Cell surface RNAs, notably glycoRNAs, have been reported, yet the precise compositions of surface RNAs across different primary cell types remain unclear. Here, we introduce a comprehensive suite of methodologies for profiling, imaging, and quantifying specific surface RNAs. We present AMOUR, a method leveraging T7-based linear amplification, to accurately profile surface RNAs while preserving plasma membrane integrity. By integrating fluorescently labeled DNA probes with live primary cells, and employing imaging along with flow cytometry analysis, we can effectively image and quantify representative surface RNAs. Utilizing these techniques, we have identified diverse non-coding RNAs present on mammalian cell surfaces, expanding beyond the known glycoRNAs. We confirm the membrane anchorage and quantify the abundance of several representative surface RNA molecules in cultured HeLa cells and human umbilical cord blood mononuclear cells (hUCB-MNCs). Our imaging and flow cytometry analyses unequivocally confirm the membrane localization of Y family RNAs, spliceosomal snRNA U5, mitochondrial rRNA MTRNR2, mitochondrial tRNA MT-TA, VTRNA1-1, and the long non-coding RNA XIST. Our study not only introduces effective approaches for investigating surface RNAs but also provides a detailed portrayal of the surface RNA landscapes of hUCB-MNCs and murine blood cells, paving the way for future research in the field of surface RNAs.
{"title":"Deciphering the RNA Landscapes on Mammalian Cell Surfaces.","authors":"Xiao Jiang,Chu Xu,Enzhuo Yang,Danhua Xu,Yong Peng,Xue Han,Jingwen Si,Qixin Shao,Zhuo Liu,Qiuxiao Chen,Weizhi He,Shuang He,Yanhui Xu,Chuan He,Xinxin Huang,Lulu Hu","doi":"10.1093/procel/pwaf079","DOIUrl":"https://doi.org/10.1093/procel/pwaf079","url":null,"abstract":"Cell surface RNAs, notably glycoRNAs, have been reported, yet the precise compositions of surface RNAs across different primary cell types remain unclear. Here, we introduce a comprehensive suite of methodologies for profiling, imaging, and quantifying specific surface RNAs. We present AMOUR, a method leveraging T7-based linear amplification, to accurately profile surface RNAs while preserving plasma membrane integrity. By integrating fluorescently labeled DNA probes with live primary cells, and employing imaging along with flow cytometry analysis, we can effectively image and quantify representative surface RNAs. Utilizing these techniques, we have identified diverse non-coding RNAs present on mammalian cell surfaces, expanding beyond the known glycoRNAs. We confirm the membrane anchorage and quantify the abundance of several representative surface RNA molecules in cultured HeLa cells and human umbilical cord blood mononuclear cells (hUCB-MNCs). Our imaging and flow cytometry analyses unequivocally confirm the membrane localization of Y family RNAs, spliceosomal snRNA U5, mitochondrial rRNA MTRNR2, mitochondrial tRNA MT-TA, VTRNA1-1, and the long non-coding RNA XIST. Our study not only introduces effective approaches for investigating surface RNAs but also provides a detailed portrayal of the surface RNA landscapes of hUCB-MNCs and murine blood cells, paving the way for future research in the field of surface RNAs.","PeriodicalId":20790,"journal":{"name":"Protein & Cell","volume":"316 1","pages":""},"PeriodicalIF":21.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breast cancer is a prevalent malignancy worldwide. The majority of breast cancers belong to the estrogen receptor (ER)-positive luminal subtype that can be effectively treated with antiestrogen therapies. However, a significant portion of such malignancies become hormone-refractory and incurable. Cancer cells often uptake more cystines to increase glutathione (GSH) biosynthesis and reduce reactive oxygen species (ROS), thereby preventing ROS-induced ferroptosis and leading to therapeutic resistance. However, few molecules of these processes are targetable for cancer therapy. However, few therapeutic targets have been established that target these processes. Here, we report that the gene for SLC7A13, a member of the SLC7A13-SLC3A1 cystine transporter, was amplified and overexpressed in 19.7% and 49.7% of breast cancers, respectively. SLC7A13 amplification and overexpression were associated with worse overall survival and disease-free survival in patients with luminal breast cancer. Functionally, SLC7A13 overexpression promoted, while its silencing attenuated, cell survival or proliferation. Molecularly, SLC7A13 silencing reduced cystine uptake and GSH biosynthesis, leading to increased lipid ROS levels. The cryo-EM structure of the human SLC7A13-SLC3A1 complex was determined at 2.64 Å, revealing a dimer-of-heterodimers architecture similar to that of other SLC3A1-linked transporters. A specific substrate-binding pocket was identified, containing distinct residues, which suggests a regulatory role in the cystine transporter. These findings suggest that the SLC7A13-SLC3A1 cystine transporter is a therapeutic target for treating luminal breast cancer. They also provide the structural insights for therapeutic development targeting the cystine transporter.
{"title":"Oncogenic role of the SLC7A13-SLC3A1 cystine transporter in human luminal breast cancer and its cryo-EM structure.","authors":"Jing Dong,Tianhao Shi,Bingbiao Lin,Xuetong Liu,Waner Wei,Zichi Geng,Mingcheng Liu,Renhong Yan,Jin-Tang Dong","doi":"10.1093/procel/pwaf076","DOIUrl":"https://doi.org/10.1093/procel/pwaf076","url":null,"abstract":"Breast cancer is a prevalent malignancy worldwide. The majority of breast cancers belong to the estrogen receptor (ER)-positive luminal subtype that can be effectively treated with antiestrogen therapies. However, a significant portion of such malignancies become hormone-refractory and incurable. Cancer cells often uptake more cystines to increase glutathione (GSH) biosynthesis and reduce reactive oxygen species (ROS), thereby preventing ROS-induced ferroptosis and leading to therapeutic resistance. However, few molecules of these processes are targetable for cancer therapy. However, few therapeutic targets have been established that target these processes. Here, we report that the gene for SLC7A13, a member of the SLC7A13-SLC3A1 cystine transporter, was amplified and overexpressed in 19.7% and 49.7% of breast cancers, respectively. SLC7A13 amplification and overexpression were associated with worse overall survival and disease-free survival in patients with luminal breast cancer. Functionally, SLC7A13 overexpression promoted, while its silencing attenuated, cell survival or proliferation. Molecularly, SLC7A13 silencing reduced cystine uptake and GSH biosynthesis, leading to increased lipid ROS levels. The cryo-EM structure of the human SLC7A13-SLC3A1 complex was determined at 2.64 Å, revealing a dimer-of-heterodimers architecture similar to that of other SLC3A1-linked transporters. A specific substrate-binding pocket was identified, containing distinct residues, which suggests a regulatory role in the cystine transporter. These findings suggest that the SLC7A13-SLC3A1 cystine transporter is a therapeutic target for treating luminal breast cancer. They also provide the structural insights for therapeutic development targeting the cystine transporter.","PeriodicalId":20790,"journal":{"name":"Protein & Cell","volume":"30 1","pages":""},"PeriodicalIF":21.1,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ran Wei,Zhehao Du,Jue Wang,Jinlong Bi,Wencong Lyu,Haochen Wang,Jianuo He,Fanju Meng,Lijun Zhang,Chao Zhang,Chen Zhang,Wei Tao
The endocrine system is crucial for maintaining overall homeostasis. However, its cellular signatures have not been elucidated during aging. Here, we conducted the first-ever single-cell transcriptomic profiles from eight endocrine organs in young and aged mice, revealing the activation of cell-type-specific aging pathways, such as loss of proteostasis, genomic instability and reactive oxygen species (ROS). Among six sex-shared endocrine organs, aging severely impaired gene expression networks in functional endocrine cells, accompanied by enhanced immune infiltration and unfolded protein response (UPR). Mechanism investigations showed that expanded aging-associated exhausted T cells activated MHC-I-UPR axis across functional endocrine cells by releasing GZMK. The inhibition of GZMK receptors by small chemical molecules counteracted the UPR and senescence, suggesting the immune infiltration is a possible driver of endocrine aging. Machine learning identified CD59 as a novel aging feature in sex-shared functional endocrine cells. For two sex-specific endocrine organs, both aged ovaries and testes showed enhanced immune responses. Meanwhile, cell-type-specific aging-associated transcriptional changes revealed an enhanced ROS mainly in aged theca cells of ovaries, while aged spermatogonia in testes showed impaired DNA repair. This study provides a comprehensive analysis of endocrine system aging at single-cell resolution, offering profound insights into mechanisms of endocrine aging.
{"title":"A single-cell transcriptomic landscape characterizes the endocrine system aging in the mouse.","authors":"Ran Wei,Zhehao Du,Jue Wang,Jinlong Bi,Wencong Lyu,Haochen Wang,Jianuo He,Fanju Meng,Lijun Zhang,Chao Zhang,Chen Zhang,Wei Tao","doi":"10.1093/procel/pwaf074","DOIUrl":"https://doi.org/10.1093/procel/pwaf074","url":null,"abstract":"The endocrine system is crucial for maintaining overall homeostasis. However, its cellular signatures have not been elucidated during aging. Here, we conducted the first-ever single-cell transcriptomic profiles from eight endocrine organs in young and aged mice, revealing the activation of cell-type-specific aging pathways, such as loss of proteostasis, genomic instability and reactive oxygen species (ROS). Among six sex-shared endocrine organs, aging severely impaired gene expression networks in functional endocrine cells, accompanied by enhanced immune infiltration and unfolded protein response (UPR). Mechanism investigations showed that expanded aging-associated exhausted T cells activated MHC-I-UPR axis across functional endocrine cells by releasing GZMK. The inhibition of GZMK receptors by small chemical molecules counteracted the UPR and senescence, suggesting the immune infiltration is a possible driver of endocrine aging. Machine learning identified CD59 as a novel aging feature in sex-shared functional endocrine cells. For two sex-specific endocrine organs, both aged ovaries and testes showed enhanced immune responses. Meanwhile, cell-type-specific aging-associated transcriptional changes revealed an enhanced ROS mainly in aged theca cells of ovaries, while aged spermatogonia in testes showed impaired DNA repair. This study provides a comprehensive analysis of endocrine system aging at single-cell resolution, offering profound insights into mechanisms of endocrine aging.","PeriodicalId":20790,"journal":{"name":"Protein & Cell","volume":"19 1","pages":""},"PeriodicalIF":21.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: the following articles.","authors":"","doi":"10.1093/procel/pwaf065","DOIUrl":"https://doi.org/10.1093/procel/pwaf065","url":null,"abstract":"","PeriodicalId":20790,"journal":{"name":"Protein & Cell","volume":" ","pages":""},"PeriodicalIF":12.8,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144966390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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