bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2025–05–11
thirteen papers selected by
William Grey, University of York
  1. Clec12a is required for the pathogenesis of NUP98::NSD1 AML.
  2. TET3 regulates hematopoietic stem cell homeostasis during embryonic and adult hematopoiesis.
  3. PIEZO1 Activation-Mediated Generation of Transgene-Free Long-Term Hematopoietic Stem Cells.
  4. Critical role of the potential O-linked glycosylation sites of CXCR4 in cell migration and bone marrow homing of hematopoietic stem progenitor cells.
  5. Monocytes/macrophages contamination disrupts functional and transcriptional characteristics of murine bone marrow- and bone-derived stromal cells.
  6. Paraoxonase-like APMAP maintains endoplasmic-reticulum-associated lipid and lipoprotein homeostasis.
  7. Targeting leukemic stem cell dormancy in NPM1c/FLT3-ITD-driven acute myeloid leukemia.
  8. m6A/IGF2BP3-driven serine biosynthesis fuels AML stemness and metabolic vulnerability.
  9. Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias.
  10. The m5C methyltransferase NSUN2 promotes progression of acute myeloid leukemia by regulating serine metabolism.
  11. PPIL2 is a target of the JAK2/STAT5 pathway and promotes myeloproliferation via p53-mediated degradation.
  12. Molecular basis of SIFI activity in the integrated stress response.
  13. p97/VCP is required for piecemeal autophagy of aggresomes.
  1. Blood Adv. 2025 May 07. pii: bloodadvances.2024015739. [Epub ahead of print]
    Clec12a is required for the pathogenesis of NUP98::NSD1 AML.
    Sagarajit Mohanty, Fiorella Charles Cano, Razif Gabdoulline, Courteney K Lai, Basem Othman, Harish Sudarsanam, Thomas Eder, Florian Grebien, Daniel B Lipka, Reinhard Henschler, Michael Heuser.
      NUP98::NSD1 is one of the most recurring nucleoporin 98 (NUP98) fusions in acute myeloid leukemia (AML). NSD1-driven AML is associated with adverse outcomes and poor response to conventional treatments. However, limited studies have been done to identify new potential targets to develop better treatment approaches. The C-type lectin domain family 12, member A (CLEC12A) is a cell surface receptor that is differentially expressed in leukemic stem cells (LSCs) compared to healthy hematopoietic stem cells (HSCs). We demonstrated a strong overexpression of CLEC12A in both NUP98::NSD1 patients and murine AML cells transformed with NUP98::NSD1. To understand the role of Clec12a in NUP98::NSD1 AML, we depleted Clec12a expression in NUP98::NSD1+NRASG12D immortalized cells using the CRISPR/Cas9 approach. NUP98::NSD1+NRASG12D/Clec12a knockout cells showed higher levels of apoptosis and lower colony numbers in vitro compared to NUP98::NSD1+NRASG12D/Clec12a wildtype cells. Importantly, the deletion of Clec12a significantly reduced leukemic engraftment and prolonged survival of the NUP98::NSD1+NRASG12D murine model. Our data suggest to further explore CLEC12A as a potential target for the treatment of NUP98::NSD1 AML.
    DOI:  https://doi.org/10.1182/bloodadvances.2024015739
  2. Hemasphere. 2025 May;9(5): e70140
    TET3 regulates hematopoietic stem cell homeostasis during embryonic and adult hematopoiesis.
    Harmony C Ketchum, Claudia Morganti, Chie Yanase, Blake Ebert, Keisuke Ito, Meelad M Dawlaty.
      The ten-eleven translocation family of enzymes (TET1/2/3) promotes DNA demethylation and is essential for hematopoiesis. While the roles of TET1 and TET2 are well-studied in hematopoiesis, the requirement of TET3 in embryonic and adult hematopoiesis is less investigated. In this study, by characterizing embryonic and adult hematopoiesis in Tie2 +/cre ; Tet3 f/f mice, we have established a requirement for TET3 in regulating hematopoietic stem cells (HSCs; CD150+CD48-). We found that loss of TET3 in the fetal liver and adult bone marrow causes a reduction in the percent of long-term HSCs (LT-HSCs; CD150+CD48-CD34-). This was accompanied by reduced colony forming capacity of TET3-deficient HSCs in vitro and reduced contribution of HSCs after a competitive bone marrow transplantation in vivo. TET3 deficiency increased DNA methylation at several cell cycle regulator genes leading to their down regulation. This is consistent with, and likely underpins, the reduced number of quiescent HSCs in TET3-deficient bone marrow. These findings uncover a new role for TET3 in HSC homeostasis during embryonic and adult hematopoiesis.
    DOI:  https://doi.org/10.1002/hem3.70140
  3. Am J Hematol. 2025 May 04.
    PIEZO1 Activation-Mediated Generation of Transgene-Free Long-Term Hematopoietic Stem Cells.
    Giorgia Scapin, Jennifer L Cillis, Marie C Goulard, Taylor C Patch, Cintia E Gomez Limia, Yichen Ding, Wenqiang Du, Priyanka R Dharampuriya, Elliott J Hagedorn, Heidi Anderson, Gabriel A Musso, Caitlyn R Curley, Emily M Teets, Calum A MacRae, Lalit Sehgal, Tzung K Hsiai, Bradley W Blaser, Dhvanit I Shah.
      The development of engraftable, long-term reconstituting hematopoietic stem cells (LT-HSC) from human pluripotent stem cells (hPSC) has been a long-sought goal. Since HSCs are formed by a subset of endothelial cells in the ventral part of the dorsal aorta, we analyzed heartbeat-mediated pulsatile displacement experienced by the walls of the dorsal aorta in zebrafish embryos. We found that pulsation-mediated circumferential stretch was restricted to the ventral part of the dorsal aorta and activated Piezo1 to stimulate LT-HSC formation. Stimulation of pulsation or Yoda1-mediated Piezo1 activation promoted the formation of de novo LT-HSCs from hemogenic endothelial cells derived from murine embryos or human pluripotent stem cells. These HSCs gave long-term multilineage reconstitution of hematopoietic cells upon transplantation into immunocompromised mice. The formation of transgene-free human LT-HSCs that can engraft and reconstitute the hematopoietic system will facilitate the generation of off-the-shelf HSCs from hPSCs for use in cellular therapies.
    Keywords:  Circumferential stretch; Hematopoiesis; Hematopoietic stem cells; Mechanosensation; Off‐the‐shelf; Piezo1; Pluripotent stem cells
    DOI:  https://doi.org/10.1002/ajh.27689
  4. Stem Cells. 2025 May 04. pii: sxaf025. [Epub ahead of print]
    Critical role of the potential O-linked glycosylation sites of CXCR4 in cell migration and bone marrow homing of hematopoietic stem progenitor cells.
    Xuchi Pan, Chie Naruse, Tomoko Matsuzaki, Ojiro Ishibashi, Kazushi Sugihara, Hidetsugu Asada, Masahide Asano.
      The C-X-C chemokine receptor type 4 (CXCR4) and its ligand, C-X-C motif chemokine ligand 12 (CXCL12), are critical for the homing of hematopoietic stem progenitor cells (HSPCs) to bone marrow (BM). Our previous study revealed that carbohydrate chains on HSPCs are vital in the homing and engraftment of HSPCs. However, the relationship between the glycosylation of CXCR4 and HSPCs homing remains unclear. In this study, we analyzed the glycosylation sites of the N-terminal 38 amino acids of mouse CXCR4, which is indispensable for CXCL12 binding. Among these, simultaneous mutations of possible glycosylation sites, Serine-5 and Serine-9 of mouse CXCR4 lost cell migration activity through CXCL12 in cultured cells and mouse HSPCs. Furthermore, Serine-5 and Serine-9 mutations in HSPCs caused a deficiency in the homing to the BM. Our findings suggest that the glycosylation of mouse CXCR4 is essential for homing HSPCs to the BM, which can be used to screen cord blood HSPCs suitable for transplantation.
    Keywords:  CXCL12; CXCR4; glycosylation; hematopoietic stem cell homing; mouse
    DOI:  https://doi.org/10.1093/stmcls/sxaf025
  5. JBMR Plus. 2025 Jun;9(6): ziaf047
    Monocytes/macrophages contamination disrupts functional and transcriptional characteristics of murine bone marrow- and bone-derived stromal cells.
    Yuko Kawano, Hiroki Kawano, Stephanie Busch, Allison J Li, Jane Zhang, Noah A Salama, Emily R Quarato, Mary Georger, Nataliia Vdovichenko, Mitra Azadniv, Daniel K Byun, Elizabeth A LaMere, Mark W LaMere, Jane L Liesveld, Michael W Becker, Laura M Calvi.
      Stromal cells are critical regulators of hematopoietic stem/progenitor cells and skeletal homeostasis. Although precise systems for functional analysis are critical to investigate mechanistically bone and bone marrow (BM)-derived stromal cells, the establishment of reproducible, highly enriched ex vivo methods for stromal cell isolation, culture and evaluation have been challenging, leading to inconsistent data on stromal cell function. In this work, we carefully tested ex vivo culture of murine stromal cells from BM and bone and discovered abundant and persistent contamination of monocytes and macrophages. We succeeded in establishing highly enriched ex vivo culture system for stromal cells by eliminating persistent monocytes and macrophages using selection against the immunological markers F4/80, Ly6C, and CD45. Transcriptional and functional assays of enriched stromal cell culture revealed differential characteristics of stromal cells from different origins, a dormant signature for bone-derived cells and a highly proliferative progenitor-like signature for BM-derived cells. Monocyte and macrophage contamination reduced signatures of immature stromal cells such as expression levels of SOX9 and CD140a as well as the cells' ability to support hematopoietic stem and progenitor cells based on our growth factor-free co-culture system of hematopoietic cells and stromal cells followed by in vivo functional assays. The inhibitory effects of macrophages on stromal cells may be explained by their potent production of inflammatory cytokines such as CXCL2, CCL3, and complement factor (C1q) confirmed by protein immunoassay of culture supernatant, as well as the differential contribution of pre-osteoblasts to the stromal cell population. This study highlights the functional diversity of stromal cells depending on the microenvironment of origin while addressing a critical limitation of murine ex vivo systems. Our robust culture system enables the study of isolated stromal cells function as well as the impact of stromal cells-macrophage crosstalk.
    Keywords:  ex vivo co-culture system; macrophage-stromal cell crosstalk; monocyte/macrophage; stromal cells; supporting effect of hematopoietic cells
    DOI:  https://doi.org/10.1093/jbmrpl/ziaf047
  6. Dev Cell. 2025 Apr 27. pii: S1534-5807(25)00210-2. [Epub ahead of print]
    Paraoxonase-like APMAP maintains endoplasmic-reticulum-associated lipid and lipoprotein homeostasis.
    Blessy Paul, Holly Merta, Rupali Ugrankar-Banerjee, Monica R Hensley, Son Tran, Goncalo Dias do Vale, Lauren Zacherias, Charles K Hewett, Jeffrey G McDonald, Joan Font-Burgada, Thomas P Mathews, Steven A Farber, W Mike Henne.
      Oxidative stress perturbs lipid homeostasis and contributes to metabolic diseases. Though ignored when compared with mitochondrial oxidation, the endoplasmic reticulum (ER) generates reactive oxygen species requiring antioxidant quality control. Using multi-organismal profiling featuring Drosophila, zebrafish, and mammalian hepatocytes, here we characterize the paraoxonase-like C20orf3/adipocyte plasma-membrane-associated protein (APMAP) as an ER-localized antioxidant that suppresses ER lipid oxidation to safeguard ER function. APMAP-depleted cells exhibit defective ER morphology, ER stress, and lipid peroxidation dependent on ER-oxidoreductase 1α (ERO1A), as well as sensitivity to ferroptosis and defects in ApoB-lipoprotein homeostasis. Similarly, organismal APMAP depletion in Drosophila and zebrafish perturbs ApoB-lipoprotein homeostasis. Strikingly, APMAP loss is rescued with chemical antioxidant N-acetyl-cysteine (NAC). Lipidomics identifies that APMAP loss elevates phospholipid peroxidation and boosts ceramides-signatures of lipid stress. Collectively, we propose that APMAP is an ER-localized antioxidant that promotes lipid and lipoprotein homeostasis in the ER network.
    Keywords:  ER; PON; ceramide; endoplasmic reticulum; lipoprotein; paraoxonase; redox homeostasis
    DOI:  https://doi.org/10.1016/j.devcel.2025.04.008
  7. Haematologica. 2025 May 08.
    Targeting leukemic stem cell dormancy in NPM1c/FLT3-ITD-driven acute myeloid leukemia.
    Patrick Stelmach.
      Not available.
    DOI:  https://doi.org/10.3324/haematol.2025.287644
  8. Nat Commun. 2025 May 06. 16(1): 4214
    m6A/IGF2BP3-driven serine biosynthesis fuels AML stemness and metabolic vulnerability.
    Feng Huang, Yushuai Wang, Xiuxin Zhang, Weiwei Gao, Jingwen Li, Ying Yang, Hongjie Mo, Emily Prince, Yifei Long, Jiacheng Hu, Chuang Jiang, Yalin Kang, Zhenhua Chen, Yueh-Chiang Hu, Chengwu Zeng, Lu Yang, Chun-Wei Chen, Jianjun Chen, Huilin Huang, Hengyou Weng.
      Metabolic reprogramming of amino acids represents a vulnerability in cancer cells, yet the mechanisms underlying serine metabolism in acute myeloid leukemia (AML) and leukemia stem/initiating cells (LSCs/LICs) remain unclear. Here, we identify RNA N6-methyladenosine (m6A) modification as a key regulator of serine biosynthesis in AML. Using a CRISPR/Cas9 screen, we find that depletion of m6A regulators IGF2BP3 or METTL14 sensitizes AML cells to serine and glycine (SG) deprivation. IGF2BP3 recognizies m6A on mRNAs of key serine synthesis pathway (SSP) genes (e.g., ATF4, PHGDH, PSAT1), stabilizing these transcripts and sustaining serine production to meet the high metabolic demand of AML cells and LSCs/LICs. IGF2BP3 silencing combined with dietary SG restriction potently inhibits AML in vitro and in vivo, while its deletion spares normal hematopoiesis. Our findings reveal the critical role of m6A modification in the serine metabolic vulnerability of AML and highlight the IGF2BP3/m6A/SSP axis as a promising therapeutic target.
    DOI:  https://doi.org/10.1038/s41467-025-58966-1
  9. Sci Transl Med. 2025 May 07. 17(797): eadr1471
    Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias.
    Meenakshi Venkatasubramanian, Leya Schwartz, Nandini Ramachandra, Joshua Bennett, Krithika R Subramanian, Xiaoting Chen, Shanisha Gordon-Mitchell, Ariel Fromowitz, Kith Pradhan, David Shechter, Srabani Sahu, Diane Heiser, Peggy Scherle, Kashish Chetal, Aishwarya Kulkarni, Davy Lee, Jeff Zhou, Kasiani C Myers, Elizabeth Tseng, Matthew T Weirauch, H Leighton Grimes, Daniel T Starczynowski, Amit Verma, Nathan Salomonis.
      The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations remains poorly understood. Prompted by the finding that splicing uniquely resolved genetic subtypes of cancer, we developed an unsupervised computational workflow called OncoSplice to comprehensively define tumor molecular landscapes. In adult and pediatric acute myeloid leukemia (AML), OncoSplice identified the spectrum of driver genetics from splicing profiles alone, defined more than a dozen previously unreported molecular subtypes recurrent across AML cohorts, and discovered a dominant splicing subtype that partially phenocopies U2AF1-mutant splicing. Although pediatric leukemias lack splicing factor mutations, this U2AF1-like subtype similarly spanned pediatric and adult AML genetics and consistently predicted poor prognosis. Using long-read single-cell RNA sequencing, we confirmed that discovered U2AF1-like splicing was shared across cell states, co-opted a healthy circadian gene program, was stable through relapse, and induced a leukemic stem cell program. Pharmacological inhibition of an implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia missplicing and inhibited leukemic cell growth. Finally, genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treatment, blocked leukemia development in xenograft models and induced differentiation. This work suggests that broad splicing dysregulation, in the absence of select mutations, is a therapeutic target in heterogeneous leukemias.
    DOI:  https://doi.org/10.1126/scitranslmed.adr1471
  10. Cell Rep. 2025 May 07. pii: S2211-1247(25)00432-2. [Epub ahead of print]44(5): 115661
    The m5C methyltransferase NSUN2 promotes progression of acute myeloid leukemia by regulating serine metabolism.
    Songyu Li, Ya Liu, Xiang Wu, Minjia Pan, Hongxia Zhao, Yunguang Hong, Qinghua Zhang, Shushu Hu, Aorong Ouyang, Guangru Li, Minhui Wu, Shanshan Fan, Zhirong Jia, Shanchao Zhao, Guocai Wu, Xiangwei Gao, Zhigang Yang, Zhanghui Chen.
      Acute myeloid leukemia (AML) is one of the most prevalent heterogeneous hematologic malignancies with a complicated etiology. RNA post-transcriptional modifications have been linked to the incidence and progression of AML, while the detailed mechanism remains to be elucidated. In this study, we find that NOP2/Sun domain family member 2 (NSUN2), a methyltransferase of 5-methylcytosine (m5C) RNA methylation, is upregulated in AML and predicts a poor prognosis for patients with AML. Knockdown of NSUN2 in AML cells inhibits proliferation and colony formation and promotes apoptosis. Depletion of NSUN2 in AML mice reduces the tumor burden and prolongs survival. Mechanistically, NSUN2 promotes the expression of phosphoglycerate dehydrogenase (PHGDH) and serine hydroxymethyltransferase 2 (SHMT2), two key enzymes in the serine/glycine biosynthesis pathway, by stabilizing the corresponding mRNAs through regulation of m5C modifications. Overall, our findings demonstrate a critical role of NSUN2 in AML development and highlight the therapeutic potential of targeting the NSUN2/m5C axis for the treatment of this cancer.
    Keywords:  5-methylcytosine; AML; Acute myeloid leukemia; CP: Cancer; CP: Metabolism; NOP2/Sun RNA methyltransferase 2; NSUN2; m(5)C; serine metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2025.115661
  11. J Clin Invest. 2025 May 08. pii: e181394. [Epub ahead of print]
    PPIL2 is a target of the JAK2/STAT5 pathway and promotes myeloproliferation via p53-mediated degradation.
    Pan Wang, Xu Han, Kehan Ren, Ermin Li, Honghao Bi, Inci Aydemir, Madina Sukhanova, Yijie Liu, Jing Yang, Peng Ji.
      The activated JAK2/STAT pathway is characteristic of myeloproliferative neoplasms (MPNs). Pleckstrin-2 (PLEK2) signalosome is downstream of the JAK2/STAT5 pathway and plays an important role in MPN development. The detailed molecular composition of this signalosome is unclear. Here, we revealed peptidylprolyl isomerase-like 2 (PPIL2) as a critical component of the complex in regulating human and murine erythropoiesis. PPIL2 was a direct target of STAT5 and was upregulated in MPN patients and a Jak2V617F MPN mouse model. Mechanistically, PPIL2 interacted with and catalyzed p53 polyubiquitination and proteasome-mediated degradation to promote cell growth. Ppil2 deficiency, or inhibition by cyclosporin A, led to a marked upregulation of p53 in vivo and ameliorated myeloproliferative phenotypes in Jak2V617F mice. Cyclosporin A also markedly reduced JAK2 mutated erythroid and myeloid proliferation in an induced pluripotent stem cell-derived human bone marrow organoid model. Our findings revealed PPIL2 as a critical component of the PLEK2 signalosome in driving MPN pathogenesis through negatively regulating p53, thus providing a target and an opportunity for drug repurposing by using cyclosporin A to treat MPNs.
    Keywords:  Bone marrow; Cancer; Cell biology; Hematology
    DOI:  https://doi.org/10.1172/JCI181394
  12. Nature. 2025 May 06.
    Molecular basis of SIFI activity in the integrated stress response.
    Zhi Yang, Diane L Haakonsen, Michael Heider, Samuel R Witus, Alex Zelter, Tobias Beschauner, Michael J MacCoss, Michael Rapé.
      Chronic stress response activation impairs cell survival and causes devastating degenerative di-seases 1-3. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase SIFI, to terminate stress response signaling and ensure cellular homeostasis 4. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here, we combine cryo-electron microscopy of endogenous SIFI with AlphaFold modeling and biochemical analyses to report the structural and mechanistic basis of integrated stress response silencing. SIFI detects both stress-indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and hence allows a single enzyme to monitor and, if needed, modulate a complex cellular state.
    DOI:  https://doi.org/10.1038/s41586-025-09074-z
  13. Nat Commun. 2025 May 07. 16(1): 4243
    p97/VCP is required for piecemeal autophagy of aggresomes.
    Maria Körner, Paul Müller, Hirak Das, Felix Kraus, Timo Pfeuffer, Sven Spielhaupter, Silke Oeljeklaus, Christina Schülein-Völk, J Wade Harper, Bettina Warscheid, Alexander Buchberger.
      Metazoan cells adapt to the exhaustion of protein quality control (PQC) systems by sequestering aggregation-prone proteins in large, pericentriolar structures termed aggresomes. Defects in both aggresome formation and clearance affect proteostasis and have been linked to neurodegenerative diseases, but aggresome clearance pathways are still underexplored. Here we show that aggresomes comprising endogenous proteins are cleared via selective autophagy requiring the cargo receptor TAX1BP1. TAX1BP1 proximitomes reveal the presence of various PQC systems at aggresomes, including Hsp70 chaperones, the 26S proteasome, and the ubiquitin-selective unfoldase p97/VCP. While Hsp70 and p97/VCP with its cofactors UFD1-NPL4 and FAF1 play key roles in aggresome disassembly, the 26S proteasome is dispensable. We identify aggresomal client proteins that are degraded via different routes, in part in a p97/VCP-dependent manner via aggrephagy. Upon acute inhibition of p97/VCP, aggresomes fail to disintegrate and cannot be incorporated into autophagosomes despite the presence of factors critical for aggrephagosome formation, including p62/SQSTM1, TAX1BP1, and WIPI2. We conclude that the p97/VCP-mediated removal of ubiquitylated aggresomal clients is essential for the disintegration and subsequent piecemeal autophagy of aggresomes.
    DOI:  https://doi.org/10.1038/s41467-025-59556-x
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