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Nechanitzky, Robert; Ramachandran, Parameswaran; Nechanitzky, Duygu; Li, Wanda Y.; Wakeham, Andrew C.; Haight, Jillian; Saunders, Mary E.; Epelman, Slava; Mak, Tak W.
doi: 10.1038/s41418-024-01268-8pmid: 38383888
PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB-related functions in macrophages at steady-state, we generated and compared single-cell RNA-sequencing (scRNAseq) datasets obtained from myeloid cell subsets of wild type (WT) and PirB-deficient knockout (PirB KO) mice. To facilitate this analysis, we developed a novel approach to clustering parameter optimization called “Cluster Similarity Scoring and Distinction Index” (CaSSiDI). We demonstrate that CaSSiDI is an adaptable computational framework that facilitates tandem analysis of two scRNAseq datasets by optimizing clustering parameters. We further show that CaSSiDI offers more advantages than a standard Seurat analysis because it allows direct comparison of two or more independently clustered datasets, thereby alleviating the need for batch-correction while identifying the most similar and different clusters. Using CaSSiDI, we found that PirB is a novel regulator of Cebpb expression that controls the generation of Ly6Clo patrolling monocytes and the expansion properties of peritoneal macrophages. PirB’s effect on Cebpb is tissue-specific since it was not observed in splenic red pulp macrophages (RPMs). However, CaSSiDI revealed a segregation of the WT RPM population into a CD68loIrf8+ “neuronal-primed” subset and an CD68hiFtl1+ “iron-loaded” subset. Our results establish the utility of CaSSiDI for single-cell assay analyses and the determination of optimal clustering parameters. Our application of CaSSiDI in this study has revealed previously unknown roles for PirB in myeloid cell populations. In particular, we have discovered homeostatic functions for PirB that are related to Cebpb expression in distinct macrophage subsets.
Jiao, Huipeng; James, Sharmy J.; Png, Chin Wen; Cui, Chaoyu; Li, Heng; Li, Liang; Chia, Wan Ni; Min, Nyo; Li, Weiyun; Claser, Carla; Rénia, Laurent; Wang, Hongyan; Chen, Mark I-Cheng; Chu, Justin Jang Hann; Tan, Kevin Shyong Wei; Deng, Yinyue; Zhang, Yongliang
Guo, Dong; Zhang, Mingming; Qi, Bingchao; Peng, Tingwei; Liu, Mingchuan; Li, Zhelong; Fu, Feng; Guo, Yanjie; Li, Congye; Wang, Ying; Hu, Lang; Li, Yan
doi: 10.1038/s41418-023-01241-xpmid: 38017147
Lipid droplet (LD) accumulation is a notable feature of obesity-induced cardiomyopathy, while underlying mechanism remains poorly understood. Here we show that mice fed with high-fat diet (HFD) exhibited significantly increase in cardiac LD and RTN3 expression, accompanied by cardiac function impairment. Multiple loss- and gain-of function experiments indicate that RTN3 is critical to HFD-induced cardiac LD accumulation. Mechanistically, RTN3 directly bonds with fatty acid binding protein 5 (FABP5) to facilitate the directed transport of fatty acids to endoplasmic reticulum, thereby promoting LD biogenesis in a diacylglycerol acyltransferase 2 dependent way. Moreover, lipid overload-induced RTN3 upregulation is due to increased expression of CCAAT/enhancer binding protein α (C/EBPα), which positively regulates RTN3 transcription by binding to its promoter region. Notably, above findings were verified in the myocardium of obese patients. Our findings suggest that manipulating LD biogenesis by modulating RTN3 may be a potential strategy for treating cardiac dysfunction in obese patients.
Zhang, Bin; Li, Jie; Wang, Yijun; Liu, Xixi; Yang, Xiao; Liao, Zhiyun; Deng, Suke; Deng, Yue; Zhou, Zhiyuan; Tian, Yu; Wei, Wenwen; Meng, Jingshu; Hu, Yan; Wan, Chao; Zhang, Zhanjie; Huang, Fang; Wen, Lu; Wu, Bian; Sun, Yajie; Li, Yan; Yang, Kunyu
Hu, Rui; Chen, Xiangyi; Su, Qiang; Wang, Zhaoyue; Wang, Xushu; Gong, Mengting; Xu, Minglu; Le, Rongrong; Gao, Yawei; Dai, Peng; Zhang, Zhen-Ning; Shao, Li; Li, Weida
doi: 10.1038/s41418-024-01258-wpmid: 38321214
Pancreatic β-cell failure by WFS1 deficiency is manifested in individuals with wolfram syndrome (WS). The lack of a suitable human model in WS has impeded progress in the development of new treatments. Here, human pluripotent stem cell derived pancreatic islets (SC-islets) harboring WFS1 deficiency and mouse model of β cell specific Wfs1 knockout were applied to model β-cell failure in WS. We charted a high-resolution roadmap with single-cell RNA-seq (scRNA-seq) to investigate pathogenesis for WS β-cell failure, revealing two distinct cellular fates along pseudotime trajectory: maturation and stress branches. WFS1 deficiency disrupted β-cell fate trajectory toward maturation and directed it towards stress trajectory, ultimately leading to β-cell failure. Notably, further investigation of the stress trajectory identified activated integrated stress response (ISR) as a crucial mechanism underlying WS β-cell failure, characterized by aberrant eIF2 signaling in WFS1-deficient SC-islets, along with elevated expression of genes in regulating stress granule formation. Significantly, we demonstrated that ISRIB, an ISR inhibitor, efficiently reversed β-cell failure in WFS1-deficient SC-islets. We further validated therapeutic efficacy in vivo with β-cell specific Wfs1 knockout mice. Altogether, our study provides novel insights into WS pathogenesis and offers a strategy targeting ISR to treat WS diabetes.
Saunders, Tahnee L.; Windley, Simon P.; Gervinskas, Gediminas; Balka, Katherine R.; Rowe, Caitlin; Lane, Rachael; Tailler, Maximilien; Nguyen, Thanh Ngoc; Ramm, Georg; Lazarou, Michael; De Nardo, Dominic; Kile, Benjamin T.; McArthur, Kate
doi: 10.1038/s41418-024-01260-2pmid: 38396150
During apoptosis mediated by the intrinsic pathway, BAX/BAK triggers mitochondrial permeabilization and the release of cytochrome-c, followed by a dramatic remodelling of the mitochondrial network that results in mitochondrial herniation and the subsequent release of pro-inflammatory mitochondrial components. Here, we show that mitochondrial herniation and subsequent exposure of the inner mitochondrial membrane (IMM) to the cytoplasm, initiates a unique form of mitophagy to deliver these damaged organelles to lysosomes. IMM-induced mitophagy occurs independently of canonical PINK1/Parkin signalling and is driven by ubiquitination of the IMM. Our data suggest IMM-induced mitophagy is an additional safety mechanism that cells can deploy to contain damaged mitochondria. It may have particular relevance in situations where caspase activation is incomplete or inhibited, and in contexts where PINK1/Parkin-mitophagy is impaired or overwhelmed.
Jia, Fei; Wang, Xiaoman; Fu, Yuhua; Zhao, Shi-Min; Lu, Boxun; Wang, Chenji
doi: 10.1038/s41418-024-01261-1pmid: 38332048
Hereditary spastic paraplegia (HSP) is a group of inherited neurodegenerative disorders characterized by progressive lower limb spasticity and weakness. One subtype of HSP, known as SPG54, is caused by biallelic mutations in the DDHD2 gene. The primary pathological feature observed in patients with SPG54 is the massive accumulation of lipid droplets (LDs) in the brain. However, the precise mechanisms and roles of DDHD2 in regulating lipid homeostasis are not yet fully understood. Through Affinity Purification-Mass Spectroscopy (AP-MS) analysis, we identify that DDHD2 interacts with multiple members of the ATG8 family proteins (LC3, GABARAPs), which play crucial roles in lipophagy. Mutational analysis reveals the presence of two authentic LIR motifs in DDHD2 protein that are essential for its binding to LC3/GABARAPs. We show that DDHD2 deficiency leads to LD accumulation, while enhanced DDHD2 expression reduces LD formation. The LC3/GABARAP-binding capacity of DDHD2 and the canonical autophagy pathway both contribute to its LD-eliminating activity. Moreover, DDHD2 enhances the colocalization between LC3B and LDs to promote lipophagy. LD·ATTEC, a small molecule that tethers LC3 to LDs to enhance their autophagic clearance, effectively counteracts DDHD2 deficiency-induced LD accumulation. These findings provide valuable insights into the regulatory roles of DDHD2 in LD catabolism and offer a potential therapeutic approach for treating SPG54 patients.
Xu, Tong; Verhagen, Mathijs P.; Teeuwssen, Miriam; Sun, Wenjie; Joosten, Rosalie; Sacchetti, Andrea; Ewing-Graham, Patricia C.; Jansen, Maurice P. H. M.; Boere, Ingrid A.; Bryce, Nicole S.; Zeng, Jun; Treutlein, Herbert R.; Hook, Jeff; Hardeman, Edna C.; Gunning, Peter W.; Fodde, Riccardo
Showing 1 to 9 of 9 Articles
Detection of cytosolic nucleic acids by pattern recognition receptors, including STING and RIG-I, leads to the activation of multiple signalling pathways that culminate in the production of type I interferons (IFNs) which are vital for host survival during virus infection. In addition to protective immune modulatory functions, type I IFNs are also associated with autoimmune diseases. Hence, it is important to elucidate the mechanisms that govern their expression. In this study, we identified a critical regulatory function of the DUSP4 phosphatase in innate immune signalling. We found that DUSP4 regulates the activation of TBK1 and ERK1/2 in a signalling complex containing DUSP4, TBK1, ERK1/2 and IRF3 to regulate the production of type I IFNs. Mice deficient in DUSP4 were more resistant to infections by both RNA and DNA viruses but more susceptible to malaria parasites. Therefore, our study establishes DUSP4 as a regulator of nucleic acid sensor signalling and sheds light on an important facet of the type I IFN regulatory system.
doi: 10.1038/s41418-024-01257-xpmid: 38287116
Cisplatin-based chemotherapy improves the control of distant metastases in patients with nasopharyngeal carcinoma (NPC); however, around 30% of patients fail treatment due to acquired drug resistance. Epigenetic regulation is known to contribute to cisplatin resistance; nevertheless, the underlying mechanisms remain poorly understood. Here, we showed that lysine-specific demethylase 5B (KDM5B) was overexpressed and correlates with tumor progression and cisplatin resistance in patients with NPC. We also showed that specific inhibition of KDM5B impaired the progression of NPC and reverses cisplatin resistance, both in vitro and in vivo. Moreover, we found that KDM5B inhibited the expression of ZBTB16 by directly reducing H3K4me3 at the ZBTB16 promoter, which subsequently increased the expression of Topoisomerase II- α (TOP2A) to confer cisplatin resistance in NPC. In addition, we showed that the deubiquitinase USP7 was critical for deubiquitinating and stabilizing KDM5B. More importantly, the deletion of USP7 increased sensitivity to cisplatin by disrupting the stability of KDM5B in NPC cells. Therefore, our findings demonstrated that USP7 stabilized KDM5B and promoted cisplatin resistance through the ZBTB16/TOP2A axis, suggesting that targeting KDM5B may be a promising cisplatin-sensitization strategy in the treatment of NPC.
doi: 10.1038/s41418-024-01267-9pmid: 38365970
Phenotypic plasticity, defined as the ability of individual cells with stable genotypes to exert different phenotypes upon exposure to specific environmental cues, represent the quintessential hallmark of the cancer cell en route from the primary lesion to distant organ sites where metastatic colonization will occur. Phenotypic plasticity is driven by a broad spectrum of epigenetic mechanisms that allow for the reversibility of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions (EMT/MET). By taking advantage of the co-existence of epithelial and quasi-mesenchymal cells within immortalized cancer cell lines, we have analyzed the role of EMT-related gene isoforms in the regulation of epithelial mesenchymal plasticity (EMP) in high grade serous ovarian cancer. When compared with colon cancer, a distinct spectrum of downstream targets characterizes quasi-mesenchymal ovarian cancer cells, likely to reflect the different modalities of metastasis formation between these two types of malignancy, i.e. hematogenous in colon and transcoelomic in ovarian cancer. Moreover, upstream RNA-binding proteins differentially expressed between epithelial and quasi-mesenchymal subpopulations of ovarian cancer cells were identified that underlie differential regulation of EMT-related isoforms. In particular, the up- and down-regulation of RBM24 and ESRP1, respectively, represent a main regulator of EMT in ovarian cancer cells. To validate the functional and clinical relevance of our approach, we selected and functionally analyzed the Tropomyosin 1 gene (TPM1), encoding for a protein that specifies the functional characteristics of individual actin filaments in contractile cells, among the ovarian-specific downstream AS targets. The low-molecular weight Tpm1.8/9 isoforms are specifically expressed in patient-derived ascites and promote invasion through activation of EMT and Wnt signaling, together with a broad spectrum of inflammation-related pathways. Moreover, Tpm1.8/9 expression confers resistance to taxane- and platinum-based chemotherapy. Small molecule inhibitors that target the Tpm1 isoforms support targeting Tpm1.8/9 as therapeutic targets for the development of future tailor-made clinical interventions.