bims-scepro 2026-01-11 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2026–01–11
eighteen papers selected by
William Grey, University of York

Transient mechanical activation of the Piezo1 channel facilitates ex vivo expansion of hematopoietic stem cells.
A Druggable Tumor Suppressor and Leukemic Stem Cell Marker.
Chronic alcohol consumption drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells.
A human pathophysiological 3D-bone marrow model reveals immune and stromal cell heterogeneity.
ΔNp73 isoform defines a TP53-mutant-like poor-risk subgroup of acute myeloid leukemia.
Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia.
The clinically available supplement pyruvate enhances the therapeutic effect of bortezomib in MM by modulating mitochondrial metabolism.
Mitochondrial presequences harbor variable strengths to maintain organellar function.
Nanoengineered 3D culture substrate enables superior persistence and polyclonal engraftment of genetically engineered hematopoietic stem cells.
CK2 inhibitor, CX-4945, enhances BH3 priming and promotes apoptosis of venetoclax-resistant AML by targeting antiapoptotic proteins.
ATGL suppresses ferroptosis in acute myeloid leukemia cells by modulating the CEBPα/SCD1 axis and induces gilteritinib resistance.
Nat10-mediated ac4C epitranscriptomics orchestrates hematopoietic stem/progenitor cell fate determination via translation control.
Improved surfactant-assisted one-pot sample preparation for robust convenient single cell proteomics.
Gene regulatory network inference with popInfer reveals the dynamic regulation of hematopoietic stem cell quiescence.
A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.
Thioredoxin interacting protein (TXNIP), a redox regulator, mediates the RAPGEF3/4 signaling dependency in primary melanoma.
Safety of gemtuzumab ozogamicin with cytarabine, daunorubicin, and midostaurin induction in FLT3-mutated AML.
Loss of TMEM55B modulates lipid metabolism through dysregulated lipophagy and mitochondrial function.

Cell Res. 2026 Jan 09.

Transient mechanical activation of the Piezo1 channel facilitates ex vivo expansion of hematopoietic stem cells.

Qiwei Wang, Xin Zeng, Haoxiang Yang, Huan Lu, Lingli Jiang, Lizhen Xu, Jinxin Li, Jingyi Li, Yingli Han, Xiaoyan Wu, Yuanhong Zhou, Xiaolan Chen, Yanmin Zhao, Jimin Shi, Yi Luo, Fang Ni, Jie Sun, Qian Zhao, Fan Yang, Peng Xia, Hongyuan Jiang, He Huang, Pengxu Qian.

Achieving long-term ex vivo expansion of functional hematopoietic stem cells (HSCs) is essential for advancing HSC-based clinical therapies. Although mechanosensitive ion channels are known to play key roles in the hematopoietic system, their involvement in HSC expansion remains unclear. Here, we show that Piezo1 is highly expressed in HSCs. Both genetic deletion and prolonged chemical activation of Piezo1 impair cultured HSC function, indicating that transient mechanical activation of Piezo1 is required for maintenance of HSCs in culture. To achieve this, we screened various microspheres and found that PS500 (500-nm polystyrene microspheres) significantly enhanced ex vivo expansion of mouse bone marrow HSCs with long-term repopulating capacity. PS500 also expanded human umbilical cord blood HSCs capable of engraftment in immunodeficient mice. Mechanistically, PS500 activates Piezo1, triggering Ca2+-dependent expression of proliferative cytokines and subsequent STAT3 activation, which support HSC self-renewal and proliferation. Together, these findings show that PS500 enables transient Piezo1 activation and efficient, non-toxic expansion of functional HSCs, offering a promising approach for the generation of transplantable HSCs for clinical use.

DOI: https://doi.org/10.1038/s41422-025-01209-1
bioRxiv. 2025 Dec 22. pii: 2025.10.16.682831. [Epub ahead of print]

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker.

Yi Pan, Xiaduo Meng, Chen Wang, Wenxuan Zhou, Yibo Chen, Richard D Hammer, Hong Zheng, Gerhard Hildebrandt, Xunlei Kang.

Acute myeloid leukemia (AML) often enters remission after chemotherapy but frequently relapses due to chemotherapy-resistant leukemic stem cells (LSCs). Relapsed AML remains largely unresponsive to current therapies and carries a poor prognosis. We developed a large-language model (LLM) agent that incorporates multi-modal data to nominate druggable therapeutic targets for AML. We identified that higher expression of AGTR2 (encoding AT2R) is associated with better chemotherapy response and longer survival. In functional studies of 68 primary human AML samples, we found that LSCs consistently lacked AT2R expression. Across both CD34-expressing and -non-expressing AML samples, AT2R expression positively correlated with CD34 and CD117 expression. In patient-derived xenograft (PDX) models using 21 primary AML samples, AT2R⁻ cells initiated leukemia, whereas AT2R⁺ cells failed to do so. AT2R⁻ cells gave rise to both AT2R⁺ and AT2R⁻ progeny, suggesting hierarchical differentiation. Following chemotherapy in AML PDX mice, bone marrow analysis showed a marked enrichment of AT2R⁻ cells and depletion of AT2R⁺ cells, indicating that AT2R⁻ cells drive minimal residual disease and relapse. These results support the role of AT2R absence as a marker of LSCs. We observed reduced AT2R expression in AML cells compared to healthy peripheral blood and bone marrow mononuclear cells, suggesting a tumor suppressor role. Whole-genome sequencing of AML patients revealed no functional mutations in AGTR2 . However, 3D chromatin and epigenetic analyses uncovered frequent chromatin rearrangements involving AGTR2 promoter-silencer interactions, indicating epigenetic silencing as a likely mechanism for AT2R downregulation in AML. To validate the tumor suppressor role of AT2R, we developed murine AML models driven by MLL-AF9 or AML1-ETO9a fusions with either Agtr2 knockdown or enforced expression. Agtr2 knockdown accelerated leukemogenesis, while enforced Agtr2 expression delayed AML progression. In these models, enforced Agtr2 expression reduced LSC frequency, impaired cell cycle progression, and decreased AML stemness, as confirmed by limiting dilution assays and analysis of LSC-enriched populations. Mechanistically, enforced Agtr2 expression suppressed fatty acid metabolism - a key driver of AML stemness and growth - and inhibited downstream signaling pathways, including GSK3, PI3K/AKT, and Wnt/β-catenin. This led to reduced SREBF1 activity, confirmed by protein level changes and CUT&Tag assays. We tested buloxibutid (C21), a small-molecule AT2R agonist currently in phase II trials for idiopathic pulmonary fibrosis, in AML PDX models derived from 20 de novo and 6 relapsed AML samples. C21 significantly inhibited AML progression and enhanced the efficacy of chemotherapy, particularly in relapsed AML models.

DOI: https://doi.org/10.1101/2025.10.16.682831
bioRxiv. 2025 Dec 26. pii: 2025.12.25.696246. [Epub ahead of print]

Chronic alcohol consumption drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells.

Ridzky A A Yuda, Habin Bea, Valerie Kellett, Jungwoo Kim, Fan Yang, Haruna B Choijilsuren, Yejie Park, Yaojie Fu, Zewen Ha, Juhye Choi, Li Z Luo, Zhaoli Sun, Bin Gao, Sangmoo Jeong, Linda M S Resar, Moonjung Jung.

Chronic alcohol use causes pancytopenia and diminished immune responses against pathogens. However, it remains unclear whether chronic alcohol consumption directly induces inflammation in human hematopoietic stem progenitor cells (HSPCs), and if aging modifies the impact of chronic alcohol consumption in HSPCs. To examine how chronic alcohol use affects HSPCs, we performed single-cell RNA-seq in human and murine HSPCs and single-cell ATAC-seq in aged murine HSPCs following alcohol exposure. In xenotransplanted human HSPCs, chronic alcohol feeding resulted in a significant myeloid bias, heightened inflammation, double-stranded RNA (dsRNA) sensor upregulation, and type 1 interferon responses. In the native murine bone marrow, chronic alcohol exposure primed HSPCs to differentiate into myeloid cells and to exhibit heightened inflammation, DNA damage, and epigenetic reactivation of transposable elements (TEs) in an age-dependent manner. Alcohol-exposed aged long-term hematopoietic stem cells (LT-HSCs) displayed increased chromatin accessibility at TE-containing loci correlated with aberrant TE transcription. This transposon derepression was associated with the accumulation of dsRNAs in aged bone marrow cells, and activation of innate immune pathways, perpetuating HSC inflammaging. Furthermore, old mice showed two epigenomically distinct LT-HSC clusters, LT-HSC1 and LT-HSC2, in which the LT-HSC2 cluster expanded in response to chronic alcohol drinking and resembled inflammatory HSCs. Notably, secondary transplantation revealed unperturbed long-term self-renewal capacity in both human and murine HSCs, suggesting that HSC function may recover following alcohol cessation. Our data illuminate potential interactions between alcohol and aging that can reinforce inflammaging and epigenetic dysregulation in HSPCs.
Keypoints: Chronic alcohol consumption triggers age-dependent myeloid bias and inflammation in HSPCs without impairing self-renewalChronic alcohol consumption alters epigenome, driving heightened transposon upregulation in aged HSPCs.

DOI: https://doi.org/10.64898/2025.12.25.696246
Commun Biol. 2026 Jan 03.

A human pathophysiological 3D-bone marrow model reveals immune and stromal cell heterogeneity.

Mariette Giannini, Giulia Campione, Lea Torcq, Sylvain Donadelli, Maroua Bencheikh, Sophia Bounaud, Sandrine Jeanpierre, Kevin Geistlich, Veronique Maguer-Satta, Sylvain Lefort, Julie Leca.

The bone marrow niche is a complex microenvironment composed of stromal, endothelial, immune and hematopoietic cells. Dysregulated interactions within this niche can contribute to hematological malignancies and also occur in the context of solid cancer metastases. Here, we present a standardized three-dimensional human bone marrow (3D-BOM) model that recapitulates key features of the human niche. Indeed, we show that monocytes/macrophages from different sources acquire enhanced pro-inflammatory phenotype in 3D compared to 2D cultures. Hematopoietic progenitor cells are also influenced by this 3D niche while maintaining stemness characteristics over extended serial culture. Single-cell transcriptomics analysis highlighted human-like stromal and endothelial cells heterogeneity. In addition, we observed monocyte/macrophage and endothelial cell remodeling in the context of acute myeloid leukemia, suggesting dynamic interactions within the 3D-BOM. These findings highlight the potential of this model to investigate cellular dynamics underlying human bone marrow physiology and pathology.

DOI: https://doi.org/10.1038/s42003-025-09433-6
Cell Rep Med. 2026 Jan 08. pii: S2666-3791(25)00613-5. [Epub ahead of print] 102540

ΔNp73 isoform defines a TP53-mutant-like poor-risk subgroup of acute myeloid leukemia.

Diego A Pereira-Martins, Cesar Ortiz, Isabel Weinhäuser, Albertus T J Wierenga, Vincent van den Boom, Fatemeh Mojallali, Dominique Sternadt, Nisha K van der Meer, Shanna M Hogeling, Thiago M Bianco, Prodromos Chatzikyriakou, Douglas R Silveira, Emanuele Ammatuna, Antonio R Lucena-Araujo, Lynn Quek, Gerwin Huls, Eduardo M Rego, Jan Jacob Schuringa.

  Among acute myeloid leukemia (AML) patients, a subgroup remains notoriously refractory to current treatment options, with underlying mechanisms poorly understood. Here, using a multi-omics approach, we reveal that this resistant patient subgroup is characterized by high expression of the oncogenic TP73 isoform ΔNp73, exhibiting similarly poor outcomes as TP53-mutant AML. ΔNp73, which lacks a transcriptional activation domain but retains chromatin-binding properties, competes with TP53 for specific gene targets, thereby downregulating TP53 signaling. We demonstrate that the transcription factor CEBPA controls ΔNp73 expression in AML cells by binding to an intragenic enhancer region. Genetic or pharmacological inhibition of the transcriptional activity of CEBPA with guanfacine reduces ΔNp73 levels and restores drug sensitivity involving ferroptosis-mediated cell death, acting synergistically with venetoclax. Our study sheds light on a previously undercharacterized poor-risk subgroup of AML, which may support patient stratification and inform treatment considerations.

Keywords:  AML PDX models; CEBPA; SREBP/SREBF; TP53-mutated AML; TP73; acute myeloid leukemia; drug resistance; ferroptosis; guanfacine; poor prognosis prediction

DOI:  https://doi.org/10.1016/j.xcrm.2025.102540
Cell Chem Biol. 2026 Jan 06. pii: S2451-9456(25)00395-2. [Epub ahead of print]

Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia.

Emma E Uible, Issac Choi, Courtnee A Clough, Aishlin Hassan, Annabelle J Anandappa, Julianna Fisher, Bibek Karki, Kathleen Hueneman, Kwangmin Choi, Eric J Vick, William Seibel, Kenneth D Greis, Lynn Lee, Courtney Jones, Timothy M Chlon, Jorge Henao-Mejia, Chandrashekhar Pasare, John T Cunningham, Andrew G Volk, Daniel T Starczynowski.

  Caspase-1 (CASP1) is best known for regulating IL-1β processing and pyroptosis; however, its role in leukemia has not been clearly defined. Here, we show that loss of CASP1 impairs leukemic cell growth, drives differentiation, and reduces leukemic burden in vivo, independent of its CASP1 protease activity. Instead, CASP1 functions as a scaffolding hub, controlling nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) signaling via its interaction with raptor (RPTOR), a component of mTORC1. Deletion of CASP1 or disruption of its CARD domain induces excessive NF-κB activity and impairs leukemic cell function. We further developed a proteolysis-targeting chimera (PROTAC) degrader that selectively depletes Pro-CASP1 and suppresses leukemic cells. These findings reveal CASP1 as a regulator of mTORC1-NF-κB signaling in leukemia and highlight its scaffolding activity as a therapeutic vulnerability.

Keywords:  AML; CASP1; NF-κB; RAPTOR; inflammasome; mTOR

DOI:  https://doi.org/10.1016/j.chembiol.2025.12.002
Cancer Lett. 2026 Jan 07. pii: S0304-3835(26)00008-X. [Epub ahead of print] 218245

The clinically available supplement pyruvate enhances the therapeutic effect of bortezomib in MM by modulating mitochondrial metabolism.

Chenggong Tu, Arne Van der Vreken, Sylvia Faict, Gamze Ates, Ann Massie, Kim De Veirman, Elke De Bruyne, Karin Vanderkerken, Eline Menu.

  Multiple myeloma (MM) is a hematological malignancy characterized by plasma cells residing in the bone marrow. Despite advancements in treatment, including proteasome inhibitors (PIs) such as bortezomib (Bz), drug resistance remains a major challenge. Metabolic reprogramming supports MM survival and drug resistance, with mitochondria emerging as promising therapeutic targets through their control of OXPHOS and mitochondrial reactive oxygen species (Mito-ROS). Using metabolic flux analyses, flow cytometry, and Western blot analysis, we identified pyruvate as a central metabolic intermediate, which not only enhances mitochondrial respiration and Mito-ROS production, but also the Integrated Stress Response (ISR) pathway. Conversely, metformin, an inhibitor of OXPHOS, was still able to activate the ISR pathway, but rather reduced Bz-induced cytotoxicity by decreasing both protein synthesis, and ROS production. Results were confirmed on primary murine and patient samples. Moreover, analysis of the CoMMpass study revealed that patients with prolonged progression-free survival under PI treatment showed enrichment in OXPHOS-related gene, highlighting the importance of mitochondrial metabolism in regulating MM responses to Bz. These data suggest that targeting pyruvate metabolism to increase ROS production could offer a strategy to enhance Bz activity in MM.

Keywords:  ISR; bortezomib; metformin; multiple myeloma; pyruvate

DOI:  https://doi.org/10.1016/j.canlet.2026.218245
J Cell Biol. 2026 Apr 06. pii: e202507116. [Epub ahead of print]225(4):

Mitochondrial presequences harbor variable strengths to maintain organellar function.

Youmian Yan, Baigalmaa Erdenepurev, Thiago N Menezes, Ian Collinson, Natalie M Niemi.

Hundreds of mitochondrial proteins rely on N-terminal presequences for organellar targeting and import. While generally described as positively charged amphiphilic helices, presequences lack a consensus motif and thus likely promote protein import into mitochondria with variable efficiencies. Indeed, the concept of presequence strength underlies biological models such as stress sensing, yet a quantitative analysis of what dictates strong versus weak presequences is lacking. Furthermore, the extent to which presequence strength affects mitochondrial function and cellular fitness remains unclear. Here, we capitalize on the MitoLuc protein import assay to define multiple aspects of presequence strength. We find that select presequences, including those that regulate the mitochondrial unfolded protein response (UPRmt), impart differential import efficiencies during mitochondrial uncoupling. Surprisingly, we find that presequences beyond those associated with stress signaling promote highly variable import efficiency in vitro, suggesting presequence strength may influence a broader array of processes than currently appreciated. We exploit this variability to demonstrate that only presequences that promote robust in vitro import can fully rescue defects in respiratory growth in complex IV-deficient yeast, suggesting that presequence strength dictates metabolic potential. Collectively, our findings demonstrate that presequence strength can describe numerous metrics, such as total imported protein, maximal import velocity, or sensitivity to uncoupling, suggesting that the annotation of presequences as weak or strong requires more nuanced characterization than typically performed. Importantly, we find that such variability in presequence strength meaningfully affects cellular fitness beyond stress signaling, suggesting that organisms may broadly exploit presequence strength to fine-tune mitochondrial import and thus organellar homeostasis.

DOI: https://doi.org/10.1083/jcb.202507116
Cell Stem Cell. 2026 Jan 08. pii: S1934-5909(25)00450-3. [Epub ahead of print]

Nanoengineered 3D culture substrate enables superior persistence and polyclonal engraftment of genetically engineered hematopoietic stem cells.

Federico Midena, Laura Alessandrini, Claudio Conci, Matteo Barcella, Francesco Gazzo, Emanuela Jacchetti, Edoardo Carsana, Fabrizio Benedicenti, Roberta Vacca, Lucrezia Della Volpe, Sergio Arévalo, Kety Giannetti, Dafne Barozzi, Martina Franchino, Erika Zonari, Francesca Ferrua, Giacomo Farina, Chiara Brombin, Federica Cugnata, Martina Fiumara, Teresa Tavella, Leonardo Cherubin, Federico Fraschetta, Giulio Cerullo, Roberto Osellame, Marina Radrizzani, Samuele Ferrari, Ivan Merelli, Bernhard Gentner, Cristina Scielzo, Andrea Brendolan, Luigi Naldini, Alessandro Aiuti, Eugenio Montini, Manuela T Raimondi, Raffaella Di Micco.

  Ex vivo culture of hematopoietic stem and progenitor cells (HSPCs) is required for gene therapy applications but inadvertently triggers detrimental cellular responses, potentially threatening clinical success. In this study, we employ nichoids, biocompatible 3D culture substrates with cell-scale resolution, to provide HSPCs with mechanical support during ex vivo manipulation. This innovative 3D system improves HSPC multi-lineage differentiation and engraftment capacity by leveraging mechanobiological control over nuclear morphology, cytoskeleton organization, metabolism, and DNA integrity. Notably, 3D culture enables efficient genetic engineering across multiple platforms, including long-range gene editing, base- and prime-editing, and lentiviral-mediated gene addition. Moreover, this scaffold increases the clonal output and persistence of genetically engineered cells in xenotransplantation experiments, including a clinical protocol for lentiviral gene addition in Wiskott-Aldrich syndrome. Overall, we propose a transformative approach to enhance the efficacy and safety of emerging and established hematopoietic stem cell-based gene therapy applications.

Keywords:  3D culture; Wiskott-Aldrich syndrome; clonal tracking; genome editing; hematopoietic stem cells; lentiviral gene transfer; mechanobiology

DOI:  https://doi.org/10.1016/j.stem.2025.12.016
bioRxiv. 2025 Dec 26. pii: 2025.12.24.696284. [Epub ahead of print]

CK2 inhibitor, CX-4945, enhances BH3 priming and promotes apoptosis of venetoclax-resistant AML by targeting antiapoptotic proteins.

Muhammad Daniyal, Rajesh Rajaiah, Upendarrao Golla, Marudhu Pandiyan Shanmugam, Koby Duke, Katherine Mercer, Yasin Uzun, Hannah Valensi, Jeremy Hengst, Sinisa Dovat, Yi Qiu, Suming Huang, Chandrika G Behura.

Acute myeloid leukemia (AML), the most common hematologic malignancy, generally has a poor prognosis. Despite initial favorable responses to the BCL2 inhibitor venetoclax (VEN), remission is transient, and AML is eventually fatal. Resistance to VEN is primarily due to the overexpression of anti-apoptotic proteins, including MCL-1, BCL2L1 (BCL-XL), and BCL2A1. Casein kinase II (CK2) is a serine-threonine kinase and a known suppressor of apoptosis. We and others have reported that protein kinase CK2 activity is high in leukemic stem cells (LSCs) and associated with resistance to chemotherapy. We have shown that the selective CK2 inhibitor, CX-4945, suppresses BCL-XL and has a significant anti-tumor effect in AML preclinical models. CK2 expression and activity are high in venetoclax-resistant AML (VR-AML) cell lines. Genetic and pharmacological inhibition of CK2 significantly altered VR-AML gene signature, decreased MCL-1 protein level, increased BH3 priming and sensitized VR-AML cells to apoptosis. More importantly, CX-4945 selectively targeted LSCs (CD34+CD38-) and chemoresistant (CD123+CD47+) subpopulation in VR-AML. CX-4945 combined with VEN decreased leukemia burden and prolonged the survival of VR-AML cell line-derived and patient-derived xenografts compared to either drug alone. The combinatorial treatment was well tolerated in mice without additional myelosuppression or organ toxicity. CX-4945 (silmitasertib) is being tested in several early-phase clinical trials against adult and pediatric cancers. These preclinical results support the use of CX-4945 in combination with VEN to overcome resistance to apoptosis and re-sensitize VR-AML to chemotherapy.

DOI: https://doi.org/10.64898/2025.12.24.696284
Cell Death Dis. 2026 Jan 09.

ATGL suppresses ferroptosis in acute myeloid leukemia cells by modulating the CEBPα/SCD1 axis and induces gilteritinib resistance.

Shiyi Yuan, Ying Zhou, Wenrui Xiao, Ning Liu, Ping Zhang, Ying Zhang, Jianchuan Deng, Liang Fang, Xi Zhang, Shifeng Lou.

Metabolic reprogramming disrupts energy homeostasis and promotes tumor cell proliferation. In the present study, high expression of adipose triglyceride lipase (ATGL) in patients with acute myeloid leukemia (AML) predicted a poor clinical prognosis. Furthermore, the aberrant upregulation of ATGL was confirmed to promote the malignant progression of AML through gene ablation, overexpression, and pharmacological inhibition of ATGL, particularly in FLT3-ITD-mutated AML. RNA sequencing, lipid peroxidation, cellular iron, and ROS assays were performed to confirm the association of ATGL with ferroptosis. Mechanistically, ATGL is positively correlated with stearoyl-CoA decarboxylase 1 (SCD1) and promotes the malignant progression of AML by inhibiting ferroptosis through the CEBPα/SCD1 axis. We established gilteritinib-resistant MOLM-13 and MV4-11 cell lines and collected cells from patients with FLT3-ITD mutations to confirm that ATGL inhibitors increased the efficacy of gilteritinib. Consequently, we constructed an AML xenograft model using cells derived from patients with FLT3-ITD-mutated AML to confirm the efficacy of combining ATGL inhibitors with gilteritinib in vivo. This study provides novel therapeutic targets and monitoring indicators for AML, along with new treatment strategies for patients with FLT3-ITD-mutated AML and those with relapsed/refractory FLT3-ITD-mutated AML.

DOI: https://doi.org/10.1038/s41419-025-08388-0
Sci Adv. 2026 Jan 09. 12(2): eady0301

Nat10-mediated ac4C epitranscriptomics orchestrates hematopoietic stem/progenitor cell fate determination via translation control.

Feng Huang, Yushuai Wang, Weiwei Gao, Xiuxin Zhang, Jiajia Zhou, Ying Yang, Hongjie Mo, Minhan Wang, Qi Chen, Guangdun Peng, Jianjun Chen, Huilin Huang, Hengyou Weng.

Epigenetic regulation is crucial for balancing hematopoietic stem cell (HSC) self-renewal and differentiation, thereby maintaining hematopoietic homeostasis. Although Nat10-mediated RNA ac4C modification has been implicated in malignant hematopoiesis, its role in normal hematopoiesis remains unexplored. Here, we developed ULAC-seq to map ac4C in rare hematopoietic stem/progenitor cells (HSPCs) and revealed dynamic, cell-type-specific ac4C patterns, peaking in megakaryocyte-erythroid progenitors (MEPs), correlating with elevated Nat10 expression. Nat10 knockout disrupts HSC self-renewal and arrests MEP differentiation, leading to fetal and postnatal hematopoietic failure. Mechanistically, Nat10 deposits ac4C on mRNAs encoding key hematopoietic transcription regulators (e.g., Nfix), thereby enhancing their translation. Nat10 loss reduces Nfix protein levels and suppresses expression of its target genes (e.g., Mpl) that govern HSPC fate, while Nfix reconstitution rescues colony-forming defects in Nat10-null HSPCs. Our findings reveal that Nat10 orchestrates hematopoiesis through ac4C-dependent translational control of transcriptional factors, establishing an epitranscriptome-transcriptome regulatory axis essential for HSC maintenance and function.

DOI: https://doi.org/10.1126/sciadv.ady0301
bioRxiv. 2025 Dec 27. pii: 2025.12.26.696642. [Epub ahead of print]

Improved surfactant-assisted one-pot sample preparation for robust convenient single cell proteomics.

Reta Birhanu Kitata, Zhangyang Xu, Nadia Bayou, Rui Zhao, William B Christler, Matthew J Gaffrey, Karl K Weitz, Mara Serena Serafini, Elisabetta Molteni, Vladislav A Petyuk, Massimo Cristofanilli, Tao Liu, Carolina Reduzzi, Tujin Shi.

Recent advances in mass spectrometry-based single-cell proteomics (SCP) technologies have revolutionized the SCP field for comprehensive characterization of cellular heterogeneity. However, most of the current SCP approaches employ sub-µL to 1 µL processing volume for effective single-cell sample preparation using either ultralow-volume specialized devices or a 384-well plate by frequently adding water to the plate well to compensate water evaporation, which greatly limits their broad accessibility and analytical robustness. Here we report a robust convenient SCP method termed iSOP ( i mproved S urfactant-assisted O ne- P ot processing) for processing of single cells at the low µL processing volume using the 384-well plate with tight sealing to avoid sample drying loss. This iSOP SCP method was built upon our previously developed SOP method by the replacement of a PCR tube or 96-well plate with the low-volume 384-well plate and systematic optimization of the single-cell processing conditions. After optimization, 3 µL was selected as the processing volume with a mixture of 2 ng trypsin and 2 ng Lys-C enzymes in terms of robustness, detection sensitivity, and operation convenience. With a commonly accessible LC-MS platform, iSOP-MS can detect and quantify ∼1,200-1,800 protein groups from single HeLa or MCF7 cells. Application of iSOP-MS to two neuroblastoma cell lines has demonstrated that iSOP-MS enabled reliable identification of an average of ∼1,700 and ∼2,050 protein groups from single BE2-C and SK-N-SH cells, respectively, and precise characterization of cellular heterogeneity between the two distinct cell types and within the same cell type. When compared to other available SCP methods, iSOP-MS is more robust and convenient for routine, cost-effective quantitative SCP analysis.

DOI: https://doi.org/10.64898/2025.12.26.696642
iScience. 2025 Dec 19. 28(12): 114010

Gene regulatory network inference with popInfer reveals the dynamic regulation of hematopoietic stem cell quiescence.

Megan K Rommelfanger, Marthe Behrends, Yulin Chen, Jonathan Martinez, Nikith Kurella, Nino Geisler, Deepthi Guturu, Martin Bens, Lingyun Xiong, Zijin Xiang, K Lenhard Rudolph, Adam L MacLean.

  Inference of gene regulatory networks (GRNs) can reveal cell state transitions from single-cell genomics data. However, obstacles to temporal inference from snapshot data are difficult to overcome. Single-nuclei multiomic data offer a means to bridge this gap and derive temporal information using joint measurements of gene expression and chromatin accessibility in the same single cells. We developed popInfer to infer networks that characterize lineage-specific dynamic cell state transitions from joint gene expression and chromatin accessibility data. Benchmarking against alternative methods for GRN inference, we showed that popInfer achieves higher accuracy in the GRNs inferred. popInfer was applied to study single-cell multiomics data characterizing hematopoietic stem cells (HSCs) and the transition from HSC to a multipotent progenitor cell state during murine hematopoiesis across age and dietary conditions. From the networks predicted by popInfer, we discovered gene interactions controlling entry to/exit from HSC quiescence that are perturbed in response to diet or aging.

Keywords:  cell biology; gene network; molecular physiology

DOI:  https://doi.org/10.1016/j.isci.2025.114010
Nat Cancer. 2026 Jan 09.

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

Immune Atlas Consortium

Multiple myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We developed an Immune Atlas of MM by generating profiles of 1,397,272 single cells from the bone marrow (BM) of 337 newly diagnosed participants and characterized immune and hematopoietic cell populations. Cytogenetic risk-based analysis revealed heterogeneous associations with T cells of BM, with 17p13 deletion showing distinct enrichment of a type 1 interferon signature. The disease progression-based analysis revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing participants. Furthermore, signaling analyses suggested active intercellular communication involving a proliferation-inducing ligand and B cell maturation antigen, potentially promoting tumor growth and survival. Lastly, using independent discovery and validation cohorts, we demonstrated that integrating immune cell signatures with known tumor cytogenetics and individual characteristics significantly improves stratification for the prediction of survival.

DOI: https://doi.org/10.1038/s43018-025-01072-4
bioRxiv. 2025 Dec 29. pii: 2025.12.29.696903. [Epub ahead of print]

Thioredoxin interacting protein (TXNIP), a redox regulator, mediates the RAPGEF3/4 signaling dependency in primary melanoma.

Sireesh Kumar Teertam, Mithalesh K Singh, Sarah Altameemi, Sonia Gude, Sushmita Roy, Ryan Rossman, Michael A Newton, Daniel D Bennett, Nihal Ahmad, Xiaodong Cheng, Vijayasaradhi Setaluri.

RAP guanine exchange factors (RAPGEF3/4) also known as EPAC1/2 (Exchange Protein Activated by cyclic AMP) are important signaling proteins. In cutaneous melanoma, we reported that loss of dependency on RAPGEF3/4 is associated with metastatic progression. Here, we investigated the molecular mechanisms underlying EPAC1/2 signaling in melanoma. Using transformed human melanocytes, chemical inhibition and genetic deletion of EPAC in Braf/Pten mice, we show that EPAC activation is an early event in melanomagenesis and is required for the growth of transformed melanocytes in vitro and melanomagenesis in vivo . Query of the Cancer Genome Atlas (TCGA) and immunohistochemical analysis of melanoma tumors showed that low EPAC mRNA and RAP1-GTP protein correlate with better diseases free survival of patients with primary melanoma. RNAseq analysis of patient-matched primary and metastatic melanoma cells treated with EPAC inhibitor ESI-09 revealed that TXNIP, an important regulator of redox homeostasis, is a downstream effector of EPAC-RAP1 signaling. Our data also show that EPACs promote melanoma growth by regulation of redox homeostasis and mitochondrial reactive oxygen species through activation of mechanistic target of rapamycin complex 1 (mTORC1) that stabilizes hypoxia-inducible factor 1-alpha (HIF-1α), a transcriptional activator of TXNIP and glycolytic enzymes. Our data suggest that targeting mechanisms that metastatic melanoma cells employ to bypass EPAC dependency as a potential therapeutic approach for melanoma.

DOI: https://doi.org/10.64898/2025.12.29.696903
Blood Neoplasia. 2026 Feb;3(1): 100171

Safety of gemtuzumab ozogamicin with cytarabine, daunorubicin, and midostaurin induction in FLT3-mutated AML.

Jayanshu Jain, Kelly Pugh, Shivani Handa, Kaitlyn M Dvorak-Kornaus, Qiuhong Zhao, Roland B Walter, Rachel Cook, Jennifer Saultz, Ronan Swords, Junyang Li, George S Laszlo, Nicole R Grieselhuber, Alice S Mims, Karilyn T M Larkin, Kieran Sahasrabudhe, James S Blachly, Gregory K Behbehani, Ann-Kathrin Eisfeld, Meixiao Long, Andrew Srisuwananukorn, Kristin L Koenig, Uma Borate.

This phase 1 study investigated the addition of gemtuzumab ozogamicin (GO) to intensive chemotherapy with cytarabine, daunorubicin, and midostaurin in 21 patients with newly diagnosed (ND) FMS-like tyrosine kinase 3 (FLT3)-mutated acute myeloid leukemia (AML). Four dose levels of GO were evaluated. The use of GO was tolerable, with all dose-limiting toxicities similar to those seen in standard-of-care treatment. After induction, the median time to platelet recovery was 26 days, and the median time to absolute neutrophil count (ANC) recovery was 27 days. The maximum tolerated dose was cytarabine 100 mg/m2 on days 1 to 7, midostaurin 50 mg twice daily on days 8 to 21, daunorubicin 60 mg/m2 on days 1 to 3, and GO 3 mg/m2 on days 1 and 4. For the 18 patients who were evaluable for response after induction therapy, 16 patients (76%) achieved a composite complete response (complete remission [CR] + CR with incomplete hematologic recovery), and 2 (10%) had stable disease. Of the 14 patients who proceeded to consolidation, 5 discontinued the study for transplant, 1 for disease progression, and 1 for physician discretion. Seven patients completed consolidation therapy, all of whom achieved a CR. In total, 13 of the 21 patients (62%) received a hematopoietic stem cell transplant. Our results show that GO can safely be combined with intensive chemotherapy with midostaurin in ND, FLT3-mutated AML. This trial was registered at www.clinicaltrials.gov as #NCT03900949.

DOI: https://doi.org/10.1016/j.bneo.2025.100171
Cell Death Dis. 2026 Jan 09. 17(1): 26

Loss of TMEM55B modulates lipid metabolism through dysregulated lipophagy and mitochondrial function.

Yuanyuan Qin, Sheila S Teker, Nilsa La Cunza, Yao Tong, Elizabeth Theusch, Neil V Yang, Leela Venkatesan, Julia Su, Xuanwen Wang, Ronald M Krauss, Aparna Lakkaraju, Aras N Mattis, Marisa W Medina.

Lipophagy is a form of selective autophagy that targets the lipid droplets for lysosomal decay and has been implicated in the onset and progression of metabolic dysfunction-associated steatotic liver disease (MASLD). Factors that augment lipophagy have been identified as targets for MASLD therapeutic development. TMEM55B is a key regulator of lysosomal positioning, which is critical for lysosome fusion with the autophagosome, but is less well studied. Here, we demonstrate that the absence of TMEM55B in murine models accelerates MASLD onset and progression to metabolic dysfunction-associated steatohepatitis (MASH). In cellular models, TMEM55B deficiency enhances incomplete lipophagy, whereby lysosome-lipid droplet interactions are increased, but lysosomal cargo is not fully degraded and/or released, leading to the development of lipid-filled lysosomes (lipolysosomes). Loss of TMEM55B also impairs mitophagy, causing an accumulation of dysfunctional mitochondria. This imbalance leads to increased lipid accumulation and oxidative stress, worsening MASLD. These findings underscore the importance of lysosomal positioning in lipid metabolism and suggest that targeting lipophagy for MASLD therapeutic development should be carefully considered to ensure promotion of the entire lipophagic flux pathway and whether it occurs in the context of mitochondrial dysfunction.

DOI: https://doi.org/10.1038/s41419-025-08210-x