bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2024–05–12
25 papers selected by
William Grey, University of York
  1. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.
  2. Inducible CXCL12/CXCR4-dependent extramedullary hematopoietic niches in the adrenal gland.
  3. Early megakaryocyte lineage-committed progenitors in adult mouse bone marrow.
  4. Establishment of human hematopoietic organoids for evaluation of hematopoietic injury and regeneration effect.
  5. p21/Zbtb18 repress the expression of cKit to regulate the self-renewal of hematopoietic stem cells.
  6. Building bones for blood and beyond: the growing field of bone marrow niche model development.
  7. Crosstalk between DNA Damage Repair and Metabolic Regulation in Hematopoietic Stem Cells.
  8. Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing.
  9. Tracing embryonic hematopoiesis guides induction of pluripotent stem cells to hematopoietic progenitors.
  10. AML/T cell interactomics uncover correlates of patient outcomes and the key role of ICAM1 in T cell killing of AML.
  11. Pin1-Catalyzed Conformation Changes Regulate Protein Ubiquitination and Degradation.
  12. Tetrahydroxy stilbene glucoside rejuvenates aging hematopoietic stem cells with predilection for lymphoid differentiation via AMPK and Tet2.
  13. Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs.
  14. An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.
  15. Roquin-2 promotes oxidative stress-induced cell death by ubiquitination-dependent degradation of TAK1.
  16. Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication.
  17. Oxidative stress is two-sided in the treatment of acute myeloid leukemia.
  18. A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3KLHL22.
  19. Targetable leukaemia dependency on noncanonical PI3Kγ signalling.
  20. TurboID-Based IRE1 Interactome Reveals Participants of the Endoplasmic Reticulum-Associated Protein Degradation Machinery in the Human Mast Cell Leukemia Cell Line HMC-1.2.
  21. Single cell sequencing of zebrafish kidney marrows reveals AHR2-dependent endogenous regulation of hematopoiesis.
  22. Sclerostin blockade inhibits bone resorption through PDGF receptor signaling in osteoblast lineage cells.
  23. Human IL-6 fosters long-term engraftment of patient derived disease-driving myeloma cells in immunodeficient mice.
  24. Giant organelle vesicles to uncover intracellular membrane mechanics and plasticity.
  25. Resolvin E1 improves efferocytosis and rescues severe aplastic anemia in mice.
  1. Cell. 2024 May 02. pii: S0092-8674(24)00408-2. [Epub ahead of print]
    Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.
    Shovik Bandyopadhyay, Michael P Duffy, Kyung Jin Ahn, Jonathan H Sussman, Minxing Pang, David Smith, Gwendolyn Duncan, Iris Zhang, Jeffrey Huang, Yulieh Lin, Barbara Xiong, Tamjid Imtiaz, Chia-Hui Chen, Anusha Thadi, Changya Chen, Jason Xu, Melissa Reichart, Zachary Martinez, Caroline Diorio, Chider Chen, Vinodh Pillai, Oraine Snaith, Derek Oldridge, Siddharth Bhattacharyya, Ivan Maillard, Martin Carroll, Charles Nelson, Ling Qin, Kai Tan.
      Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.
    Keywords:  CODEX; bone marrow; hematopoiesis; leukemia; mesenchymal; microenvironment; neighborhood; signaling; single-cell; spatial omics
    DOI:  https://doi.org/10.1016/j.cell.2024.04.013
  2. Blood. 2024 May 10. pii: blood.2023020875. [Epub ahead of print]
    Inducible CXCL12/CXCR4-dependent extramedullary hematopoietic niches in the adrenal gland.
    Frederica Schyrr, Alejandro Alonso Calleja, Anjali Vijaykumar, Jessica Sordet-Dessimoz, Sandra Gebhard, Rita Sarkis, Charles Bataclan, Silvia Ferreira Lopes, Aurélien Laurent Jean-Charles Oggier, Laurence L de Leval, Cesar Nombela-Arrieta, Olaia M Naveiras.
      Adult hematopoietic Stem and Progenitor Cells (HSPCs) reside in the bone marrow hematopoietic niche, which regulates HSPC quiescence, self-renewal, and commitment in a demand-adapted manner. While the complex bone marrow niche is responsible for adult hematopoiesis, evidence exists for simpler, albeit functional and more accessible, extramedullary hematopoietic niches. Inspired by the anecdotal description of retroperitoneal hematopoietic masses occurring at higher frequency upon hormonal dysregulation within the adrenal gland, we hypothesized that the adult adrenal gland could be induced into a hematopoietic supportive environment in a systematic manner, thus revealing mechanisms underlying de novo niche formation in the adult. Here we show that upon splenectomy and hormonal stimulation, the adult adrenal gland of mice can be induced to recruit and host functional HSPCs, capable of serial transplantation, and that this phenomenon is associated with de novo formation of platelet-derived growth factor receptor α (PDGFRα) expressing stromal nodules. We further show in CXCL12-GFP reporter mice that adrenal glands contain a stromal population reminiscent of the CXCL12-Abundant Reticular (CAR) cells which compose the bone marrow HSPC niche. Mechanistically, HSPC homing to hormonally-induced adrenal glands was found dependent on the CXCR4/CXCL12 axis. Mirroring our findings in mice, we found reticular CXCL12+ cells co-expressing master niche-regulator FOXC1 in primary samples from human adrenal myelolipomas, a benign tumor composed of adipose and hematopoietic tissue. Our findings reignite long-standing questions regarding hormonal regulation of hematopoiesis and provide a novel model to facilitate the study of adult-specific inducible hematopoietic niches which may pave the way to therapeutic applications.
    DOI:  https://doi.org/10.1182/blood.2023020875
  3. Blood Sci. 2024 Apr;6(2): e00187
    Early megakaryocyte lineage-committed progenitors in adult mouse bone marrow.
    Zixian Liu, Jinhong Wang, Yao Ma, Miner Xie, Peng Wu, Sen Zhang, Xiaofang Wang, Fang Dong, Hui Cheng, Ping Zhu, Mingzhe Han, Hideo Ema.
      Hematopoietic stem cells (HSCs) have been considered to progressively lose their self-renewal and differentiation potentials prior to the commitment to each blood lineage. However, recent studies have suggested that megakaryocyte progenitors (MkPs) are generated at the level of HSCs. In this study, we newly identified early megakaryocyte lineage-committed progenitors (MgPs) mainly in CD201-CD48- cells and CD48+ cells separated from the CD150+CD34-Kit+Sca-1+Lin- HSC population of the bone marrow in adult mice. Single-cell colony assay and single-cell transplantation showed that MgPs, unlike platelet-biased HSCs, had little repopulating potential in vivo, but formed larger megakaryocyte colonies in vitro (on average 8 megakaryocytes per colony) than did previously reported MkPs. Single-cell RNA sequencing supported that HSCs give rise to MkPs through MgPs along a Mk differentiation pathway. Single-cell reverse transcription polymerase chain reaction (RT-PCR) analysis showed that MgPs expressed Mk-related genes, but were transcriptionally heterogenous. Clonal culture of HSCs suggested that MgPs are not direct progeny of HSCs. We propose a differentiation model in which HSCs give rise to MgPs which then give rise to MkPs, supporting a classic model in which Mk-lineage commitment takes place at a late stage of differentiation.
    Keywords:  Differentiation; Hematopoietic progenitor cells; Hematopoietic stem cells; Lineage commitment; Megakaryocytes
    DOI:  https://doi.org/10.1097/BS9.0000000000000187
  4. Stem Cell Res Ther. 2024 May 04. 15(1): 133
    Establishment of human hematopoietic organoids for evaluation of hematopoietic injury and regeneration effect.
    Keyi Chen, Yunqiao Li, Xumin Wu, Xuan Tang, Bowen Zhang, Tao Fan, Lijuan He, Xuetao Pei, Yanhua Li.
       BACKGROUND: Human hematopoietic organoids have a wide application value for modeling human bone marrow diseases, such as acute hematopoietic radiation injury. However, the manufacturing of human hematopoietic organoids is an unaddressed challenge because of the complexity of hematopoietic tissues.
    METHODS: To manufacture hematopoietic organoids, we obtained CD34+ hematopoietic stem and progenitor cells (HSPCs) from human embryonic stem cells (hESCs) using stepwise induction and immunomagnetic bead-sorting. We then mixed these CD34+ HSPCs with niche-related cells in Gelatin-methacryloyl (GelMA) to form a three-dimensional (3D) hematopoietic organoid. Additionally, we investigated the effects of radiation damage and response to granulocyte colony-stimulating factor (G-CSF) in hematopoietic organoids.
    RESULTS: The GelMA hydrogel maintained the undifferentiated state of hESCs-derived HSPCs by reducing intracellular reactive oxygen species (ROS) levels. The established hematopoietic organoids in GelMA with niche-related cells were composed of HSPCs and multilineage blood cells and demonstrated the adherence of hematopoietic cells to niche cells. Notably, these hematopoietic organoids exhibited radiation-induced hematopoietic cell injury effect, including increased intracellular ROS levels, γ-H2AX positive cell percentages, and hematopoietic cell apoptosis percentages. Moreover, G-CSF supplementation in the culture medium significantly improved the survival of HSPCs and enhanced myeloid cell regeneration in these hematopoietic organoids after radiation.
    CONCLUSIONS: These findings substantiate the successful manufacture of a preliminary 3D hematopoietic organoid from hESCs-derived HSPCs, which was utilized for modeling hematopoietic radiation injury and assessing the radiation-mitigating effects of G-CSF in vitro. Our study provides opportunities to further aid in the standard and scalable production of hematopoietic organoids for disease modeling and drug testing.
    Keywords:  Gelatin-methacryloyl; Granulocyte colony-stimulating factor; Hematopoietic organoids; Hematopoietic stem/progenitor cells; Radiation injury
    DOI:  https://doi.org/10.1186/s13287-024-03743-y
  5. Protein Cell. 2024 May 09. pii: pwae022. [Epub ahead of print]
    p21/Zbtb18 repress the expression of cKit to regulate the self-renewal of hematopoietic stem cells.
    Nini Wang, Shangda Yang, Yu Li, Fanglin Gou, Yanling Lv, Xiangnan Zhao, Yifei Wang, Chang Xu, Bin Zhou, Fang Dong, Zhenyu Ju, Tao Cheng, Hui Cheng.
      The maintenance of hematopoietic stem cells (HSCs) is a complex process involving numerous cell-extrinsic and -intrinsic regulators. The first member of the cyclin-dependent kinase family of inhibitors to be identified, p21, has been reported to perform a wide range of critical biological functions, including cell cycle regulation, transcription, differentiation, and so on. Given the previous inconsistent results regarding the functions of p21 in HSCs in a p21-knockout mouse model, we employed p21-tdTomato (tdT) mice to further elucidate its role in HSCs during homeostasis. The results showed that p21-tdT+ HSCs exhibited increased self-renewal capacity compared to p21-tdT- HSCs. Zbtb18, a transcriptional repressor, was upregulated in p21-tdT+ HSCs, and its knockdown significantly impaired the reconstitution capability of HSCs. Furthermore, p21 interacted with ZBTB18 to co-repress the expression of cKit in HSCs and thus regulated the self-renewal of HSCs. Our data provide novel insights into the physiological role and mechanisms of p21 in HSCs during homeostasis independent of its conventional role as a cell cycle inhibitor.
    Keywords:  Zbtb18; cKit; hematopoietic stem cells; p21; self-renewal
    DOI:  https://doi.org/10.1093/procel/pwae022
  6. Exp Hematol. 2024 May 08. pii: S0301-472X(24)00091-2. [Epub ahead of print] 104232
    Building bones for blood and beyond: the growing field of bone marrow niche model development.
    W Sebastian Doherty-Boyd, Monica P Tsimbouri, Hannah Donnelly, Matthew J Dalby.
      The bone marrow (BM) niche is a complex microenvironment that provides the signals required for regulation of hematopoietic stem cells (HSCs) and the process of haematopoiesis they are responsible for. Bioengineered models of the BM niche incorporate various elements of the in vivo BM microenvironment, including cellular components, soluble factors, a 3D environment, mechanical stimulation of included cells, and perfusion. Recent advances in the bioengineering field have resulted in a spate of new models that shed light on BM function and are approaching precise imitation of the BM niche. These models promise to improve our understanding of the in vivo microenvironment in health and disease. They also aim to serve as platforms for HSC manipulation, or as preclinical models for screening novel therapies for BM-associated disorders and diseases.
    DOI:  https://doi.org/10.1016/j.exphem.2024.104232
  7. Cells. 2024 Apr 24. pii: 733. [Epub ahead of print]13(9):
    Crosstalk between DNA Damage Repair and Metabolic Regulation in Hematopoietic Stem Cells.
    Jian Xu, Peiwen Fei, Dennis W Simon, Michael J Morowitz, Parinda A Mehta, Wei Du.
      Self-renewal and differentiation are two characteristics of hematopoietic stem cells (HSCs). Under steady physiological conditions, most primitive HSCs remain quiescent in the bone marrow (BM). They respond to different stimuli to refresh the blood system. The transition from quiescence to activation is accompanied by major changes in metabolism, a fundamental cellular process in living organisms that produces or consumes energy. Cellular metabolism is now considered to be a key regulator of HSC maintenance. Interestingly, HSCs possess a distinct metabolic profile with a preference for glycolysis rather than oxidative phosphorylation (OXPHOS) for energy production. Byproducts from the cellular metabolism can also damage DNA. To counteract such insults, mammalian cells have evolved a complex and efficient DNA damage repair (DDR) system to eliminate various DNA lesions and guard genomic stability. Given the enormous regenerative potential coupled with the lifetime persistence of HSCs, tight control of HSC genome stability is essential. The intersection of DDR and the HSC metabolism has recently emerged as an area of intense research interest, unraveling the profound connections between genomic stability and cellular energetics. In this brief review, we delve into the interplay between DDR deficiency and the metabolic reprogramming of HSCs, shedding light on the dynamic relationship that governs the fate and functionality of these remarkable stem cells. Understanding the crosstalk between DDR and the cellular metabolism will open a new avenue of research designed to target these interacting pathways for improving HSC function and treating hematologic disorders.
    Keywords:  DNA damage repair (DDR); Fanconi anemia (FA) pathway; cellular metabolism; hematopoietic stem cells (HSCs)
    DOI:  https://doi.org/10.3390/cells13090733
  8. Front Oncol. 2024 ;14 1365330
    Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing.
    Jianbiao Zhou, Wee-Joo Chng.
      Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence of diverse and functionally distinct populations of leukemia cells within the same patient's bone marrow or blood poses a significant challenge in diagnosing and treating AML. A substantial proportion of AML patients demonstrate resistance to induction chemotherapy and a grim prognosis upon relapse. The rapid advance in next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding of AML pathogenesis by enabling high-resolution interrogation of the cellular heterogeneity in the AML ecosystem, and their transcriptional signatures at a single-cell level. New studies have successfully characterized the inextricably intertwined interactions among AML cells, immune cells and bone marrow microenvironment and their contributions to the AML development, therapeutic resistance and relapse. These findings have deepened and broadened our understanding the complexity and heterogeneity of AML, which are difficult to detect with bulk RNA-seq. This review encapsulates the burgeoning body of knowledge generated through scRNA-seq, providing the novel insights and discoveries it has unveiled in AML biology. Furthermore, we discuss the potential implications of scRNA-seq in therapeutic opportunities, focusing on immunotherapy. Finally, we highlight the current limitations and future direction of scRNA-seq in the field.
    Keywords:  acute myeloid leukemia (AML); bone marrow microenvironment; immunotherapy; intratumoral heterogeneity; leukemia stem cell (LSC); novel therapy; single cell RNA-sequencing (scRNA-seq)
    DOI:  https://doi.org/10.3389/fonc.2024.1365330
  9. Dev Cell. 2024 May 06. pii: S1534-5807(24)00226-0. [Epub ahead of print]59(9): 1093-1095
    Tracing embryonic hematopoiesis guides induction of pluripotent stem cells to hematopoietic progenitors.
    Xinjian Mao, Linheng Li.
      In this issue of Developmental Cell, Fowler et al. applied genetic lineage-tracing mouse models to support the notion that artery endothelial cells are the predominant source of hematopoietic stem cells. They leveraged this and developed a method capable of efficiently differentiating human pluripotent stem cells into HLF+HOXA+ hematopoietic progenitors.
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.001
  10. Leukemia. 2024 May 09.
    AML/T cell interactomics uncover correlates of patient outcomes and the key role of ICAM1 in T cell killing of AML.
    Ece Canan Sayitoglu, Bogdan A Luca, Allison Paige Boss, Benjamin Craig Thomas, Robert Arthur Freeborn, Molly Javier Uyeda, Pauline Ping Chen, Yusuke Nakauchi, Colin Waichler, Norman Lacayo, Rosa Bacchetta, Ravindra Majeti, Andrew J Gentles, Alma-Martina Cepika, Maria Grazia Roncarolo.
      T cells are important for the control of acute myeloid leukemia (AML), a common and often deadly malignancy. We observed that some AML patient samples are resistant to killing by human-engineered cytotoxic CD4+ T cells. Single-cell RNA-seq of primary AML samples and CD4+ T cells before and after their interaction uncovered transcriptional programs that correlate with AML sensitivity or resistance to CD4+ T cell killing. Resistance-associated AML programs were enriched in AML patients with poor survival, and killing-resistant AML cells did not engage T cells in vitro. Killing-sensitive AML potently activated T cells before being killed, and upregulated ICAM1, a key component of the immune synapse with T cells. Without ICAM1, killing-sensitive AML became resistant to killing by primary ex vivo-isolated CD8+ T cells in vitro, and engineered CD4+ T cells in vitro and in vivo. While AML heterogeneity implies that multiple factors may determine their sensitivity to T cell killing, these data show that ICAM1 acts as an immune trigger, allowing T cell killing, and could play a role in AML patient survival in vivo.
    DOI:  https://doi.org/10.1038/s41375-024-02255-1
  11. Cells. 2024 Apr 23. pii: 731. [Epub ahead of print]13(9):
    Pin1-Catalyzed Conformation Changes Regulate Protein Ubiquitination and Degradation.
    Jessica Jeong, Muhammad Usman, Yitong Li, Xiao Zhen Zhou, Kun Ping Lu.
      The unique prolyl isomerase Pin1 binds to and catalyzes cis-trans conformational changes of specific Ser/Thr-Pro motifs after phosphorylation, thereby playing a pivotal role in regulating the structure and function of its protein substrates. In particular, Pin1 activity regulates the affinity of a substrate for E3 ubiquitin ligases, thereby modulating the turnover of a subset of proteins and coordinating their activities after phosphorylation in both physiological and disease states. In this review, we highlight recent advancements in Pin1-regulated ubiquitination in the context of cancer and neurodegenerative disease. Specifically, Pin1 promotes cancer progression by increasing the stabilities of numerous oncoproteins and decreasing the stabilities of many tumor suppressors. Meanwhile, Pin1 plays a critical role in different neurodegenerative disorders via the regulation of protein turnover. Finally, we propose a novel therapeutic approach wherein the ubiquitin-proteasome system can be leveraged for therapy by targeting pathogenic intracellular targets for TRIM21-dependent degradation using stereospecific antibodies.
    Keywords:  E3 ligase; Pin1; TRIM21; cancer; cis–trans conformational changes; neurodegeneration; phosphorylation signaling; protein ubiquitination; proteosome pathway
    DOI:  https://doi.org/10.3390/cells13090731
  12. J Adv Res. 2024 May 03. pii: S2090-1232(24)00170-X. [Epub ahead of print]
    Tetrahydroxy stilbene glucoside rejuvenates aging hematopoietic stem cells with predilection for lymphoid differentiation via AMPK and Tet2.
    Dan Gao, Wei-Wei Yi, Bo Liu, Cong-En Zhang, Cui-Cui Yang, Li Zeng, Lin Li, Guangbin Luo, Lan Zhang, Zhen-Yu Ju, Jia-Bo Wang.
       INTRODUCTION: Aging of hematopoietic stem cells (HSCs) has emerged as an important challenge to human health. Recent advances have raised the prospect of rejuvenating aging HSCs via specific medical interventions, including pharmacological treatments. Nonetheless, efforts to develop such drugs are still in infancy until now.
    OBJECTIVES: We aimed to screen the prospective agents that can rejuvenate aging HSCs and explore the potential mechanisms.
    METHODS: We screened a set of natural anti-aging compounds through oral administration to sub-lethally irradiated mice, and identified 2,3,5,4'-tetrahydroxystilbene-2-O-β-D-glucoside (TSG) as a potent rejuvenating agent for aging HSCs. Then naturally aged mice were used for the follow-up assessment to determine the HSC rejuvenating potential of TSG. Finally, based on the transcriptome and DNA methylation analysis, we validated the role of the AMP-activated protein kinase (AMPK)-ten-eleven-translocation 2 (Tet2) axis (the AMPK-Tet2 axis) as the underlying mechanisms of TSG for ameliorating HSCs aging.
    RESULTS: TSG treatment not only significantly increased the absolute number of common lymphoid progenitors (CLPs) along with B lymphocytes, but also boosted the HSCs/CLPs repopulation potential of aging mice. Further elaborated mechanism research demonstrated that TSG supplementation restored the stemness of aging HSCs, as well as promoted an epigenetic reprograming that was associated with an improved regenerative capacity and an increased rate of lymphopoiesis. Such effects were diminished when the mice were co-treated with an AMPK inhibitor, or when it was performed in Tet2 knockout mice as well as senescent cells assay.
    CONCLUSION: TSG is effective in rejuvenating aging HSCs by modulating the AMPK- Tet2 axis and thus represents a potential candidate for developing effective HSC rejuvenating therapies.
    Keywords:  AMPK-Tet2 axis; Aging; Hematopoietic stem cells; Lymphoid differentiation; Tetrahydroxy stilbene glucoside
    DOI:  https://doi.org/10.1016/j.jare.2024.04.027
  13. Nat Commun. 2024 May 08. 15(1): 3894
    Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs.
    Linda Lauinger, Anna Andronicos, Karin Flick, Clinton Yu, Geetha Durairaj, Lan Huang, Peter Kaiser.
      The F-box domain is a highly conserved structural motif that defines the largest class of ubiquitin ligases, Skp1/Cullin1/F-box protein (SCF) complexes. The only known function of the F-box motif is to form the protein interaction surface with Skp1. Here we show that the F-box domain can function as an environmental sensor. We demonstrate that the F-box domain of Met30 is a cadmium sensor that blocks the activity of the SCFMet30 ubiquitin ligase during cadmium stress. Several highly conserved cysteine residues within the Met30 F-box contribute to binding of cadmium with a KD of 8 µM. Binding induces a conformational change that allows for Met30 autoubiquitylation, which in turn leads to recruitment of the segregase Cdc48/p97/VCP followed by active SCFMet30 disassembly. The resulting inactivation of SCFMet30 protects cells from cadmium stress. Our results show that F-box domains participate in regulation of SCF ligases beyond formation of the Skp1 binding interface.
    DOI:  https://doi.org/10.1038/s41467-024-48184-6
  14. Nat Commun. 2024 May 07. 15(1): 3793
    An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.
    Stephen M Coscia, Andrew S Moore, Cameron P Thompson, Christian F Tirrito, E Michael Ostap, Erika L F Holzbaur.
      Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.
    DOI:  https://doi.org/10.1038/s41467-024-48189-1
  15. Free Radic Biol Med. 2024 May 08. pii: S0891-5849(24)00438-6. [Epub ahead of print]
    Roquin-2 promotes oxidative stress-induced cell death by ubiquitination-dependent degradation of TAK1.
    Yusuke Hirata, Yuya Nakata, Hiromu Komatsu, Yuki Kodoh, Miki Takahashi, Soma Taguchi, Takuya Noguchi, Atsushi Matsuzawa.
      Reactive oxygen species (ROS) are highly reactive and its accumulation causes oxidative damage to cells. Cells maintain survival upon mild oxidative stress with anti-oxidative systems, such as the kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) system. On the other hand, upon severe oxidative stress, cells undergo regulated cell death, including apoptosis, for eliminating damaged cells. To execute efficient cell death, cells need to turn off the anti-oxidant systems, while triggering cell death. However, it remains unknown how cells orchestrate these two conflicting systems under excessive oxidative stress. Herein, we show that when cells are exposed to excessive oxidative damage, an E3 ubiquitin ligase Roquin-2 (also known as RC3H2) plays a key role in switching cell fate from survival to death by terminating activation of transforming growth factor-β-activated kinase (TAK1), a positive regulator for Nrf2 activation. Roquin-2 interacted with TAK1 via four cysteine residues in TAK1 (C96, C302, C486, and C500) that are susceptible to oxidative stress and participate in oligomer formation via disulfide bonds, promoting K48-linked polyubiquitination and degradation of TAK1. Nrf2 was inactivated upon lethal oxidative stress in wild-type mouse embryonic fibroblast (MEF) cells, whereas it sustained activation and conferred resistance to Roquin-2 deficient cells, which was reversed by pharmacological or genetic inhibition of TAK1. These data demonstrate that in response to excessive ROS exposure, Roquin-2 promotes ubiquitination and degradation of TAK1 to suppress Nrf2 activation, and thereby contribute to an efficient cell death, providing insight into the pathogenesis of oxidative stress-related diseases, including cancer.
    Keywords:  Nrf2; Roquin-2; TAK1; cell death; oxidative stress; redox; ubiquitin ligase; ubiquitination
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.05.009
  16. Annu Rev Biomed Data Sci. 2024 May 09.
    Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication.
    Jarrod Shilts, Gavin J Wright.
      Proteins on the surfaces of cells serve as physical connection points to bridge one cell with another, enabling direct communication between cells and cohesive structure. As biomedical research makes the leap from characterizing individual cells toward understanding the multicellular organization of the human body, the binding interactions between molecules on the surfaces of cells are foundational both for computational models and for clinical efforts to exploit these influential receptor pathways. To achieve this grander vision, we must assemble the full interactome of ways surface proteins can link together. This review investigates how close we are to knowing the human cell surface protein interactome. We summarize the current state of databases and systematic technologies to assemble surface protein interactomes, while highlighting substantial gaps that remain. We aim for this to serve as a road map for eventually building a more robust picture of the human cell surface protein interactome.
    DOI:  https://doi.org/10.1146/annurev-biodatasci-102523-103821
  17. Cancer Med. 2024 May;13(9): e6806
    Oxidative stress is two-sided in the treatment of acute myeloid leukemia.
    Chenyang Fan, Xiangdong Yang, Lixiang Yan, Zhexin Shi.
       INTRODUCTION: Oxidative stress caused by elevated ROS, as a novel therapeutic mechanism, has been implicated in various tumors including AML. AML cells are chronically under oxidative stress, yet overreliance on ROS production makes tumor cells increasingly vulnerable to further damage. Reducing the cytotoxic effect of ROS on normal cells while killing leukemia stem cell (LSC) with high levels of reactive oxygen species is a new challenge for oxidative stress therapy in leukemia.
    METHODS: By searching literature databases, we summarized recent relevant studies. The relationship of ROS on AML genes, signaling pathways, and transcription factors, and the correlation of ROS with AML bone marrow microenvironment and autophagy were summarized. In addition, we summarize the current status of research on ROS and AML therapeutics. Finally, we discuss the research progress on redox resistance in AML.
    RESULTS: This review discusses the evidence showing the link between redox reactions and the progression of AML and compiles the latest research findings that will facilitate future biological studies of redox effects associated with AML treatment.
    CONCLUSION: We believe that exploiting this unique oxidative stress property of AML cells may provide a new way to prevent relapse and drug resistance.
    Keywords:  ROS; acute myeloid leukemia; autophagy; chemoresistance; niche; oxidative stress
    DOI:  https://doi.org/10.1002/cam4.6806
  18. Nat Commun. 2024 May 06. 15(1): 3789
    A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3KLHL22.
    Weize Wang, Ling Liang, Zonglin Dai, Peng Zuo, Shang Yu, Yishuo Lu, Dian Ding, Hongyi Chen, Hui Shan, Yan Jin, Youdong Mao, Yuxin Yin.
      The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. However, how and why such a dimeric assembly is required for its ligase activity remains elusive. Here, we report the cryo-EM structure of the dimeric CRL3KLHL22 complex and reveal a conserved N-terminal motif in CUL3 that contributes to the dimerization assembly and the E3 ligase activity of CRL3KLHL22. We show that deletion of the CUL3 N-terminal motif impairs dimeric assembly and the E3 ligase activity of both CRL3KLHL22 and several other CRL3s. In addition, we found that the dynamics of dimeric assembly of CRL3KLHL22 generates a variable ubiquitination zone, potentially facilitating substrate recognition and ubiquitination. These findings demonstrate that a CUL3 N-terminal motif participates in the assembly process and provide insights into the assembly and activation of CRL3s.
    DOI:  https://doi.org/10.1038/s41467-024-48045-2
  19. Nature. 2024 May 08.
    Targetable leukaemia dependency on noncanonical PI3Kγ signalling.
    Qingyu Luo, Evangeline G Raulston, Miguel A Prado, Xiaowei Wu, Kira Gritsman, Karley S Whalen, Kezhi Yan, Christopher A G Booth, Ran Xu, Peter van Galen, John G Doench, Shai Shimony, Henry W Long, Donna S Neuberg, Joao A Paulo, Andrew A Lane.
      Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1-4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukaemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid and dendritic lineages. This dependency is characterized by innate inflammatory signalling and activation of phosphoinositide 3-kinase regulatory subunit 5 (PIK3R5), which encodes a regulatory subunit of PI3Kγ5 and stabilizes the active enzymatic complex. We identify p21 (RAC1)-activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency and find that dephosphorylation of PAK1 by PI3Kγ inhibition impairs mitochondrial oxidative phosphorylation. Treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukaemias with activated PIK3R5. In addition, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukaemia xenografts with low baseline PIK3R5 expression, as residual leukaemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Together, our study reveals a targetable dependency on PI3Kγ-PAK1 signalling that is amenable to near-term evaluation in patients with acute leukaemia.
    DOI:  https://doi.org/10.1038/s41586-024-07410-3
  20. Cells. 2024 Apr 25. pii: 747. [Epub ahead of print]13(9):
    TurboID-Based IRE1 Interactome Reveals Participants of the Endoplasmic Reticulum-Associated Protein Degradation Machinery in the Human Mast Cell Leukemia Cell Line HMC-1.2.
    Nabil Ahmed, Christian Preisinger, Thomas Wilhelm, Michael Huber.
      The unfolded protein response is an intricate system of sensor proteins in the endoplasmic reticulum (ER) that recognizes misfolded proteins and transmits information via transcription factors to either regain proteostasis or, depending on the severity, to induce apoptosis. The main transmembrane sensor is IRE1α, which contains cytoplasmic kinase and RNase domains relevant for its activation and the mRNA splicing of the transcription factor XBP1. Mast cell leukemia (MCL) is a severe form of systemic mastocytosis. The inhibition of IRE1α in the MCL cell line HMC-1.2 has anti-proliferative and pro-apoptotic effects, motivating us to elucidate the IRE1α interactors/regulators in HMC-1.2 cells. Therefore, the TurboID proximity labeling technique combined with MS analysis was applied. Gene Ontology and pathway enrichment analyses revealed that the majority of the enriched proteins are involved in vesicle-mediated transport, protein stabilization, and ubiquitin-dependent ER-associated protein degradation pathways. In particular, the AAA ATPase VCP and the oncoprotein MTDH as IRE1α-interacting proteins caught our interest for further analyses. The pharmacological inhibition of VCP activity resulted in the increased stability of IRE1α and MTDH as well as the activation of IRE1α. The interaction of VCP with both IRE1α and MTDH was dependent on ubiquitination. Moreover, MTDH stability was reduced in IRE1α-knockout cells. Hence, pharmacological manipulation of IRE1α-MTDH-VCP complex(es) might enable the treatment of MCL.
    Keywords:  ERAD pathway; mastocytosis; metadherin; ubiquitination; valosin-containing protein
    DOI:  https://doi.org/10.3390/cells13090747
  21. bioRxiv. 2024 Apr 28. pii: 2024.04.23.590755. [Epub ahead of print]
    Single cell sequencing of zebrafish kidney marrows reveals AHR2-dependent endogenous regulation of hematopoiesis.
    Subham Dasgupta, Britton Goodale, Robyn Tanguay.
      The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a wide range of biological and toxicological responses. While largely studied in ligand-activated toxicant responses, AHR also plays important roles in endogenous physiological processes. We leveraged single cell sequencing and an AHR2 knockout zebrafish line to investigate the role of AHR2 in regulating hematopoiesis (production and differentiation of red and white blood cells from hematopoietic stem cells). Our objectives were to determine if absence of AHR2-1) alters proportions of immune cell populations and/or 2) impacts gene expression within individual immune cell types. We dissected kidney marrow (organ of hematopoiesis in zebrafish) from adult wildtype and AHR2 knockout zebrafish (N=3/genotype), isolated single cells and sequenced ∼ 5000 cells/sample (10X Genomics). We identified 14 cell clusters representing the expected major blood (erythrocytes, thrombocytes), immune (B cells, macrophages, lymphoid cells, granulocytes, etc), progenitors and kidney cell populations. We focused our analyses only on the progenitor and mature immune cell types. While there were no genotype-specific differences in proportion of individual cell types, gene expression differences were observed within several cell types. For known genes, such as rrm2 , changes were up to 2000-fold, signifying their importance in AHR2-hematopoesis interaction. Several of the known genes are also identified as markers of carcinoma cells for an array of cancer types. However, many of the dysregulated genes are poorly annotated, limiting our ability to examine biological processes and pathways dysregulated on AHR2 mutation. Nevertheless, our study indicates that AHR2 plays an important endogenous role in hematopoiesis. Future work will focus on better characterizing anatomy of dysregulated genes and their functions in hematopoiesis.
    DOI:  https://doi.org/10.1101/2024.04.23.590755
  22. JCI Insight. 2024 May 22. pii: e176558. [Epub ahead of print]9(10):
    Sclerostin blockade inhibits bone resorption through PDGF receptor signaling in osteoblast lineage cells.
    Cyril Thouverey, Pierre Apostolides, Julia Brun, Joseph Caverzasio, Serge Ferrari.
      While sclerostin-neutralizing antibodies (Scl-Abs) transiently stimulate bone formation by activating Wnt signaling in osteoblast lineage cells, they exert sustained inhibition of bone resorption, suggesting an alternate signaling pathway by which Scl-Abs control osteoclast activity. Since sclerostin can activate platelet-derived growth factor receptors (PDGFRs) in osteoblast lineage cells in vitro and PDGFR signaling in these cells induces bone resorption through M-CSF secretion, we hypothesized that the prolonged anticatabolic effect of Scl-Abs could result from PDGFR inhibition. We show here that inhibition of PDGFR signaling in osteoblast lineage cells is sufficient and necessary to mediate prolonged Scl-Ab effects on M-CSF secretion and osteoclast activity in mice. Indeed, sclerostin coactivates PDGFRs independently of Wnt/β-catenin signaling inhibition, by forming a ternary complex with LRP6 and PDGFRs in preosteoblasts. In turn, Scl-Ab prevents sclerostin-mediated coactivation of PDGFR signaling and consequent M-CSF upregulation in preosteoblast cultures, thereby inhibiting osteoclast activity in preosteoblast/osteoclast coculture assays. These results provide a potential mechanism explaining the dissociation between anabolic and antiresorptive effects of long-term Scl-Ab.
    Keywords:  Bone biology; Osteoclast/osteoblast biology; Osteoporosis; Signal transduction
    DOI:  https://doi.org/10.1172/jci.insight.176558
  23. JCI Insight. 2024 May 07. pii: e177300. [Epub ahead of print]
    Human IL-6 fosters long-term engraftment of patient derived disease-driving myeloma cells in immunodeficient mice.
    Zainul S Hasanali, Alfred L Garfall, Lisa Burzenski, Leonard D Shultz, Yan Tang, Siddhant Kadu, Neil C Sheppard, Wei Liu, Derek Dopkin, Dan T Vogl, Adam D Cohen, Adam J Waxman, Sandra P Susanibar-Adaniya, Martin Carroll, Edward A Stadtmauer, David Allman.
      Multiple myeloma is a largely incurable and life-threatening malignancy of antibody-secreting plasma cells. An effective and widely available animal model that recapitulates human myeloma and related plasma cell disorders is lacking. We show that busulfan-conditioned hIL-6 transgenic NSG mice (NSG+hIL6) reliably support the engraftment of malignant and pre-malignant human plasma cells including from patients diagnosed with monoclonal gammopathy of undetermined significance, pre- and post-relapse myeloma, plasma cell leukemia, and AL amyloidosis. Consistent with human disease, NSG+hIL6 mice engrafted with patient-derived myeloma cells, developed serum M spikes, and a majority developed anemia, hypercalcemia, and/or bone lesions. Single cell RNA sequencing showed non-malignant and malignant cell engraftment, the latter expressing a wide array of mRNAs associated with myeloma cell survival and proliferation. Myeloma engrafted mice given CAR T-cells targeting plasma cells or bortezomib experienced reduced tumor burden. Our results established NSG+hIL6 mice as an effective patient derived xenograft model for study and preclinical drug development of multiple myeloma and related plasma cell disorders.
    Keywords:  Bone marrow; Cancer; Hematology; Mouse models
    DOI:  https://doi.org/10.1172/jci.insight.177300
  24. Nat Commun. 2024 May 04. 15(1): 3767
    Giant organelle vesicles to uncover intracellular membrane mechanics and plasticity.
    Alexandre Santinho, Maxime Carpentier, Julio Lopes Sampaio, Mohyeddine Omrane, Abdou Rachid Thiam.
      Tools for accessing and studying organelles remain underdeveloped. Here, we present a method by which giant organelle vesicles (GOVs) are generated by submitting cells to a hypotonic medium followed by plasma membrane breakage. By this means, GOVs ranging from 3 to over 10 µm become available for micromanipulation. GOVs are made from organelles such as the endoplasmic reticulum, endosomes, lysosomes and mitochondria, or in contact with one another such as giant mitochondria-associated ER membrane vesicles. We measure the mechanical properties of each organelle-derived GOV and find that they have distinct properties. In GOVs procured from Cos7 cells, for example, bending rigidities tend to increase from the endoplasmic reticulum to the plasma membrane. We also found that the mechanical properties of giant endoplasmic reticulum vesicles (GERVs) vary depending on their interactions with other organelles or the metabolic state of the cell. Lastly, we demonstrate GERVs' biochemical activity through their capacity to synthesize triglycerides and assemble lipid droplets. These findings underscore the potential of GOVs as valuable tools for studying the biophysics and biology of organelles.
    DOI:  https://doi.org/10.1038/s41467-024-48086-7
  25. Cell Death Dis. 2024 May 09. 15(5): 324
    Resolvin E1 improves efferocytosis and rescues severe aplastic anemia in mice.
    Rachel Grazda, Allison N Seyfried, Krishna Rao Maddipati, Gabrielle Fredman, Katherine C MacNamara.
      Severe aplastic anemia (SAA) is a rare, fatal disease characterized by severe cytopenias and loss of hematopoietic stem cells (HSCs). Immune-mediated destruction and inflammation are known drivers of SAA, however, the underlying mechanisms driving persistent inflammation are unknown. Current treatments for SAA rely on immunosuppressive therapies or HSC transplantation, however, these treatments are not always effective. Using an established mouse model of SAA, we observed a significant increase in apoptotic cells within the bone marrow (BM) and impaired efferocytosis in SAA mice, relative to radiation controls. Single-cell transcriptomic analysis revealed heterogeneity among BM monocytes and unique populations emerged during SAA characterized by increased inflammatory signatures and significantly increased expression of Sirpa and Cd47. CD47, a "don't eat me" signal, was increased on both live and apoptotic BM cells, concurrent with markedly increased expression of signal regulatory protein alpha (SIRPα) on monocytes. Functionally, SIRPα blockade improved cell clearance and reduced accumulation of CD47-positive apoptotic cells. Lipidomic analysis revealed a reduction in the precursors of specialized pro-resolving lipid mediators (SPMs) and increased prostaglandins in the BM during SAA, indicative of impaired inflammation resolution. Specifically, 18-HEPE, a precursor of E-series resolvins, was significantly reduced in SAA-induced mice relative to radiation controls. Treatment of SAA mice with Resolvin E1 (RvE1) improved efferocytic function, BM cellularity, platelet output, and survival. Our data suggest that impaired efferocytosis and inflammation resolution contributes to SAA progression and demonstrate that SPMs, such as RvE1, offer new and/or complementary treatments for SAA that do not rely on immune suppression.
    DOI:  https://doi.org/10.1038/s41419-024-06705-7
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