bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2026–04–12
seventeen papers selected by
William Grey, University of York
  1. Non-necroptotic MLKL function damages mitochondria and promotes hematopoietic stem cell aging.
  2. Fetal-restricted hematopoietic progenitors arise from hemogenic endothelium in vitelline and umbilical arteries.
  3. A Function-First Legacy in Hematopoietic Stem Cell Biology: The Scientific Impact of Hal E. Broxmeyer.
  4. Mitochondrial transfer in acute myeloid leukaemia and multiple myeloma: Mechanisms, consequences and potential therapeutic opportunities.
  5. Stem cell function in vivo is supported by an alternative glycolysis endpoint.
  6. Genotype-immunophenotype relationships in NPM1-mutated AML clonal evolution uncovered by single-cell multiomic analysis.
  7. RPS19 and RPL5 haploinsufficient models reveal divergent ribosomal subunit controls of fetal hematopoiesis.
  8. Glutamine addiction is a therapeutic target to block emergency myelopoiesis.
  9. Retinoic acid regulates the development of human definitive hematopoiesis in a non-cell autonomous manner.
  10. The rise of bone marrow organoids as next-generation models for blood formation and failure.
  11. A multimodal atlas for immunotherapeutic targeting of AML surface heterogeneity.
  12. Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR.
  13. Mitochondrial Ubiquitination as a Signaling Hub: Balancing Mitophagy, Inflammation, and Cell Death.
  14. Tunneling Nanotube-Mediated Filamin A Transport Mechanosensitively Programs Osteoclastogenesis in Myeloma Bone Disease.
  15. STUB1-VCP/p97 limits PINK1 overaccumulation to safeguard mitophagy and memory.
  16. Enhanced Proteomics Analysis with a Novel Recombinant Chymotrypsin Analogue Engineered for High Cleavage Specificity.
  17. Cellector: A tool to detect foreign genotype cells in scRNAseq data with applications in leukemia and microchimerism.
  1. Nat Commun. 2026 Apr 06. pii: 2798. [Epub ahead of print]17(1):
    Non-necroptotic MLKL function damages mitochondria and promotes hematopoietic stem cell aging.
    Yuta Yamada, Jinjing Yang, Akiho Saiki-Tsuchiya, Yuji Watanabe, Shuhei Koide, Shin Murai, Yuriko Sorimachi, Yu Fukuda, Kenta Sumiyama, Hiroshi Sagara, Hiroyasu Nakano, Keiyo Takubo, Atsushi Iwama, Masayuki Yamashita.
      Hematopoietic stem cells (HSCs) survive many types of cellular stress but often lose their regenerative and lymphopoietic capacities as a result. Such functional decline also occurs with age, and dysfunctional HSCs with impaired mitochondria accumulate during aging. However, the molecular link between HSC stress response and age-related functional decline remains poorly understood. Here we show that multiple stress responses converge on the RIPK3-MLKL axis to induce age-related changes in HSCs. The necroptosis effector MLKL is readily activated by inflammation and replication stress and accumulates in HSC mitochondria. Consequently, activated MLKL does not cause cell death but impairs HSC self-renewal and lymphoid differentiation. Such MLKL-mediated functional decline also occurs in HSCs during organismal aging, with activated MLKL primarily mediating age-related mitochondrial damage and reduced glycolytic flux. Collectively, our results establish the RIPK3-MLKL axis as a key mediator of HSC aging and identify a necroptosis-independent role of MLKL in mitochondrial damage.
    DOI:  https://doi.org/10.1038/s41467-026-71060-4
  2. Nat Cardiovasc Res. 2026 Apr 08.
    Fetal-restricted hematopoietic progenitors arise from hemogenic endothelium in vitelline and umbilical arteries.
    Cristiana Barone, Giulia Quattrini, Alessandro Muratore, Giorgio Anselmi, Yurim Park, Naeema T Mehmood, Elena Morganti, Roberto Orsenigo, Filipa Timóteo-Ferreira, Anna Cazzola, Arianna Patelli, Thea Milanesi, Bianca Nesti, Francisca Soares-da-Silva, Matthew Nicholls, Gloria Zambelli, Mario Mauri, Silvia Bombelli, Sofia De Marco, Deborah D'Aliberti, Silvia Spinelli, Veronica Bonalume, Alison Domingues, Mahdieh Naghavi Alhosseini, Gianluca Sala, Arianna Colonna, Elisabetta D'Errico, Cristina D'Orlando, Cristina Bianchi, Roberto A Perego, Raffaella Meneveri, Ana Cumano, Silvia Brunelli, Marella F T R De Bruijn, Andrea Ditadi, Alessandro Fantin, Rocco Piazza, Emanuele Azzoni.
      Embryonic hematopoiesis involves successive waves of progenitors from distinct anatomical sites, but the origins and contributions of early hematopoietic stem and progenitor cells (HSPCs) remain incompletely defined. Here we use genetic fate mapping in mice to temporally label hemogenic endothelium (HE) subsets and track their progeny. We show that a wave of fetal-restricted HSPCs arises from HE in the vitelline and umbilical arteries between embryonic days 8.5 and 9.5, preceding the emergence of definitive hematopoietic stem cells. Lineage tracing, single-cell transcriptomic analyses and functional assays revealed that these progenitors are transient and distinct from erythro-myeloid progenitors, contribute extensively to fetal lympho-myelopoiesis but decline postnatally. Our findings reveal a previously unrecognized early HE wave as a key source of fetal-restricted HSPCs, refining the spatial-temporal understanding of layered hematopoiesis and informing developmental origins of blood cell diversity.
    DOI:  https://doi.org/10.1038/s44161-026-00793-8
  3. Exp Hematol. 2026 Apr 03. pii: S0301-472X(26)00059-7. [Epub ahead of print] 105426
    A Function-First Legacy in Hematopoietic Stem Cell Biology: The Scientific Impact of Hal E. Broxmeyer.
    Xuepeng Wang, Jim Patrick Ropa, Maegan Lynn Capitano, Reuben Kapur.
      Hal E. Broxmeyer profoundly shaped modern hematopoietic stem cell biology through a rigorously functional approach that defined stem and progenitor cells by what they do rather than how they appear. Across five decades, his work established a unifying principle: biological mechanisms matter most when they preserve or enhance durable, multilineage hematopoietic reconstitution, particularly in transplantation. This function‑first philosophy guided seminal contributions spanning cytokine regulation of hematopoiesis, umbilical cord blood transplantation, stem cell mobilization, and the biology of hypoxia. Broxmeyer helped define hematopoietic regulation as emerging from a complex, context‑dependent "sea of cytokines," challenging reductionist models that assigned fixed roles to individual factors. This conceptual framework informed translational advances, including the identification of dipeptidyl peptidase‑4 (DPP4/CD26) as a key regulator of chemokine activity, stem cell homing, mobilization, and engraftment, ultimately influencing clinical mobilization strategies and cord blood transplantation outcomes. His pioneering demonstration that human umbilical cord blood contains functionally competent hematopoietic stem cells transformed discarded biological material into a globally used graft source. Equally transformative was his recognition of oxygen tension as a critical, often overlooked determinant of stem cell integrity. By defining extraphysiological oxygen shock/stress (EPHOSS), Broxmeyer revealed how routine handling conditions compromise stem cell function and identified mechanistic strategies to preserve engraftment capacity. Together, these contributions reshaped experimental standards, aligned basic discovery with clinical reality, and trained generations of scientists to prioritize functional validation. Broxmeyer's legacy endures not only in clinical practice worldwide, but in a way of thinking that anchors discovery to biological and therapeutic relevance. TEASER ABSTRACT: Hal E. Broxmeyer helped define modern hematopoietic stem cell biology through a singular guiding principle: stem and progenitor cells must ultimately be judged by function durable, multilineage hematopoietic reconstitution rather than phenotype alone. This tribute synthesizes five decades of his scientific impact across cytokine biology, umbilical cord blood transplantation, stem cell mobilization, DPP4/CD26-mediated regulation of homing and engraftment, and the recognition of hypoxia and extra-physiologic oxygen stress as critical determinants of stem cell integrity. From conceptualizing hematopoietic regulation as a context-dependent "sea of cytokines," to establishing umbilical cord blood as a clinically viable graft source, to translating mechanistic insights into mobilization and engraftment strategies, Broxmeyer consistently linked molecular discovery to transplantation-relevant outcomes. His work reshaped experimental standards, clinical practice, and translational thinking in hematology. In an era increasingly dominated by descriptive depth, his legacy remains a powerful reminder that the highest measure of discovery is enduring biological function.
    DOI:  https://doi.org/10.1016/j.exphem.2026.105426
  4. FEBS J. 2026 Apr 10.
    Mitochondrial transfer in acute myeloid leukaemia and multiple myeloma: Mechanisms, consequences and potential therapeutic opportunities.
    Ebubechukwu Nwarunma, Mark T S Williams.
      Haematological malignancies, such as acute myeloid leukaemia (AML) and multiple myeloma (MM), which develop from malignant transformations within the bone marrow, represent the most critical unmet needs in the haemato-oncology field. Sub-optimal clinical outcomes in patients with AML and MM are often driven by resistance to chemotherapy. It is well established that cells within the bone marrow microenvironment (BMME) support the proliferation and survival of these blood cancer cells. One of the mechanisms by which these BMME-resident cells support the malignant cells is through horizontal mitochondrial transfer (HMT), a mechanism well documented as occurring under steady-state conditions as well as in many cancers. Recent research implicates mitochondrial transfer in BMME-driven chemoresistance in AML and MM. In this review, we critically analyse current understanding of the role of HMT in supporting the survival and proliferation of AML and MM cells, as well as driving resistance to cytotoxic effects of chemotherapy. We further elucidate various mechanisms, molecular triggers, functional consequences, and therapeutic implications for HMT in AML and MM. Our review also highlights unanswered questions within the HMT field and provides a theoretical basis for further study, giving direction on what is important in translating this knowledge into effective future therapeutic strategies.
    Keywords:  Horizontal mitochondrial transfer (HMT); Multiple myeloma (MM); acute myeloid leukaemia (AML); bone marrow microenvironment (BMME); chemoresistance
    DOI:  https://doi.org/10.1111/febs.70544
  5. bioRxiv. 2026 Apr 01. pii: 2026.03.30.715412. [Epub ahead of print]
    Stem cell function in vivo is supported by an alternative glycolysis endpoint.
    Edward O Kwarteng, Yafeng Li, Dieu Linh Nguyen, Michalis Agathocleous.
      Carbohydrates are classically catabolized by fermentation or oxidation, a choice that impacts many cellular functions including proliferation. Proliferating cells including somatic stem and progenitor cells are thought to favor fermentation over oxidation, and most proliferating cells in vitro depend on lactate production. However, it has not been tested if fermentation and oxidation are the universal obligatory terminal fates for carbohydrates in vivo because the key enzymes, lactate dehydrogenase (LDH) and pyruvate dehydrogenase (PDH), have not been simultaneously deleted in any cell type. Here we show that both fermentation and oxidation are dispensable for the survival and function of hematopoietic stem cells (HSC). Combined LDHA and LDHB deletion to ablate LDH did not impair HSC function, suggesting that HSCs and rapidly proliferating hematopoietic progenitors surprisingly do not require fermentation. Combined LDHA, LDHB, and PDH deletion abolished both glucose oxidation and fermentation, but did not impair HSC function. Glycolysis was preserved, suggesting the operation of an alternative endpoint. LDH/PDH-deficient HSCs terminated glycolysis through pyruvate export. Pyruvate export by HSCs and progenitors was a physiological response to changing nutrient levels. Quadruple deletion of LDHA/B, PDH, and the pyruvate transporter MCT1 impaired HSC function. This suggested that an essential role of glycolysis termination is not to produce acetyl-CoA or lactate but to remove pyruvate. Therefore, in contrast to classical theories and to in vitro metabolism, carbohydrate metabolism in vivo does not require oxidation or fermentation but can terminate directly in pyruvate export, and this alternative pathway is sufficient to support stem cell function.
    DOI:  https://doi.org/10.64898/2026.03.30.715412
  6. Blood. 2026 Apr 08. pii: blood.2025030772. [Epub ahead of print]
    Genotype-immunophenotype relationships in NPM1-mutated AML clonal evolution uncovered by single-cell multiomic analysis.
    Morgan Drucker, Darren Lee, Michael S Bowman, Xuan Zhang, Bailee Nicole Kain, Deedra Nicolet, Roopsha Bandopadhyay, Varsha Singh, Zhe Wang, Richard M Stone, Caner Saygin, Krzysztof Mrózek, Andrew J Carroll, Daniel T Starczynowski, Ross L Levine, John C Byrd, Nathan Salomonis, Sarah J Skuli, H Leighton Grimes, Ann-Kathrin Eisfeld, Robert L Bowman, Linde A Miles.
      Acute myeloid leukemia (AML) is a multi-clonal disease, existing as a milieu of clones with unique but related genotypes as initiating clones acquire subsequent mutations. However, bulk sequencing cannot fully capture AML clonal architecture or the clonal evolution that occurs as patients undergo therapy. To interrogate clonal evolution, we performed simultaneous single-cell molecular profiling and immunophenotyping on 43 samples from 32 NPM1-mutated AML patients at different timepoints in disease progression. Here we show that diagnosis and relapse AML samples display similar clonal architecture patterns, but signaling mutations drive increased clonal complexity, specifically at relapse that correlates with overall survival. We uncovered unique genotype-immunophenotype relationships regardless of disease state, suggesting leukemic lineage trajectories can be hard-wired by the mutations present. Analysis of longitudinal samples from patients on front-line AML therapy identified dynamic clonal and immunophenotypic changes consistent with the genotype-immunophenotype relationships we identified.
    DOI:  https://doi.org/10.1182/blood.2025030772
  7. Nat Commun. 2026 Apr 08.
    RPS19 and RPL5 haploinsufficient models reveal divergent ribosomal subunit controls of fetal hematopoiesis.
    Yuefeng Tang, Te Ling, Rashid Mehmood, Alexis Bertrand, Julien Papoin, Mushran Khan, Riaz Rao, Jianing Xu, Vincent Schulz, James Palis, Laurie A Steiner, Betsy J Barnes, Yong-Rui Zou, Philippe Marambaud, Robert A J Signer, Irene Roberts, Deena Iskander, Leonard I Zon, Senthil Velan Bhoopalan, Mitchell J Weiss, Jeffrey M Lipton, Patrick G Gallagher, Narla Mohandas, Naomi Taylor, Sébastien Durand, John Crispino, Lionel Blanc.
      Diamond Blackfan anemia syndrome (DBAS) is a congenital ribosomopathy caused by haploinsufficiency of ribosomal proteins (RPs), but how RP stoichiometry and activity regulates erythroid development remains enigmatic. Using in vivo models, we uncover divergent functions for the small and large ribosomal subunit proteins RPS19 and RPL5 in fetal hematopoiesis. While RPL5 haploinsufficiency causes hematopoietic stem and progenitor cell (HSPC) accumulation and prenatal lethality via p53-mediated ferroptosis of mature erythroid progenitors, RPS19 haploinsufficiency leads to HSPC depletion and impaired erythroid expansion through p53-dependent apoptosis. The latter is accompanied by translational and transcriptional dysregulation, including the upregulation of RUNX1, which is also observed in RPS- haploinsufficient DBAS patients. Importantly, Runx1 deletion in RPS19-haploinsufficient mice partially rescues HSPC numbers. These findings reveal subunit-specific RP functions in controlling fetal hematopoiesis and demonstrate how imbalanced RP stoichiometry disrupts developmental programs, providing crucial mechanistic insights into DBAS pathogenesis and the basis for its clinical heterogeneity.
    DOI:  https://doi.org/10.1038/s41467-026-71727-y
  8. bioRxiv. 2026 Mar 30. pii: 2026.03.26.714544. [Epub ahead of print]
    Glutamine addiction is a therapeutic target to block emergency myelopoiesis.
    Oakley C Olson, Ruiyuan Zhang, Melissa A Proven, James C Swann, Kexuan Huang, William E Lowry, Emmanuelle Passegue.
      Inflammation-driven emergency myelopoiesis (EM) contributes to the progression of many solid cancers and inflammatory diseases, yet therapeutic strategies to selectively suppress EM without compromising hematopoiesis remain lacking. Here, we use functional and single-cell transcriptomic analyses to determine metabolic programs organizing the hematopoietic hierarchy, myeloid lineage commitment, and myeloid differentiation. We identify de novo glutamine biosynthesis as a stem cell-specific survival mechanism allowing independence from exogenous glutamine. We show that myeloid differentiation is characterized by Myc-driven upregulation of mitochondrial respiration, which is hyperactivated during EM and renders myeloid progenitors dependent on glutaminolysis to fuel the TCA cycle. Both genetic and pharmacologic targeting of glutaminase suppresses EM and impairs breast tumor progression by reducing intratumoral neutrophil infiltration. Our study defines a central role for Myc-glutaminolysis in driving EM, identifies glutaminolysis as a therapeutic target to normalize maladaptive EM, and highlights myeloid overproduction as a systemic problem requiring HSPC targeting.
    DOI:  https://doi.org/10.64898/2026.03.26.714544
  9. Development. 2026 Apr 08. pii: dev.205213. [Epub ahead of print]
    Retinoic acid regulates the development of human definitive hematopoiesis in a non-cell autonomous manner.
    Nestor A Fernandez, Lauren J Durland, Analucia Garcia, Michael H Atkins, Marion Kennedy, Christopher M Sturgeon, Gordon Keller.
      The developing embryo harbors multiple hematopoietic programs, categorized as either intra-embryonic or extra-embryonic yolk-sac, that differ in their spatio-temporal origins and developmental potential. In the vertebrate embryo, the hematopoietic stem cell (HSC) derives from the definitive intra-embryonic hematopoietic program and is dependent on stage-specific retinoic acid (RA) signaling. We have recently modelled aspects of this developmental process in vitro using human pluripotent stem cells (hPSCs) and identified a KDR+CXCR4+ mesodermal population that generates definitive hematopoietic progeny in a uniquely RA-dependent manner. A subpopulation of this mesoderm expresses ALDH1A2, an enzyme involved in RA synthesis. Here, we sought to characterize the role of ALDH1A2 in the development of the human RA-dependent hematopoietic lineage and to map its mesodermal origin. Using two different engineered reporter hPSC lines, we show that specification of this lineage requires a functional ALDH1A2 enzyme at the mesoderm stage. Through functional analyses of different mesoderm subpopulations, we demonstrate that this RA-dependent lineage derives from ALDH1A2neg mesoderm by non-cell autonomous RA signaling. Collectively, these studies provide new insight into the differentiation trajectory of hPSCs towards the definitive hematopoietic lineage.
    Keywords:  Definitive hematopoiesis; Human pluripotent stem cells; Non-cell autonomous; Retinoic acid
    DOI:  https://doi.org/10.1242/dev.205213
  10. Exp Hematol. 2026 Apr 02. pii: S0301-472X(26)00061-5. [Epub ahead of print] 105428
    The rise of bone marrow organoids as next-generation models for blood formation and failure.
    Anne Stolz, Lauren M Harmon, Jingjing Li, Jasmin Rettkowski, Alba Rodriguez-Meira, Kohei Shiroshita, Vu L Tran, Abdullah Khan, Christoph Klein.
      Bone marrow organoids (BMOs) are three-dimensional cell culture models that recapitulate key structural and functional features of the bone marrow (BM) niche. BMOs offer important advantages in hematopoietic research by modeling key aspects of human hematopoiesis compared to classical in vitro two- and three-dimensional cellular models including bioreactors, BM-on-a-chip platforms, 2D models or BM ossicles by better recreating the three-dimensional architecture, cellular heterogeneity, and spatial organization of the BM microenvironment. They offer a scalable and cost-effective alternative to animal models and reduce the need for animal experiments. Induced pluripotent stem cell (iPSC)-derived BMOs can be generated from a patient's own cells, enabling personalized disease modeling and drug testing and are highly amenable to gene editing technologies allowing precise modifications to study gene function or model diseases. Recent landmark studies from Christoph Klein and Abdullah Khan have established protocols for the generation of BMOs and demonstrated their applications in disease modeling. Here, we review the critical steps in BMO generation, their structural/ functional validation and discuss how BMOs can be applied to model inflammatory responses, rare genetic bone marrow failure syndromes, and multiple myeloma. These advances demonstrate BMOs' growing potential as powerful tools in hematopoietic research and will pave the way for further innovation and increasingly refined systems in future studies.
    Keywords:  bone marrow niche; bone marrow organoid; disease modeling
    DOI:  https://doi.org/10.1016/j.exphem.2026.105428
  11. iScience. 2026 Apr 17. 29(4): 115337
    A multimodal atlas for immunotherapeutic targeting of AML surface heterogeneity.
    Matthew Ung, Julia Etchin, Amanda Halfond, Julia DiFazio, Yonina Keschner, Alyssa Pyclik, Anne Campbell, Ruijia Wang, Mariana Silva, Brikena Gjeci, Antonino Montalbano, Reid Williams, Guy Mundelboim, Andrea Arruda, Mark Minden, Julian Scherer, Tirtha Chakraborty, Huanying Gary Ge, John R Lydeard.
      Acute myeloid leukemia (AML) is a hematologic malignancy with high relapse rates and limited treatment options due to extensive intra-tumor heterogeneity across patients. To characterize this heterogeneity, we profiled matched bone marrow mononuclear cell (BMMC) samples from 26 patients with adult AML at diagnosis and relapse using the cellular indexing of transcriptome and epitope sequencing (CITE-seq) and quantitative flow cytometry. These data together represent a comprehensive multimodal and longitudinal single-cell resource that reveals the transcriptomic and immunophenotypic landscape of AML. Data integration of CITE-seq and flow cytometry surface antigen readouts enabled systematic quantitation of surface antigen co-expression across individual leukemic cells, providing a granular framework for the design of immunotherapeutic strategies to target heterogeneous AML. With this resource, we identified CD33, CLL-1, LAIR1, ITGA4, DEC-205, and CD244 as antigens that induced cytotoxicity in AML cell lines in vitro when co-targeted by antibody drug conjugates (ADCs) or chimeric antigen receptor T (CAR-T) cells, demonstrating the exploitation of AML heterogeneity for immunotherapeutic innovation.
    Keywords:  Cancer; Immune response; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2026.115337
  12. bioRxiv. 2026 Mar 13. pii: 2026.03.12.711310. [Epub ahead of print]
    Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR.
    Avijit Mallick, Yunguang Du, Cole Haynes.
      Mitochondrial dysfunction and extracellular protein aggregation occur in neurodegenerative diseases such as Alzheimer's disease (AD). However, it remains unclear if these processes are functionally linked. Here, we identify a signaling pathway that is activated upon accumulation of aggregation-prone proteins in the extracellular space. We find that the transcription factor ATFS-1, which regulates the mitochondrial unfolded protein response, also regulates transcripts required for endosomal recycling, multiple plasma membrane-localized signaling receptors, and secreted proteins that bind aggregation-prone proteins in the extracellular space, including transthyretin and Aβ, and promote their degradation. Interestingly, Aβ(1-42) aggregation induces atfs-1 -dependent transcription by promoting degradation of the bZIP protein ZIP-3, which antagonizes ATFS-1. ZIP-3 accumulates in the cytosol when it is phosphorylated by kinases that function downstream of plasma membrane-localized signaling receptors, including the WNT and glutamate receptors. Upon ligand binding, the signaling receptors stimulate the cognate kinase, many of which we found phosphorylate ZIP-3, impeding ZIP-3 degradation, allowing it to antagonize atfs-1 -dependent transcription. However, accumulation of aggregation-prone proteins such as Aβ(1-42) causes endosomal swelling, which impairs endosomal recycling, instead diverting signaling receptors to lysosomes for degradation. In turn, the depletion of signaling receptors reduces the level of ZIP-3 phosphorylation, resulting in ZIP-3 degradation and activation of atfs-1 -dependent transcription, which promotes extracellular proteostasis. Our findings uncover an unexpected coupling between endocytic quality control and mitochondrial signaling, revealing a circuit that preserves extracellular proteostasis and promotes organismal resilience.
    DOI:  https://doi.org/10.64898/2026.03.12.711310
  13. Biochemistry. 2026 Apr 06.
    Mitochondrial Ubiquitination as a Signaling Hub: Balancing Mitophagy, Inflammation, and Cell Death.
    Ashwini Kumar, Emmanouil Zacharioudakis.
      Mitochondria are increasingly recognized as signaling organelles that coordinate cell-fate decisions during stress. Because outer mitochondrial membrane (OMM) proteins are exposed to the cytosol, they are prominent substrates for ubiquitination, a dynamic post-translational modification that encodes information through diverse chain architectures and linkage types. In this review, we examine how ubiquitination of OMM proteins functions as a molecular switch that integrates mitochondrial stress signals and engages three major, often antagonistic, stress-response mechanisms: mitophagy, cell death, and innate immune signaling. We highlight an emerging concept that a stress-responsive "ubiquitin code" is written on OMM substrates, in which pathway selection is coordinated by the identity of ubiquitinated OMM proteins together with the linkage type and branching of attached polyubiquitin chains. We provide an updated overview of the E3 ubiquitin ligases and deubiquitinases (DUBs) that write and erase this code and summarize ubiquitin linkage types reported on key OMM substrates across these pathways. For mitophagy, we cover both PARKIN-dependent and PARKIN-independent mechanisms mediated by other E3 ligases and counteracted by DUBs. For innate immunity, we discuss how ubiquitination of OMM proteins regulates the MDA5/RIG-I-MAVS axis and NF-κB signaling. For cell death, we describe how ubiquitination of anti- and pro-apoptotic BCL-2 family proteins can either lower or increase the threshold for the induction of apoptosis. We also highlight the newfound role of PARKIN to drive apoptosis through a BAX/BAK-independent mechanism. Finally, we discuss therapeutic opportunities to reprogram OMM ubiquitination by targeting E3 ligases or DUBs directly, or by using PROTAC- and DUBTAC-based strategies.
    Keywords:  E3 ubiquitin ligases; apoptosis; deubiquitinases; innate immune signaling; mitophagy; ubiquitin
    DOI:  https://doi.org/10.1021/acs.biochem.6c00007
  14. Blood. 2026 Apr 08. pii: blood.2025031627. [Epub ahead of print]
    Tunneling Nanotube-Mediated Filamin A Transport Mechanosensitively Programs Osteoclastogenesis in Myeloma Bone Disease.
    Jing Guo, Jingjing Wang, Ying Xie, Yixuan Wang, Ziyi Peng, Mengqi Wang, Hao Cheng, Tiantian Li, Linchuang Jia, Hongwei Xu, Danchen Su, Mu Qiao, Huanhuan Liu, Xinyang Li, Wenjing Li, Di Wu, Jianyong Huang, P Leif Bergsagel, Feng Li, Zhigang Zhao, Zhiqiang Liu.
      Intercellular communications between multiple myeloma (MM) cells and osteoclast precursor cells (pre-OCs) contribute extensively to the occurrence and development of myeloma-related bone destruction. However, key interacting modes and the substances exchanged involved in this communication remain unclear. In this study, we discover that tunnelling nanotubes (TNT) directly connect MM and pre-OCs. Using stable isotope labeling with amino acids in cell culture (SILAC) assay and a positive-negative double selection strategy, we identify Filamin-A (FLNA) as a major protein transported from MM to pre-OCs. FLNA acts as a molecular clutch linking ECM-bound MAC1 to the cytoskeleton, activating Rho and MAPK signaling pathways and promoting F-actin polymerization, which subsequently enhances osteoclast differentiation by modulating cellular stiffness, traction force, and deformability. Additionally, FLNA directly binds vinculin and promotes its recruitment to podosome, thereby enhancing functions of podosome and bone resorption capacity of osteoclasts. Conditional depletion of Flna in mice suppresses podosome activity and reduces stiffness, traction force, and deformability in pre-OCs, leading to significantly impaired osteoclast differentiation and increased bone mass. In the Vk*MYC mouse model of myeloma, administration of the TNT inhibitor Latrunculin B disrupts FLNA transport to osteoclasts and alleviates osteolytic bone disease. These findings highlight the critical role of MM-transferred FLNA in osteoclastogenesis and suggest that targeting TNTs may represent a therapeutic strategy to limit pathological bone resorption associated with multiple myeloma.
    DOI:  https://doi.org/10.1182/blood.2025031627
  15. Autophagy. 2026 Apr 11.
    STUB1-VCP/p97 limits PINK1 overaccumulation to safeguard mitophagy and memory.
    Jin-Yi Lin, Ze-Bo Huang, Evandro F Fang, Guang Lu.
      PINK1 serves as the central regulator of PINK1-PRKN-mediated mitophagy, and its precise regulation is critical for efficient mitochondrial clearance. Although the cleavage of PINK1 and its subsequent degradation via the N-end rule pathway under basal conditions are well understood, how full-length PINK1 stability is regulated following mitochondrial damage has remained elusive. In our recent study, we identified the STUB1-VCP/p97 axis as a mechanism that fine-tunes full-length PINK1 levels during mitophagy. We demonstrate that STUB1 functions as an E3 ubiquitin ligase that catalyzes K48-linked polyubiquitination of full-length PINK1, which is subsequently recognized and extracted by VCP/p97 for proteasomal degradation. Disruption of this axis results in excessive accumulation of full-length PINK1, accelerated turnover of PRKN, and impaired mitophagy. Moreover, we find that this regulatory mechanism is compromised in the brains of patients with Alzheimer disease (AD), and its disruption leads to neuronal mitophagy defects and impaired associated learning capability in C. elegans. These findings demonstrate that the STUB1-VCP/p97 complex fine-tunes PINK1 levels to ensure efficient mitophagy and preserve mitochondrial homeostasis.Abbreviations: AD, Alzheimer disease; CALCOCO2/NDP52, calcium binding and coiled-coil domain 2; MPP, mitochondrial processing peptidase; MQC, mitochondrial quality control; OMM, outer mitochondrial membrane; OPTN, optineurin; PARL, presenilin associated rhomboid like; PINK1, PTEN induced kinase 1; PRKN, parkin RBR E3 ubiquitin protein ligase; SILAC, stable isotope labeling by amino acids in cell culture; STUB1, STIP1 homology and U-box containing protein 1; TPR, tetratricopeptide repeat; VCP/p97, valosin containing protein; WIPI2, WD repeat domain, phosphoinositide interacting 2.
    Keywords:  Alzheimer disease; PINK1; PRKN; STUB1; VCP/p97; memory; mitochondrial homeostasis; mitophagy; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/15548627.2026.2658848
  16. J Proteome Res. 2026 Apr 10.
    Enhanced Proteomics Analysis with a Novel Recombinant Chymotrypsin Analogue Engineered for High Cleavage Specificity.
    Kish R Adoni, Jonathan E Ditcham, Alba Katiria González Rivera, Georgina H Charlton, Sergei V Saveliev, Konstantinos Thalassinos, Riccardo Zenezini Chiozzi.
      Chymotrypsin is widely used in shotgun proteomics, owing to its orthogonal cleavage specificity relative to trypsin, which enhances sequence coverage of hydrophobic protein regions. However, commercial preparations often display variable cleavage specificity, trypsin contamination, and elevated missed cleavage rates, which can collectively reduce the proteome coverage and data reproducibility. To address these limitations, we present a novel recombinant chymotrypsin (rChymoSelect) engineered for improved cleavage specificity and robustness in proteomics workflows. Benchmarking against standard bovine chymotrypsin revealed 97% C-terminal cleavages after tyrosine (Y), phenylalanine (F), and leucine (L) for rChymoSelect, compared to 72% for the standard enzyme. This enhanced cleavage specificity reduced missed cleavages and increased peptide-spectrum matches across charge states. Across 3,638 identified proteins, rChymoSelect yielded 22.2% unique identifications compared with 8.2% for standard chymotrypsin, while maintaining similar peptide length, m/z, and hydrophobicity distributions. The enzyme remained active in up to 6 M urea and achieved near-maximal proteome coverage within 2 h (only a 2.4% gain after overnight digestion). These results establish rChymoSelect as an advanced tool with improved cleavage specificity that reduces analytical complexity and enhances the reliability of proteomic analysis, while expanding chymotryptic digestion to hydrophobic and high-denaturant proteomics applications.
    Keywords:  chymotrypsin; missed cleavages; protein digestion; proteomics; sample preparation
    DOI:  https://doi.org/10.1021/acs.jproteome.5c01262
  17. bioRxiv. 2026 Mar 30. pii: 2026.03.26.714571. [Epub ahead of print]
    Cellector: A tool to detect foreign genotype cells in scRNAseq data with applications in leukemia and microchimerism.
    Haynes Heaton, Reza Behboudi, Collin Ward, Minindu Weerakoon, Sami Kanaan, Skylar Reichle, Nathan Hunter, Scott Furlan.
      The existence of rare, genetically distinct cells can occur in various samples such as transplant patients, naturally occurring microchimerism between maternal and fetal tissues, and cancer samples with sufficient mutational burden. Computational methods for detecting these foreign cells are vital to studying these biological conditions. An application that is of particular interest is that of leukemia patients post hematopoietic cell transplant (HCT). In many leukemias, a primary therapy is HCT, after which, the primary genotype of the bone marrow and blood cells should be of donor origin. If cells exist that are of the patient's genotype and the cell type lineage of the particular leukemia, this is known as measurable residual disease (MRD). If the MRD is high enough, this may represent a relapse of the patient's leukemia. Furthermore, accurately estimating the MRD is important for driving clinical decision making for these patients. Here we present Cellector, a computational method for identifying rare foreign genotype cells in single cell RNAseq (scRNAseq) datasets. We show cellector accurately detects microchimeric cells down to an exceedingly low percentage of these cells present (0.05% or lower).
    DOI:  https://doi.org/10.64898/2026.03.26.714571
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