bims-scepro 2026-10-18 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2026–10–18
twenty-six papers selected by
William Grey, University of York

Single-cell CRISPR screen maps epigenetic regulators of lineage specification and malignancies in human HSPCs.
Molecular Consequences and Targeting of PPM1D Overexpression in Myeloproliferative Neoplasms.
Ambient oxygen disrupts amino acid homeostasis and impairs human hematopoietic stem and progenitor cell engraftment.
Megakaryopoiesis and its dysregulation in paediatric acute megakaryoblastic leukaemia.
Perinatal nicotine exposure disrupts hematopoietic stem cell development and elevates influenza severity in adulthood.
TNFα drives platelet hyperreactivity and thromboinflammation through regulation of hematopoietic stem and progenitor cells.
Inhibition of PHB2/PINK1-mediated mitophagy potentiates venetoclax activity in acute myeloid leukemia.
Elp1 is required for myeloid differentiation and brain repopulation.
Bone marrow ECM-based vascular niche modeling for the evaluation of HSC/leukemic cell interaction with niche cells.
Hematopoietic stem cell culture comes of age.
Stem cell factor acts locally in the bone marrow to promote stem and progenitor cell maintenance.
Cord blood-derived natural killer cells engineered with a novel, highaffinity chimeric antigen receptor can eliminate acute myeloid leukemia cells with minimal C-type lectin-like molecule-1 expression.
Nicotinic acid restriction potentiates NAMPT inhibition in acute myeloid leukemia xenograft models.
Current understanding and new promises of umbilical cord blood in emerging clinical applications.
Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response.
Chemogenetic ubiquitin E1 inhibitor TAK-243 CRISPR screen uncovers HAPSTR1/HUWE1 axis in chromatin proteostasis and cell cycle control.
Combining the Telomerase Inhibitor Imetelstat with the BCL-2 Inhibitor Venetoclax Enhances Apoptosis and Improves Survival in Acute Myeloid Leukemia Cellular and Animal Models.
Controller for Maintaining Hematopoietic Stem Cell Stemness: Genetic Information Transmission.
TET2 loss triggers ssDNA gap accumulation and heightened PARP inhibitor sensitivity.
Dynamic protein phosphorylation shapes mitochondrial catalysis, import, and architecture.
An Open Infrastructure for Mass Spectrometry Data in R.
Rank Normalization Enables Cross Pathway Comparison in Degradation Resolved Proteome Turnover Analysis.
Fibroblast growth factor receptor-signaling confers stroma-mediated drug resistance in malignant B cells.
An Ex Vivo 3D Co-Culture Model of the Bone Marrow Niche Better Predicts Clinically Relevant Epigenetic Target Modulation to Improve Immunotherapy in Multiple Myeloma.
Aging as a Potential Modulator of Extramedullary Hematopoiesis: A Hypothesis-Generating Niche-HSPC Competence-Trigger Model.
The SKP2-Substrate Axis in Hematological Malignancies: Mechanisms of Oncogenesis and Opportunities for Targeted Therapy.

Cell Stem Cell. 2026 Oct 13. pii: S1934-5909(26)00347-4. [Epub ahead of print]

Single-cell CRISPR screen maps epigenetic regulators of lineage specification and malignancies in human HSPCs.

Shiru Yuan, Shangda Yang, Yaojin Huang, Baowei Ma, Qian Wu, Xinghui Zhang, Tong Yin, Lianting Chen, Baixuan Zhang, Guohuan Sun, Yicheng He, Honglin Duan, Linping Hu, Sha Hao, Hui Cheng, Jun Wei, Tao Cheng.

  Mapping how genetic perturbations influence cell fate is key to understanding human development and disease. Here, we developed a massively parallel single-cell CRISPR (scCRISPR) screening platform in primary human hematopoietic stem and progenitor cells (HSPCs), profiling 322 regulators across 172,382 single-perturbed cells. The resulting multi-layered regulatory framework captured known associations and enabled functional annotation of regulator-phenotype relationships. Specifically, our atlas revealed that regulators acted within perturbation clusters to govern distinct gene programs that shaped cell fate. As proof of concept, we illustrated several examples. SMYD3 emerged as a negative regulator of long-term regenerative capacity. Analysis of lineage output further identified KMT5B, TRIM24, SETD7, and NSD3 as regulators associated with lineage-biased outputs. Finally, integration with clinical datasets identified PRDM10 as a candidate dependency in acute myeloid leukemia (AML). This work establishes a scalable functional genomics platform in a primary human stem cell system.

Keywords:  acute myeloid leukemia; epigenetic regulation; functional genomics; hematopoietic differentiation; hematopoietic stem and progenitor cells; human hematopoiesis; lineage output; single-cell CRISPR screening

DOI:  https://doi.org/10.1016/j.stem.2026.09.005
Blood. 2026 Oct 13. pii: blood.2025030377. [Epub ahead of print]

Molecular Consequences and Targeting of PPM1D Overexpression in Myeloproliferative Neoplasms.

Md Babu Mia, Christoph Schaniel, Cara Clementelli, Sarah Elisabeth Haines, Malgorzata Olszewska, JoAnn Arandela, Sebastian Elghaity-Beckley, Sophie Klingborg, Zinedine Hoque, Ayman Mohammad, Shwetha Hara Sridhar, Brianna Kelly, Xiaoli Wang, Emmanuel Olivier, Alan H Shih, Blake T Langlais, Allison Cote, Noushin Farnoud, Raajit K Rampal, Duke Butterfield, Amylou C Dueck, Min Lu, Kristin G Beaumont, Robert Sebra, John O Mascarenhas, Eirini P Papapetrou, Ronald Hoffman, Bridget K Marcellino.

Phosphatase Mg2+/Mn2+ dependent 1D protein (PPM1D) is a serine threonine phosphatase known to regulate oncogenic pathways. PPM1D mutations are enriched in therapy-related MDS and AML, but the role of PPM1D in myeloproliferative neoplasms (MPN) remains largely unexplored. By sequencing 519 MPN patients, we detected activating PPM1D mutations in 3.1% of them. Importantly, PPM1D was overexpressed in hematopoietic stem and progenitor cells (HSPCs) in most PPM1D wild-type (WT) MPN cases. To elucidate the impact of PPM1D mutations on MPN HSPCs, we generated isogenic JAK2V617F+/PPM1D-WT and JAK2V617F+/PPM1D mutant (MUT) induced pluripotent stem cell (iPSC) lines from a MPN patient. Single-cell RNA-sequencing (scRNA-seq) of iPSC derived HSPCs revealed altered TP53, DNA damage response and cell cycle regulation. scRNA-seq analysis of primary PPM1D-MUT MPN patient mononuclear cells (MNCs) further confirmed upregulation of MYC, mTORC1, OXPHOS, JAK/STAT, and NF-κB pathways and corresponding genes in HSCs. The allosteric PPM1D inhibitor (PPM1Di) GSK2830371 preferentially inhibited colony formation in myelofibrosis (MF) samples. Combination treatment of GSK2830371 with low dose inhibition of HDM2, a negative regulator of p53, significantly improved targeting of JAK2V617F+ HSPCs, while sparing normal HSPCs. Single-cell mutational and protein analysis of a clonally complex MF patient sample treated with this combination strategy revealed reduced mutated clones and increased WT clones by >4-fold. Dual PPM1D and HDM2 targeting also significantly decreased leukemic burden in a xenograft MPN model. These findings support PPM1D as a critical MPN HSPCs regulator and support dual PPM1D/HDM2 inhibition as a treatment strategy for MF patients.

DOI: https://doi.org/10.1182/blood.2025030377
Blood. 2026 Oct 13. pii: blood.2026034288. [Epub ahead of print]

Ambient oxygen disrupts amino acid homeostasis and impairs human hematopoietic stem and progenitor cell engraftment.

Xuepeng Wang, Sankalp Srivastava, Rahul Kanumuri, Ramesh Kumar, Minghua Zhong, Ji Zhang, Reuben Kapur.

Hematopoietic stem cell transplantation is limited not only by donor cell number and recipient conditioning, but also by loss of stem-cell fitness during collection and processing. Hematopoietic stem and progenitor cells normally reside in a physiologically hypoxic marrow environment, yet routine ex vivo handling exposes them to ambient oxygen outside this niche. Although ambient oxygen exposure during ex vivo handling impairs hematopoietic stem cell (HSC) function, the metabolic basis for this effect remains incompletely defined. Using hypoxic handling as a physiologic reference, we examined whether functionally relevant consequences of ambient oxygen exposure remain modifiable in human CD34+ cells during ex vivo handling. Quantitative LC-MS profiling revealed that ambient oxygen exposure rapidly increased intracellular amino acids, including branched-chain amino acids, together with activation of nutrient-sensing pathways. This metabolic shift was associated with increased mTORC1 signaling, attenuation of lysosomal programs, and impaired primary and secondary engraftment. Complementary single-cell analyses supported a coordinated transition toward nutrient-activated states under ambient oxygen, whereas hypoxia preserved relative metabolic restraint. Transient restriction of essential amino acids or branched-chain amino acids during ex vivo handling restored lysosomal programs and improved engraftment of normoxia-handled human CD34+ cells. Pharmacologic LAT1 inhibition similarly improved engraftment. Together, these findings identify disruption of amino acid homeostasis as a previously underappreciated consequence of ambient oxygen exposure during routine ex vivo handling and demonstrate that a functionally relevant component of this injury remains modifiable after exposure to improve human HSPC engraftment.

DOI: https://doi.org/10.1182/blood.2026034288
Leuk Res. 2026 Oct 13. pii: S0145-2126(26)00187-6. [Epub ahead of print]171 108343

Megakaryopoiesis and its dysregulation in paediatric acute megakaryoblastic leukaemia.

Faakhir Butt, Marry Lin, Jacqueline Cloos, Bianca F Goemans, Tom Reuvekamp.

  Megakaryocytes (Mks) are haematopoietic cells responsible for platelet production. They arise from haematopoietic stem cells (HSCs) through a differentiation process known as megakaryopoiesis, which is classically viewed as occurring in a stepwise manner. However, recent studies have challenged this model, suggesting an alternative direct differentiation route producing functionally distinct Mk subtypes. Understanding this process is important, as dysregulation can lead to the development of diseases such as paediatric acute megakaryoblastic leukaemia (AMKL). This is a rare subtype of acute myeloid leukaemia (AML) that has a significantly worse prognosis compared to other AML subtypes. Accurate classification of AML increasingly relies on an integrated genetic and immunophenotypic diagnostic pathway. The poor prognosis of AML is largely driven by the presence of therapy-resistant leukaemia stem cells (LSCs). Furthermore, LSCs are often resistant to targeted therapies like the BCL-2 inhibitor venetoclax, yet they show a distinct dependency on other proteins within the same apoptosis pathway, notably BCL-XL. Therefore, this review aims to summarise current knowledge on normal megakaryopoiesis and explore how its dysregulation contributes to LSC emergence in paediatric AMKL, while also highlighting the therapeutic implications of both BCL-XL dependency and emerging subtype-specific therapies.

Keywords:  Acute megakaryocytic leukaemia; Leukaemia stem cells; Megakaryocytes; Megakaryopoiesis

DOI:  https://doi.org/10.1016/j.leukres.2026.108343
Stem Cell Reports. 2026 Oct 15. pii: S2213-6711(26)00329-2. [Epub ahead of print] 103118

Perinatal nicotine exposure disrupts hematopoietic stem cell development and elevates influenza severity in adulthood.

M G E Rommel, T Cool, A Rodriguez Y Baena, S Saini, P Medina, C Mattingly, E Bachinsky, S Chattopadhyaya, B A Manso, S Rajendiran, A K Worthington, D M Poscablo, A Deguzman, P Q Wimer, I M Voelker, T Berger-Cahn, L Langroudi, A F Svendsen, A Shariati, S Carpenter, D F Boyd, E C Forsberg.

  Developmental exposures profoundly shape lifelong health by altering disease resilience later in life. One potential cause of increased disease susceptibility is an altered immune system, originating in epigenetically maladaptive hematopoietic stem cells (HSCs). Here, we establish perinatal nicotine exposure (PNE) as a mouse model of developmental maladaptive immunity, wherein early-life environmental insults permanently alter HSCs. We show that PNE selectively disrupts the establishment of HSCs and tissue-resident, but not circulating, immune cells. Remarkably, the specific decrease of HSCs and lung-resident immune cells persists into adulthood. Single-cell transcriptomics revealed durable molecular reprogramming of adult PNE HSCs, with inverse regulation of positive trained immunity signatures. Functionally, adult PNE offspring challenged with respiratory virus exhibit exacerbated immune maladaptation, marked by increased weight loss, deteriorated lung pathology, hyper-permeability of pulmonary vasculature, tissue-resident macrophage depletion, and exaggerated neutrophil recruitment. Together, our findings establish that PNE imprints durable maladaptive immunity involving changes in HSCs and their progeny, suggesting a hematopoietic origin for the PNE-induced respiratory vulnerability.

Keywords:  fetal and neonatal hematopoiesis; hematopoietic stem cell; influenza A virus infection; maldapative trained immunity; maternal smoking; perinatal nicotine exposure; respiratory disease susceptibility and severity; tissue-resident macrophages; transcriptional memory

DOI:  https://doi.org/10.1016/j.stemcr.2026.103118
bioRxiv. 2026 Sep 29. pii: 2026.09.28.755049. [Epub ahead of print]

TNFα drives platelet hyperreactivity and thromboinflammation through regulation of hematopoietic stem and progenitor cells.

Joshua I Siner, Molly Brakhane, Kimsey Platten, Abigail Ajanel, Ei Thanda Tun, Lilian Antunes Heck, Thomas Girard, Nina Lasky, Mary Fulbright, Chris Letson, Yoon-A Kang, Craig N Morrel, Stephen T Oh, Jorge Di Paola.

TNFα is the primary age-related cytokine responsible for hyperreactive platelet formation. In mouse models, increased TNFα induced abnormal megakaryocyte development and platelet activity. Here, we extend these findings to demonstrate that TNFα drives this thrombotic phenotype through expansion of the hematopoietic stem and progenitor cell (HSPCs) compartment. Using HSPC-specific TNFα receptor labeling and single cell RNA sequencing, we found that TNFα receptors are absent from megakaryocytes and their progenitors (MkPs) indicating that TNFα does not directly act on these cells. Chronic TNFα exposure expanded HSPCs in the bone marrow and extramedullary tissues - and these expanded HSPCs retained functional repopulation capacity. Using species-specificity TNFα receptor activation, we further demonstrate that TNFαR1 signaling is sufficient to induce platelet hyperreactivity independent of HSPC expansion. Unlike emergency hematopoiesis, chronic TNFα promoted megakaryopoiesis through the canonical hematopoietic hierarchy as demonstrated by lineage-tracing studies. Mechanistically, chronic TNFα induced a distinct transcriptional program in single cell RNA sequencing of HSPCs and megakaryocytes. Together, these findings establish that chronic TNFα promotes hyperreactive platelet formation not through direct effects on megakaryocytes or MkPs but by expanding and transcriptionally reprogramming HSPCs, thereby imprinting a TNFα dependent program that persists through megakaryopoiesis and ultimately produces hyperreactive platelets.
Key Points: Chronic TNFα exposure drives HSC expansion and myeloid biasing of progenitors.TNFα regulates platelet hyperreactivity by signaling through HSPCs, not Mks.

DOI: https://doi.org/10.64898/2026.09.28.755049
Leukemia. 2026 Oct 13.

Inhibition of PHB2/PINK1-mediated mitophagy potentiates venetoclax activity in acute myeloid leukemia.

Romain Vazquez, Maxime Sajot, Jad Nasrallah, Rudy Birsen, Ismaël Boussaid, Morgane Plevenage, Zubaidan Tuerdi, Axelle Guedon, Lilia Cantero Aguilar, Tony Huynh, Natacha Johnson, Chloé Friedrich, Eric Grignano, Justine Decroocq, Lise Willems, Carole Almire, Marie-Clotilde Alves-Guerra, Evelyne Lauret, Yannick Simoni, Michaela Fontenay, Olivier Kosmider, Didier Bouscary, Clement Larrue, Nicolas Chapuis.

Acute myeloid leukemia (AML) cells are highly dependent on mitochondrial activity for survival, with this metabolic reliance driven in part by BCL-2, which is therapeutically targeted by venetoclax-based therapies. The regulation of mitochondrial dynamics in leukemic cells is therefore essential for maintaining mitochondrial homeostasis. However, the mechanisms that enable selective degradation of damaged mitochondria (mitophagy) are still poorly understood in AML. In this study, we sought to elucidate the role of PTEN-induced putative kinase 1 (PINK1), a key sensor of mitochondrial stress, in regulating mitophagy in leukemic cells. Our results identified PINK1 as a central modulator of mitophagy. Genetic depletion of PINK1 reduced both basal and stress-induced mitophagy, leading to mitochondria accumulation and functional impairment. Additionally, we discovered that PINK1 stabilization during mitochondrial stress is regulated by Prohibitin 2 (PHB2), and that depletion or inhibition of PHB2 mirrored the biological effects of PINK1 loss. Notably, both genetic depletion of PINK1 or PHB2, as well as pharmacological inhibition of PHB2, significantly increased AML cell sensitivity to venetoclax both in vitro and in vivo. Together, these findings highlight the potential of targeting the PHB2/PINK1 signalling pathway to improve the efficacy of venetoclax-based therapies in AML by disrupting the mitophagy process.

DOI: https://doi.org/10.1038/s41375-026-03160-5
Nature. 2026 Oct 14.

Elp1 is required for myeloid differentiation and brain repopulation.

Marius Marc-Daniel Mader, Wanhua Li, Alexa Scavetti, Yongjin Yoo, Gernot Neumayer, Katie Han, Yohei Shibuya, Michael Haney, Tony Wyss-Coray, Lynn George, Frances Lefcort, Michael Bassik, Hiromitsu Nakauchi, Adam C Wilkinson, Marius Wernig.

Haematopoietic stem and progenitor cell (HSPC) transplantation-mediated replacement of microglia-the reconstitution of the central nervous system microglial niche with donor-derived myeloid cells-represents a promising strategy for brain cell therapies1-7. However, the cell-intrinsic molecular regulators of HSPC-derived myeloid lineage commitment in the brain have remained largely uncharacterized. This is partially because the scarcity of primary HSPCs has rendered large-scale genetic interrogation intractable. Here we explored whether ex vivo expansion of primary cultured HSPCs (cHSPCs) enables unbiased genetic interrogation of haematopoietic differentiation. We established that cHSPCs can be genetically manipulated and readily differentiate into myeloid cells and repopulate microglia niches of the brain after transplantation. Moreover, primary neonatal astrocytes contained strong signals to induce myeloid specification of cHSPCs in vitro. To identify genes that regulate glia-induced myeloid differentiation, we successfully screened around 20,000 individual genetic perturbations and characterized genes involved in the regulation of cell signalling, cell cycle, mitochondrial function and protein translation. Among these genes was elongator acetyltransferase complex subunit 1 (Elp1), which suppressed the unfolded protein response during myeloid specification and was essential for the generation but not maintenance of myeloid cells. Our work establishes a platform to investigate the molecular mechanisms of brain myeloid biology.

DOI: https://doi.org/10.1038/s41586-026-11112-3
Biomater Adv. 2026 Oct 05. pii: S2772-9508(26)00524-8. [Epub ahead of print]191 215224

Bone marrow ECM-based vascular niche modeling for the evaluation of HSC/leukemic cell interaction with niche cells.

Yutian Huang, Pei Peng, Tongtong Huang, Yulu Ying, Cao Yao, Siying Cai, Pujie An, Linhan Ye, Wei Li, Yang Xiong, Mancang Gu, Chaofeng Mu, Guilin Cheng.

  Bone marrow vascular niche regulates both hematopoiesis and hematopoietic disorders, including acute and chronic leukemia. However, it is still not fully understood at the structural and functional levels owing to its inaccessibility in situ. Here, a biomimetic bovine decellularized bone marrow extracellular matrix (dbECM) mixed hydrogel was developed. Proteomics validation confirmed its retention of bone marrow-specific ECM components. The mechanical properties and microstructure of the mixed hydrogel provided a biomimetic platform that integrates biochemical and physical cues for niche functional studies. Vascular networks with multilayered murine C166 endothelial cells (ECs) and mesenchymal stromal cells (MSCs: C3H10T1/2 cells or primary murine bone marrow-derived MSCs) were successfully formed in the mixed hydrogel scaffold. This murine vascular niche model can be utilized to unravel the dynamic events of Lin-c-Kit+ hematopoietic cells /leukemic cell interaction with niche components. MSCs mainly contributed to hematopoietic stem cell preservation, whereas the ECM served as permissive scaffolding but did not directly instruct stemness maintenance. The dynamic disruption of leukemic cells to the vascular integrity was recapitulated in this vascular niche model. Even though leukemic cells adhere to both ECs and MSCs, their adhesion to MSCs was the main niche factor maintaining leukemic stem cells and leading to chemoresistance in the bone marrow. Collectively, this bioengineered short-term static niche delineates the specific roles of dbECM as a structural foundation, ECs as spatial organizers, and MSCs as functional regulators, advancing our understanding of niche-directed physiology and pathology and accelerating the development of microenvironment-targeted therapies.

Keywords:  Bone marrow extracellular matrix; Chemotherapeutic resistance; Endothelial cells; Hematopoietic stem cells; Leukemic stem cells; Mesenchymal stromal cells

DOI:  https://doi.org/10.1016/j.bioadv.2026.215224
Blood. 2026 Oct 15. 148(16): 1943-1945

Hematopoietic stem cell culture comes of age.

Adam C Wilkinson, Berthold Göttgens.

DOI: https://doi.org/10.1182/blood.2026035565
bioRxiv. 2026 Sep 29. pii: 2026.09.28.755094. [Epub ahead of print]

Stem cell factor acts locally in the bone marrow to promote stem and progenitor cell maintenance.

Maria Angelica Freitas-Cortez, Stefano Comazzetto, Xiang Gao, Bo Shen, Lei Ding, Zhiyu Zhao, Sean J Morrison.

Stem cell factor (SCF) from Leptin Receptor-expressing (LepR + ) mesenchymal stromal cells and endothelial cells is required for hematopoietic stem and progenitor cell maintenance in bone marrow. Consistent with this, Scf is highly expressed by LepR + cells and at lower levels by endothelial cells in bone marrow. However, endothelial cells outside the bone marrow produce circulating SCF, raising the question of whether the SCF that promotes stem and progenitor cell maintenance is produced inside or outside bone marrow. We found that Scf deletion in spleen and liver endothelial cells reduces SCF levels in the blood without affecting stem or progenitor numbers in the bone marrow. Moreover, deletion of Scf from mesenchymal cells in the long bones, but not vertebrae, of Prx1 Cre ; Scf fl/fl mice depletes stem and progenitor cells in long bones but not vertebrae. SCF thus acts locally within the bones in which it is made to promote stem and progenitor cell maintenance.
Key Points: Scf deletion in endothelial cells outside of BM reduces SCF levels in blood without affecting stem or progenitor cell frequencies in BM Scf deletion from mesenchymal cells in long bones, but not vertebrae, depletes stem and progenitor cells in long bones but not vertebrae.

DOI: https://doi.org/10.64898/2026.09.28.755094
Haematologica. 2026 Oct 15.

Cord blood-derived natural killer cells engineered with a novel, highaffinity chimeric antigen receptor can eliminate acute myeloid leukemia cells with minimal C-type lectin-like molecule-1 expression.

Makiko Suga, Shuhei Kida, Yo Mizutani, Yosuke Kogue, Yuta Yamaguchi, Shunya Ikeda, Ryuhei Kawamoto, Mana Tachikawa, Tsubasa Seto, Hiroto Takekawa, Yuto Maehara, Kumi Shibata, Kazuhito Tsutsumi, Hiraku Murakami, Emiko Mizuta, Kyoko Yoshihara, Satoshi Yoshihara, Hirohisa Nakamae, Takafumi Nakao, Megumu Inoue, Shuji Ueda, Satoru Kosugi, Yasutaka Ueda, Hisashi Kato, Shinsuke Kusakabe, Hidenori Kasahara, Akihisa Hino, Jiro Fujita, Tomoaki Ueda, Michiko Ichii, Kentaro Fukushima, Naoki Hosen.

CAR NK cell therapy is expected to be developed to treat acute myeloid leukemia (AML). C-type lectin-like molecule 1 (CLL-1) is a candidate target. However, AML cells with minimal CLL-1 expression (CLL-1dim) may not be eliminated by CAR NK cells. Here we demonstrate that cord blood (CB)-derived NK cells transduced with a novel high-affinity CAR that recognizes CLL-1 can eliminate CLL-1dim AML cells. A newly established anti- CLL-1 monoclonal antibody (mAb) designated as 2-23 exhibits a higher affinity for CLL- 1 than the widely used anti-CLL-1 mAb M26. CB-derived NK cells transduced with a CAR derived from 2-23, but not M26, killed CLL-1dim AML cells in vitro. Additionally, treatment with 2-23 CAR NK cells, but not M26 CAR NK cells, significantly enhanced the survival of the mice transplanted with CLL-1dim AML cells in vivo. Furthermore, in AML patient-derived xenograft models, the 2-23 CAR NK cells expanded robustly, persisted, and eradicated AML cells.

DOI: https://doi.org/10.3324/haematol.2026.301327
Cancer Res Commun. 2026 Oct 12.

Nicotinic acid restriction potentiates NAMPT inhibition in acute myeloid leukemia xenograft models.

Kyoji Tsurumi, Miyuki Nomura, Mai Ohuchi, Ryoma Kizu, Naohiko Kikuchi, Taku Sato, Mami Morita, Yoji Yamashita, Kayoko Hayashi, Tomoyoshi Soga, Yuki Sugiura, Tatsuro Fukuhara, Nobuhiro Tanuma.

NAMPT, a key enzyme in NAD biosynthesis, is a potential therapeutic target in cancer. Acute myeloid leukemia (AML) is among cancer types exhibiting high NAMPT dependence, and elevated NAMPT activity is implicated in venetoclax resistance. Thus, pharmacological NAMPT inhibitors (NAMPTi) have been developed as a promising therapeutic approach in some cancers. However, our current knowledge of in vivo factors that determine NAMPTi therapeutic efficacy is incomplete. Here, using mouse models we found that NAMPTi efficacy against AML is limited by dietary nicotinic acid (NA). Specifically, NA and nicotinic acid riboside (NAR), an NA-derived metabolite, promoted NAD biosynthesis independent of NAMPT and rescued AML cells from NAMPTi-mediated toxicity in vitro. Importantly, in AML xenograft models, dietary NA restriction, which selectively reduces circulating NAR levels, enhanced antitumor efficacy of NAMPTi and prolonged animal survival. Although the combination treatment caused transient hematological toxicity, peripheral blood cell counts largely recovered after treatment. Our findings highlight systemic NAD precursor metabolism, including NAR, as a determinant of responses to NAMPT-targeted therapies. We conclude that NA restriction may improve the therapeutic efficacy of NAMPT inhibitors in AML.

DOI: https://doi.org/10.1158/2767-9764.CRC-26-0274
Sci China Life Sci. 2026 Oct 12.

Current understanding and new promises of umbilical cord blood in emerging clinical applications.

Xinyu Feng, Yuxuan Liu, Sha Hao, Tao Cheng, Linping Hu.

  Umbilical cord blood (UCB) has become an important resource for regenerative medicine owing to its unique cellular composition, immune immaturity, and abundance of bioactive factors. Although UCB was initially applied in hematopoietic stem cell transplantation, accumulating evidence indicates that its diverse cellular and paracrine components possess broad regenerative potential. Beyond conventional hematopoietic stem cell transplantation, substantial progress has expanded the therapeutic scope of UCB to immune cell-based therapies, the treatment of genetic and metabolic disorders, and tissue repair. In this review, we focus on the biological characteristics of the key cellular and noncellular components of UCB and analyze how these properties support tissue repair, immunomodulation, and regeneration across multiple organ systems. We further summarize recent technological advances, including cell engineering, gene modification, and manufacturing technologies, that have enhanced the scalability and therapeutic potential of UCB-derived products. In addition, we highlight current challenges that limit their widespread clinical application. This review aims to provide a framework for optimizing UCB-based therapies and accelerating their clinical translation. Optimizing UCB collection, processing, and application strategies may further unlock its therapeutic potential, thereby improving clinical efficacy and expanding its applicability to a broader range of diseases.

Keywords:  cell therapy; clinical applications; gene editing; hematopoietic stem cell; immune cell; regenerative medicine; umbilical cord blood

DOI:  https://doi.org/10.1007/s11427-026-3460-2
bioRxiv. 2026 Sep 28. pii: 2026.09.25.754245. [Epub ahead of print]

Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response.

Lorena Alamillo, Thalia Paiz, Alexander Black, Matthew C Juber, Ethan M Arends, Jacob G Cox, Dominic C M Ng, Timothy A McKinsey, Maggie P Y Lam, Edward Lau.

Endoplasmic reticulum (ER) stress is associated with many human diseases, but current understanding of how ER stress responses reshape the stressed proteome over time is still emerging. Specifically, how organellar protein quality control and clearance pathways coordinate to maintain proteostasis in early and prolonged ER stress is unclear. Here we describe a spatiotemporal proteomic strategy termed simultaneous proteome localization and turnover analysis with time resolution (SPLAT-TR) to interrogate the synthesis, degradation, and localization changes of over 4,000 proteins in early (1-4 hours) and prolonged (16-24 hours) ER stress. As ER stress progresses, each time point is distinguished by distinct protein translocation and clearance regulations, coupled to differential organellar proteostasis and usage of protein degradation pathways. Mitochondria show a bimodal response, with a shift from early activation of respiratory protein towards protein quality control pathways in prolonged stress, coinciding with energetics decline. In the Golgi, the increased clearance of collagen proteins is paradoxically coupled to an increased synthesis of secretory pathway components, suggesting removal by secretion. In the ER, the proteome remodels under prolonged stress via increased synthesis of UFMylation and ER-phagy-related proteins coupled to the selective degradation of ER membrane and microdomain proteins. Inhibition of UFMylation alters ER-phagy receptor usage and synergistically induces stress-induced cell death. These results present a systematic delineation of cell compartment proteostasis under unfolded protein response and highlight the utility of SPLAT-TR to investigate time-dependent cellular events.

DOI: https://doi.org/10.64898/2026.09.25.754245
Sci Adv. 2026 Oct 16. 12(42): eaea3388

Chemogenetic ubiquitin E1 inhibitor TAK-243 CRISPR screen uncovers HAPSTR1/HUWE1 axis in chromatin proteostasis and cell cycle control.

Nila K van Overbeek, Linda Clijsters, Martina Wirth, Ilona J de Graaf, Klaas de Lint, Sidrit Uruci, Amina F A S Teunisse, Vyacheslav Akimov, Arnoud H de Ru, Maja Vukic, Idil Kirdök, Lucia Daxinger, Peter A van Veelen, Blagoy Blagoev, Martijn S Luijsterburg, Rob M F Wolthuis, Ilana Berlin, Alfred C O Vertegaal.

In this study, we sought to comprehensively map ubiquitin signaling networks at the crossroads of cellular proliferation and proteostasis, both crucial in cancer. Genome-wide CRISPR knockout screening in the presence of the ubiquitin E1 inhibitor TAK-243 identified 239 genes whose ablation sensitizes cells to ubiquitination blockade. Follow-up studies reveal a role for the nuclear protein, C16orf72/HECT, UBA, and WWE domain containing E3 ubiquitin protein ligase 1 (HUWE1)-Associated Protein modifying Stress Responses (HAPSTR1), in chromatin proteostasis and DNA replication. We show that HAPSTR1 recruits the E3 ligase HUWE1 to the chromatin, keeping the chromatin-associated proteome in check, and is itself turned over by HUWE1 during cell cycle progression. Structural modeling of the HAPSTR1/HUWE1 complex, supported by mutational analysis, demonstrates that loss of HUWE1 binding renders HAPSTR1 unable to support cellular proliferation when ubiquitin signaling is suppressed. Consequently, HAPSTR1 ablation impairs clearance of chromatin-associated proteins, triggering global transcriptional and proteostatic adaptations. Under diminished ubiquitin signaling, these adaptive mechanisms give way to replication stress and premature S phase entry, culminating in cell cycle collapse and DNA damage. Our findings uncover protein networks exhibiting synthetic lethality with ubiquitin signaling blockade and highlight vulnerabilities of actively proliferating cells to proteostatic imbalance at the chromatin.

DOI: https://doi.org/10.1126/sciadv.aea3388
J Clin Med. 2026 Sep 23. pii: 7399. [Epub ahead of print]15(19):

Combining the Telomerase Inhibitor Imetelstat with the BCL-2 Inhibitor Venetoclax Enhances Apoptosis and Improves Survival in Acute Myeloid Leukemia Cellular and Animal Models.

Fei Huang, Joshua J Rusbuldt, Leopoldo Luistro, Heidi Colton, Joseph Eid.

  Background/Objectives: Acute myeloid leukemia (AML) is a heterogeneous disease with limited treatment options. New therapies with novel mechanisms of action are needed. Telomerase and BCL-2 are overexpressed in AML and correlate with disease severity and poor prognosis, suggesting dual targeting may be beneficial. Methods: We evaluated the effect of imetelstat, a telomerase inhibitor, in combination with venetoclax, a BCL-2 inhibitor, in AML cell lines, AML patient-derived samples, and in a MOLM-13 AML xenograft model. Results: In AML cell lines and patient samples, imetelstat plus venetoclax demonstrated dose-dependent synergistic activity to induce apoptosis. Studying AML patient samples ex vivo showed the effect is preferentially in CD34+ leukemic cells, and not in lymphocytes. The synergy induced by venetoclax plus imetelstat was stronger than venetoclax plus hypomethylating agents in AML cell lines. The in vivo MOLM-13 AML xenograft model demonstrated that imetelstat plus venetoclax prolonged survival of tumor-bearing mice compared to either agent alone. Forty percent of mice in the combination group were still alive eighty days after the end of treatment, whereas all mice in the single-agent groups succumbed to disease within two weeks. Mechanisms of synergy elicited by the combination were further illustrated through reduction of hTERT expression and telomerase activity, decreases in the interaction of BCL-2 with BAX, and enhanced mitochondrial dysfunction via loss of mitochondrial membrane potential, and these led to marked increases in the intrinsic mitochondrial apoptosis pathway in AML cells. Conclusions: This study supports the clinical evaluation of imetelstat plus venetoclax for the treatment of AML in the Phase 1 IMAGINE trial (NCT07320235).

Keywords:  BCL-2; acute myeloid leukemia; apoptosis; imetelstat; mechanism of action; synergy; telomerase; venetoclax

DOI:  https://doi.org/10.3390/jcm15197399
Stem Cells Dev. 2026 Oct 14. 15473287261490008

Controller for Maintaining Hematopoietic Stem Cell Stemness: Genetic Information Transmission.

XinYu Tang, Yan Li, Yan Wang, Ruirong Xu.

  Hematopoietic stem cell (HSC) has self-renewal and multilineage differentiation capacities. They sustain lifelong homeostasis and repair of damaged tissues, serving as the core cellular foundation for long-term homeostasis and regenerative repair. Maintaining HSC stemness is essential for normal hematopoiesis; this is not a static property but a dynamically regulated process that directly governs the stable operation of regular hematopoiesis. Recent studies show that HSC quiescence, self-renewal, and lineage differentiation are coordinately controlled by multiple signaling cues. Transcription factor networks, the extracellular matrix, metabolic reprogramming, and epigenetic modifications interact to form a regulatory network that governs stemness maintenance. Under physiological conditions, these factors establish stemness homeostasis; when aberrantly remodeled, they drive diseases such as leukemia and bone marrow failure. This review summarizes the factors that modulate HSC function and stemness during genetic information transmission, and discusses their biological significance. It further elaborates on the regulatory network, compares its distinct patterns in physiological versus pathological states, and explores its translational clinical value. Ultimately, this work aims to provide basic researchers with an integrated conceptual framework and to offer feasible forward-looking strategies for clinical translation.

Keywords:  DNA replication regulation; hematopoietic stem cells; multipotency maintenance; transcriptional regulation; translational regulation

DOI:  https://doi.org/10.1177/15473287261490008
Nat Commun. 2026 09 12. pii: 10765. [Epub ahead of print]17(1):

TET2 loss triggers ssDNA gap accumulation and heightened PARP inhibitor sensitivity.

Sumedha Agashe, Nidhi Athreya, William Jacobs, Christopher T Letson, Vladislav O Sviderskiy, Celia D Rouault, Yixuan Xie, Carolina Brás-Costa, Emily Zahn, Mary Claire Kendall, Alice Meroni, Matthew Wood, Barbara Soares, Jin Shao, Maggie J Cox, Luis Francisco Zirnberger Batista, Grant A Challen, John Krais, Matthew J Walter, Stephen T Oh, Benjamin A Garcia, John Edwards, Priyanka Verma, Alessandro Vindigni.

Somatic mutations in the de novo methyltransferase DNMT3A and cytosine demethylase TET2 are common in age-related clonal hematopoiesis and hematopoietic neoplasms. TET2 mutations, unlike DNMT3A mutations, increase sensitivity to PARP inhibitors (PARPi). We find that TET2 loss, but not DNMT3A loss, alters DNA replication fork progression upon treatment with PARPi Olaparib, resulting in longer DNA replication tracts and increased DNA breaks. This reveals a new link between abnormal fork elongation and PARPi sensitivity in TET2-deficient cells. The elongated forks of TET2-deficient cells contain PRIMPOL-dependent single-stranded (ss)-DNA gaps. This phenotype is dependent on the catalytic activity of TET2 and is mitigated by TET1/3 depletion. Furthermore, TET2 loss causes an imbalance in cytosine methylation and an increase in 5hmU modifications. These modifications are processed by SMUG1, creating abasic sites, detectable via a modified DNA fiber method. A CRISPR screen identified the base excision repair nuclease APE1 as linked to increased PARPi sensitivity in TET2-deficient cells. We propose that abasic sites, skipped by PRIMPOL repriming, lead to ssDNA gaps that are converted into DNA breaks by APE1, increasing PARPi toxicity. Finally, we identify TET2 mutations as an unrecognized predictor of PARPi response in bone marrow samples from patients with myeloid malignancies.

DOI: https://doi.org/10.1038/s41467-026-77587-w
bioRxiv. 2026 Sep 29. pii: 2026.09.28.755151. [Epub ahead of print]

Dynamic protein phosphorylation shapes mitochondrial catalysis, import, and architecture.

Andrew J Smith, Patrick Forny, Sean W Rogers, Merima Forny, David J Pagliarini.

Phosphorylation is a pervasive mitochondrial protein post-translational modification, yet the extent of its influence over mitochondrial functions remains unclear. To identify dynamic mitochondrial phosphoisoforms, we profiled the phosphoproteome of AML12 cells following individual genetic perturbations of 10 resident mitochondrial phosphatases. Guided by these results, we investigated the functional implications of phosphorylation on mitochondrial processes related to catalysis, import, and morphology. We find that phosphorylation of adenylate kinase 2 suppresses its nucleotide binding and catalytic activity. Elevated phosphorylation proximal to the mitochondrial targeting sequence of branched chain ketoacid dehydrogenase kinase disrupts its import and processing, resulting in enhanced catabolism of branched chain amino acids. Most notably, we discover extensive phosphorylation on proteins involved in mitochondrial cristae architecture, including multiple members of the MICOS complex and ATP synthase, upon silencing the phosphatase PGAM5. Collectively, our work connects reversible phosphorylation and resident phosphatases to the regulation of diverse mitochondrial processes.
HIGHLIGHTS: Perturbation of 10 mitochondrial resident phosphatases maps dynamic phosphosites.AK2 S151 phosphorylation tunes catalysis by augmenting adenine nucleotide binding.MTS-proximal BCKDK phosphorylation impairs protein import and gates BCAA catabolism.MIC19 and ATP5I phosphorylation remodels cristae and modulates bioenergetics.

DOI: https://doi.org/10.64898/2026.09.28.755151
Methods Mol Biol. 2027 ;3071 29-54

An Open Infrastructure for Mass Spectrometry Data in R.

Johannes Rainer, Marilyn De Graeve, Philippine Louail, Sebastien Gibb, Laurent Gatto.

  We present the Spectra software, an R/Bioconductor package, defining an efficient infrastructure for storing, handling, and visualizing mass spectrometry data. We describe how Spectra adapts to different data types, sizes, and use cases, addressing scalability while keeping a consistent user interface. We also demonstrate how it can integrate with third-party Python tools and follow modern tidyomics principles, seamlessly integrating with more general tidy data science tools.

Keywords:  Bioconductor; Mass spectrometry; Metabolomics; Proteomics; R; Reproducible research; Software

DOI:  https://doi.org/10.1007/978-1-0716-5519-1_3
bioRxiv. 2026 Oct 01. pii: 2026.09.30.755414. [Epub ahead of print]

Rank Normalization Enables Cross Pathway Comparison in Degradation Resolved Proteome Turnover Analysis.

Zi Gao, Qiang Xiao, Jeffery W Kelly, Evan T Powers.

Protein homeostasis, or proteostasis, is essential for cellular health, and its disruption contributes to cancer, aging, and neurodegenerative disease. Proteostasis is maintained largely by two intracellular degradation systems: the ubiquitin proteasome system (UPS) and the autophagy lysosomal pathway (ALP). Here, we combine pulse stable isotope labeling by amino acids in cell culture (pSILAC) with selective inhibition of the UPS or ALP to quantify pathway-dependent protein turnover and identify substrates that are preferentially cleared through each route. Direct comparison of these perturbations is complicated by their markedly different response distributions. To address the mismatch in dynamic range, we developed a normalization strategy based on within-condition ranks. Protein stabilization values are converted to percentile scores before comparison across pathways, placing both perturbations on a common relative response scale. Across two independent pSILAC experiments, 5,518 proteins were quantified in at least one condition, and 3,814 yielded high confidence half-life measurements in control, proteasome-inhibited, and lysosome-inhibited conditions. Rank normalization resolved pathway sensitivities that were obscured by direct comparison of absolute half-life changes. Importantly, the method reports relative pathway preference rather than absolute pathway contribution, exchanging effect size magnitude for comparability across perturbations with unequal response distributions. Integration with a curated proteostasis network annotation revealed coherent pathway preferences, including coordinated stabilization of proteasome core and regulatory subunits following lysosomal inhibition. This finding provides proteome-wide quantitative evidence for proteaphagy that complements previous targeted observations. Together, these results establish rank normalization as a practical strategy for comparing degradation resolved proteome turnover across perturbations with different dynamic ranges.

DOI: https://doi.org/10.64898/2026.09.30.755414
Leukemia. 2026 Oct 13.

Fibroblast growth factor receptor-signaling confers stroma-mediated drug resistance in malignant B cells.

Matthew A Timmins, Jingyu Chen, Andrew Moore, Sophie Kogut, Hana Paculova, Seth Frietze, Ingo Ringshausen.

DOI: https://doi.org/10.1038/s41375-026-03143-6
Cancers (Basel). 2026 Sep 23. pii: 3093. [Epub ahead of print]18(19):

An Ex Vivo 3D Co-Culture Model of the Bone Marrow Niche Better Predicts Clinically Relevant Epigenetic Target Modulation to Improve Immunotherapy in Multiple Myeloma.

Christine Greil, Johannes Jung, Julia Felthaus, Dagmar Wider, Monika Engelhardt, Ralph Wäsch.

  Background: In the last decade, treatment options for multiple myeloma have increased remarkably, including antibodies or CAR-T cells targeting myeloma surface markers with unprecedented efficacy. To enhance immunomodulation and clinical efficacy even more, the combination of these agents with other drugs is highly relevant. A significant association between CD38 expression on myeloma cells and the cytotoxicity of the anti-CD38 antibody daratumumab has been shown. All-trans retinoic acid, the pan-histone deacetylase inhibitor panobinostat, and the enhancer of the zeste homolog 2 inhibitor tazemetostat induce CD38 upregulation and can augment the anti-myeloma effect of daratumumab in conventional cell culture. However, translation into a clinical trial failed. Methods: To better predict in vivo drug effects preclinically, we used an ex vivo 3D model, allowing long-term propagation of myeloma cell lines and primary cells from 12 patients in co-culture with human stromal cells in a milieu that more closely resembles the physiological conditions in the bone marrow niche. Results: While epigenetic CD38 upregulation with different drugs leading to enhanced daratumumab efficacy was reproducible in conventional 2D culture, this effect was not confirmed in the optimized 3D model. Here, the epigenetic modification of CD38 expression and the impact on the cytotoxic effect of daratumumab seem to depend on the individual plasma cell and its interaction with the bone marrow microenvironment, which could be a plausible explanation for the lack of clinical efficacy of this combination treatment. Conclusions: Epigenetically induced CD38 upregulation to enhance the effect of anti-CD38 antibodies does not appear to be clinically relevant when using an optimized preclinical model.

Keywords:  3D model; CD38 expression; epigenetic modulation; immunotherapy; multiple myeloma; stromal cell support

DOI:  https://doi.org/10.3390/cancers18193093
Aging Dis. 2026 Oct 09.

Aging as a Potential Modulator of Extramedullary Hematopoiesis: A Hypothesis-Generating Niche-HSPC Competence-Trigger Model.

Zoe Bezirgiannidou, Iliana Stamatiou, Konstantinos Liapis, Emmanouil Spanoudakis, Evdokia Mandala, Ioannis Kotsianidis, Timoleon-Achilleas Vyzantiadis, Efthymia Vlachaki.

Extramedullary hematopoiesis (EMH) is a compensatory response to hematopoietic stress that occurs unevenly across disorders with ineffective erythropoiesis (IE). The mechanisms underlying differing EMH patterns despite similarly severe IE remain poorly understood. Thalassemia and congenital dyserythropoietic anemias frequently develop overt EMH, whereas myelodysplastic syndromes (MDS), despite severe IE, rarely show overt EMH. We propose the Niche- HSPC Competence-Trigger Model as a hypothesis-generating framework in which EMH expression reflects the interaction among erythropoietic trigger load, intrinsic hematopoietic stem and progenitor cell (HSPC) competence, and extramedullary niche fitness. Erythropoietic trigger load reflects the intensity and persistence of erythropoietic stress, particularly anemia and hypoxia, in disorders characterized by ineffective erythropoiesis. HSPC competence refers to the intrinsic capacity of HSPCs for proliferation and differentiation, whereas extramedullary niche fitness denotes the capacity of target tissues to support HSPC homing, engraftment, survival, expansion, and productive hematopoiesis; this capacity is shaped by stromal and vascular integrity, inflammatory and fibrotic remodeling, metabolic support, and iron availability. Within this framework, overt EMH is hypothesized to be favored when erythropoietic drive coincides with preserved HSPC competence and extramedullary niche fitness. Conversely, impaired HSPC competence or reduced niche fitness may limit overt EMH, while whether subclinical extramedullary hematopoietic activity occurs in MDS remains unresolved. We hypothesize that aging may modulate this balance by influencing both HSPC competence and niche fitness, thereby potentially contributing to the rarity of overt EMH in MDS. These hypotheses, including the contribution of aging and the possible occurrence of subclinical extramedullary hematopoietic activity, require experimental and clinical validation.

DOI: https://doi.org/10.14336/AD.2026.0896
Cells. 2026 Sep 30. pii: 1796. [Epub ahead of print]15(19):

The SKP2-Substrate Axis in Hematological Malignancies: Mechanisms of Oncogenesis and Opportunities for Targeted Therapy.

Yueying Zhang, Omar Faruq, Mariusz Shrestha, Shamila D Alipoor, Hong Chang.

  S-phase kinase-associated protein 2 (SKP2), a key substrate-recognition subunit of the Skp1-Cul1-F-box (SCF) E3 ubiquitin ligase complex, promotes the ubiquitin-proteasome-mediated degradation of tumor suppressors such as p27Kip1 and p21(Cip1/Waf1). Through these activities, SKP2 regulates critical cellular processes, including cell cycle progression, apoptosis, metabolic reprogramming, maintenance of cancer stem cell stemness, and contributes to the pathogenesis, therapeutic resistance, and clinical progression of hematological malignancies. Recent advances in protein degradation technologies and regulatory network analysis have highlighted SKP2 and its substrate interactions as promising targets for precision therapies. In this review, we examine the biological functions of SKP2 and regulatory mechanisms governing its substrate spectrum across hematological malignancies, including acute myeloid leukemia, chronic myeloid leukemia, B/NK/T-cell lymphoma, and multiple myeloma. We further review currently available SKP2-targeted therapeutic strategies, including small-molecule inhibitors, molecular glue degraders, and proteolysis-targeting chimeras (PROTACs), and discuss SKP2-related prognostic biomarkers in hematological malignancies. Finally, we outline the key challenges and future directions to guide the development of SKP2-centered therapeutic approaches.

Keywords:  SCF complex; SKP2; hematological malignancies; prognostic marker; targeted therapy; ubiquitination

DOI:  https://doi.org/10.3390/cells15191796