bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2026–08–23
twenty papers selected by
William Grey, University of York
  1. Human CEBPA -N AML exhibits enhanced engraftment and a C/EBP α -p30-driven leukemic stem cell program.
  2. Mutant TP53 allelic states in human hematopoietic stem and progenitor cells.
  3. Geneformer-guided multiomics integration identifies Pbx1 as a network hub of hematopoietic stem cell aging.
  4. Dual MYC and GSPT1 Protein Degrader for MYC-Driven Hematologic Malignancies.
  5. A novel role for transcription factor NFE2 in redox regulation and chemotherapy resistance in acute myeloid leukemia.
  6. Hematopoietic stem cell aging: a review of transcriptional and multi-omics insights and potential paths for AI integration.
  7. Oncogenic DHX15 mutation enhances mitochondrial metabolism and sustains leukemia stemness.
  8. NRAS knockdown reverses monocytic cell state and resensitizes resistant FLT3-AML cells to gilteritinib.
  9. FLT3-ITD signals for CEBPA and p53 proteolysis by the ubiquitin-proteosome pathway.
  10. CD55 promotes hematopoietic stem and progenitor cell survival in a mouse model of immune-mediated aplastic anaemia.
  11. In-depth characterization of stem cell potency and genotoxicity for clinical-scale ex vivo CRISPR-Cas9 gene editing.
  12. PKM2 modulation regulates leukemia cell survival.
  13. Modeling KRAS mutations in KMT2A::MLLT3 acute myeloid leukemia promotes leukemic progression and transcriptional rewiring.
  14. STING agonists in combination with epigenetic drugs potentiate ZNFX1-driven inflammatory necroptosis in TP53 -mutated AML.
  15. CXCR4-dependent migratory differences between peripheral Tregs and Tcons preserve GvL while limiting GvHD after HSCT.
  16. Injury-driven stromal exhaustion disrupts intrinsic regenerative capability.
  17. Multi-omic analyses of the same sample using metabolomics, lipidomics, proteomics, phosphoproteomics, and glycoproteomics.
  18. Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics.
  19. BAG6-RNF115 Couples Protein Quality Control with Ribosome Assembly.
  20. Development of a universal imaging "phenome" using shape, appearance and motion (SAM) features and the SAM Phenotype Observation Tool (SPOT).
  1. bioRxiv. 2026 Aug 04. pii: 2026.08.03.742558. [Epub ahead of print]
    Human CEBPA -N AML exhibits enhanced engraftment and a C/EBP α -p30-driven leukemic stem cell program.
    Philomina Sona Peramangalam, Mayuresh Konde, Onur Karakaslar, Sebastian Wolf, Shikan Zheng, Akmal Salimov, Sridevi Surapally, Marieke Griffioen, Tongjun Gu, Sridhar Rao, Daniel G Tenen, Thomas Oellerich, Erik van den Akker, Martin Carroll, Caner Saygin, John A Pulikkan.
      Leukemic stem cells (LSCs) play a central role in disease progression, therapeutic resistance, and relapse in acute myeloid leukemia (AML). However, the identification and characterization of LSCs remain challenging because of their low abundance and their close phenotypic resemblance to normal hematopoietic stem and progenitor cells. Although patient-derived xenograft (PDX) models have provided important insights into AML biology and LSC heterogeneity, the relative engraftment potential of distinct CEBPA mutation subtypes and the immunophenotypic identity of LSCs in CEBPA N-terminal mutant AML ( CEBPA - N -AML) remain poorly defined. To address these questions, we compared the engraftment characteristics of primary human CEBPA-mutated AML samples representing the major mutational subtypes using the highly permissive NSGS xenograft model. Primary CEBPA -N-AML samples exhibited markedly greater engraftment efficiency and leukemogenic potential than other CEBPA -mutated AML subtypes. Furthermore, we identified a CD366⁺CD73⁺CD123⁺CD117⁺CD371⁺CD247⁺ cell population that is highly enriched for functional LSCs in CEBPA-N -AML, demonstrating enhanced clonogenic activity, leukemia-initiating capacity, and long-term self-renewal. Collectively, our findings demonstrate that the leukemogenic potential of CEBPA -mutated AML is strongly influenced by mutation subtype, with CEBPA-N -AML exhibiting superior leukemia-propagating capacity in vivo. We further define a novel immunophenotypic LSC signature specific to CEBPA-N -AML, providing new insights into LSC heterogeneity in CEBPA -mutated AML and establishing a foundation for the development of LSC-directed therapeutic strategies.
    DOI:  https://doi.org/10.64898/2026.08.03.742558
  2. Leukemia. 2026 Aug 18.
    Mutant TP53 allelic states in human hematopoietic stem and progenitor cells.
    Karin Lind, Sayantanee Dutta, Marco Raffaele Cosenza, Thomas Eder, Johannes Foßelteder, Gabriel Pabst, Wolfgang Schöll, Andreas Prokesch, Holger W Auner, Albert Wölfler, Armin Zebisch, Andreas Reinisch, Florian Grebien, Jan O Korbel, Heinz Sill.
      
    DOI:  https://doi.org/10.1038/s41375-026-03106-x
  3. Sci Adv. 2026 Aug 21. 12(34): eaeb1346
    Geneformer-guided multiomics integration identifies Pbx1 as a network hub of hematopoietic stem cell aging.
    Hiroshi Kobayashi, Shintaro Watanuki, Yusuke Shiozawa, Motohiko Oshima, Shuhei Koide, Naoya Takayama, Takayuki Morikawa, Miho Haraguchi, Shinpei Tamaki, Takayoshi Asakura, Toshio Miyata, Atsushi Iwama, Seishi Ogawa, Keiyo Takubo.
      Hematopoietic stem cells (HSCs) constitute an organized hematopoietic system that undergoes age-related alterations, including increased platelet production and decreased erythropoiesis. The fundamental mechanisms driving these shifts remain incompletely understood. We used single-cell RNA sequencing data to show that old HSCs contain two distinct transcriptional programs: one shared with megakaryocytes and the other reflecting the most primitive HSC state. Developmental time-series profiling further suggests that the acquisition of these programs begins early in life, with the primitive module rising prenatally and megakaryocytic priming emerging after birth. Using a fine-tuned Geneformer (transformer-based deep learning model) to capture higher-order differences between young and old HSCs, coupled with transcriptomic and epigenetic profiling, as well as transcription factor screens, we identified Pbx1 as a key regulator of these age-related transcriptional and differentiation changes. Specifically, Pbx1 suppresses erythroid differentiation by repressing Gata1 expression. These findings provide insight into HSC aging and may inform approaches to modulate age-associated HSC dysfunction.
    DOI:  https://doi.org/10.1126/sciadv.aeb1346
  4. Blood. 2026 Aug 17. pii: blood.2025030170. [Epub ahead of print]
    Dual MYC and GSPT1 Protein Degrader for MYC-Driven Hematologic Malignancies.
    Yuki Nishida, Valeria Impedovo, Edward Ayoub, Natalia Baran, Darah A Scruggs, Hideaki Mizuno, Shayaun Khazaei, Lauren B Ostermann, Kazuharu Kamachi, Liang Zhang, Jo Ishizawa, Sandeep Singh, Andrea D Bedoy, Po Yee Mak, Bing Z Carter, Eiji Sugihara, Tetsuya Takimoto, Youzhi Tong, Honghua Yan, Dong Chen, Ji Huang, Hsu-Feng Chu, Liang Tong, Zamal Ahmed, Sarita Namjoshi, John Tainer, Mihai Gagea, Thomas Huynh, Abhishek Maiti, Koji Sasaki, Branko Cuglievan, Steffen Boettcher, Torsten Haferlach, Stefano Tiziani, Liandong Ma, Michael Andreeff.
      Direct targeting of the oncoprotein MYC has not yet been successful. We here report a novel dual protein degrader, GT19630, which binds directly to MYC and G1 to S phase transition protein 1 (GSPT1). GT19630 disrupts a novel feedforward loop of MYC and GSPT1, where MYC promotes transcription of GSPT1, and GSPT1 senses the stop codon of MYC to properly terminate its translation. The agent induces integrated stress response and abrogates oxidative phosphorylation through inhibition of the TCA cycle, resulting in apoptosis. GT19630 has superior activity compared to GSPT1- targeting molecular glues. GT19630 induces profound anti-proliferative effects and apoptosis at low nanomolar concentrations in a multitude of leukemia and lymphoma cell lines and primary samples, including those with TP53 mutations. GT19630 is highly active in vivo in models of therapy-resistant hematologic malignancies, including Burkitt's lymphoma, acute myeloid leukemia (AML) and multiple myeloma. CD34+ AML blasts overexpress MYC protein compared to normal hematopoietic stem/progenitor cells (HSPCs) and GT19630 induces greater cytotoxicity in AML cells compared to normal HSPCs. Further, GT19630 restores sensitivity to venetoclax and profoundly prolongs survival in vivo in venetoclax-resistant AML. GT19630 was well tolerated in humanized Crbn mice. In conclusion, our data support the development of the MYC/GSPT1 degrader GT19630 as a therapeutic strategy of MYC-driven hematologic malignancies.
    DOI:  https://doi.org/10.1182/blood.2025030170
  5. Leukemia. 2026 Aug 19.
    A novel role for transcription factor NFE2 in redox regulation and chemotherapy resistance in acute myeloid leukemia.
    Anne Marie Staehle, Florian Perner, Hans Felix Staehle, Katharina Gellrich, Fiona Preiß, Annika Grafemeyer, Jana Schulze, Jean-Luca Funk, Albert Gründer, Julia Berner, Sander Bekeschus, Christoph Koellerer, Heike L Pahl.
      Elevated activity of transcription factor NFE2 is sufficient to cause leukemic transformation in absence of a classical leukemic driver. However, the molecular mechanism promoting NFE2-driven leukemogenesis is not known. Here we report a previously unrecognized role for NFE2 as a key regulator of the oxidative stress response in leukemic cells. Through a comprehensive analysis of NFE2 genomic occupancy and its effect on chromatin accessibility and transcription, we demonstrate that NFE2 regulates glutathione homeostasis as well as the expression of central detoxifying enzymes. NFE2 constituted one of the highest scoring gene dependencies in MLL-AF9-transformed primary leukemic cells under redox stress, substantially more significant than the universally recognized redox regulator NRF2. Consequently, NFE2 knockdown sensitized leukemic cells to GSH depletion, ferroptosis induction, as well as to cytarabine treatment. Deriving an NFE2 RedOx score, we demonstrate that increased NFE2 activity constitutes an independent predictor of inferior outcome in AML patients at diagnosis.
    DOI:  https://doi.org/10.1038/s41375-026-03095-x
  6. Exp Mol Med. 2026 Aug 19.
    Hematopoietic stem cell aging: a review of transcriptional and multi-omics insights and potential paths for AI integration.
    Bongsoo Park, Hagai Yanai, Jun Ding, Isabel Beerman.
      Hematopoietic stem cell (HSC) aging underlies age-related immune decline, anemia and increased risk of hematologic malignancies, including clonal hematopoiesis and leukemia. Many available microarray and bulk RNA sequencing studies have elucidated conserved transcriptional hallmarks, such as myeloid bias, inflammation dysregulation, and self-renewal reinforcement in aged HSCs across mouse and human models. Here, we review key publicly available transcriptome and epigenome datasets from landmark studies, highlighting their contributions to defining HSC molecular aging signatures. We also summarize recent single-cell RNA sequencing, HSC aging intervention, and sex difference datasets. Despite these advances in technology and available sequencing datasets, fragmented data access, limited cross-species integration, and scarcity of multi-omics and single-cell contexts hinder progress. We discuss strategies for dataset harmonization, incorporation of multi-omics (transcriptome, epigenome, and proteome) and single-cell resolution to uncover heterogeneity and trajectories, as well as introduce the application of artificial intelligence and machine learning for predictive modeling, epigenome aging clocks, variant calling, clonal hematopoiesis detection, chromatin-based age prediction, and trajectory inference. Bridging insights from genetic mutant mouse models to emerging human bone marrow organoids offers translational potential for modeling HSC aging in vitro. We propose a curated, centralized, interactive database as a community resource to integrate these layers, enabling meta-analyses, artificial intelligence-driven discoveries, and accelerated therapeutic interventions for age-related hematopoietic disorders.
    DOI:  https://doi.org/10.1038/s12276-026-01805-0
  7. Leukemia. 2026 Aug 21.
    Oncogenic DHX15 mutation enhances mitochondrial metabolism and sustains leukemia stemness.
    Qilong Li, Peiqi Xing, Jin Xu, Jifei Li, Liangjie Chen, Xinlu Li, Yinpeng Bai, Gang Li, Ting Xie, Luzhen Wang, Yuan Wang, Guoliang Qing, Huafeng Wang, Liang Shao, Wei Wu, Zhaoqi Liu, Hudan Liu.
      The RUNX1::RUNX1T1 translocation, also termed AML1-ETO, is one of the most frequent cytogenetic abnormalities in acute myeloid leukemia (AML) and is associated with variable clinical outcomes. The R222G hotspot mutation, located in the RNA helicase gene DHX15, is enriched and predominantly found in AML with this translocation, but its diagnostic significance and underlying mechanism remain largely unclear. In this study, we show that pediatric AML patients carrying DHX15 mutations exhibit an inferior prognosis. Functional analysis demonstrates that DHX15R222G cooperates with AML1-ETO fusion protein to enhance AML leukemia stem cell (LSC) activity and promote resistance to standard chemotherapy. Mechanistically, AML1-ETO transcriptionally upregulates mitochondrial transcription factor A (TFAM), while DHX15R222G promotes TFAM protein stabilization and nuclear translocation, resulting in robust activation of oxidative phosphorylation (OXPHOS) gene expression and mitochondrial respiration. Inhibition of oxidative phosphorylation by the Complex V inhibitor S-Gboxin exerts strong anti-leukemic effects and efficiently circumvents chemotherapy resistance in AML1-ETO+ DHX15R222G leukemia. These findings underscore the pivotal role of oncogenic DHX15 mutations in regulating AML LSC activity and identify DHX15R222G as a potential genetic biomarker for AML risk stratification. Moreover, this mutation may predict therapeutic vulnerability to OXPHOS inhibition.
    DOI:  https://doi.org/10.1038/s41375-026-03102-1
  8. Blood. 2026 Aug 11. pii: blood.2026033305. [Epub ahead of print]
    NRAS knockdown reverses monocytic cell state and resensitizes resistant FLT3-AML cells to gilteritinib.
    Sunil K Joshi, Hadi Maazi, Janét Pittsenbarger, Belinda B Garana, Andy Kaempf, Ariane Huang, Marina A Gritsenko, Chelsea Hutchinson-Bunch, Karl K Weitz, Rosalie K Chu, Sara J C Gosline, Paul D Piehowski, Ann-Kathrin Eisfeld, Martin P Carroll, Alexander E Perl, Karin D Rodland, Bill H Chang, Alexey S Revenko, Jeffrey W Tyner, Brian J Druker, Elie Traer.
      While the FLT3 inhibitor gilteritinib is initially effective in patients with FLT3-mutated acute myeloid leukemia (AML), patients invariably relapse within months of treatment. Gilteritinib resistance is commonly driven by the emergence of NRAS mutations and a shift towards a more monocytic cell state. We hypothesized that directly targeting and depleting NRAS protein would reverse these adaptive differentiation changes and restore therapeutic sensitivity. To test this, we utilized a mutation-agnostic antisense oligonucleotide (ASO) to selectively knock down NRAS expression across gilteritinib-resistant AML cell lines, in vivo cell-line-derived xenografts, and primary patient samples. NRAS ASO successfully resensitized gilteritinib resistant cells with multiple distinct NRAS mutations, displaying superior efficacy compared to downstream MEK inhibition. This therapeutic efficacy was independent of NRAS mutant variant allele frequency, suggesting that wild-type NRAS may also contribute to resistance. Comprehensive multi-omic profiling (transcriptomics, proteomics, phosphoproteomics) revealed that NRAS knockdown consistently reversed monocytic phenotype, shifting cells back toward a more primitive cell state. Monocytic differentiation and NRAS mutations are established drivers of resistance to diverse targeted regimens in AML, including FLT3, IDH, and BCL2 inhibitors, so we also tested venetoclax resistant primary cells with NRAS mutations. Resistant cells were resensitized to venetoclax after NRAS knockdown, suggesting that NRAS knockdown may be more broadly applicable in overcoming monocytic cell state and drug resistance in AML.
    DOI:  https://doi.org/10.1182/blood.2026033305
  9. Res Sq. 2026 Jul 30. pii: rs.3.rs-10436387. [Epub ahead of print]
    FLT3-ITD signals for CEBPA and p53 proteolysis by the ubiquitin-proteosome pathway.
    Yogen Saunthararajah, Xiaorong Gu, Sudipta Biswas, Zeinab Zahran, Songa Bae, Ramesh Balusu, Babal Jha, Jaroslaw Maciejewski.
      FLT3-ITD mutations in acute myeloid leukemias (AMLs) cause ligand-independent signaling. One way signaling pathways potently and immediately influence cell fates is by phosphorylating key fate-determining proteins to trigger their proteolysis. We investigated the master transcription factor (MTF) driver of granulo-monocytic lineage-fates, CEBPA, for regulation by this mechanism because we found high CEBPA mRNA but little CEBPA protein in FLT3-ITD versus FLT3 -wildtype AML cells, and inhibiting FLT3-ITD signaling with tyrosine kinase inhibitors (TKI) rapidly rescued CEBPA protein. Mass spectrometry revealed that CEBPA interacts with major ubiquitin-proteasome pathway (UPP) components: the ubiquitin-ligase UHRF1 and the deubiquitinase USP7. TKI treatment decreased the phosphorylation of CEBPA (Ser21) and USP7 (Ser18) alongside shifts in CEBPA interactions from degradative UHRF1 to protective USP7, stabilizing CEBPA and activating differentiation. Similarly, TKIs and UPP inhibitors stabilized the USP7 client p53, triggering apoptosis specifically in FLT3-ITD cells. Notably, UPP inhibitors (such as bortezomib) successfully stabilized CEBPA and p53 even in TKI-resistant FLT3-ITD cells. Because FLT3-ITD signaling functionally suppresses CEBPA and p53, genetic mutations in CEBPA or TP53 were mutually exclusive with FLT3-ITD in clinical series. In summary, FLT3-ITD drives the UPP-mediated destruction of CEBPA and p53, positioning UPP inhibitors as promising therapeutic candidates acting downstream of TKIs.
    DOI:  https://doi.org/10.21203/rs.3.rs-10436387/v1
  10. Blood Adv. 2026 Aug 20. pii: bloodadvances.2025018656. [Epub ahead of print]
    CD55 promotes hematopoietic stem and progenitor cell survival in a mouse model of immune-mediated aplastic anaemia.
    Foteini Kalampalika, Raul Sanchez-Lanzas, Amanda Jimenez-Pompa, Abigail Hateley, Miguel Ganuza.
      Idiopathic aplastic anaemia (AA) is a life-threatening autoimmune bone marrow (BM) failure syndrome characterized by a hypocellular BM and peripheral pancytopenia. While dysregulation of the complement system has been implicated in the pathogenesis of several autoimmune diseases, including rheumatoid arthritis and systemic lupus erythematosus, its role in AA remains poorly understood. Notably, autoantibodies are frequently detected in AA patients and have the potential to activate the complement cascade. Using an immune-mediated murine model of AA, we found that allogeneic transplantation of splenocytes induced BM failure accompanied by activation of the complement system, as evidenced by elevated plasma levels of complement components C3 and C5. To functionally dissect the contributions of direct cytotoxic T-cell effects versus indirect mechanisms such as complement activation, we co-transplanted hematopoietic stem and progenitor cells (HSPCs) congenic to the donor splenocytes into allogeneic recipient mice. In this context, HSPCs deficient in the complement inhibitor Cd55 were negatively selected, indicating increased susceptibility to complement-mediated attack in vivo. Importantly, pharmacological inhibition of the complement cascade rescued the selective disadvantage of Cd55-deficient HSPCs in AA mice, demonstrating that complement activation imposes a negative selective pressure on HSPCs in this model. Together, these findings support a functional role for the complement pathway in the pathogenesis of immune-mediated AA. Further studies are warranted to evaluate the therapeutic potential of combining complement inhibition with standard immunosuppressive therapy in patients with AA.
    DOI:  https://doi.org/10.1182/bloodadvances.2025018656
  11. Mol Ther Adv. 2026 Sep 10. 34(3): 201816
    In-depth characterization of stem cell potency and genotoxicity for clinical-scale ex vivo CRISPR-Cas9 gene editing.
    Asma Naseem, Winston Vetharoy, Thomas E Whittaker, Federica Zinghirino, Antonio Carusillo, Roopkatha Ghosh, Eduardo Gomez-Castaneda, Hashim Ali, Carlo Cipriani, Eugenio Montini, Adrian J Thrasher, Giorgia Santilli, Daniela Cesana, Giandomenico Turchiano, Alessia Cavazza.
      Translating CRISPR-Cas9-based homology-directed repair (HDR) strategies into clinical application remains a major challenge due to limited standardization, concerns over safety, and efficacy issues. Here, we present a comprehensive and clinically compliant preclinical framework for the ex vivo correction of Wiskott-Aldrich syndrome (WAS) using a CRISPR-Cas9-AAV6 platform targeting hematopoietic stem and progenitor cells (HSPCs). In this study, we established a clinical-compatible platform enabling large-scale manufacturing while preserving HSPC viability, stemness, and multilineage functionality. To overcome low HSPC long-term engraftment, we fine-tuned AAV dosing and transiently modulated p53BP-dependent DNA damage response pathway, achieving significantly improved in vivo correction and repopulation. Importantly, we implemented a multi-tiered genotoxicity assessment strategy, integrating in silico, genome-wide, and orthogonal assays, revealing a largely favorable safety profile with minimal off-target risks and no evidence of clonal dominance or transformation during the study period. Longitudinal in vivo safety monitoring revealed donor-specific rare off-target events and structural variants. This highlights the crucial importance of patient monitoring after transplantation, further emphasized by the identification of a de novo chromosomal rearrangement that could be detected exclusively following cell engraftment in mice. This work offers a robust and adaptable roadmap for future HDR-based gene editing platforms, establishing critical benchmarks for efficacy, safety, and regulatory readiness in the development of advanced therapeutic medicinal products.
    Keywords:  gene editing; hematopoietic stem and progenitor cells; homology-directed repair; preclinical
    DOI:  https://doi.org/10.1016/j.omta.2026.201816
  12. Cancer Metab. 2026 Jul 24. pii: 26. [Epub ahead of print]14(1):
    PKM2 modulation regulates leukemia cell survival.
    Nikolina Vrdoljak, Ekaterina N Parfenova, Alessia Roma, Drake A Mosca, Mark D Minden, Paul A Spagnuolo.
      Acute myeloid leukemia (AML) cells exhibit aberrant metabolism defined by a shift away from oxidative phosphorylation and towards anaerobic glycolysis, favouring cell growth. Glycolytic enzymes are altered for this change to occur, including pyruvate kinase (PK), where the tetrameric and high activity M1 isoform (PKM1) is replaced with the predominantly dimeric and low activity M2 isoform (PKM2). Dimeric PKM2 produces less pyruvate and acts as a protein kinase in the nucleus, demonstrating divergent roles in both cell metabolism and as a transcriptional co-activator. In this study, the role of PKM2 in AML was defined, as PKM2 levels were elevated but PK enzymatic activity was reduced in AML cells compared to normal hematopoietic cells. Genetic and pharmacological studies show that decreasing and increasing PKM2 activity resulted in anti-AML effects both in vitro and in vivo. Indeed, these models show that inhibition and activation of PKM2 disrupt the native oligomeric state of the protein, resulting in reduced nuclear PKM2 accumulation and c-Myc expression, ultimately leading to cell death. Together, these results highlight the importance of PKM2 in AML, uncover the mechanisms by which both inhibition and activation cause AML cell death, and identify a novel modulator of PKM2 activity.
    DOI:  https://doi.org/10.1186/s40170-026-00440-7
  13. Leukemia. 2026 Aug 18.
    Modeling KRAS mutations in KMT2A::MLLT3 acute myeloid leukemia promotes leukemic progression and transcriptional rewiring.
    Nayeli Esparza, Joan Defrêne, Eva Bresson, Anne-Cécile Soufflet, Martha María Juárez-Rodríguez, Veronique Lisi, Alberto Hernández-Sánchez, Lars Bullinger, Vincent-Philippe Lavallée, Brian T Wilhelm, Frédéric Barabé.
      
    DOI:  https://doi.org/10.1038/s41375-026-03112-z
  14. bioRxiv. 2026 Jul 28. pii: 2026.07.27.741029. [Epub ahead of print]
    STING agonists in combination with epigenetic drugs potentiate ZNFX1-driven inflammatory necroptosis in TP53 -mutated AML.
    Kaushlendra Tripathi, Lora Stojanovic, Zahra Gohari, Mostafa Abdelrheem, Gabriella Santos, Aviva Tyler, Brandon Cooper, Rena G Lapidus, Darren Perkins, Alonso Heredia, Kenneth P Nephew, Stephen B Baylin, Michael J Topper, Maria R Baer, Feyruz V Rassool.
      TP53 -mutated acute myeloid leukemia (AML) has dismal outcomes with current treatments and represents a critical unmet need. TP53 -mutated AML is proposed to be susceptible to immunotherapeutic approaches but, to date, there is no established immunotherapy for this sub-group. Expression of stimulator of interferon genes (STING), a key innate immune driver that activates interferon (IFN) signaling, is decreased by epigenetic silencing or mutation in many cancers, including those with TP53 mutations. Here, we report that response to the next-generation synthetic STING agonist C92 is potentiated in AML cell lines and primary cells with TP53- mutated versus wild-type (WT) cells, representing a previously undescribed vulnerability of these leukemia cells to STING small molecule therapies. Moreover, combining treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC), significantly increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes. Cell death in TP53 KO versus WT AML is specifically dependent on innate immune zinc finger NFX1-type containing 1 (ZNFX1) and Z-DNA-binding protein 1 (ZBP1) driving increased cleavage and activation of Receptor-Interacting-Serine/Threonine-Protein Kinase 3 (RIPK3) and mixed lineage kinase domain-like protein (MLKL), suggesting mechanisms of necroptosis. Finally, C92 and DAC combination significantly reduces leukemia burden in humanized AML mouse models, accompanied by increased immune responses, including cytokines and cytotoxic T lymphocytes in the leukemia microenvironment. These results support development of clinical trial strategies combining STING agonists with DNMTis for patients with TP53 -mutated AML.
    Summary: TP53-mutated AML potentiates effects of novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, inducing increased STING activation and cytokine release STING agonists and DNMTis, synergistically increase STING activation with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes in TP53 -mutated AML STING agonists induce necroptosis via a STING-ZNFX1-ZBP1-necroptosis axis in TP53 -mutated AML. This drug combination reduces leukemia burden, activates immune responses in AML models and supports translation for high-risk AML patients.
    Statement of Translational Relevance: This pre-clinical study identifies a novel therapeutic vulnerability in ( TP53 )-mutated acute myeloid leukemia (AML), a poor prognosis subtype with a critical unmet need. Novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, induces increased STING activation and cytokine release, compared with WT TP53 in AML cell lines and primary cells, and has superior STING activity with respect to several STING agonists currently in clinical studies. Combining C92 treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC) synergistically increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes, driving ZNFX1-driven inflammatory necroptotic cell death. Utilizing humanized mouse models, C92 in combination with DAC significantly reduces leukemia burden and enhances cytotoxic T-cell responses in the tumor microenvironment, supporting clinical translation for high-risk AML patients.
    DOI:  https://doi.org/10.64898/2026.07.27.741029
  15. Blood Adv. 2026 Aug 19. pii: bloodadvances.2025017997. [Epub ahead of print]
    CXCR4-dependent migratory differences between peripheral Tregs and Tcons preserve GvL while limiting GvHD after HSCT.
    Loredana Ruggeri, Antonio Pierini, Elena Urbani, Sara Ciardelli, Rachele Del Sordo, Rosaria Sola, Tiziana Zei, Roberta Iacucci Ostini, Simonetta Saldi, Francesco Maria Adamo, Antonella Mancusi, Karim Enrico Jardini, Eni Hoxha, Valerio Viglione, Rebecca Sembenico, Francesco Zorutti, Susanta K Hui, Mauro Di Ianni, Franca Falzetti, Maria Paola Martelli, Cristina Mecucci, Cynthia Aristei, Alessandra Carotti, Massimo F Martelli, Andrea Velardi.
      Although studies on HLA-haploidentical hematopoietic stem cells transplant (HSCT) for high-risk acute myeloid leukemia (AML) showed that regulatory and conventional T-lymphocyte (Treg/Tcon) immunotherapy prevents graft-versus-host disease (GvHD) while it exerts T-cell dependent graft-versus-leukemia (GvL) effect, its mechanism is less known. The present study clarifies the mechanisms underlying this finding. In a xenogenic immunotherapy model, non-obese diabetic-scidIl2rgtm mice were engrafted with human primary AML and were treated with allogeneic human peripheral blood Tregs followed by Tcons. Treg/Tcon immunotherapy cleared leukemia without causing GvHD. Peripheral blood Tregs are largely CD45RO+ and express low levels of CXCR4 bone marrow (BM) homing receptor. They localised in peripheral tissues (i.e., liver, gut), but not in the BM. Consequently, in the BM Tcon effector function was not downregulated and indeed Tcons killed leukemia. In contrast, in peripheral tissues, they showed no alloreactivity suggesting their effector function had been downregulated by the Tregs. Thus, the GvL effect without GvHD was due to the migratory features of peripheral blood Tregs. These data were confirmed in an MHC-mismatched BM transplant model using H-2b mice as recipients and H-2d mice as donors. Remarkably, in patients receiving haploidentical T-cell depleted HSCT with Treg/Tcon immunotherapy, the infused Tregs were not found in the BM in the first month post-transplant. In contrast, donor Tcons homed to the BM where they exerted leukemia killing. In conclusion, for the first time we show the mechanism whereby immunotherapy with Tregs/Tcons protects from GvHD while it preserves GvL in murine transplantation models and in transplanted leukemia patients.
    DOI:  https://doi.org/10.1182/bloodadvances.2025017997
  16. Nat Commun. 2026 Aug 19. pii: 8259. [Epub ahead of print]17(1):
    Injury-driven stromal exhaustion disrupts intrinsic regenerative capability.
    Sixun Wu, Hirotaka Matsumoto, Keita Kondo, Aiko Kuroda, Jumpei Morita, Takeshi Moriishi, Shawn A Hallett, Yuki Matsuo, Azumi Noguchi, Mitsuaki Ono, Makoto Abe, Kosei Ito, Shinsuke Ohba, Noriaki Ono, Yuki Matsushita.
      Bone marrow stromal cells, marked by leptin receptor (Lepr) and C-X-C motif chemokine ligand 12 (Cxcl12), orchestrate osteogenesis and maintain bone homeostasis. Following injury, these stromal cells directly generate reparative bone and subsequently restore the marrow microenvironment, a process widely regarded as a reliable regenerative response. However, it remains unclear whether stromal cells retain full regenerative capacity after prior injury. Here, we show that Lepr+Cxcl12+ stromal cells have limited regenerative capacity and become dysfunctional upon repeated activation, defining a state of stromal exhaustion. Lepr-Cre-labeled stromal cells progressively lose osteogenic potential after repeated injury and instead differentiate into bone marrow adipocytes. Exhausted stromal cells are distinct from aging stromal cells, exhibiting metabolic abnormalities, chronic inflammation associated with stress responses, and impaired regenerative plasticity. Furthermore, β-catenin deletion during injury repair induces adipogenesis through stromal lineage switching, whereas pharmacological and genetic activation of Wnt/β-catenin signaling partially rescues osteogenesis, indicating that dysregulated Wnt/β-catenin signaling drives stromal exhaustion and impaired regeneration. As repeated regenerative activation may occur in recurrent fractures, orthopedic surgeries, osteoporosis, and osteogenesis imperfecta, stromal exhaustion represents a critical barrier to bone regeneration and a potential therapeutic target for restoring stromal plasticity.
    DOI:  https://doi.org/10.1038/s41467-026-76108-z
  17. Chem Commun (Camb). 2026 Aug 20.
    Multi-omic analyses of the same sample using metabolomics, lipidomics, proteomics, phosphoproteomics, and glycoproteomics.
    Yuefan Wang, Xuejun Peng, Hongyi Liu, Mia Gidley, Beth Kelly, Erika L Pearce, Edward J Pearce, Xianlin Han, Hui Zhang.
      Mass spectrometry (MS)-based multi-omics offers powerful tools to comprehensively characterize proteins, post-translational modifications, metabolites, and lipids. However, these measurements are typically performed using separate sample preparation workflows and modality-specific liquid chromatography mass spectrometry (LC-MS) platforms, limiting integration and constraining applications to small amounts of sample materials, especially scarce clinical specimens. Here, we describe a unified nano-LC-MS framework that enables metabolomic, lipidomic, proteomic, phosphoproteomic, and glycoproteomic analyses from the same starting material using a single nano-LC-MS platform, with only the chromatographic conditions, acquisition methods, and enrichment procedures tailored to each omics. This integrated strategy reduces workflow complexity and sample consumption while improves analytical continuity across molecular layers. By enabling deep multi-omics characterization from the same sample, this platform provides a practical foundation for comprehensive analysis of precious clinical samples.
    DOI:  https://doi.org/10.1039/d6cc03477b
  18. bioRxiv. 2026 Jul 30. pii: 2026.07.29.741525. [Epub ahead of print]
    Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics.
    Samantha A O'Connor, Romell B Gletten, Ritin Sharma, Zoe N Jensen, Brooke Lovell, Krystine Garcia-Mansfield, Lucy Y Ghoda, Bin Zhang, David E Frankhouser, Russell C Rockne, Jeffrey M Trent, Guido Marcucci, Patrick Pirrotte.
      Single-cell proteomics (SCP) currently lacks validated benchmarking standards, and cell annotation often relies on transcriptomic proxies. Unsupervised clustering offers a proxy-free alternative, but its success depends on biological signal outweighing technical variation. In homogeneous samples this is achievable, but in heterogeneous populations, where closely related cell types differ only subtly, technical variation can dominate the clustering and obscure the biology needed for annotation. To address this, we developed an integrated experimental and computational pipeline for protein-level cell annotation and applied it to human PBMCs as an immune-cell test case. We isolated T cells, B cells, monocytes, and NK cells by negative-selection sorting to build a high-fidelity reference. In parallel, unsorted PBMCs from the same donor were processed on a cellenONE and acquired using label-free DIA on an Orbitrap Astral Zoom. Using the labeled reference dataset, we systematically benchmarked normalization, imputation, and clustering methods to assess their effect on cell-type separation. Unsupervised analysis resolved functional subpopulations within each lineage, and a probabilistic SCP classifier trained on these annotations identified the corresponding cell types and states in the unsorted PBMC fraction, validating the pipeline on unenriched, heterogeneous samples. Together, this work delivers an analytically benchmarked SCP workflow that resolves immune lineage and cell-state heterogeneity in human PBMCs and provides a classifier-ready, protein-level reference for immune-cell assignment.
    DOI:  https://doi.org/10.64898/2026.07.29.741525
  19. bioRxiv. 2026 Aug 07. pii: 2026.08.06.742952. [Epub ahead of print]
    BAG6-RNF115 Couples Protein Quality Control with Ribosome Assembly.
    Anat Raiff, Colin Zenge, Alban Ordureau, Itay Koren.
      Protein homeostasis relies on protein quality control (PQC) pathways that survey the proteome to eliminate aberrant polypeptides. The BAG6 complex is a central PQC factor that recognizes exposed hydrophobic regions, a feature commonly associated with misfolded, mislocalized, and mistranslated proteins. Whether this surveillance machinery also regulates intact, functional proteins as part of physiological proteostasis has remained unclear. Using unbiased quantitative proteomics, we identify the ribosomal protein RPL22L1 as an endogenous BAG6 substrate whose abundance is controlled by continuous proteasomal degradation. This turnover requires the RNF115 E3 ligase activity but not the canonical BAG6 partner RNF126, defining RPL22L1 as a selective RNF115-dependent substrate. Mechanistically, we map a bipartite hydrophobic degron that distinguishes RPL22L1 from its stable paralog RPL22, and show that BAG6-RNF115-mediated degradation is governed by substrate assembly state. Accordingly, RPL22L1 is protected from degradation upon incorporation into the 60S ribosome, where it substitutes for RPL22. When RPL22 is lost, either genetically or through recurrent inactivating mutations in microsatellite-unstable cancers, the vacant ribosomal binding site permits RPL22L1 incorporation, protecting it from BAG6-mediated degradation. These findings establish unassembly-coupled degradation as a mechanism by which BAG6 regulates the abundance of functional protein components, ensuring that they accumulate only when incorporated into their native macromolecular complexes.
    DOI:  https://doi.org/10.64898/2026.08.06.742952
  20. Nat Commun. 2026 Aug 17. pii: 8409. [Epub ahead of print]17(1):
    Development of a universal imaging "phenome" using shape, appearance and motion (SAM) features and the SAM Phenotype Observation Tool (SPOT).
    Felix Y Zhou, Adam Norton-Steele, Lewis Marsh, Helen M Byrne, Heather A Harrington, Xin Lu.
      Cells are plastic, highly heterogeneous and change over time. High-content timelapse imaging promises to reveal dynamic cell behaviors, enabling more accurate identification of cell state and cell fate prediction for biological hypothesis generation and perturbation screens. To empower live-cell imaging based screening, we report the development of (1) a Shape, Appearance, Motion (SAM) "phenome"; a universal set of 2185 image-derived features that act as a image-"transcriptome" to comprehensively quantify an object's instantaneous phenotype; (2) the SAM-Phenotype-Observation-Tool (SPOT), for image-"sequencing" analysis of phenomes. We validate the effectiveness of unbiased SAM-SPOT workflow on publicly available computer vision and 2D single cell imaging datasets. Importantly, we demonstrate that SAM-phenome outperforms features generated by deep learning AI models trained on >1 million fixed single cell and >5000 single cell video frames, respectively. SAM-phenome and SPOT deliver high-throughput, object-treatment-agnostic, comprehensive screening readouts of dynamics, promising to advance novel molecular target discovery and new medicine development.
    DOI:  https://doi.org/10.1038/s41467-026-75505-8
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