bims-scepro 2026-09-27 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2026–09–27
eighteen papers selected by
William Grey, University of York

Multipotent Progenitor-3 Cells Are Reprogrammed by Bone-derived DKK1 to Drive Myelopoiesis in Breast Cancer.
Melatonin, circadian metabolism, mitochondrial remodeling, and cell size dynamics in primitive hematopoietic stem cells.
Mutant ASXL1 Cooperates with MECOM and BRD4 to Drive Transcriptional Dysregulation in Human Hematopoiesis.
Increasing H3K9 Methylation Level Reduces the Proliferation of Leukemic Stem Cells.
Characterization of disease-initiating hematopoietic stem cells in calreticulin-mutated myeloproliferative neoplasms.
SLIT2 modulates leukaemic cell proliferation and stromal support in acute myeloid leukaemia models.
p38 MAPK inhibition safeguards genome integrity during gene editing of hematopoietic stem and progenitor cells.
Systemic delivery of phagocytosis-shielded retroviral vectors enables in vivo HSC gene therapy for sickle cell disease.
Targeting BIRC6 rejuvenates hematopoietic stem cell aging and immunosenescence.
Inducing oxidative stress by targeting the cholesterol biosynthesis pathway augments the efficacy of bortezomib in multiple myeloma.
Electroporation for High-Efficiency Delivery of CRISPR to Hematopoietic Cells.
The molecular interplay between USP32 and ERP44 in driving multiple myeloma progression and tumor growth.
MCUB restricts mitochondrial calcium to support metabolic adaptation and homeostasis in glioblastoma.
Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.
Artificial Intelligence-Powered Histopathology in Stem Cell Research: Bridging Morphology, Function, and Omics.
Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets.
Fatty acid oxidation fuels mitochondrial respiration to drive epidermal stem cell fate and differentiation.
The predicted interactome of the human mitochondrial proteome.

Blood. 2026 Sep 25. pii: blood.2026033782. [Epub ahead of print]

Multipotent Progenitor-3 Cells Are Reprogrammed by Bone-derived DKK1 to Drive Myelopoiesis in Breast Cancer.

Emily Eul, Giulia Furesi, Wentao Han, Seunghyun Lee, Mark Watson, Rebecca Aft, Grant Challen, Roberta Faccio.

The expansion of immunosuppressive myeloid cells drives tumor progression, yet clinical strategies aimed at depleting these populations have shown limited effects and high toxicity. Because myeloid cells arise from hematopoietic progenitors, we asked whether solid tumors durably reprogram hematopoietic stem and progenitor cells (HSPCs) to sustain pathological myeloid bias. Here, we show treatment-naïve stage-III breast cancer (BC) patients and murine models of primary BC exhibited expansion of bone marrow HSPCs with enhanced myeloid output. Transplantation assays further demonstrated that tumor-educated HSPCs retained durable myeloid bias following transfer into healthy recipients and promoted tumor progression upon secondary challenge, accompanied by selective expansion of multi-potent progenitors (MPPs) and mature myeloid cells. In contrast, transplantation of long-term HSCs did not confer durable hematopoietic changes or enhanced tumor growth, indicating that tumor-induced myeloid bias is mediated by downstream progenitors. Consistently, depletion of mature myeloid cells did not alter HSCs but triggered rapid MPP expansion and myeloid rebound in tumor-bearing mice compared to no-tumor controls. Among progenitor subsets, MPP3s emerged as the principal drivers of tumor-associated myelopoiesis. Single-cell RNA sequencing of BC patient bone marrow revealed reduced Wnt-β-catenin signaling in HSPCs and identified DKK1, a bone-derived Wnt inhibitor elevated during BC progression, as a mediator of MPP3 reprogramming. Targeting bone-derived DKK1 limited HSPC engraftment following transplantation into naïve mice, and reduced BC progression, MPP3 expansion, and myeloid output in tumor bearing mice. These findings highlight solid tumor-induced hematopoietic reprogramming and identify bone-derived DKK1 as a regulator of MPP3 fate.

DOI: https://doi.org/10.1182/blood.2026033782
Blood. 2026 Sep 21. pii: blood.2026034660. [Epub ahead of print]

Melatonin, circadian metabolism, mitochondrial remodeling, and cell size dynamics in primitive hematopoietic stem cells.

Priyasmita Chakrabarti, Abhishek K Singh, Nicola K Wilson, Iwo Kucinski, Orit Kollet, Lizeth-Alejandra Ordonez Moreno, Arturo Simoni-Nieves, M S Vijayabaskar, Sarah J Kinston, Tzu-Hsuan Chang, Yi-Hao Wang, Montaser Haddad, Angelica Varesi, Ekaterina Petrovich-Kopitman, Ziv Porat, Tatiana Smirnova, Jiffin Paulose, Avik Choudhuri, John Hogenesch, You-Yang Zhao, Ping-Chih Ho, Amnon Buxboim, Leonard I Zon, Marie-Dominique Filippi, Regina P Markus, John E Dick, Stephanie Z Xie, Berthold Gottgens, Jose A Cancelas, Tsvee Lapidot.

Primitive hematopoietic stem cells (pHSCs) sustain lifelong hematopoiesis through tightly regulated transitions between quiescence and activation. Circadian oscillations influence hematopoiesis; however, the mechanisms coordinating metabolic state and stem cell function daily remain incompletely defined. Here, we show that circadian cues coordinated a program of mitochondrial remodeling, metabolic reprogramming, and structural adaptation in pHSCs. At night, peak melatonin levels were associated with reduced mitochondrial membrane potential, increased mitochondrial reactive oxygen species, and activation of DRP1 and PINK1 dependent mitophagy, resulting in enhanced long term repopulating capacity. In parallel, pHSCs exhibited increased glycolytic activity characterized by elevated glucose uptake, GLUT1 expression, AMPK phosphorylation, and HIF1α signaling. Mechanistically, mitochondrial remodeling was regulated in part by melatonin signaling, whereas glycolytic reprogramming was modulated by systemic circadian inputs, including feeding associated cues and Wnt/β-catenin signaling. FoxM1 and DRP1 contributed to mitochondrial quality control, while PGC1α dependent transcription supported compensatory mitochondrial biogenesis across the daily circadian cycle. These metabolic transitions were accompanied by dynamic changes in cell and nuclear size, linked to lamin A/C phosphorylation modulation. These coordinated processes defined a nocturnal state of enhanced stem cell fitness characterized by improved regenerative potential. Key features of glycolytic regulation were conserved in human HSCs, and in vitro melatonin treatment reduced the mitochondrial membrane potential and cell size of human pHSCs. Together, these findings establish a temporally regulated metabolic framework in which circadian cues partition mitochondrial and glycolytic programs to preserve stem cell maintenance and function, adding a new layer to pHSC metabolic physiology with clinical transplantation implications.

DOI: https://doi.org/10.1182/blood.2026034660
Blood. 2026 Sep 22. pii: blood.2026034001. [Epub ahead of print]

Mutant ASXL1 Cooperates with MECOM and BRD4 to Drive Transcriptional Dysregulation in Human Hematopoiesis.

Madison L Hall, Aliya Quintal, Sonia N Acharya, Samantha Worme, Thai T Nguyen, Zachary Schonrock, Mitsuhiro Tsuchiya, Hanqian L Carlson, Itallia V Pacentine, Shawn B Shrestha, Jommel Macaraeg, Randall Armstrong, Nicole Szczepanski, James Adler, James McGann, Sara Evans-Dutson, Theresa A Lusardi, Brendan L O'Connell, Andrew C Adey, Galip Gürkan Yardımcı, Julia E Maxson, Theodore P Braun.

Mutations in the epigenetic regulator ASXL1 are common in myeloid malignancies and portend a near-universally poor prognosis. While multiple mechanisms for mutant ASXL1-dependent oncogenesis have been proposed, none have been functionally validated in the context of the human hematopoietic stem cell, where these mutations almost certainly arise. Here, we extensively characterized a CRISPR-engineered human hematopoietic stem and progenitor cell model of ASXL1 mutations. In this context, mutant ASXL1 expression decreases differentiation, increases clonogenicity in serial replating experiments, and improves engraftment in immunodeficient mice. We also show that endogenous truncating ASXL1 mutations stabilize the protein and confirm that mutant ASXL1 resists proteasomal degradation. At the transcriptional level, these phenotypes are driven by significant repression of immediate early genes and subtle global transcriptional upregulation, especially of genes repressed during normal differentiation. Using protein-interaction screens, genomic and functional approaches, we link the phenotypic changes in ASXL1-mutant cells to increased chromatin binding of RNAPII, BRD4, and the transcription factor MECOM. The association between ASXL1 and MECOM may reflect a direct or indirect interaction. We also observe aberrant RNA polymerase II pausing dynamics, especially at immediate early genes, in ASXL1-mutated cells. Finally, we demonstrate that ASXL1-mutant AML exhibits increased MECOM activity, consistent with our gene-editing models. Collectively, these studies highlight a highly reproducible model of mutant ASXL1 in the appropriate cell context. Further, they are the first to functionally describe the mutant ASXL1 interactome in the context of human HSCs, identifying MECOM and BRD4 as actionable dependencies with therapeutic potential for ASXL1-mutant myeloid malignancies.

DOI: https://doi.org/10.1182/blood.2026034001
Cancers (Basel). 2026 Sep 14. pii: 2969. [Epub ahead of print]18(18):

Increasing H3K9 Methylation Level Reduces the Proliferation of Leukemic Stem Cells.

Barbara Walter, Polina Zjablovskaja, Sara Montserrat-Vazquez, Eva Mejia-Ramirez, Laia Solé-Castilla, Javier Lozano-Bartolome, Miroslava Kari Adamcová, Meritxell Alberich-Jorda, Chang Sun, Qin Peng, Michael Lübbert, Amanda Amoah, Liam MacPhee, Melika Bakharzi, Florian Kuchenbauer, Arefeh Rouhi, Jasson Villarreal-Hernandez, Montserrat Arnan-Sangerman, Maria Carolina Florian.

  Background/Objectives: Genetic and epigenetic alterations accumulate throughout life in hematopoietic stem and progenitor cells (HSPCs), leading to an increased risk of age-related hematological malignancies, such as acute myeloid leukemia (AML). While a few epigenetic drugs have entered clinical practice, studies focusing on histone post-translational modifications (PTMs) altered in AML remain limited. Methods: Here, we used murine HSPCs, murine AML mouse models, human leukemic cell lines, and leukemic patient samples to investigate whether targeting the methylation of histone 3 at lysine 9 (H3K9 methylation) affects HSPCs upon aging and leukemogenesis and might represent a possible target. Results: Our data show that H3K9 methylation changes upon aging in HSPCs and is linked to a pre-malignant phenotype. Low levels of H3K9 methylation in leukemic cells are required to maintain proliferative capacities in vitro. Increasing H3K9 methylation reduces the leukemogenesis of both young and aged murine and patient-derived leukemic cells. Conclusions: Thus, H3K9 methylation might be a potential and selective therapeutic target in AML patients.

Keywords:  HoxA9-Meis1; IOX1; acute myeloid leukemia (AML); aging; hematopoietic stem cell (HSC); histone 3 lysine 9 methylation (H3K9 methylation)

DOI:  https://doi.org/10.3390/cancers18182969
Blood. 2025 Sep 25. pii: blood.2026033236. [Epub ahead of print]

Characterization of disease-initiating hematopoietic stem cells in calreticulin-mutated myeloproliferative neoplasms.

Camélia Benlabiod, Laetitia Borderon, Gurvan Hermange, Quentin Blampey, Maxime Evrard, Antonio Rodriguez-Romera, Stephanie G Moreno, Nathalie Gault, Philippe Rameau, Cyril Catelain, Elodie Rosa, Guillemette Fouquet, Lionel Faivre, Florence Pasquier, Bethan Psaila, Claus Nerlov, Sten Eirik W Jacobsen, William Vainchenker, Hana Raslova, Paul-Henry Cournède, Isabelle Plo, Caroline Marty.

Myeloproliferative neoplasms (MPNs) arise following the acquisition of a mutation in a hematopoietic stem cell (HSC) that causes oncogenic cytokine receptor signaling. Mutations in the calreticulin (CALR) gene are the second most common key driver mutations in MPNs, yet the identity of the disease-initiating HSCs and the mechanisms underlying their clonal expansion remain elusive. Knock-in mice bearing CALRdel52 and CALRins5 mutations recapitulate disease phenotypes, with a greater HSC amplification in CALRdel52 mice. Here, we crossed these strains with transgenic reporter mice expressing GFP under the control of the Von willebrand factor (Vwf) promoter, enabling discrimination between different HSC subsets. We show that CALR-mutated MPNs are mainly initiated from the expansion of platelet-biased, Vwf-positive HSCs, without substantially altering their lineage bias. Notably, the selective amplification of Vwf-positive CALRdel52 compared to CALRins5 HSCs is associated with increased signaling of the thrombopoietin receptor MPL and activation of the integrated stress response as evidenced by eIF2a phosphorylation downstream of PERK kinase triggered by endoplasmic reticulum stress. This pathway is also transcriptionally upregulated in CALRdel52-like compared with CALRins5-like patient hematopoietic stem and progenitor cells (HSPCs), as supported by reanalysis of a previous dataset, and is associated with increased phosphorylation of eIF2a. Pharmacological inhibition of PERK markedly reduces the proliferation of mouse CALRdel52 HSCs and impairs the megakaryocytic differentiation of CALRdel52-like HSPCs from patients while sparing cells from healthy donors. These findings identify the PERK/eIF2a pathway as a mechanistic vulnerability in the MPN cell-of-origin and offer a rationale for exploring new treatment approaches.

DOI: https://doi.org/10.1182/blood.2026033236
Br J Haematol. 2026 Sep 24.

SLIT2 modulates leukaemic cell proliferation and stromal support in acute myeloid leukaemia models.

Luise Albuquerque-Simões, Isabel Weinhäuser, Diego A Pereira-Martins, César Alexander Ortiz Rojas, Lúcio Henrique Sousa Pinheiro, Livia Bassani Lins de Miranda, Thiago Mantello Bianco, Rita de Cássia Cavaglieri, Mariane Cristina do Nascimento, Lynn Quek, Steffen Boettcher, Jan Jacob Schuringa, Eduardo Magalhães Rego.

  Acute myeloid leukaemia (AML) is supported by leukaemic stem cells (LSCs), whose continued existence and growth are dependent upon signals derived from their bone marrow (BM) microenvironment. Although the highly conserved glycoprotein slit guidance ligand 2 (SLIT2), implicated in axon guidance, has been proposed to support normal haematopoietic stem cell (HSC) function, its role in AML pathogenesis remains poorly defined. Here, we show that SLIT2 is downregulated in mesenchymal stem cells (MSCs) from AML patients. Patients with higher-than-normal SLIT2 protein levels had better outcomes, independently of classical risk factors. Functionally, knocking down (KD) SLIT2 in MSCs caused a reprogramming of the microenvironment. Specifically, SLIT2-KD in MSCs resulted in increased expression of LSC-supporting genes including C-X-C motif chemokne ligand 12 (CXCL12) and KIT proto-oncogene, receptor tyrosine kinase (KIT), and co-culture of primary AML cells on SLIT2-KD stromal cells prevented myeloid differentiation. Conversely, the addition of recombinant SLIT2 had cytostatic effects on AML cells, resulting in reduced proliferation and reduced clonogenicity in all tested models. Furthermore, in human xenograft models, systemic administration of recombinant SLIT2 resulted in a decrease in leukaemic burden in BM and spleen, delayed disease progression and improved survival. Overall, these data demonstrate that SLIT2 may act as a tumour suppressor, while SLIT2 loss impairs myeloid terminal differentiation, suggesting that SLIT2 signalling could serve as a potential therapeutic axis in AML.

Keywords:  SLIT2; acute myeloid leukaemia; bone marrow niche

DOI:  https://doi.org/10.1111/bjh.70785
Mol Ther. 2026 Sep 22. pii: S1525-0016(26)00794-X. [Epub ahead of print]

p38 MAPK inhibition safeguards genome integrity during gene editing of hematopoietic stem and progenitor cells.

Roberta Vacca, Lucrezia Della Volpe, Nicolò Gualandi, Kohei Shiroshita, Edoardo Carsana, Kety Giannetti, Chiara Gaddoni, Fabrizio Benedicenti, Barbara Gega, Sergio Arévalo, Parinaz Zarghamian, Stefano Beretta, Maria Carmina Castiello, Chiara Brombin, Daniele Canarutto, Ivan Merelli, Toni Cathomen, Eugenio Montini, Anna Villa, Luigi Naldini, Raffaella Di Micco.

Ex vivo genome editing of hematopoietic stem and progenitor cells (HSPCs) holds significant therapeutic potential but remains constrained by genotoxic risks associated with nuclease-induced DNA double-strand breaks, DNA donor template delivery and sensing, and proliferation-induced stress during ex vivo manipulation. These processes can lead to chromosomal instability, large on-target deletions, donor mis-integration, off-target events, and impaired long-term stem cell function, raising safety concerns for clinical translation. Here, we evaluate the impact of transient p38 MAPK inhibition on genomic integrity during clinically relevant CRISPR-Cas9 editing and show that this intervention attenuates ex vivo culture-associated stress without increasing detectable genotoxic outcomes. Comprehensive genotoxicity analyses, including quantification of large on-target deletions, adeno-associated viral vector mis-integration, and CAST-seq mapping of translocations, reveal no measurable differences in gene editing-associated structural alterations upon p38 MAPK inhibition, while micronuclei were significantly reduced. Importantly, long-term xenotransplantation followed by whole-exome sequencing shows that p38i-treated HSPCs display a reduced mutational burden without evidence of increased genomic alterations. Collectively, these findings identify transient p38 MAPK inhibition as a strategy to improve the quality and long-term fitness of gene-edited HSPCs without detectable adverse effects on the genome editing outcomes, supporting its further evaluation as a refinement to clinically relevant CRISPR-Cas9 editing workflows.

DOI: https://doi.org/10.1016/j.ymthe.2026.09.024
Cell Stem Cell. 2026 Sep 24. pii: S1934-5909(26)00343-7. [Epub ahead of print]

Systemic delivery of phagocytosis-shielded retroviral vectors enables in vivo HSC gene therapy for sickle cell disease.

Denise Klatt, Adele Mucci, Boya Liu, Marie Peschers, Giulia Schiroli, Axel Schambach, John Manis, Myriam Armant, David T Scadden, Els Verhoeyen, Danilo Pellin, David A Williams, Christian Brendel.

  Ex vivo hematopoietic stem cell (HSC) gene therapy is effective for non-malignant blood disorders including sickle cell disease (SCD), but requires hospitalization, ex vivo cell manipulation, and conditioning. Direct in vivo gene delivery could remove these barriers and widen access. Here, we explore phagocytosis-shielded lentiviral and alpha-retroviral vectors pseudotyped with the baboon endogenous retrovirus glycoprotein variant BaEVRLess for in vivo HSC gene transfer. Vector injection into mobilized humanized mice yielded up to 8.8% gene marking in hCD45+ cells, which chemoselection enriched to 70% of hCD45+ cells and 54% of HSCs. Barcode analysis showed polyclonal reconstitution in over 90% of mice, which remained stable in secondary recipients. For SCD, we targeted BCL11A and ZNF410 selectively in erythroid cells using miRNA-embedded shRNAs to derepress gamma-globin, reaching therapeutically relevant levels of 61.5% of beta-like globins. In summary, BaEVRLess-pseudotyped lentiviral vectors enable clinically relevant in vivo gene transfer and fetal globin induction for SCD.

Keywords:  BaEV; HSC; SCD; alpha-retroviral vector; baboon endogenous retrovirus glycoprotein; hematopoietic stem cell; in vivo gene therapy; lentiviral vector; sickle cell disease

DOI:  https://doi.org/10.1016/j.stem.2026.09.001
Signal Transduct Target Ther. 2026 Sep 23. pii: 404. [Epub ahead of print]11(1):

Targeting BIRC6 rejuvenates hematopoietic stem cell aging and immunosenescence.

Weinian Liao, Fangze Shao, Shaoyan Wang, Yetong Wang, Xinliang Chen, Yue Zhang, Zhang Zhang, Xiaodong Zai, Yilong Yang, Ying Yin, Youliang Wang, Jun Zhang, Junping Wang, Junjie Xu.

Immunosenescence represents a central hallmark of organismal aging, characterized by a progressive decline in immune function, which compromises host defense and accelerates systemic aging. Hematopoietic stem cell (HSC) aging is a key contributor to this process, characterized by aberrant expansion, myeloid-biased differentiation, and impaired self-renewal, culminating in hematopoietic-immune imbalance. Although the expansion and survival advantages of aged HSCs have been well-demonstrated, the underlying mechanisms remain elusive. Here, we reveal that regulatory T cells (Tregs) within the bone marrow (BM) microenvironment actively safeguard the survival of aged HSCs via a previously uncharacterized signaling pathway. We identify a novel aged HSC subpopulation characterized by high expression of Baculoviral IAP Repeat Containing 6 (BIRC6), an apoptosis inhibitor. This BIRC6-high subpopulation is markedly expanded in aged mice and recapitulates the hallmarks of HSC aging. Mechanistically, cAMP derived from BM Tregs activates the PKA-CREB pathway in HSCs, activating Birc6 transcription, which reduces apoptotic priming in aged HSCs, thereby promoting hematopoietic-immune imbalance. Strikingly, targeted BIRC6 inhibition in HSCs using antibody-conjugated lipid nanoparticle-encapsulated antisense oligonucleotides (LNP-ASOs) significantly reverses hematopoietic-immune aging phenotypes and ameliorates age-associated immune dysfunction in middle-aged mice. LNP-ASO treatment dramatically rebalances immune cell production, reduces immunosenescence markers, and enhances vaccine responses in middle-aged mice. More importantly, this strategy was also effective in HSCs from middle-aged human donors, highlighting its potential for clinical translation. These findings elucidate a key microenvironmental pathway (Treg-cAMP-PKA-CREB-BIRC6) driving HSC aging and offer a novel strategy to ameliorate the aged hematopoietic system and combat age-related immune decline.

DOI: https://doi.org/10.1038/s41392-026-02787-1
Free Radic Biol Med. 2026 Sep 21. pii: S0891-5849(26)01170-6. [Epub ahead of print]256 650-663

Inducing oxidative stress by targeting the cholesterol biosynthesis pathway augments the efficacy of bortezomib in multiple myeloma.

Chunfan Li, Fuqiang Wang, Hongwei Peng, Meng Chen, Yafang Pu, Xiang Lin, Shuai Wang, Fei Li, Zhimin Gu.

  Proteasome inhibitors, particularly bortezomib (BTZ) which induces oxidative stress, remain the cornerstone of multiple myeloma (MM) therapy. However, resistance driven by metabolic reprogramming and redox adaptation limits their long-term efficacy. Here, we identify a cholesterol biosynthesis-dependent antioxidant mechanism that shields MM cells from BTZ-induced generation of reactive oxygen species (ROS). High cholesterol biosynthesis activity characterizes BTZ-nonresponsive plasma cells and correlates with poor prognosis. Genetic silencing of SREBF2, the master transcriptional regulator of cholesterol metabolism, sensitized MM cells to BTZ both in vitro and in vivo. Pharmacological inhibition of HMG-CoA reductase, the rate-limiting enzyme of cholesterol biosynthesis, with the clinically approved atorvastatin likewise enhanced the anti-myeloma activity of BTZ in vitro and in vivo. Mechanistically, the lipid raft protein FLOT1 promoted FOXO3 nuclear translocation and SREBF2 activation, thereby driving increased cholesterol biosynthesis and accumulation of the intermediate metabolite 7-dehydrocholesterol (7-DHC), a critical antioxidant that mitigated BTZ-induced cytotoxicity. Decreasing 7-DHC production by disrupting SREBF2 activation or treating with atorvastatin impaired the cellular ROS detoxification capacity and enhanced BTZ-induced cytotoxicity. Collectively, our findings identify that MM cells resist therapy-induced ROS by accumulating 7-DHC through activation of cholesterol biosynthesis, and provide preclinical evidence for repurposing statins to augment the efficacy of BTZ therapy.

Keywords:  7-Dehydrocholesterol; Bortezomib resistance; Cholesterol biosynthesis; Multiple myeloma; Oxidative stress

DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.09.019
Methods Mol Biol. 2027 ;3075 341-366

Electroporation for High-Efficiency Delivery of CRISPR to Hematopoietic Cells.

Nikoletta Y Papaioannou, Panayiota L Papasavva, Petros Patsali, Carsten W Lederer.

  Recent advances in genome editing technologies have enabled transformative therapeutic strategies for hematological disorders. Efficient implementation of these approaches requires reliable delivery of genome editing components into primary hematopoietic stem and progenitor cells (HSPCs), which are particularly sensitive and resistant to conventional transfection methods. Electroporation has emerged as the most widely used strategy for ex vivo delivery of genome editing reagents into CD34⁺ hematopoietic cells. Genome editing tools can be delivered in multiple formats, including plasmid DNA, messenger RNA (mRNA), and ribonucleoprotein (RNP) complexes. In HSPCs, mRNA- and RNP-based approaches are generally better tolerated than plasmid DNA and allow transient expression with reduced cytotoxicity. In this chapter, we describe optimized protocols for electroporation-based delivery of CRISPR/Cas9 RNP complexes and mRNA-encoded base editors into HSPCs using the Amaxa™ 4D-Nucleofector™ system. Detailed procedures are provided for cell preparation, guide RNA design, assembly of Cas9 RNPs, in vitro transcription and purification of base editor mRNA, electroporation parameters, and assessment of editing efficiency. Emphasis is placed on maximizing editing performance while preserving stem cell viability and functionality.

Keywords:  Base editor; CRISPR/Cas9; Delivery; Editing efficiency; Electroporation; Genome editing; HSPCs; HUDEP-2; In vitro transcription; Nucleofection

DOI:  https://doi.org/10.1007/978-1-0716-5547-4_18
Cell Signal. 2026 Sep 24. pii: S0898-6568(26)00563-2. [Epub ahead of print] 112904

The molecular interplay between USP32 and ERP44 in driving multiple myeloma progression and tumor growth.

Yujuan Gao, Hongjia Wang, Jiayue Sun, Guibo Ma.

  Multiple myeloma (MM) is a malignancy of plasma cells with complex pathogenesis and unmet clinical needs. ERP44 is an Endoplasmic Reticulum (ER)-resident protein involved in protein folding, but its role in MM remains unclear. Kaplan-Meier survival analysis showed that high ERP44 expression correlated with poor prognosis in MM patients, prompting us to investigate its biological function and regulatory mechanisms. Using lentiviral-mediated overexpression and knockdown strategies in MM cell lines, we demonstrated that ERP44 significantly promoted cell proliferation in vitro, and ERP44 knockdown suppressed tumor growth in a xenograft mouse model. Mechanistically, we identified USP32 as an upstream regulator that interacted with and stabilized ERP44 through deubiquitination. Functional rescue experiments showed that ERP44 overexpression partially reversed USP32 knockdown-induced proliferation inhibition, confirming that USP32 promoted MM cell proliferation through ERP44. RNA sequencing combined with Western blotting revealed that ERP44 activated the PI3K-AKT signaling pathway, leading to upregulation of CDK2 and Cyclin D1 and driving cell cycle progression. Notably, the PI3K-AKT inhibitor LY294002 significantly attenuated the proliferative advantage conferred by ERP44 overexpression, suggesting this pathway as a critical downstream effector. Furthermore, ERP44 overexpression upregulated UPR markers (GRP78, XBP1, and CHOP) as well as osteolytic factors (DKK1, RANKL, and MIP-1α), indicating its broader role in UPR and bone destruction. Collectively, these findings identify ERP44 as a pro-proliferative factor in MM and establish a USP32-ERP44-PI3K-AKT regulatory axis.

Keywords:  Cell apoptosis; Cell proliferation; ERP44; Multiple myeloma; Ubiquitin-proteasome

DOI:  https://doi.org/10.1016/j.cellsig.2026.112904
Cell Rep. 2026 Sep 24. pii: S2211-1247(26)01114-9. [Epub ahead of print]45(10): 118036

MCUB restricts mitochondrial calcium to support metabolic adaptation and homeostasis in glioblastoma.

Nan Sun, Penggang Sun, Feiyue Xuan, Junzhe Zhong, Wenbin Ma, Yu Song, Hanwen Xuan, Daohan Yu, Zhengwei Sun, Yunlei Zhao, Yiwei Wang, Tian Tian, Jiazheng Guo, Jingze Hu, Jiaqi Dong, Zhuang Chen, Wenhang Jia, Weinan Liu, Runyu Tian, Fan Xu, Hao Chen, Shuaiyu Liu, Xintong Hou, Hongkai Yang, Xiangqi Meng, Qun Chen, Jinquan Cai, Chuanlu Jiang.

  The refractory nature of glioblastoma (GBM) is largely attributed to metabolic plasticity and stress adaptation. However, the role of precise mitochondrial calcium (mCa2+) flux gating in this context remains elusive. Here, we identify MCUB as a key gatekeeper upregulated in GBM, establishing a restricted mCa2+ threshold associated with malignancy. Mechanistically, MCUB limits mCa2+ uptake, attenuating pyruvate dehydrogenase activity and enforcing a glycolytic shift. MCUB deficiency triggers mCa2+ overload and reactive oxygen species bursts, sensitizing GBM cells to oxidative stress and radiotherapy. Moreover, hypoxia drives this adaptation via HIF-1α, which upregulates MCUB and reinforces its interaction with MCU to tune mCa2+ flux. Through high-throughput screening, we identify TF-PPAO as a compound interfering with the MCUB-MCU interaction. TF-PPAO exerts antitumor and radiosensitizing effects in xenografts, patient-derived xenografts (PDXs), and GBM organoids. Our findings reveal MCUB-mediated mCa2+ restriction as a mechanism of GBM metabolic adaptation and mitochondrial homeostasis, highlighting MCUB as a therapeutic target.

Keywords:  CP: cancer; MCUB; glioblastoma; metabolic reprogramming; mitochondrial calcium; mitochondrial homeostasis; radiosensitization

DOI:  https://doi.org/10.1016/j.celrep.2026.118036
Nat Commun. 2026 Aug 25. pii: 10135. [Epub ahead of print]17(1):

Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.

Yang Jiang, Anushka Jain, Sina Ghaemmaghami, Edward P O'Brien.

A novel class of protein misfolding involving changes in entanglement status occurs across the bacterial cytosolic proteome and likely exists in many other organisms. Here, we test whether this class of misfolding has measurable consequences for protein homeostasis by examining its relationship with ubiquitin-mediated proteasomal degradation immediately after protein synthesis. Integrating protein structural information with ubiquitin mass spectrometry (Ubq-MS) data from human fibroblasts, we find that proteins containing native non-covalent lasso entanglements (NCLEs), which are known to be more prone to misfolding, are 93% (95% Confidence Interval: 44-160%) more likely to be ubiquitinated and targeted for proteasomal degradation than proteins lacking native entanglements. Coarse-grained folding simulations further show that ubiquitinated proteins with native entanglements are four-fold more likely to misfold than non-ubiquitinated proteins without entanglements. These results suggest that entanglement misfolding, primarily through failure to form native entanglements, increases susceptibility to proteasomal degradation. We further estimate that approximately one-third of the globular proteome populates near-native entanglement-misfolded states that evade proteasomal degradation because they remain structurally similar to the native ensemble. Given that entanglement misfolding is inherent to the polymeric nature of proteins, these findings are likely applicable across diverse organisms.

DOI: https://doi.org/10.1038/s41467-026-76875-9
Curr Issues Mol Biol. 2026 Aug 25. pii: 859. [Epub ahead of print]48(9):

Artificial Intelligence-Powered Histopathology in Stem Cell Research: Bridging Morphology, Function, and Omics.

Mashael Saleh Al-Toub.

  The histopathology area is being redefined with the use of artificial intelligence (AI), providing robust tools to help bridge cellular morphology, functional assays, and multi-omics data in stem cell research. The ability of stem cells to undergo self-renewal and differentiation is key in regenerative medicine, but their research requires the careful characterization of morphological and molecular phenotypic traits. Traditional histopathology is invaluable, but its application can be limited by inter-observer variability and restricted scalability. These limitations are circumvented by AI-based techniques, such as machine learning and deep learning, which are capable of classifying cells, performing quantitative morphometry, and forecasting stem cell behavior. Adding AI to genomics, proteomics, and metabolomics will contribute to the further identification of biomarkers and pathways that regulate stem cell fate. This convergence provides new possibilities for precision medicine, personalized therapies, and translational uses like drug discovery and disease modeling. However, its potential has not yet been realized because of the existing difficulties in data quality, variability, regulatory control, and ethical issues, especially in terms of the transparency and justice of AI systems. Emphasized areas for the future include explainable AI, federated learning, and a multimodal framework that integrates imaging, sequencing, and clinical data. Interdisciplinary partnerships and adequate regulatory frameworks will help AI-enabled histopathology reshape stem cell studies and speed up the process of translating regenerative medicine into clinical applications.

Keywords:  artificial intelligence; digital pathology; histopathology; morphology; multi-omics; multimodal AI; regenerative medicine; stem cells

DOI:  https://doi.org/10.3390/cimb48090859
bioRxiv. 2026 Sep 18. pii: 2026.09.16.752145. [Epub ahead of print]

Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets.

Benson M George, Anna Rodriguez-Pöhnlein, Donavelle J DeCastro, Jennifer Porat, Benyu Zhou, Dinah M Abeja, Ryan J Lumpkin, Rebecca J Metivier, Anna Schmoker, Wencke Walter, Torsten Haferlach, Yana Pikman, Katherine A Donovan, Kimberly Stegmaier, Eric S Fischer, Franziska Wachter, Ryan A Flynn.

Cell surface proteomics provides a direct topological assessment of the outer membrane of cells and enables the capture of low abundance proteins that may be missed by whole cell proteomics. Here we present an unbiased atlas of the whole cell and surface proteomes of 25 commonly used leukemic cell lines, encompassing both lymphoid and myeloid lineages, and a variety of driver mutations. Paired-wise analysis highlights recurrent surface proteins that are not detected by whole cell proteomics. Coupling this dataset to RNA-sequencing, we also discovered genes where protein and RNA abundances are discordant. In KMT2A -rearranged AML, CD70 expression was increased across cell lines and validated in primary patient samples, supporting CD70 as a candidate therapeutic target in this disease. Several proteins are enriched in the surface proteomes but lack surface annotation, adding to the growing list of potential non-canonical cell surface proteins. These findings reveal a substantial pool of proteins absent from conventional surface annotations, including RNA-binding proteins, an emerging class of candidate immunotherapeutic targets.
Key Points: Direct surface proteomics identifies leukemia cell-surface proteins not reliably predicted by transcriptomic or whole-proteome profilingSurface profiling reveals genotype-specific therapeutic targets, including CD70 in KMT2A-rearranged AML.

DOI: https://doi.org/10.64898/2026.09.16.752145
Nat Commun. 2026 Aug 21. pii: 10037. [Epub ahead of print]17(1):

Fatty acid oxidation fuels mitochondrial respiration to drive epidermal stem cell fate and differentiation.

Kristina Todorova, Stefano Sol, Fabiana Boncimino, Andrea Clocchiatti, Kazuki Takagaki, Enkhtuul Gantumur, Mihaela Ruseva, Meaghan Cadieux, Michelle Liu, Victor A Neel, Amy S Colwell, Christine G Lian, George F Murphy, Peter Carmeliet, Anna Mandinova.

Skin barrier function relies on the epidermis, whose integrity is maintained by basal stem cells that continuously renew and differentiate into a multilayered architecture. Disrupted epidermal differentiation underlies numerous hyperproliferative and inflammatory skin disorders. While transcriptional and epigenetic mechanisms are known to regulate late differentiation, the molecular events driving early commitment remain elusive. Here, we reveal that early mitochondrial reprogramming, characterized by the activation of oxidative phosphorylation, is a determinant of differentiation initiation. We identify fatty acid oxidation as the primary metabolic pathway fueling oxidative phosphorylation during this process. Pharmacological and genetic inhibition of fatty acid oxidation, in vitro and in vivo, disrupts differentiation and compromises stratification, causing defective responses to physical insults. Mechanistically, fatty acid oxidation enables ATP production in committed epidermal cells to support the differentiation process, linking lipid metabolism and epidermal homeostasis. These results uncover an unrecognized role for metabolic reprogramming in epidermal stem cell fate and highlight fatty acid oxidation as a promising therapeutic target for restoring differentiation defects in disease.

DOI: https://doi.org/10.1038/s41467-026-77023-z
Nat Commun. 2026 Aug 25. pii: 10162. [Epub ahead of print]17(1):

The predicted interactome of the human mitochondrial proteome.

Abhinav B Swaminathan, Mohammad Zulkifli, Rachel M Guerra, Sofia M Calabrese, Dimitris T Kalafatis, David J Pagliarini, Vishal M Gohil.

Despite the fundamental importance of mitochondria in cellular metabolism, the molecular function(s) of many mitochondrial proteins remain unknown. Since protein function can be inferred from their interacting partners, we repurpose the protein structure prediction algorithm AlphaFold Multimer (AFM) as a classification model to predict protein-protein interactions of the entire human mitochondrial proteome. By screening 630,003 protein pairs, we create a compendium of 2,895 previously known and newly observed interactions, which include the interacting partner(s) of 85 uncharacterized mitochondrial proteins, thereby linking them to a known biochemical pathway. Extending the AFM-based analysis to 11 diverse eukaryotes identifies evolutionarily conserved interactions among human hits, including regulators of core bioenergetic pathways. Our experiments, guided by these predictions, nominate protein interactions that form the coenzyme Q metabolon and define the mitochondrial copper delivery pathway to cytochrome c oxidase. Our compendium represents a powerful resource for the systematic, structure-based functionalization of the human mitochondrial proteome.

DOI: https://doi.org/10.1038/s41467-026-77112-z