bims-scepro 2025-06-01 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2025–06–01
twenty-six papers selected by
William Grey, University of York

BCLAF1 restrains stress responses in hematopoietic stem cells to support expansion and repopulation.
Tetraspanin CD82 regulates Transforming Growth Factor β signaling in Hematopoietic Stem and Progenitor Cells.
Intra-bone marrow diversity of endothelial cells and its impact on hematopoietic stem cell development and maintenance.
CD97-directed CAR-T cells with enhanced persistence eradicate acute myeloid leukemia in diverse xenograft models.
PERK Maintains Hematopoietic Stem Cell Pool Integrity under Endoplasmic Reticulum Stress by Promoting Proliferation.
Multiplex base editing to protect from CD33 directed drugs for immune and gene therapy.
Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity.
WNK1 signalling regulates amino acid transport and mTORC1 activity to sustain acute myeloid leukaemia growth.
The Sympathetic Nervous Influence on Hematopoiesis Up To Date.
SFRP1 and SFRP2 jointly regulate normal and malignant hematopoietic progenitors by influencing mesenchymal cells in the hematopoietic niche.
Inhibition of mitochondrial protein import and proteostasis by a pro-apoptotic lipid.
Improving predictive accuracy in multiple myeloma using a plasma cell profile derived from single-cell RNA sequencing.
A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.
Acetylation profiling by Iseq-Kac reveals insights into HSC aging and lineage decision.
Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes.
In vivo haemopoietic stem cell gene therapy enabled by postnatal trafficking.
The ubiquitin ligase HUWE1 enhances WNT signaling by antagonizing destruction complex-mediated β-catenin degradation and through a mechanism independent of changes in β-catenin abundance.
The progression of multiple myeloma is regulated by LILRB1 via the GATA2-SAGE1 pathway.
Mesoscale regulation of microtubule-organizing centers by the E3 ligase TRIM37.
RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation.
Microtubule dynamics are defined by conformations and stability of clustered protofilaments.
The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets.
Impact of proteostasis workload on sensitivity to proteasome inhibitors in multiple myeloma.
IRF2-driven upregulation of OAS3 promotes AML cell proliferation by modulating the JAK-STAT signaling pathway.
hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments.
Galectin-9 induces IL-1β production as a key inflammatory cytokine in the acute myeloid leukemia cell line (U937).

Blood Adv. 2025 May 29. pii: bloodadvances.2024014916. [Epub ahead of print]

BCLAF1 restrains stress responses in hematopoietic stem cells to support expansion and repopulation.

Stephanie J Crowley, Wei Yang, Lynn S White, Jun Wu, Yanan Li, Haley Schmidt, Kyunghee Choi, Jeffrey A Magee, Jeffrey J Bednarski.

Hematopoietic stem cells (HSC) rapidly expand during fetal development and after stress. Here, we identify BCLAF1 as a regulator of HSC repopulation activity with functions in expansion of fetal HSCs and hematopoietic reconstitution after stem cell transplantation. Using mice with hematopoietic-specific and inducible deletion of Bclaf1, we find that BCLAF1 promotes fetal HSC development but is dispensible for maintenance of adult HSCs at steady state. Loss of BCLAF1 in either fetal or adult HSCs significantly impairs their self-renewal and multi-lineage reconstitution activity after stem cell transplantation. Single-cell RNA sequencing of fetal hematopoietic progenitors reveals that loss of BCLAF1 reduces long-term HSCs and restrains expression of stress response genes. BCLAF1 associates with chromatin throughout the genome of fetal and adult hematopoietic cells, likely through indirect mechanisms, to regulate transcriptional programs. These results establish a novel function for the transcriptional regulator BCLAF1 in limiting stress responses in HSCs to preserve HSC development during embryogenesis and repopulation function after stem cell transplant.

DOI: https://doi.org/10.1182/bloodadvances.2024014916
Mol Biol Cell. 2025 May 28. mbcE24100474

Tetraspanin CD82 regulates Transforming Growth Factor β signaling in Hematopoietic Stem and Progenitor Cells.

Erica Pascetti, Muskan Floren, Tatiane da Silva Fernandes, Carina Anastasio, Levi Doyle, Jennifer Gillette.

The cellular demand of the hematopoietic system is maintained by a rare pool of tissue-specific, hematopoietic stem cells (HSCs). HSCs are primarily maintained in a quiescent state but can be activated to exit quiescence and undergo self-renewal and differentiation in response to stress. The cytokine Transforming Growth Factor-β (TGF-β) plays an essential role in supporting HSC quiescence and activation, as one of the most potent inhibitors of HSPC growth. Therefore, how TGF-β signaling can be regulated in the context of HSCs is of significant interest as it may uncover novel mechanisms to target HSC activity. Previous studies revealed that the tetraspanin CD82 modulates the long-term HSC population, with CD82 knockout (KO) mice displaying increased HSC activation. Here, in this study, we connect the CD82 scaffold with the regulation of TGF-β signaling in hematopoietic stem and progenitor cells (HSPCs). We show that CD82KO leads to decreased TGF-β signaling, whereas increased CD82 expression promotes TGF-β activation. These changes in CD82-mediated TGF-β signaling are associated with extracellular matrix interactions, as fibronectin engagement is critical for promoting TGF-β signaling. Mechanistically, we find that CD82 stimulates enhanced TGF-β activation by promoting receptor crosstalk between TGF-β receptor I and integrin β1, resulting in downstream changes in cell proliferation. Collectively, these findings demonstrate that CD82 modulates canonical TGF-β signaling through receptor crosstalk mechanisms that may be targeted to alter the balance between HSC quiescence and activation.

DOI: https://doi.org/10.1091/mbc.E24-10-0474
Exp Hematol. 2025 May 26. pii: S0301-472X(25)00108-0. [Epub ahead of print] 104817

Intra-bone marrow diversity of endothelial cells and its impact on hematopoietic stem cell development and maintenance.

Shota Shimizu, Yoshiaki Kubota.

  In addition to supplying oxygen and nutrients, blood vessels secrete paracrine molecules known as angiocrine factors to promote tissue homeostasis and repair. The bone marrow (BM) vasculature in long bones has differing properties between the diaphysis, metaphysis, and epiphysis in terms of its morphology, plasticity, perivascular cellular components, and angiocrine profiles. Blood vessel formation is linked with bone formation through paracrine interactions between endothelial cells (ECs) and osteolineage cells, so-called angiogenic-osteogenic coupling. ECs also play essential roles in maintenance of hematopoietic stem cells (HSCs) by forming vascular niches together with perivascular stromal cells. Recent studies highlight the heterogeneity of vascular niches at different bone regions, suggesting that HSCs are regulated by locally distinct mechanisms. Here, we provide an overview of the BM vasculature and discuss how the heterogeneous vasculature contributes to bone formation and HSC maintenance. TEASER ABSTRACT: The bone marrow (BM) vasculature in long bones has differing properties across different bone regions. Blood vessel formation is closely linked with bone formation, a process known as angiogenic-osteogenic coupling. The BM vasculature also supports hematopoietic stem cells (HSCs) by establishing vascular niches. Recent studies highlight regional heterogeneity of vascular niches at different bone regions, suggesting that HSCs are regulated by locally distinct mechanisms. This review outlines the BM vasculature and examine how its heterogeneity influences bone formation and HSC maintenance.

Keywords:  Angiogenesis; angiogenic-osteogenic coupling; bone marrow vasculature; hematopoietic stem cells; stem cell niche

DOI:  https://doi.org/10.1016/j.exphem.2025.104817
Cell Rep Med. 2025 May 16. pii: S2666-3791(25)00221-6. [Epub ahead of print] 102148

CD97-directed CAR-T cells with enhanced persistence eradicate acute myeloid leukemia in diverse xenograft models.

Kai Shang, Deyu Huang, Jun Liu, Zebin Yu, Wei Bian, Jiangqing Chen, Yin Zhao, Lina Liu, Jie Jiang, Yajie Wang, Yanting Duan, Jingyu Ge, Shize Zhang, Chun Zhou, Yingli Han, Yongxian Hu, Weiyan Zheng, Jie Sun, He Huang, Shanshan Pei, Pengxu Qian, Jie Sun.

  Chimeric antigen receptor (CAR)-T therapy on acute myeloid leukemia (AML) is hindered by the absence of a suitable tumor-specific antigen. Here, we propose CD97 as a potential target for CAR-T therapy against AML based on its broader and higher expression on AML cells compared to normal hematopoietic stem and progenitor cells (HSPCs). To resolve the fratricide problem caused by CD97 expression on T cells, we knock out CD97 in CAR-T cells using CRISPR-Cas9. Our CD97KO CAR-T cells eliminate both AML cell lines and primary AML cells effectively while showing tolerable toxicity to HSPCs. Furthermore, we mutate the CD3ζ domain of the CAR and find that the optimized CD97 CAR-T cells exhibit persistent anti-tumor activity both in vitro and in multiple xenograft models. Mechanistically, transcriptional profiles reveal that the optimized CAR-T cells delay differentiation and resist exhaustion. Collectively, our study supports CD97 as a promising target for CAR-T therapy against AML.

Keywords:  CD97; acute myeloid leukemia; chimeric antigen receptor; exhaustion; immunotherapy

DOI:  https://doi.org/10.1016/j.xcrm.2025.102148
Blood. 2025 May 28. pii: blood.2024027846. [Epub ahead of print]

PERK Maintains Hematopoietic Stem Cell Pool Integrity under Endoplasmic Reticulum Stress by Promoting Proliferation.

Manxi Zheng, Qinlu Peng, Erin M Kropp, Zhejuan Shen, Suxuan Liu, Zhengyou Yin, Sho Matono, Takao Iwawaki, Xiang Wang, Ken Inoki, Yang Mei, Qing Li, Lu Liu.

The integrity of the hematopoietic stem cell (HSC) pool depends on effective long-term self-renewal and the timely elimination of damaged or differentiation-prone HSCs. While the PERK branch of the unfolded protein response (UPR) has been shown to initiate pro-apoptotic signaling in response to ER stress in vitro, its role in regulating HSC fate in vivo remains incompletely understood. Here, we demonstrate that PERK is dispensable for steady-state hematopoiesis and HSC self-renewal under homeostatic conditions. However, under ER stress induced by disruption of ER-associated degradation (ERAD), via knockout of key components such as Sel1L or Hrd1, PERK becomes activated and drives HSC proliferation and depletion. Notably, deletion of PERK or expression of a kinase-dead PERK mutant significantly rescues the HSC defects caused by Sel1L or Hrd1 loss. Mechanistically, ERAD deficiency does not lead to increased HSC apoptosis or elevated reactive oxygen species (ROS), and PERK knockout has minimal impact on HSC apoptosis. Instead, PERK activation promotes aberrant mTOR signaling and HSC hyperproliferation, ultimately compromising self-renewal capacity. This PERK-driven elimination of stressed HSCs may function as a protective mechanism to maintain overall HSC pool integrity. Collectively, our findings reveal a previously unrecognized, proliferative, and apoptosis-independent role for PERK in regulating HSC fate under ER stress, highlighting a novel mechanism for preserving HSC homeostasis.

DOI: https://doi.org/10.1182/blood.2024027846
Nat Commun. 2025 May 27. 16(1): 4899

Multiplex base editing to protect from CD33 directed drugs for immune and gene therapy.

Florence Borot, Olivier Humbert, Jeffrey T Ehmsen, Emily Fields, Sajeev Kohli, Stefan Radtke, Kyle Swing, Dnyanada Pande, Mark R Enstrom, George S Laszlo, Thiyagaraj Mayuranathan, Abdullah Mahmood Ali, Mitchell J Weiss, Jonathan S Yen, Gregory A Newby, Roland B Walter, David R Liu, Siddhartha Mukherjee, Hans-Peter Kiem.

The selection of genetically engineered immune or hematopoietic cells in vivo after gene editing remains a clinical problem and requires a method to spare on-target toxicity to normal cells. Here, we develop a base editing approach exploiting a naturally occurring CD33 single nucleotide polymorphism leading to removal of full-length CD33 surface expression on edited cells. CD33 editing in human and nonhuman primate hematopoietic stem and progenitor cells protects myeloid progeny from CD33-targeted therapeutics without affecting normal hematopoiesis in vivo, thus demonstrating potential for improved immunotherapies with reduced off-leukemia toxicity. For broader application to gene therapies, we demonstrate highly efficient (>70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in nonhuman primates. Using the CD33 antibody-drug conjugate Gemtuzumab Ozogamicin, we show resistance of engrafted, multiplex edited human cells in vivo, and a 2-fold enrichment for edited cells in vitro. Together, our results highlight the potential of adenine base editors for improved immune and gene therapies.

DOI: https://doi.org/10.1038/s41467-025-59713-2
Cancer Cell. 2025 May 28. pii: S1535-6108(25)00211-9. [Epub ahead of print]

Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity.

Andrew W Daman, Anthony C Antonelli, Gil Redelman-Sidi, Lucinda Paddock, Shireen Khayat, Mythili Ketavarapu, Jin Gyu Cheong, Leonardo F Jurado, Anna Benjamin, Song Jiang, Dughan Ahimovic, Victoria R Lawless, Michael J Bale, Oleg Loutochin, Victor A McPherson, Maziar Divangahi, Rachel E Niec, Dana Pe'er, Eugene Pietzak, Steven Z Josefowicz, Michael S Glickman.

  Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the vaccine against tuberculosis and an immunotherapy for bladder cancer. When administered intravenously, BCG reprograms bone marrow hematopoietic stem and progenitor cells (HSPCs), leading to heterologous protection against infections. Whether HSPC reprogramming contributes to the anti-tumor effects of BCG administered into the bladder is unknown. We demonstrate that BCG administered in the bladder colonizes the bone marrow and, in both mice and humans, reprograms HSPCs to alter and amplify myelopoiesis. BCG-reprogrammed HSPCs are sufficient to confer augmented anti-tumor immunity through production of neutrophils, monocytes, and dendritic cells that broadly remodel the tumor microenvironment, drive T cell-dependent anti-tumor responses, and synergize with checkpoint blockade. We conclude that bladder BCG acts systemically through hematopoiesis, highlighting the broad potential of HSPC reprogramming to enhance the innate drivers of T cell-dependent tumor immunity.

Keywords:  BCG; bladder cancer; epigenetics; hematopoiesis; immunotherapy; innate immune memory; trained immunity; tumor immunity

DOI:  https://doi.org/10.1016/j.ccell.2025.05.002
Nat Commun. 2025 May 27. 16(1): 4920

WNK1 signalling regulates amino acid transport and mTORC1 activity to sustain acute myeloid leukaemia growth.

Shunlei Duan, Karl Agger, Jan-Erik Messling, Koutarou Nishimura, Xuerui Han, Isabel Peña-Rømer, Pavel Shliaha, Helene Damhofer, Max Douglas, Manas Kohli, Akos Pal, Yasmin Asad, Aaron Van Dyke, Raquel Reilly, Robert Köchl, Victor L J Tybulewicz, Ronald C Hendrickson, Florence I Raynaud, Paolo Gallipoli, George Poulogiannis, Kristian Helin.

The lack of curative therapies for acute myeloid leukaemia (AML) remains an ongoing challenge despite recent advances in the understanding of the molecular basis of the disease. Here we identify the WNK1-OXSR1/STK39 pathway as a previously uncharacterised dependency in AML. We show that genetic depletion and pharmacological inhibition of WNK1 or its downstream phosphorylation targets OXSR1 and STK39 strongly reduce cell proliferation and induce apoptosis in leukaemia cells in vitro and in vivo. Furthermore, we show that the WNK1-OXSR1/STK39 pathway controls mTORC1 signalling via regulating amino acid uptake through a mechanism involving the phosphorylation of amino acid transporters, such as SLC38A2. Our findings underscore an important role of the WNK1-OXSR1/STK39 pathway in regulating amino acid uptake and driving AML progression.

DOI: https://doi.org/10.1038/s41467-025-59969-8
J Neuroimmune Pharmacol. 2025 May 30. 20(1): 61

The Sympathetic Nervous Influence on Hematopoiesis Up To Date.

Georges Maestroni.

  Hematopoiesis is a tightly regulated process taking place in specialized bone marrow structures called hematopoietic niches. In these structures, hematopoietic stem cells produce all hematopoietic lineages by their self-renewal and differentiation abilities. Sympathetic nerve fibers, entering the bone marrow in association with blood vessels, regulate on a circadian basis the hematopoietic stem cells and leukocytes migration in and out the bone marrow. This cellular traffic, that is mainly regulated by beta-adrenergic receptors expressed on mesenchymal stem cells, is needed to maintain an efficient hematopoietic niche and for immunosurveillance against infections. Both alpha- and beta-adrenergic receptors seem involved in the regeneration of hematopoiesis after myeloablative treatments. Likewise, the effects of psychogenic stress and of ageing on the hematopoietic system are also mediated by adrenergic signals. Yet, the exact mechanisms regulating hematopoietic regeneration and the differentiation ratio between lymphoid and myeloid cells are still obscure. A comprehensive understanding of the adrenergic influence on hematopoiesis holds the potential for novel therapeutic approaches in a variety of hematological diseases.

Keywords:  Adrenergic receptors; Hematopoiesis; Hematopoietic stem cells niche; Sympathetic nervous system

DOI:  https://doi.org/10.1007/s11481-025-10220-7
Biochem Biophys Res Commun. 2025 May 24. pii: S0006-291X(25)00795-8. [Epub ahead of print]774 152081

SFRP1 and SFRP2 jointly regulate normal and malignant hematopoietic progenitors by influencing mesenchymal cells in the hematopoietic niche.

Hikaru Tsutsumi, Fuki Kumagai, Kazuki Tsutsui, Akio Maekawa, Aya Ohno, Hikari Okamoto, Ayana Ueno, Ayano Kuga, Natsumi Hasegawa, Mitsuhiro Ito.

  Secreted frizzled-related proteins (SFRPs) are secreted proteins identified as antagonists of the Wnt signaling pathway. Sfrp1 or Sfrp2 deletion in mice attenuates the hematopoietic stem/progenitor cell (HSPC) pool; however, the mechanisms by which SFRP1/2 support hematopoietic cells remain unclear. Here, we showed that SFRP1/2 functions as a niche factor for both normal and malignant HSPCs by acting on mesenchymal stromal cells (MSCs). Addition of SFRP1/2-blocking antibodies to a co-culture of OP-9 MSCs and normal mouse bone marrow hematopoietic cells reduced the long-term culture-initiating cell number. Addition of these antibodies to the co-culture of MSCs and MB-1 myeloblastoma cells reduced the cobblestone area, which is a characteristic feature of leukemic stem cells. During co-culture with MB-1 cells, these antibodies upregulated the target genes of the Wnt and bone morphogenetic protein pathways in OP-9 MSCs, but not in MB-1 cells. Additionally, addition of blocking antibodies to OP-9 MSC monoculture attenuated cell growth. Overall, our findings suggest that SFRP1 and SFRP2 maintain normal and malignant HSPC functions in the hematopoietic niche by modulating the Wnt and bone morphogenetic protein pathways in MSCs.

Keywords:  Hematopoietic stem/progenitor cells; Mesenchymal stromal cells; SFRP1; SFRP2

DOI:  https://doi.org/10.1016/j.bbrc.2025.152081
Elife. 2025 May 30. pii: RP93621. [Epub ahead of print]13

Inhibition of mitochondrial protein import and proteostasis by a pro-apoptotic lipid.

Josep Fita-Torró, José Luis Garrido-Huarte, Lucía López-Gil, Agnès H Michel, Benoit Kornmann, Amparo Pascual-Ahuir, Markus Proft.

  Mitochondria-mediated cell death is critically regulated by bioactive lipids derived from sphingolipid metabolism. The lipid aldehyde trans-2-hexadecenal (t-2-hex) induces mitochondrial dysfunction from yeast to humans. Here, we apply unbiased transcriptomic, functional genomics, and chemoproteomic approaches in the yeast model to uncover the principal mechanisms and biological targets underlying this lipid-induced mitochondrial inhibition. We find that loss of Hfd1 fatty aldehyde dehydrogenase function efficiently sensitizes cells for t-2-hex inhibition and apoptotic cell death. Excess of t-2-hex causes a profound transcriptomic response with characteristic hallmarks of impaired mitochondrial protein import, like activation of mitochondrial and cytosolic chaperones or proteasomal function and severe repression of translation. We confirm that t-2-hex stress induces rapid accumulation of mitochondrial pre-proteins and protein aggregates and subsequent activation of Hsf1- and Rpn4-dependent gene expression. By saturated transposon mutagenesis, we find that t-2-hex tolerance requires an efficient heat shock response and specific mitochondrial and ER functions and that mutations in ribosome, protein, and amino acid biogenesis are beneficial upon t-2-hex stress. We further show that genetic and pharmacological inhibition of protein translation causes t-2-hex resistance, indicating that loss of proteostasis is the predominant consequence of the pro-apoptotic lipid. Several TOM subunits, including the central Tom40 channel, are lipidated by t-2-hex in vitro and mutation of accessory subunits Tom20 or Tom70 confers t-2-hex tolerance. Moreover, the Hfd1 gene dose determines the strength of t-2-hex mediated inhibition of mitochondrial protein import, and Hfd1 co-purifies with Tom70. Our results indicate that the transport of mitochondrial precursor proteins through the outer mitochondrial membrane is sensitively inhibited by the pro-apoptotic lipid and thus represents a hotspot for pro- and anti-apoptotic signaling.

Keywords:  S. cerevisiae; apoptosis; biochemistry; chemical biology; genetics; genomics; lipid signaling; mitochondrial protein import; proteostasis; sphingolipid metabolism; yeast

DOI:  https://doi.org/10.7554/eLife.93621
Haematologica. 2025 May 29.

Improving predictive accuracy in multiple myeloma using a plasma cell profile derived from single-cell RNA sequencing.

Lanting Liu, Hao Sun, Fangshuo Feng, Xiyue Sun, Jingyuan Ma, Rui Lv, Tengteng Yu, Linhai Ye, Xiuchun Li, Zhen Yu, Xiaoyu Zhang, Huaqing Jing, Yao Yao, Fengxia Ma, Lugui Qiu, Mu Hao.

Multiple myeloma (MM) shows inherent clinical and biological heterogeneity, leading to variable treatment responses and outcomes. The complex molecular landscape of MM makes precise risk stratification through clinical genetic testing difficult. Thus, identifying better biomarkers is essential to enhance existing stratification methods and guide personalized therapy decisions. Here, we systematically analyzed the intratumor heterogeneity of tumor cells from 12 newly diagnosed MM patients with different outcomes at single-cell resolution, especially those with an overall survival of less than two years, considered extremely high-risk in the real world. Among the eight heterogeneous tumor cell subclusters in these patients' myeloma cells, a particularly aggressive subset was discovered, characterized by severe chromosomal instability, high-level drug resistance, and high-risk genes. Survival analysis indicated that a high rate of this aggressive cell subset was associated with patients' poor outcomes. We revealed a seven genes signature (LILRB4, CD74, TUBA1B, CCND2, HIST1H4C, ITGB7, and CRIP1) extremely highly expression within this aggressive myeloma cell subset. Multivariate Cox analysis showed that the 7-gene signature score was a worst factor for patients' outcome independent with cytogenetic aberrant and the International Staging System (ISS) stages. We then established an integrated risk stratification model combined with the 7-gene signature score. This model could significantly improve the risk discrimination capabilities, especially to distinguish the ultra-high-risk myeloma patients with the worst outcome in our cohort and validated in five independent datasets of MM patients. We further devised a simply digital PCR method for feasible quantifying the 7-gene signature, which still significantly differentiated the survival of MM patients and possesses considerable clinical application value. Overall, this integrated risk-scoring model derived from scRNA-seq data was significantly associated with a more advanced stage of myeloma patients, facilitating guided risk-adapted treatment strategies for such ultra-high-risk patients.

DOI: https://doi.org/10.3324/haematol.2025.287586
Nat Commun. 2025 May 30. 16(1): 5034

A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.

Barbora Salovska, Wenxue Li, Oliver M Bernhardt, Pierre-Luc Germain, Qinyue Wang, Tejas Gandhi, Lukas Reiter, Yansheng Liu.

Quantifying protein turnover is fundamental to understanding cellular processes and advancing drug discovery. Multiplex-DIA mass spectrometry (MS), combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC) reliably measures protein turnover and degradation kinetics. Previous multiplex-DIA-MS workflows have employed various strategies including leveraging the highest isotopic labeling channels to enhance the detection of isotopic signal pairs. Here we present a robust workflow that integrates a machine learning algorithm and channel-specific statistical filtering, enabling dynamic adaptation to channel ratio changes across multiplexed experiments and enhancing both coverage and accuracy of protein turnover profiling. We also introduce KdeggeR, a data analysis tool optimized for pSILAC-DIA experiments, which determines and visualizes peptide and protein degradation profiles. Our workflow is broadly applicable, as demonstrated on 2-channel and 3-channel DIA datasets and across two MS platforms. Applying this framework to an aneuploid cancer cell model before and after cisplatin resistance, we uncover strong proteome buffering of key protein complex subunits encoded by the aneuploid genome mediated by protein degradation. We identify resistance-associated turnover signatures, including mitochondrial metabolic adaptation via accelerated degradation of respiratory complexes I and IV. Our approach provides a powerful platform for high-throughput, quantitative analysis of proteome dynamics and stability in health and disease.

DOI: https://doi.org/10.1038/s41467-025-60319-x
Nat Chem Biol. 2025 May 26.

Acetylation profiling by Iseq-Kac reveals insights into HSC aging and lineage decision.

Yanqiu Gong, Huiwen Zhan, Ni Wei, Min Liu, Yu Liu, Pengbo Guan, Yusi Xie, Yujun Deng, Qianlun Pu, Xiaoxian Lou, Xiaodong Wang, Rou Zhang, Ping Wang, Xiuxiu Jin, Xiuxuan Wang, Zhiqiang Xu, Li Gao, Xinyuan Wang, Siyu He, Ying Lu, Meng Hu, Wanmeng Li, Kun Zheng, Yong Peng, Peng Lei, Heng Xu, Yujun Shi, Jun Qin, Hongbo Hu, Huiyuan Zhang, Lunzhi Dai.

Profiling post-translational modifications face challenges with low-input samples. We developed Iseq-Kac (internal standard-assisted enrichment-free approach for high-throughput quantitative analysis of lysine acetylation) to profile the acetylome in as few as 103-104 cells. By using a hyperacetylated internal standard, Iseq-Kac can be used in mass spectrometry (MS) to enhance MS1 signals and facilitate MS2 fragmentation of acetylated peptides. Using Iseq-Kac, we quantified 675-1,471 acetylated peptides per analysis from 104 hematopoietic stem cells (HSCs) or multipotent progenitors. Validation by targeted MS, site-specific antibodies and functional assays linked aging-related proteome and acetylome changes to HSC lineage decision. A pronounced decrease in acetylation at H4 lysine 77 (H4K77ac) was observed in aged HSCs, linked to histone deacetylase 3 (HDAC3) activity. HDAC3 inhibition or knockdown in HSCs significantly promoted lymphocyte differentiation. Mimicking H4K77ac through H4K77Q expression enhanced B cell differentiation while repressing myeloid differentiation. Overall, Iseq-Kac enables robust low-input acetylome profiling and reveals epigenetic mechanisms underlying lineage skewing in aged HSCs.

DOI: https://doi.org/10.1038/s41589-025-01916-1
J Clin Invest. 2025 May 27. pii: e189266. [Epub ahead of print]

Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes.

Srinivas Aluri, Te Ling, Ellen Fraint, Samarpana Chakraborty, Kevin Zhang, Aarif Ahsan, Leah Kravets, Gowri Poigaialwar, Rongbao Zhao, Kith Pradhan, Anitria Cotton, Kimo Bachiashvili, Jung-In Yang, Anjali Budhathoki, Beamon Agarwal, Shanisha Gordon-Mitchell, Milagros Carbajal, Srabani Sahu, Jacqueline Boultwood, Andrea Pellagatti, Ulrich Steidl, Amittha Wickrema, Satish Nandakumar, Aditi Shastri, Rajasekhar Nvs Suragani, Teresa V Bowman, John D Crispino, Sadanand Vodala, Amit Verma.

  Anemia is the primary clinical manifestation of myelodysplastic syndromes (MDS), but the molecular pathogenesis of ineffective erythropoiesis remains incompletely understood. Luspatercept, an activin receptor 2B (ACVRIIB-Fc) ligand trap, has been approved to treat anemia, however its molecular mechanism of action is unclear. We found that the ACVR2B, its ligand GDF11, and effector, SMAD2, are upregulated in MDS patient samples. GDF11 inhibited human erythropoiesis in vitro and caused anemia in zebrafish, effects that were abrogated by luspatercept. Upon GDF11 stimulation of human erythroid progenitors, SMAD2 binding occurred in the erythroid regulatory regions, including at GATA1 intron. Intronic SMAD2 binding led to skipping of exon 2 of GATA1, resulting in a shorter, hypomorphic isoform (GATA1s). CRISPR deletion of the SMAD2 binding intronic region decreased GATA1s production upon GDF11 stimulation. Expression of gata1s in a mouse model led to anemia, rescued by a murine ActRIIB-Fc (RAP-536). Finally, RNA-seq analysis of samples from the Phase 3 MEDALIST trial revealed that responders to Luspatercept had a higher proportion of GATA1s compared to non-responders. Moreover, the increase RBCs post-treatment was linked to a relative decrease in GATA1s isoform. Our study indicates that GDF11-mediated SMAD2 activation results in an increase in functionally impaired GATA1 isoforms, consequently contributing to anemia and influencing responses to Luspatercept in MDS.

Keywords:  Cell biology; Hematology; Hematopoietic stem cells

DOI:  https://doi.org/10.1172/JCI189266
Nature. 2025 May 28.

In vivo haemopoietic stem cell gene therapy enabled by postnatal trafficking.

Michela Milani, Anna Fabiano, Marta Perez-Rodriguez, Raisa Jofra Hernandez, Alessandra Zecchillo, Erika Zonari, Sofia Ottonello, Luca Basso-Ricci, Cesare Canepari, Monica Volpin, Valeria Iannello, Valentina Capo, Pamela Quaranta, Luca Seffin, Fabio Russo, Mauro Biffi, Leonardo Ormoli, Chiara Brombin, Filippo Carlucci, Antonella Forlino, Marta Filibian, Eugenio Montini, Serena Scala, Anna Villa, Juan Antonio Bueren, Paula Rio, Alessandro Aiuti, Alessio Cantore, Luigi Naldini.

Lentiviral vector (LV)-mediated ex vivo gene therapy for haematopoietic stem and progenitor cells (HSPCs) has delivered on the promise of a 'one-and-done' treatment for several genetic diseases1. However, ex vivo manipulation and patient conditioning before transplantation are major hurdles that could be overcome by an in vivo approach. Here we demonstrate that in vivo gene delivery to HSPCs after systemic LV administration is enabled by the substantial trafficking of these cells from the liver to the bone marrow in newborn mice. We improved gene-transfer efficiency using a phagocytosis-shielded LV, successfully reaching bona fide HSPCs capable of long-term multilineage output and engraftment after serial transplantation, as confirmed by clonal tracking. HSPC mobilization further increased gene transfer, extending the window of intervention, although permissiveness to LV transduction declined with age. We successfully tested this in vivo strategy in mouse models of adenosine deaminase deficiency, autosomal recessive osteopetrosis and Fanconi anaemia. Interestingly, in vivo gene transfer provided a selective advantage to corrected HSPCs in Fanconi anaemia, leading to near-complete haematopoietic reconstitution and prevention of bone marrow failure. Given that circulating HSPCs in humans are also most abundant shortly after birth, in vivo HSPC gene transfer holds strong translational potential across multiple diseases.

DOI: https://doi.org/10.1038/s41586-025-09070-3
PLoS Genet. 2025 May 27. 21(5): e1011677

The ubiquitin ligase HUWE1 enhances WNT signaling by antagonizing destruction complex-mediated β-catenin degradation and through a mechanism independent of changes in β-catenin abundance.

Joseph K McKenna, Yalan Wu, Praveen Sonkusre, Caleb K Sinclear, Raj Chari, Andres M Lebensohn.

WNT/β-catenin signaling is mediated by the transcriptional coactivator β-catenin (CTNNB1). CTNNB1 abundance is regulated by phosphorylation and proteasomal degradation, promoted by a destruction complex composed of the scaffold proteins APC and AXIN1 or AXIN2, and the kinases casein kinase 1α (CSNK1A1) and GSK3A or GSK3B. Loss of CSNK1A1 increases CTNNB1 abundance, resulting in hyperactive WNT signaling. Previously, we demonstrated that the HECT domain E3 ubiquitin ligase HUWE1 is necessary for hyperactive WNT signaling in HAP1 haploid human cells lacking CSNK1A1. Here, we investigated the mechanism underlying this requirement. In HAP1 cells lacking CSNK1A1, GSK3A/GSK3B still phosphorylated a fraction of CTNNB1, promoting its degradation. HUWE1 loss enhanced GSK3A/GSK3B-dependent CTNNB1 phosphorylation, further reducing CTNNB1 abundance. However, the reduction in CTNNB1 caused by HUWE1 loss was smaller than the reduction in WNT target gene transcription. To test whether the reduction in WNT signaling caused by HUWE1 loss resulted from reduced CTNNB1 alone, we engineered the endogenous CTNNB1 locus in HAP1 cells to encode a CTNNB1 variant insensitive to destruction complex-mediated phosphorylation and degradation. HUWE1 loss in these cells did not change CTNNB1 abundance but still reduced WNT signaling, demonstrating that another mechanism was at play. Genetic interaction and overexpression analyses revealed that the reduction in WNT signaling caused by HUWE1 loss required not only GSK3A or GSK3B, but also APC and AXIN1. Therefore, in HAP1 cells lacking CSNK1A1, a residual destruction complex containing APC, AXIN1 and GSK3A or GSK3B downregulates WNT signaling by phosphorylating and targeting CTNNB1 for degradation, and HUWE1 enhances WNT signaling by antagonizing this activity. Regulation of WNT signaling by HUWE1 also requires its ubiquitin ligase activity. We conclude that HUWE1 enhances WNT/CTNNB1 signaling through two mechanisms, one that antagonizes destruction complex-mediated CTNNB1 degradation and another that is independent of changes in CTNNB1 abundance. Coordinated regulation of CTNNB1 abundance and a second signaling step by HUWE1 would be an efficient way to control WNT signaling output, enabling sensitive and robust activation of the pathway.

DOI: https://doi.org/10.1371/journal.pgen.1011677
Br J Haematol. 2025 May 25.

The progression of multiple myeloma is regulated by LILRB1 via the GATA2-SAGE1 pathway.

Chiqi Chen, Xuanyi Zhou, Liyuan Cao, Wenqian Yang, Lietao Weng, Jin Yuan, Wen Zhou, Zhuo Yu, Junke Zheng.

  Multiple myeloma (MM) is a haematological malignancy characterized by the clonal expansion of plasma cells within the bone marrow, thus resulting in the overproduction of monoclonal immunoglobulins. Despite the availability of various immunotherapeutic strategies, patient survival rates remain disappointingly low, thus underscoring the need for innovative immunotherapies to improve outcomes. Leukocyte Ig-like receptor subfamily B (LILRB1), which is a recently identified immune checkpoint, has an undefined role and molecular mechanism in MM. Herein, we demonstrated that LILRB1 was significantly upregulated in MM patients and MM cell lines and was negatively correlated with patient survival. The knockdown of LILRB1 promoted apoptosis in MM cells, enhanced sensitivity to bortezomib and diminished tumourigenicity in a subcutaneous mouse model. Mechanistically, LILRB1 triggers downstream GATA Binding Protein 2 (GATA2) and sustains MM cell proliferation via the GATA2-Sarcoma Antigen 1 (SAGE1) signalling pathway. Consequently, the targeting of LILRB1 may represent a promising therapeutic approach for MM.

Keywords:  GATA2; LILRB1; SAGE1; multiple myeloma; proliferation

DOI:  https://doi.org/10.1111/bjh.20144
Nat Struct Mol Biol. 2025 May 25.

Mesoscale regulation of microtubule-organizing centers by the E3 ligase TRIM37.

Zhong Y Yeow, Sonia Sarju, Fang-Chi Chang, Lance Y Xu, Mark van Breugel, Andrew J Holland.

Centrosomes ensure accurate chromosome segregation during cell division. Although the regulation of centrosome number is well established, less is known about the suppression of noncentrosomal microtubule-organizing centers (ncMTOCs). The E3 ligase TRIM37, implicated in Mulibrey nanism and 17q23-amplified cancers, has emerged as a key regulator of both centrosomes and ncMTOCs. Yet, the mechanism by which TRIM37 achieves enzymatic activation to target these mesoscale structures had thus far remained unknown. Here we elucidate the activation process of TRIM37, unveiling a process that initiates with TRAF domain-directed substrate recognition followed by B-box domain-mediated oligomerization and culminates in RING domain dimerization. Using optogenetics, we demonstrate that the E3 activity of TRIM37 is directly coupled to the assembly state of its substrates, being activated only when centrosomal proteins cluster into higher-order assemblies resembling MTOCs. This regulatory framework provides a mechanistic basis for understanding TRIM37-driven pathologies and echoes the restriction of the human immunodeficiency virus capsid by TRIM5, thus unveiling a conserved activation blueprint among TRIM proteins to control turnover of complexes assembled at the mesoscale level.

DOI: https://doi.org/10.1038/s41594-025-01540-6
Blood. 2025 May 28. pii: blood.2024027712. [Epub ahead of print]

RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation.

Madeline Y Mayday, Giulia Biancon, Manyi Wei, Christian Ramirez, Irene Moratti, Andreas P Pintado-Urbanc, Jether Amos Espinosa, Mi Chen, Lin Wang, Matthew D Simon, Yaara Ofir-Rosenfeld, Oliver Rausch, Toma Tebaldi, Stephanie Halene, Diane S Krause.

Acute megakaryoblastic leukemia driven by the RBM15-MKL1 fusion protein (RM-AMKL) is encoded by the recurrent t(1;22) translocation. Dysregulation of m6A modification affects RNA fate and is linked to oncogenesis. Because RBM15 is critical for bringing the m6A writer complex to specific RNAs, we hypothesized that RM disrupts m6A modification, altering RNA fate to drive leukemogenesis in RM-AMKL. Using a multi-omic approach, we show for the first time that RM retains the RNA-binding and m6A-modifying functions of RBM15 while also selectively regulating distinct mRNA targets including Frizzled genes in the WNT signaling pathway. Treating murine RM-AMKL cells with the METTL3 inhibitor STM3675, which decreases m6A deposition, induced apoptosis in vitro and prolonged survival in transplanted mice. Frizzled genes were upregulated by RM and downregulated upon METTL3 inhibition, implicating an m6A-dependent mechanism for their dysregulation. Direct Frizzled knockdown reduced RM-AMKL growth in vitro and in vivo, highlighting Wnt signaling as a key oncogenic driver. Elevated Wnt pathway and Frizzled expression in multiple forms of human AMKL underscores the relevance of our findings. Together, our results establish RM-specific m6A modifications and Wnt pathway activation as critical drivers of RM-AMKL, identifying these pathways as potential therapeutic targets.

DOI: https://doi.org/10.1182/blood.2024027712
Proc Natl Acad Sci U S A. 2025 Jun 03. 122(22): e2424263122

Microtubule dynamics are defined by conformations and stability of clustered protofilaments.

Maksim Kalutskii, Helmut Grubmüller, Vladimir A Volkov, Maxim Igaev.

  Microtubules are dynamic cytoskeletal polymers that add and lose tubulin dimers at their ends. Microtubule growth, shortening, and transitions between them are linked to GTP hydrolysis. Recent evidence suggests that flexible tubulin protofilaments at microtubule ends adopt a variety of shapes, complicating structural analysis using conventional techniques. Therefore, the link between GTP hydrolysis, protofilament structure and microtubule polymerization state is poorly understood. Here, we investigate the conformational dynamics of microtubule ends using coarse-grained modeling supported by atomistic simulations and cryoelectron tomography. We show that individual bent protofilaments organize in clusters, transient precursors to the straight microtubule lattice, with GTP-bound ends showing elevated and more persistent cluster formation. Differences in the mechanical properties of GTP- and GDP-protofilaments result in differences in intracluster tension, determining both clustering propensity and protofilament length. We propose that conformational selection at microtubule ends favors long-lived clusters of short GTP-protofilaments that are more prone to forming a straight microtubule lattice and accommodating new tubulin dimers. Conversely, microtubule ends trapped in states with unevenly long and stiff GDP-protofilaments are more prone to shortening. We conclude that protofilament clustering is the key phenomenon that links the hydrolysis state of single tubulins to the polymerization state of the entire microtubule.

Keywords:  coarse-grained modeling; cryoelectron tomography; dynamic instability; microtubule; molecular dynamics simulation

DOI:  https://doi.org/10.1073/pnas.2424263122
Cancer Cell. 2025 May 27. pii: S1535-6108(25)00212-0. [Epub ahead of print]

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets.

Jaco C Knol, Mengge Lyu, Franziska Böttger, Madalena Nunes Monteiro, Thang V Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Richard R de Goeij-de Haas, Irene V Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Jun A, Bart A Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan N M IJzermans, Hanneke W M van Laarhoven, Maarten F Bijlsma, Jan Paul Medema, Alex A Henneman, Sander R Piersma, Ruud H Brakenhoff, Jacqueline Cloos, Valentina Cordo', Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, Tessa Y S Le Large, John W M Martens, Jules P P Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E Kibbelaar, David P Noske, Renske D M Steenbergen, Nicole C T van Grieken, Winan van Houdt, Elisa Giovannetti, Geert J L H van Leenders, Jos Jonkers, Tong Liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo, Connie R Jimenez.

  Most cancer proteomics studies to date have focused on a single cancer type. We report The Pan-Cancer Proteome Atlas (TPCPA) based on data-independent acquisition mass spectrometry, to better understand cancer biology and identify therapeutic targets and biomarkers. TPCPA includes 9,670 proteins derived from 999 primary tumors representing 22 cancer types. We describe pan-cancer and cancer type-enriched proteins with extensive external annotation, prioritizing candidate drug targets and biomarkers. Relevant for proteolysis-targeting chimeras, we identify E3-ubiquitin ligases highly expressed in specific tumor types, including HERC5 (esophageal cancer) and RNF5 (liver cancer). Co-expression analysis reveals 13 modules, including unexpected hub proteins as potential drug targets (e.g., GFPT1, LRPPRC, PINK1, DOCK2, and PTPN6). Analysis of 195 colorectal cancers identifies protein markers for RNA-based consensus molecular subtypes (CMSs) and two immune subtypes with prognostic value. We report a cancer type classifier for identification of cancers of unknown primary origin. All TPCPA data can be queried in a dedicated web resource.

Keywords:  bioinformatics; biomarker/ target; colorectal cancer subtypes; mass spectrometry; multi-cancer (sub)type classification; pan-cancer; proteome

DOI:  https://doi.org/10.1016/j.ccell.2025.05.003
Clin Exp Med. 2025 May 26. 25(1): 176

Impact of proteostasis workload on sensitivity to proteasome inhibitors in multiple myeloma.

Jindrich Sedlacek.

  Genomic alterations and enormous monoclonal immunoglobulin production cause multiple myeloma to heavily depend on proteostasis mechanisms, including protein folding and degradation. These findings support the use of proteasome inhibitors for treating multiple myeloma and mantle cell lymphoma. Myeloma treatment has evolved, especially with the availability of new drugs, such as proteasome inhibitors, into therapeutic strategies for both frontline and relapsed/refractory disease settings. However, proteasome inhibitors are generally not effective enough to cure most patients. Natural resistance and eventual acquired resistance led to relapsed/refractory disease and poor prognosis. Advances in the understanding of cellular proteostasis and the development of innovative drugs that also target other proteostasis network components offer opportunities to exploit the intrinsic vulnerability of myeloma cells. This review outlines recent findings on the molecular mechanisms regulating cellular proteostasis pathways, as well as resistance, sensitivity, and escape strategies developed against proteasome inhibitors and provides a rationale and examples for novel combinations of proteasome inhibitors with FDA-approved drugs and investigational drugs targeting the NRF1 (NFE2L1)-mediated proteasome bounce-back response, redox homeostasis, heat shock response, unfolding protein response, autophagy, and VCP/p97 to increase proteotoxic stress, which can improve the efficacy of antimyeloma therapy based on proteasome inhibitors.

Keywords:  Autophagy; Heat shock response; Proteasome bounce-back response; Redox homeostasis; UPR; VCP/p97

DOI:  https://doi.org/10.1007/s10238-025-01713-z
Biochem Biophys Res Commun. 2025 May 21. pii: S0006-291X(25)00778-8. [Epub ahead of print]772 152064

IRF2-driven upregulation of OAS3 promotes AML cell proliferation by modulating the JAK-STAT signaling pathway.

Xi Zhang, Liang Zhong, Li Zhai, Haitao Li, Beizhong Liu.

  Acute myeloid leukemia (AML) presents significant treatment challenges due to its heterogeneity and resistance to conventional therapies. This study explored the role of 2'-5'-oligoadenylate synthetase 3 (OAS3) in AML progression and its potential as a prognostic and therapeutic biomarker. Through bioinformatics analysis, OAS3 was found to be significantly upregulated in AML patients and associated with poor clinical outcomes. Functional assays in AML cell lines revealed that silencing OAS3 suppressed cell proliferation, induced G1 phase arrest, and promoted apoptosis, while its overexpression enhanced cell growth. Pathway analysis and western blotting demonstrated that OAS3 regulates the JAK-STAT signaling pathway. Further investigation revealed that interferon regulatory factor 2 (IRF2) acts as a transcription factor that binds to the promoter region of OAS3 and enhances its expression, thereby indirectly modulating the JAK-STAT pathway. Cotransfection experiments with IRF2 and si-OAS3 supported this regulatory mechanism. In vivo studies using a xenograft model and subsequent immunohistochemical analysis of tumor specimens confirmed the role of OAS3 in AML progression. These findings highlight OAS3 as a critical player in AML pathogenesis, functioning through the JAK-STAT pathway activation under the transcriptional control of IRF2. The study suggests that OAS3 could serve as a valuable prognostic marker and therapeutic target, offering a promising avenue to improve AML treatment outcomes.

Keywords:  AML; IRF2; JAK-STAT signaling; OAS3; Prognosis

DOI:  https://doi.org/10.1016/j.bbrc.2025.152064
Mol Syst Biol. 2025 May 27.

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments.

Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Sara Sdelci, Sandra Orchard, Henning Hermjakob, Georg Kustatscher, Kevin Drew.

  Macromolecular protein complexes carry out most cellular functions. Unfortunately, we lack the subunit composition for many human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify >15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing nearly 70% of human proteins into their physical contexts. We globally characterize our complexes using mass spectrometry based protein covariation data (ProteomeHD.2) and identify covarying complexes suggesting common functional associations. hu.MAP3.0 generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 5871 mutually exclusive proteins in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI's Complex Portal ( https://www.ebi.ac.uk/complexportal/home ) and provide complexes through our hu.MAP3.0 web interface ( https://humap3.proteincomplexes.org/ ). We expect our resource to be highly impactful to the broader research community.

Keywords:  Disease Candidates; Machine Learning; Mutually Exclusive; Protein Complex; Protein Interaction

DOI:  https://doi.org/10.1038/s44320-025-00121-5
Res Pharm Sci. 2025 Apr;20(2): 304-315

Galectin-9 induces IL-1β production as a key inflammatory cytokine in the acute myeloid leukemia cell line (U937).

Nafiseh Behranvand, Farzad Nasri, Maryam Vakily Moghaddam, Mohammad Davoodzadeh Gholami, Elahe Safari, Nafiseh Esmaeil, Reza Falak.

   Background and purpose: T-cell immunoglobulin and mucin-domain containing protein-3 (TIM-3)/ galectin-9 (Gal-9)/ autocrine loop in myeloid leukemia stem cells provokes inflammation through the NF-κB signaling pathway, which is influential in the expression of inflammatory factors. Interleukin 1β (IL-1β) is a vital inflammatory cytokine that plays an important role in the proliferation and therapy resistance of acute myeloid leukemia (AML) cells. This study aimed to assess the effect of Gal-9 on IL-1β in the human leukemic U937 cell line.
Experimental approach: The U937 cells were cultured in different concentrations of Gal-9. Cell counting kit-8 was used to assess the effect of Gal-9 on human leukemic U937 cell proliferation. Also, its impact on the expression of TIM-3, Gal-9, IL-1β, IL-1βR, IL-1βRAP, and NLRP3 genes and IL-1β protein was studied by RT-PCR and ELISA, respectively. Moreover, the effect of Gal-9 on the NF-κB signaling pathway was evaluated by western blotting.
Findings/Results: U937 cells were expanded in the presence of Gal-9 in a concentration-dependent manner. Following treatment of U937 cells with Gal-9, the gene expression of Gal-9, IL-1B, IL-1BR, and IL-1BRAP were significantly upregulated compared to the control group. The IL-1β concentration increased following Gal-9 treatment in a concentration-dependent manner, while following time-pass its level significantly decreased. Furthermore, Gal-9 slightly increased NF-κB phosphorylation.
Conclusion and implications: Gal-9 increased IL-1β level as a critical inflammatory cytokine in the proliferation and resistance of AML cells to therapy. According to this finding, targeting and blocking the TIM-3/Gal-9 autocrine loop can suppress IL-1β production and facilitate AML treatment.

Keywords:  AML; GAL-9; IL-1β; Inflammation; NF-κB

DOI:  https://doi.org/10.4103/RPS.RPS_234_23