple injections of mobilization drugs and HDAd vectors can trigger auto-expansion of in vivo transduced HSCs resulting in transgene-marking rates that, theoretically, are curative for hemoglobinopathies.
    Keywords:  HMGA2; Sleeping Beauty transposase; gene therapy; helper-dependent adenovirus vector; hematopoietic stem cells; insertion site analysis; in vivo
    DOI:  https://doi.org/10.1016/j.omtm.2024.101319
  9. Int J Hematol. 2024 Sep 20.
    Expansion effect of romiplostim on hematopoietic stem and progenitor cells versus thrombopoietin and eltrombopag.
    Yuta Tezuka, Naoki Onoda, Tatsuya Morishima, Yoshiki Sumitomo, Keigo Nishii, Hitoshi Takizawa, Masayuki Kai.
      Romiplostim, a thrombopoietin (TPO) receptor agonist, is a clinically approved drug that is clearly effective in reconstituting hematopoiesis in refractory aplastic anemia and　idiopathic thrombocytopenic purpura. However, the mechanism underlying its biological effect is unknown, and its differences from other TPO receptor agonists remain unclear. Therefore, we determined the in vitro expansion effect of romiplostim on human CD34 + hematopoietic stem and progenitor cells (HSPCs) versus recombinant human TPO (rhTPO) and another clinically available drug, eltrombopag. We also performed single-cell RNA-seq to determine effects of romiplostim on CD34 + HSPCs at the molecular level. The maximum expansion effect of romiplostim on total CD34 + cells, CD34 + CD38 + progenitor cells, and CD34 + CD38 - immature cells was comparable to that of rhTPO, but higher than that of eltrombopag, particularly on CD34 + CD38 - immature cells. Single-cell RNA-seq analysis revealed that both romiplostim and eltrombopag induced signatures driven by rhTPO, but romiplostim induced molecular changes related to RHOA signaling in the most primitive HSPC subsets that were partially driven or not driven by eltrombopag. Additionally, romiplostim did not induce TFRC expression as was observed with eltrombopag. In conclusion, romiplostim expands and affects human HSPCs similar to rhTPO, but partially different from eltrombopag in terms of induction of gene expression.
    Keywords:  HSPC; Romiplostim; TPO
    DOI:  https://doi.org/10.1007/s12185-024-03853-6
  10. J Hematol Oncol. 2024 Sep 16. 17(1): 85
    Proteasome inhibition enhances the anti-leukemic efficacy of chimeric antigen receptor (CAR) expressing NK cells against acute myeloid leukemia.
    David Sedloev, Qian Chen, Julia M Unglaub, Nicola Schanda, Yao Hao, Eleni Besiridou, Brigitte Neuber, Anita Schmitt, Simon Raffel, Yi Liu, Maike Janssen, Carsten Müller-Tidow, Michael Schmitt, Tim Sauer.
       BACKGROUND: Relapsed and refractory acute myeloid leukemia (AML) carries a dismal prognosis. CAR T cells have shown limited efficacy in AML, partially due to dysfunctional autologous T cells and the extended time for generation of patient specific CAR T cells. Allogeneic NK cell therapy is a promising alternative, but strategies to enhance efficacy and persistence may be necessary. Proteasome inhibitors (PI) induce changes in the surface proteome which may render malignant cells more vulnerable to NK mediated cytotoxicity. Here, we investigated the potential benefit of combining PIs with CAR-expressing allogeneic NK cells against AML.
    METHODS: We established the IC50 concentrations for Bortezomib and Carfilzomib against several AML cell lines. Surface expression of class-I HLA molecules and stress-associated proteins upon treatment with proteasome inhibitors was determined by multiparameter flow cytometry. Using functional in vitro assays, we explored the therapeutic synergy between pre-treatment with PIs and the anti-leukemic efficacy of NK cells with or without expression of AML-specific CAR constructs against AML cell lines and primary patient samples. Also, we investigated the tolerability and efficacy of a single PI application strategy followed by (CAR-) NK cell infusion in two different murine xenograft models of AML.
    RESULTS: AML cell lines and primary AML patient samples were susceptible to Bortezomib and Carfilzomib mediated cytotoxicity. Conditioned resistance to Azacitidine/Venetoclax did not confer primary resistance to PIs. Treating AML cells with PIs reduced the surface expression of class-I HLA molecules on AML cells in a time-and-dose dependent manner. Stress-associated proteins were upregulated on the transcriptional level and on the cell surface. NK cell mediated killing of AML cells was enhanced in a synergistic manner. PI pre-treatment increased effector-target cell conjugate formation and Interferon-γ secretion, resulting in enhanced NK cell activity against AML cell lines and primary samples in vitro. Expression of CD33- and CD70-specific CARs further improved the antileukemic efficacy. In vivo, Bortezomib pre-treatment followed by CAR-NK cell infusion reduced AML growth, leading to prolonged overall survival.
    CONCLUSIONS: PIs enhance the anti-leukemic efficacy of CAR-expressing allogeneic NK cells against AML in vitro and in vivo, warranting further exploration of this combinatorial treatment within early phase clinical trials.
    DOI:  https://doi.org/10.1186/s13045-024-01604-y
  11. Nat Genet. 2024 Sep 18.
    Pharmacological restriction of genomic binding sites redirects PU.1 pioneer transcription factor activity.
    Samuel J Taylor, Jacob Stauber, Oliver Bohorquez, Goichi Tatsumi, Rajni Kumari, Joyeeta Chakraborty, Boris A Bartholdy, Emily Schwenger, Sriram Sundaravel, Abdelbasset A Farahat, Justin C Wheat, Mendel Goldfinger, Amit Verma, Arvind Kumar, David W Boykin, Kristy R Stengel, Gregory M K Poon, Ulrich Steidl.
      Transcription factor (TF) DNA-binding dynamics govern cell fate and identity. However, our ability to pharmacologically control TF localization is limited. Here we leverage chemically driven binding site restriction leading to robust and DNA-sequence-specific redistribution of PU.1, a pioneer TF pertinent to many hematopoietic malignancies. Through an innovative technique, 'CLICK-on-CUT&Tag', we characterize the hierarchy of de novo PU.1 motifs, predicting occupancy in the PU.1 cistrome under binding site restriction. Temporal and single-molecule studies of binding site restriction uncover the pioneering dynamics of native PU.1 and identify the paradoxical activation of an alternate target gene set driven by PU.1 localization to second-tier binding sites. These transcriptional changes were corroborated by genetic blockade and site-specific reporter assays. Binding site restriction and subsequent PU.1 network rewiring causes primary human leukemia cells to differentiate. In summary, pharmacologically induced TF redistribution can be harnessed to govern TF localization, actuate alternate gene networks and direct cell fate.
    DOI:  https://doi.org/10.1038/s41588-024-01911-7
  12. ACS Omega. 2024 Sep 10. 9(36): 37901-37909
    Inhibition of JAK/STAT3 Expression by Acute Myeloid Leukemia-Targeted Nanoliposome for Chemotherapy Enhancement.
    Yao Zuo, Hongwen Li, Xiaochao Wang, Yejin Liang, Caihong Huang, Guanye Nai, Jingrong Ruan, Wenzheng Dong, Xiang Lu.
      Acute myeloid leukemia (AML) is a relatively common malignant hematological disease whose development is mostly associated with abnormal activation of the JAK/STAT3 signaling pathway. Our previous study revealed that SAR317461, a novel JAK2/STAT3 inhibitor, can effectively inhibit the activation of the JAK2/STAT3 signaling pathway and has significant damaging and pro-apoptotic effects on AML cell lines. This project aims to build upon our prior research to enhance the application of SAR317461 in AML. The surface modification of liposomes with the CD34 antibody, along with the inclusion of the SAR317461 and cytarabine (a common AML chemotherapeutic agent), is observed. Due to the high expression of CD34 on the surface of AML cells, the nanoliposome could target AML cells specifically, further achieving an effective treatment for AML through the synergistic effect of JAK2/STAT3 inhibitors and chemotherapeutic agents. The implementation of this project will provide more theoretical support and ideas for the clinical application of JAK/STAT3 inhibitors in malignant tumors and for overcoming chemotherapy resistance.
    DOI:  https://doi.org/10.1021/acsomega.4c00710
  13. Nat Commun. 2024 Sep 18. 15(1): 8191
    Multiomic single cell sequencing identifies stemlike nature of mixed phenotype acute leukemia.
    Cheryl A C Peretz, Vanessa E Kennedy, Anushka Walia, Cyrille L Delley, Andrew Koh, Elaine Tran, Iain C Clark, Corey E Hayford, Chris D'Amato, Yi Xue, Kristina M Fontanez, Aaron A May-Zhang, Trinity Smithers, Yigal Agam, Qian Wang, Hai-Ping Dai, Ritu Roy, Aaron C Logan, Alexander E Perl, Adam Abate, Adam Olshen, Catherine C Smith.
      Despite recent work linking mixed phenotype acute leukemia (MPAL) to certain genetic lesions, specific driver mutations remain undefined for a significant proportion of patients and no genetic subtype is predictive of clinical outcomes. Moreover, therapeutic strategy for MPAL remains unclear, and prognosis is overall poor. We performed multiomic single cell profiling of 14 newly diagnosed adult MPAL patients to characterize the inter- and intra-tumoral transcriptional, immunophenotypic, and genetic landscapes of MPAL. We show that neither genetic profile nor transcriptome reliably correlate with specific MPAL immunophenotypes. Despite this, we find that MPAL blasts express a shared stem cell-like transcriptional profile indicative of high differentiation potential. Patients with the highest differentiation potential demonstrate inferior survival in our dataset. A gene set score, MPAL95, derived from genes highly enriched in the most stem-like MPAL cells, is applicable to bulk RNA sequencing data and is predictive of survival in an independent patient cohort, suggesting a potential strategy for clinical risk stratification.
    DOI:  https://doi.org/10.1038/s41467-024-52317-2
  14. J Clin Invest. 2024 Sep 19. pii: e181111. [Epub ahead of print]
    Long-lived lung megakaryocytes contribute to platelet recovery in thrombocytopenia models.
    Alison C Livada, Kathleen E McGrath, Michael W Malloy, Chen Li, Sara K Ture, Paul D Kingsley, Anne D Koniski, Leah A Vit, Katherine E Nolan, Deanne Mickelsen, Grace E Monette, Preeti Maurya, James Palis, Craig N Morrell.
      Lung megakaryocytes (Mks) are largely extravascular with an immune phenotype (1). Because bone marrow (BM) Mks are short-lived it has been assumed that extravascular lung Mks are constantly 'seeded' from the BM. To investigate lung Mk origins and how that impacts their functions, we developed methods to specifically label lung Mks using CFSE dye and biotin delivered oropharyngeal. Labeled lung Mks were present for up to four months, while BM Mks had a <1 week lifespan. In a parabiosis model, lung Mks were partially replaced over 1-month from a circulating source. Unlike tissue-resident macrophages, using MDS1-Cre-ERT2 TdTomato mice, we found that lung Mks arise from hematopoietic stem cells. However, studies with FlkSwitch mTmG mice showed that lung Mks are derived from a Flt3-independent lineage that does not go through a multipotent progenitor. CFSE labeling to track lung Mk-derived platelets showed that about 10% of circulating platelets are lung resident Mk-derived at steady state, but in sterile thrombocytopenia this was doubled (about 20%). Lung-derived platelets were similarly increased in a malaria infection model (Plasmodium yoelii) typified by thrombocytopenia. These studies indicate that lung Mks arise from a Flt3-negative BM source, are long-lived, and contribute more platelets during thrombocytopenia.
    Keywords:  Hematology; Platelets
    DOI:  https://doi.org/10.1172/JCI181111
  15. EBioMedicine. 2024 Sep 17. pii: S2352-3964(24)00352-9. [Epub ahead of print]108 105316
    Phosphoproteomics predict response to midostaurin plus chemotherapy in independent cohorts of FLT3-mutated acute myeloid leukaemia.
    Weronika E Borek, Luis Nobre, S Federico Pedicona, Amy E Campbell, Josie A Christopher, Nazrath Nawaz, David N Perkins, Pedro Moreno-Cardoso, Janet Kelsall, Harriet R Ferguson, Bela Patel, Paolo Gallipoli, Andrea Arruda, Alex J Ambinder, Andrew Thompson, Andrew Williamson, Gabriel Ghiaur, Mark D Minden, John G Gribben, David J Britton, Pedro R Cutillas, Arran D Dokal.
       BACKGROUND: Acute myeloid leukaemia (AML) is a bone marrow malignancy with poor prognosis. One of several treatments for AML is midostaurin combined with intensive chemotherapy (MIC), currently approved for FLT3 mutation-positive (FLT3-MP) AML. However, many patients carrying FLT3 mutations are refractory or experience an early relapse following MIC treatment, and might benefit more from receiving a different treatment. Development of a stratification method that outperforms FLT3 mutational status in predicting MIC response would thus benefit a large number of patients.
    METHODS: We employed mass spectrometry phosphoproteomics to analyse 71 diagnosis samples of 47 patients with FLT3-MP AML who subsequently received MIC. We then used machine learning to identify biomarkers of response to MIC, and validated the resulting predictive model in two independent validation cohorts (n = 20).
    FINDINGS: We identified three distinct phosphoproteomic AML subtypes amongst long-term survivors. The subtypes showed similar duration of MIC response, but different modulation of AML-implicated pathways, and exhibited distinct, highly-predictive biomarkers of MIC response. Using these biomarkers, we built a phosphoproteomics-based predictive model of MIC response, which we called MPhos. When applied to two retrospective real-world patient test cohorts (n = 20), MPhos predicted MIC response with 83% sensitivity and 100% specificity (log-rank p < 7∗10-5, HR = 0.005 [95% CI: 0-0.31]).
    INTERPRETATION: In validation, MPhos outperformed the currently-used FLT3-based stratification method. Our findings have the potential to transform clinical decision-making, and highlight the important role that phosphoproteomics is destined to play in precision oncology.
    FUNDING: This work was funded by Innovate UK grants (application numbers: 22217 and 10054602) and by Kinomica Ltd.
    Keywords:  Acute myeloid leukaemia; Drug response prediction; Machine learning; Midostaurin plus chemotherapy; Phosphoproteomics; Precision medicine
    DOI:  https://doi.org/10.1016/j.ebiom.2024.105316
  16. iScience. 2024 Sep 20. 27(9): 110755
    Knowledge graphs facilitate prediction of drug response for acute myeloid leukemia.
    Guangrong Qin, Yue Zhang, Jeffrey W Tyner, Christopher J Kemp, Ilya Shmulevich.
      Acute myeloid leukemia (AML) is a highly aggressive and heterogeneous disease, underscoring the need for improved therapeutic options and methods to optimally predict responses. With the wealth of available data resources, including clinical features, multiomics analysis, and ex vivo drug screening from AML patients, development of drug response prediction models has become feasible. Knowledge graphs (KGs) embed the relationships between different entities or features, allowing for explanation of a wide breadth of drug sensitivity and resistance mechanisms. We designed AML drug response prediction models guided by KGs. Our models included engineered features, relative gene expression between marker genes for each drug and regulators (e.g., transcription factors). We identified relative gene expression of FGD4-MIR4519, NPC2-GATA2, and BCL2-NFKB2 as predictive features for venetoclax ex vivo drug response. The KG-guided models provided high accuracy in independent test sets, overcame potential platform batch effects, and provided candidate drug sensitivity biomarkers for further validation.
    Keywords:  Bioinformatics; Biological sciences; Cancer
    DOI:  https://doi.org/10.1016/j.isci.2024.110755
  17. Neurotherapeutics. 2024 Sep 13. pii: S1878-7479(24)00127-2. [Epub ahead of print]21(4): e00440
    Hematopoietic stem cell gene therapy to halt neurodegeneration.
    Alessandra Biffi.
      Microglia play fundamental roles in multiple pathological primary and secondary processes affecting the central nervous system that ultimately result in neurodegeneration and for this reason they are considered as a key therapeutic target in several neurodegenerative diseases. Microglia-targeted therapies are directed at either restoring or modulating microglia function, to redirect their functional features toward neuroprotection. Among these strategies, hematopoietic stem cell gene therapy have proven to be endowed with a unique potential for replacing diseased microglia with engineered, transplant progeny cells that can integrate and exert relevant beneficial effects in the central nervous system of patients affected by inherited and acquired neurodegenerative conditions.
    Keywords:  Gene therapy; Hematopoietic stem cells; Microglia
    DOI:  https://doi.org/10.1016/j.neurot.2024.e00440
  18. Nature. 2024 Sep 18.
    Targeted protein relocalization via protein transport coupling.
    Christine S C Ng, Aofei Liu, Bianxiao Cui, Steven M Banik.
      Subcellular protein localization regulates protein function and can be corrupted in cancers1 and neurodegenerative diseases2,3. The rewiring of localization to address disease-driving phenotypes would be an attractive targeted therapeutic approach. Molecules that harness the trafficking of a shuttle protein to control the subcellular localization of a target protein could enforce targeted protein relocalization and rewire the interactome. Here we identify a collection of shuttle proteins with potent ligands amenable to incorporation into targeted relocalization-activating molecules (TRAMs), and use these to relocalize endogenous proteins. Using a custom imaging analysis pipeline, we show that protein steady-state localization can be modulated through molecular coupling to shuttle proteins containing sufficiently strong localization sequences and expressed in the necessary abundance. We analyse the TRAM-induced relocalization of different proteins and then use nuclear hormone receptors as shuttles to redistribute disease-driving mutant proteins such as SMARCB1Q318X, TDP43ΔNLS and FUSR495X. TRAM-mediated relocalization of FUSR495X to the nucleus from the cytoplasm correlated with a reduction in the number of stress granules in a model of cellular stress. With methionyl aminopeptidase 2 and poly(ADP-ribose) polymerase 1 as endogenous cytoplasmic and nuclear shuttles, respectively, we demonstrate relocalization of endogenous PRMT9, SOS1 and FKBP12. Small-molecule-mediated redistribution of nicotinamide nucleotide adenylyltransferase 1 from nuclei to axons in primary neurons was able to slow axonal degeneration and pharmacologically mimic the genetic WldS gain-of-function phenotype in mice resistant to certain types of neurodegeneration4. The concept of targeted protein relocalization could therefore inspire approaches for treating disease through interactome rewiring.
    DOI:  https://doi.org/10.1038/s41586-024-07950-8
  19. Blood Cancer J. 2024 Sep 16. 14(1): 160
    Therapy-related AML: long-term outcome in a large cohort of AML-patients with intensive and non-intensive therapy.
    Sophia Gross, Jana Ihlow, Leonie Busack, Kacper Adamiak, Jens Schrezenmeier, Julia Jesse, Michaela Schwarz, Anne Flörcken, Lam Giang Vuong, Kathrin Rieger, Jan Krönke, Philipp le Coutre, Vivien Boldt, Ann-Christin von Brünneck, David Horst, Thomas Burmeister, Igor-Wolfgang Blau, Ulrich Keller, Lars Bullinger, Jörg Westermann.
      Therapy-related acute myeloid leukemia (t-AML) often exhibits adverse (genetic) features. There is ongoing discussion on the impact of t-AML on long-term outcome in AML. Therefore, we retrospectively analyzed clinical and biological characteristics of 1133 AML patients (225 t-AML patients and 908 de novo AML patients) with a median follow-up of 81.8 months. T-AML patients showed more adverse genetic alterations, higher age and more comorbidities as compared to de novo AML. Median OS in intensively treated t-AML patients was 13.7 months as compared to 39.4 months in de novo AML (p < 0.001). With non-intensive therapy, OS did not differ significantly (p = 0.394). With intensive therapy, significant differences in favor of de novo AML were observed in the ELN intermediate I/II (p = 0.009) and adverse (p = 0.016) risk groups but not within favorable risk groups (APL p = 0.927, ELN favorable p = 0.714). However, t-AML was no independent risk factor for OS (p = 0.103), RR (p = 0.982) and NRM (p = 0.320) in the multivariate analysis. A limitation of our study is an ELN 2010 risk stratification due to a lack of more comprehensive molecular data according to ELN 2022. We conclude that therapeutic algorithms in t-AML, in particular with regard to allo-HSCT, should be guided by ELN genetic risk rather than classification as t-AML alone. Our data support the WHO and ICC 2022 classifications, which include t-AML as diagnostic qualifier rather than a separate subcategory.
    DOI:  https://doi.org/10.1038/s41408-024-01140-5
  20. Nat Protoc. 2024 Sep 16.
    CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics.
    Suoqin Jin, Maksim V Plikus, Qing Nie.
      Recent advances in single-cell sequencing technologies offer an opportunity to explore cell-cell communication in tissues systematically and with reduced bias. A key challenge is integrating known molecular interactions and measurements into a framework to identify and analyze complex cell-cell communication networks. Previously, we developed a computational tool, named CellChat, that infers and analyzes cell-cell communication networks from single-cell transcriptomic data within an easily interpretable framework. CellChat quantifies the signaling communication probability between two cell groups using a simplified mass-action-based model, which incorporates the core interaction between ligands and receptors with multisubunit structure along with modulation by cofactors. Importantly, CellChat performs a systematic and comparative analysis of cell-cell communication using a variety of quantitative metrics and machine-learning approaches. CellChat v2 is an updated version that includes additional comparison functionalities, an expanded database of ligand-receptor pairs along with rich functional annotations, and an Interactive CellChat Explorer. Here we provide a step-by-step protocol for using CellChat v2 on single-cell transcriptomic data, including inference and analysis of cell-cell communication from one dataset and identification of altered intercellular communication, signals and cell populations from different datasets across biological conditions. The R implementation of CellChat v2 toolkit and its tutorials together with the graphic outputs are available at https://github.com/jinworks/CellChat . This protocol typically takes ~5 min depending on dataset size and requires a basic understanding of R and single-cell data analysis but no specialized bioinformatics training for its implementation.
    DOI:  https://doi.org/10.1038/s41596-024-01045-4
  21. Adv Med Sci. 2024 Sep 14. pii: S1896-1126(24)00051-8. [Epub ahead of print]
    Changes in Hematopoietic Stem Cell Numbers Following Acute Exercise in Non-Athlete Marathon Runners.
    Özgür Günaştı, Çiğdem Özdemir, Kerem T Özgünen, Gizem Çiftdal, Ertuğrul Gezgin, Selcen Korkmaz Eryılmaz, Ömer Cumhur Boyraz, Abdullah Kılcı, Ümüt Adaş, Bülent Antmen, Sanlı Sadi Kurdak.
       PURPOSE: Hematopoietic stem cell (HSC) transplant is one of the curative methods for some patients with hematological malignancies. Granulocyte colony-stimulating factor (G-CSF) is the most common drug used to mobilize CD34+ cells, generally found in small numbers. Recent evidence showed that exercise causes transient mobilization in HSC. However, the type and intensity of exercise have not been fully revealed. We aimed to detect a significant increase in stem cell levels following 60 minutes of running at a personalized running pace.
    MATERIALS/METHODS: Eighteen runners, 48.2±1.9 years with peak oxygen consumption of 46.2±1.4 ml/kg/min, were enrolled in the study. The cardiopulmonary exercise test was performed to determine the individual running pace, and the participants ran 60-min on a treadmill at an intensity close to their ventilatory threshold (VT). The blood sampling for HSC count was performed before, immediately after, at the 1st, 4th and 24th hour after the 60-min running.
    RESULTS: The CD34+ HSCs were 13.9±2.3cells/μl before and significantly increased immediately after to 19.5±3.6cells/μl (p < 0.05). The consecutive HSC counts were 15.3±2.2, 19.5±4.8 and 15.1±3.4cells/μl at the 1st, 4th, and 24th hour, respectively.
    CONCLUSION: The individual data showed that some runners had higher HSC levels than the transplantation limit before and after the 60-min running trail, which was maintained for 24 hours. Pre-running high CD34+ HSCs may reflect an adaptive response to regular exercise, with a 60-min run near the VT further elevating HSCs. Individualized exercise may be a valuable tool to mobilize the CD34+ HSCs in peripheral blood for donors.
    Keywords:  cardiopulmonary exercise test; haematopoietic stem cells; marathon runners
    DOI:  https://doi.org/10.1016/j.advms.2024.09.003
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