CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.
{"title":"Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs","authors":"Kuan Ren, Fengxia Zhou, Fan Zhang, Mingyu Yin, Yuwei Zhu, Shouyu Wang, Yan Chen, Tengjin Huang, Zixuan Wu, Jiale He, Anqi Zhang, Changyou Guo, Zhiwei Huang","doi":"10.1038/s41422-024-00952-1","DOIUrl":"10.1038/s41422-024-00952-1","url":null,"abstract":"CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 5","pages":"370-385"},"PeriodicalIF":44.1,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00952-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140349225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-02DOI: 10.1038/s41422-024-00954-z
Isabella R. Gengaro, Lei S. Qi
{"title":"Persistent in vivo epigenetic silencing of Pcsk9","authors":"Isabella R. Gengaro, Lei S. Qi","doi":"10.1038/s41422-024-00954-z","DOIUrl":"10.1038/s41422-024-00954-z","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"607-608"},"PeriodicalIF":28.1,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00954-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140346070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-02DOI: 10.1038/s41422-024-00955-y
Amir Khan, Klaus Ley
{"title":"Immunotherapy for atherosclerosis by targeting pro-inflammatory T cells","authors":"Amir Khan, Klaus Ley","doi":"10.1038/s41422-024-00955-y","DOIUrl":"10.1038/s41422-024-00955-y","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 7","pages":"467-468"},"PeriodicalIF":28.1,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00955-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140751261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Atherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without Fc-binding capability. Our analysis shows that anti-PD-1 mAb with Fc-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without Fc-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.
动脉粥样硬化（AS）是导致全球心脑血管疾病的主要原因，其驱动因素是脂质含量的积累和慢性炎症。传统策略主要侧重于降低血脂，以控制动脉粥样硬化的发展，但残留的炎症风险会导致重大不良心血管事件（MACE）。虽然针对先天性免疫的抗炎疗法减少了 MACEs，但许多患者仍面临重大风险。强直性脊柱炎进展的另一个关键因素是适应性免疫，但其在预防强直性脊柱炎中的潜在作用仍不清楚。为了研究这个问题，我们对患有强直性脊柱炎斑块的肿瘤患者进行了一项回顾性队列研究。我们发现，抗程序性细胞死亡蛋白1（PD-1）单克隆抗体（mAb）能显著缩小强直性脊柱炎斑块的大小。通过多组学单细胞分析，我们全面描述了强直性脊柱炎斑块特异性PD-1+ T细胞的特征，这些细胞具有激活和促炎作用。我们证明，抗PD-1 mAb被骨髓表达的Fcγ受体（FcγRs）捕获后，会与T细胞上表达的PD-1相互作用。这种相互作用使抗PD-1 mAb成为PD-1配体的替代物，在PD-1配体缺乏的强直性脊柱炎斑块中抑制T细胞功能。此外，我们还对使用具有或不具有Fc结合能力的抗PD-1 mAb治疗的肿瘤患者进行了前瞻性队列研究。我们的分析表明，具有 Fc 结合能力的抗 PD-1 mAb 能有效缩小 AS 斑块，而不具有 Fc 结合能力的抗 PD-1 mAb 则不能。我们的研究表明，T细胞靶向免疫疗法是解决人类强直性脊柱炎的有效策略。
{"title":"Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans","authors":"Lin Fan, Junwei Liu, Wei Hu, Zexin Chen, Jie Lan, Tongtong Zhang, Yang Zhang, Xianpeng Wu, Zhiwei Zhong, Danyang Zhang, Jinlong Zhang, Rui Qin, Hui Chen, Yunfeng Zong, Jianmin Zhang, Bing Chen, Jun Jiang, Jifang Cheng, Jingyi Zhou, Zhiwei Gao, Zhenjie Liu, Ying Chai, Junqiang Fan, Pin Wu, Yinxuan Chen, Yuefeng Zhu, Kai Wang, Ying Yuan, Pintong Huang, Ying Zhang, Huiqin Feng, Kaichen Song, Xun Zeng, Wei Zhu, Xinyang Hu, Weiwei Yin, Wei Chen, Jian’an Wang","doi":"10.1038/s41422-024-00945-0","DOIUrl":"10.1038/s41422-024-00945-0","url":null,"abstract":"Atherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without Fc-binding capability. Our analysis shows that anti-PD-1 mAb with Fc-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without Fc-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 6","pages":"407-427"},"PeriodicalIF":44.1,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00945-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140139503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Neural signals can significantly influence cancer prognosis. However, how cancer cells may proactively modulate the nervous system to benefit their own survival is incompletely understood. In this study, we report an overlapping pattern of brain responses, including that in the paraventricular nucleus of the hypothalamus, in multiple mouse models of peripheral cancers. A multi-omic screening then identifies leukemia inhibitory factor (LIF) and galectin-3 (Gal3) as the key cytokines released by these cancer cell types to trigger brain activation. Importantly, increased plasma levels of these two cytokines are observed in patients with different cancers. We further demonstrate that pharmacologic or genetic blockage of cancer cell-derived LIF or Gal3 signaling abolishes the brain responses and strongly inhibits tumor growth. In addition, ablation of peripheral sympathetic actions can similarly restore antitumor immunity. These results have elucidated a novel, shared mechanism of multiple cancer cell types hijacking the nervous system to promote tumor progression.
{"title":"Multiple cancer cell types release LIF and Gal3 to hijack neural signals","authors":"Qun Xu, Ying Cao, Fanni Kong, Jiaqi Liu, Xin Chen, Yifei Zhao, Chin-Hui Lai, Xin Zhou, Hao Hu, Wei Fu, Jian Chen, Jing Yang","doi":"10.1038/s41422-024-00946-z","DOIUrl":"10.1038/s41422-024-00946-z","url":null,"abstract":"Neural signals can significantly influence cancer prognosis. However, how cancer cells may proactively modulate the nervous system to benefit their own survival is incompletely understood. In this study, we report an overlapping pattern of brain responses, including that in the paraventricular nucleus of the hypothalamus, in multiple mouse models of peripheral cancers. A multi-omic screening then identifies leukemia inhibitory factor (LIF) and galectin-3 (Gal3) as the key cytokines released by these cancer cell types to trigger brain activation. Importantly, increased plasma levels of these two cytokines are observed in patients with different cancers. We further demonstrate that pharmacologic or genetic blockage of cancer cell-derived LIF or Gal3 signaling abolishes the brain responses and strongly inhibits tumor growth. In addition, ablation of peripheral sympathetic actions can similarly restore antitumor immunity. These results have elucidated a novel, shared mechanism of multiple cancer cell types hijacking the nervous system to promote tumor progression.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 5","pages":"345-354"},"PeriodicalIF":44.1,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00946-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-06DOI: 10.1038/s41422-024-00938-z
Ran Feng, Feng Liu, Ruofei Li, Zhifen Zhou, Zhuoheng Lin, Song Lin, Shengcheng Deng, Yingying Li, Baoting Nong, Ying Xia, Zhiyi Li, Xiaoqin Zhong, Shuhan Yang, Gang Wan, Wenbin Ma, Su Wu, Zhou Songyang
Rheb is a small G protein that functions as the direct activator of the mechanistic target of rapamycin complex 1 (mTORC1) to coordinate signaling cascades in response to nutrients and growth factors. Despite extensive studies, the guanine nucleotide exchange factor (GEF) that directly activates Rheb remains unclear, at least in part due to the dynamic and transient nature of protein–protein interactions (PPIs) that are the hallmarks of signal transduction. Here, we report the development of a rapid and robust proximity labeling system named Pyrococcus horikoshii biotin protein ligase (PhBPL)-assisted biotin identification (PhastID) and detail the insulin-stimulated changes in Rheb-proximity protein networks that were identified using PhastID. In particular, we found that the lysosomal V-ATPase subunit ATP6AP1 could dynamically interact with Rheb. ATP6AP1 could directly bind to Rheb through its last 12 amino acids and utilizes a tri-aspartate motif in its highly conserved C-tail to enhance Rheb GTP loading. In fact, targeting the ATP6AP1 C-tail could block Rheb activation and inhibit cancer cell proliferation and migration. Our findings highlight the versatility of PhastID in mapping transient PPIs in live cells, reveal ATP6AP1’s role as an unconventional GEF for Rheb, and underscore the importance of ATP6AP1 in integrating mTORC1 activation signals through Rheb, filling in the missing link in Rheb/mTORC1 activation.
{"title":"The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb","authors":"Ran Feng, Feng Liu, Ruofei Li, Zhifen Zhou, Zhuoheng Lin, Song Lin, Shengcheng Deng, Yingying Li, Baoting Nong, Ying Xia, Zhiyi Li, Xiaoqin Zhong, Shuhan Yang, Gang Wan, Wenbin Ma, Su Wu, Zhou Songyang","doi":"10.1038/s41422-024-00938-z","DOIUrl":"10.1038/s41422-024-00938-z","url":null,"abstract":"Rheb is a small G protein that functions as the direct activator of the mechanistic target of rapamycin complex 1 (mTORC1) to coordinate signaling cascades in response to nutrients and growth factors. Despite extensive studies, the guanine nucleotide exchange factor (GEF) that directly activates Rheb remains unclear, at least in part due to the dynamic and transient nature of protein–protein interactions (PPIs) that are the hallmarks of signal transduction. Here, we report the development of a rapid and robust proximity labeling system named Pyrococcus horikoshii biotin protein ligase (PhBPL)-assisted biotin identification (PhastID) and detail the insulin-stimulated changes in Rheb-proximity protein networks that were identified using PhastID. In particular, we found that the lysosomal V-ATPase subunit ATP6AP1 could dynamically interact with Rheb. ATP6AP1 could directly bind to Rheb through its last 12 amino acids and utilizes a tri-aspartate motif in its highly conserved C-tail to enhance Rheb GTP loading. In fact, targeting the ATP6AP1 C-tail could block Rheb activation and inhibit cancer cell proliferation and migration. Our findings highlight the versatility of PhastID in mapping transient PPIs in live cells, reveal ATP6AP1’s role as an unconventional GEF for Rheb, and underscore the importance of ATP6AP1 in integrating mTORC1 activation signals through Rheb, filling in the missing link in Rheb/mTORC1 activation.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 5","pages":"355-369"},"PeriodicalIF":44.1,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00938-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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