Pub Date : 2025-09-25DOI: 10.1038/s41435-025-00345-3
Marcio A. Almeida, Vincent P. Diego, Kevin R. Viel, Bernadette W. Luu, Karin Haack, Raja Rajalingam, Afshin Ameri, Meera Chitlur, Natalia Rydz, David Lillicrap, Raymond G. Watts, Craig M. Kessler, Christopher Ramsey, Long V. Dinh, Benjamin Kim, Jerry S. Powell, Eron G. Manusov, Juan M. Peralta, Ruayda Bouls, Shirley M. Abraham, Yu-Min Shen, Carlos M. Murillo, Henry Mead, Paul V. Lehmann, Eli J. Fine, Miguel A. Escobar, Satish Kumar, Barbara A. Konkle, Sarah Williams-Blangero, Carol K. Kasper, Laura Almasy, Shelley A. Cole, John Blangero, Tom E. Howard
{"title":"Correction: A scan of pleiotropic immune mediated disease genes identifies novel determinants of baseline FVIII inhibitor status in hemophilia A","authors":"Marcio A. Almeida, Vincent P. Diego, Kevin R. Viel, Bernadette W. Luu, Karin Haack, Raja Rajalingam, Afshin Ameri, Meera Chitlur, Natalia Rydz, David Lillicrap, Raymond G. Watts, Craig M. Kessler, Christopher Ramsey, Long V. Dinh, Benjamin Kim, Jerry S. Powell, Eron G. Manusov, Juan M. Peralta, Ruayda Bouls, Shirley M. Abraham, Yu-Min Shen, Carlos M. Murillo, Henry Mead, Paul V. Lehmann, Eli J. Fine, Miguel A. Escobar, Satish Kumar, Barbara A. Konkle, Sarah Williams-Blangero, Carol K. Kasper, Laura Almasy, Shelley A. Cole, John Blangero, Tom E. Howard","doi":"10.1038/s41435-025-00345-3","DOIUrl":"10.1038/s41435-025-00345-3","url":null,"abstract":"","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 6","pages":"626-626"},"PeriodicalIF":4.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00345-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-24DOI: 10.1038/s41435-025-00355-1
Ning Zhang, Tangbing Chen, Yintao Chang, Mingzhi Cao, Huan Wang, Chengli Wu, Hong Jiang
Acute lung injury (ALI) is a common and life-threatening lung disease. This study investigated the mechanism by which dexmedetomidine (Dex) alleviates lipopolysaccharide (LPS)-induced ALI, focusing on its regulation of macrophage autophagy and polarization. Initially, a mouse model of LPS-induced ALI was pretreated with Dex. Pulmonary function, histopathological changes, apoptosis, macrophage numbers in bronchoalveolar lavage fluid (BALF), M1/M2 macrophage ratios, iNOS/Arg-1/LC3/P62 fluorescence intensity, and autophagy flux were assessed. Subsequently, RAW264.7 macrophages were treated with LPS and Dex, transfected with si-ACOD1 or si-HIF-1α, and co-cultured with mouse pulmonary microvessel endothelial cells (MPMVECs). The results showed that Dex relieved autophagy flux blockage and promoted autophagy in ALI mice. LPS promoted ACOD1 and HIF-1α levels, and Dex further enhanced their levels to boost macrophage autophagy and M2 polarization. ACOD1 was transcriptionally regulated by HIF-1α. Collectively, Dex mitigated LPS-induced MPMVEC injury and ALI by enhancing HIF-1α-mediated ACOD1 transcription, thus promoting macrophage autophagy and M2 polarization.
{"title":"Dexmedetomidine relieves LPS-induced acute lung injury by boosting HIF-1a/ACOD1 driven anti-inflammatory macrophage polarization","authors":"Ning Zhang, Tangbing Chen, Yintao Chang, Mingzhi Cao, Huan Wang, Chengli Wu, Hong Jiang","doi":"10.1038/s41435-025-00355-1","DOIUrl":"10.1038/s41435-025-00355-1","url":null,"abstract":"Acute lung injury (ALI) is a common and life-threatening lung disease. This study investigated the mechanism by which dexmedetomidine (Dex) alleviates lipopolysaccharide (LPS)-induced ALI, focusing on its regulation of macrophage autophagy and polarization. Initially, a mouse model of LPS-induced ALI was pretreated with Dex. Pulmonary function, histopathological changes, apoptosis, macrophage numbers in bronchoalveolar lavage fluid (BALF), M1/M2 macrophage ratios, iNOS/Arg-1/LC3/P62 fluorescence intensity, and autophagy flux were assessed. Subsequently, RAW264.7 macrophages were treated with LPS and Dex, transfected with si-ACOD1 or si-HIF-1α, and co-cultured with mouse pulmonary microvessel endothelial cells (MPMVECs). The results showed that Dex relieved autophagy flux blockage and promoted autophagy in ALI mice. LPS promoted ACOD1 and HIF-1α levels, and Dex further enhanced their levels to boost macrophage autophagy and M2 polarization. ACOD1 was transcriptionally regulated by HIF-1α. Collectively, Dex mitigated LPS-induced MPMVEC injury and ALI by enhancing HIF-1α-mediated ACOD1 transcription, thus promoting macrophage autophagy and M2 polarization.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 6","pages":"561-576"},"PeriodicalIF":4.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Innate immune memory, also called trained immunity, refers to the ability of innate immune cells to gain memory characteristics after transient stimulation, resulting in a nonspecific modified inflammatory response upon secondary remote challenge. Bronchial epithelial cells (BECs) participate in innate immune defence and are the first cells of the lower respiratory tract to encounter inhaled pathogens. We recently showed that BECs are capable of innate immune memory after preexposure to Pseudomonas aeruginosa flagellin through epigenetic mechanisms. In the present study, we investigated such mechanisms through the modification of chromatin architecture induced by flagellin preexposure that results in subsequent changes of gene expression. By conducting an unsupervised approach to jointly analyse chromatin accessibility and gene expression, we mapped the remodelling of the epigenomic and transcriptomic profiles during the establishment of BECs memory. We identified a Memory regulatory profile induced by flagellin exposure. It includes clusters of upregulated genes related to inflammation that are linked to a sustainable gain in chromatin accessibility and with an increased activity of specific transcription factors (TFs) whose binding may drive this process. In summary, we demonstrated that flagellin exposure induced changes in chromatin condensation in BECs, which sustains the reprogramming of transcriptional patterns.
{"title":"The epigenomic landscape of bronchial epithelial cells reveals the establishment of trained immunity","authors":"Jeanne Bigot, Rachel Legendre, Juliette Hamroune, Sébastien Jacques, Mathieu Le Gars, Nicolas Millet, Loïc Guillot, Harriet Corvol, Christophe Hennequin, Juliette Guitard, Jean-Yves Coppée, Viviane Balloy, Claudia Chica","doi":"10.1038/s41435-025-00357-z","DOIUrl":"10.1038/s41435-025-00357-z","url":null,"abstract":"Innate immune memory, also called trained immunity, refers to the ability of innate immune cells to gain memory characteristics after transient stimulation, resulting in a nonspecific modified inflammatory response upon secondary remote challenge. Bronchial epithelial cells (BECs) participate in innate immune defence and are the first cells of the lower respiratory tract to encounter inhaled pathogens. We recently showed that BECs are capable of innate immune memory after preexposure to Pseudomonas aeruginosa flagellin through epigenetic mechanisms. In the present study, we investigated such mechanisms through the modification of chromatin architecture induced by flagellin preexposure that results in subsequent changes of gene expression. By conducting an unsupervised approach to jointly analyse chromatin accessibility and gene expression, we mapped the remodelling of the epigenomic and transcriptomic profiles during the establishment of BECs memory. We identified a Memory regulatory profile induced by flagellin exposure. It includes clusters of upregulated genes related to inflammation that are linked to a sustainable gain in chromatin accessibility and with an increased activity of specific transcription factors (TFs) whose binding may drive this process. In summary, we demonstrated that flagellin exposure induced changes in chromatin condensation in BECs, which sustains the reprogramming of transcriptional patterns.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 6","pages":"577-588"},"PeriodicalIF":4.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00357-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hepatocellular carcinoma (HCC) is a major cause of cancer death globally, with a poor prognosis. The long non-coding RNA TUG1 has been implicated, but its specific role in HCC remains unclear. RT-qPCR was used to evaluate TUG1 and PD-L1 expression, while GEO and TCGA databases were utilized to compare TUG1 levels between HCC patients and healthy controls. In vitro, including CCK8, colony formation, and transwell, assessed cell growth. CD8 + T cell cytotoxicity was evaluated through HCC cells co-culture experiments, and the interaction of miR-377-3p with TUG1 and PD-L1 was examined using dual-luciferase reporter assays. Results indicated that TUG1 was upregulated in HCC, particularly in advanced-stage disease, and PD-L1 expression positively correlated with TUG1 levels. Notably, lenvatinib (LEN) treatment downregulated both TUG1 and PD-L1 in HCC cells, enhancing CD8 + T cell-mediated cytotoxicity. Overexpression of TUG1 diminished the efficacy of LEN, while TUG1 knockdown enhanced it. Mechanistically, TUG1 was found to sponge miR-377-3p, thereby increasing PD-L1 expression. In vivo, TUG1 knockdown combined with LEN treatment significantly reduced tumor growth and PD-L1 expression. In conclusion, TUG1 promotes HCC progression by enhancing PD-L1 through miR-377-3p, with its knockdown enhancing the therapeutic efficacy of LEN, highlighting TUG1’s potential as a novel target for HCC treatment.
{"title":"TUG1 targeting enhances anticancer immunity thereby facilitating lenvatinib efficacy in hepatocellular carcinoma","authors":"Siyao Che, Longguang He, Qinshou Chen, Yiqiao Mo, Fuliang Li, Junwei Huang, Zikang Ruan","doi":"10.1038/s41435-025-00358-y","DOIUrl":"10.1038/s41435-025-00358-y","url":null,"abstract":"Hepatocellular carcinoma (HCC) is a major cause of cancer death globally, with a poor prognosis. The long non-coding RNA TUG1 has been implicated, but its specific role in HCC remains unclear. RT-qPCR was used to evaluate TUG1 and PD-L1 expression, while GEO and TCGA databases were utilized to compare TUG1 levels between HCC patients and healthy controls. In vitro, including CCK8, colony formation, and transwell, assessed cell growth. CD8 + T cell cytotoxicity was evaluated through HCC cells co-culture experiments, and the interaction of miR-377-3p with TUG1 and PD-L1 was examined using dual-luciferase reporter assays. Results indicated that TUG1 was upregulated in HCC, particularly in advanced-stage disease, and PD-L1 expression positively correlated with TUG1 levels. Notably, lenvatinib (LEN) treatment downregulated both TUG1 and PD-L1 in HCC cells, enhancing CD8 + T cell-mediated cytotoxicity. Overexpression of TUG1 diminished the efficacy of LEN, while TUG1 knockdown enhanced it. Mechanistically, TUG1 was found to sponge miR-377-3p, thereby increasing PD-L1 expression. In vivo, TUG1 knockdown combined with LEN treatment significantly reduced tumor growth and PD-L1 expression. In conclusion, TUG1 promotes HCC progression by enhancing PD-L1 through miR-377-3p, with its knockdown enhancing the therapeutic efficacy of LEN, highlighting TUG1’s potential as a novel target for HCC treatment.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 6","pages":"549-560"},"PeriodicalIF":4.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-09DOI: 10.1038/s41435-025-00356-0
Aarón D. Ramírez-Sánchez, Stephanie Zühlke, Raúl Aguirre-Gamboa, Martijn Vochteloo, Lude Franke, Knut E. A. Lundin, Sebo Withoff, Iris H. Jonkers
In coeliac disease (CeD), the epithelial lining (EL) of the small intestine is severely damaged by a complex auto-inflammatory response, leading intraepithelial lymphocytes to attack epithelial cells. To understand the intestinal changes and genetic regulation in CeD, we investigated the heterogeneity in the transcriptomic profile of the duodenal EL using RNA-seq and eQTL analysis on predicted cell types. The study included duodenal biopsies from 82 patients, grouped into controls, gluten-free diet treated CeD and untreated CeD. We identified 1 862 differential expressed genes, which clustered into four sets. Two sets, one upregulated for cell cycle function (n = 366) and one downregulated for digestion, transmembrane transport, and laminin pathways (n = 543), defined three sample groups based on inflammation status: non-inflamed, mild inflammation or severe inflammation. The remaining two sets of genes were enriched for immune (n = 458) and extracellular matrix and barrier functions (n = 495) and were sufficient to classify samples into their disease conditions. Finally, deconvoluting eQTL effects from epithelial and immune cells identified 6 and 15 cell-type-mediated eQTL genes, respectively. In sum, we identified genes expressed in the duodenal EL whose expression reflect heterogeneity in CeD and that may be used as biomarkers to assess CeD condition and its mucosal and immune status.
{"title":"Transcriptomics and eQTLs reveal inflammatory heterogeneity in the duodenal lining in coeliac disease","authors":"Aarón D. Ramírez-Sánchez, Stephanie Zühlke, Raúl Aguirre-Gamboa, Martijn Vochteloo, Lude Franke, Knut E. A. Lundin, Sebo Withoff, Iris H. Jonkers","doi":"10.1038/s41435-025-00356-0","DOIUrl":"10.1038/s41435-025-00356-0","url":null,"abstract":"In coeliac disease (CeD), the epithelial lining (EL) of the small intestine is severely damaged by a complex auto-inflammatory response, leading intraepithelial lymphocytes to attack epithelial cells. To understand the intestinal changes and genetic regulation in CeD, we investigated the heterogeneity in the transcriptomic profile of the duodenal EL using RNA-seq and eQTL analysis on predicted cell types. The study included duodenal biopsies from 82 patients, grouped into controls, gluten-free diet treated CeD and untreated CeD. We identified 1 862 differential expressed genes, which clustered into four sets. Two sets, one upregulated for cell cycle function (n = 366) and one downregulated for digestion, transmembrane transport, and laminin pathways (n = 543), defined three sample groups based on inflammation status: non-inflamed, mild inflammation or severe inflammation. The remaining two sets of genes were enriched for immune (n = 458) and extracellular matrix and barrier functions (n = 495) and were sufficient to classify samples into their disease conditions. Finally, deconvoluting eQTL effects from epithelial and immune cells identified 6 and 15 cell-type-mediated eQTL genes, respectively. In sum, we identified genes expressed in the duodenal EL whose expression reflect heterogeneity in CeD and that may be used as biomarkers to assess CeD condition and its mucosal and immune status.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"519-530"},"PeriodicalIF":4.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00356-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145029594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-05DOI: 10.1038/s41435-025-00353-3
Matthew D. Estrada, Christopher J. Gebhardt, Mariam A. Salem, Christina N. Rau, Kruthika Sharma, Rebecca A. Glynn, Craig H. Bassing, Eugene M. Oltz, Patrick L. Collins
Double-strand breaks represent the most dangerous form of DNA damage, and in resting cells, these breaks are sealed via the non-homologous end joining (NHEJ) factor Ligase IV (LIG4). Excessive NHEJ may be genotoxic, necessitating multiple mechanisms to control NHEJ activity. However, a clear mechanism of transcriptional control for them has not yet been identified. Here, we examine mechanisms governing Lig4 transcription in mammals, finding that most tissues maintain very low levels of LIG4 production. Select tissues upregulate LIG4, employing different strategies for genomic regulation. In developing lymphocytes, the Lig4 locus is devoid of long-range chromatin contacts; instead, its expression and role in immune development depend upon a promoter-proximal intronic regulatory element. Deletion of the Lig4 intronic regulatory element results in thymocyte-specific loss of Lig4 upregulation, defects in lymphocyte development, and altered antigen receptor rearrangement. Our findings show the NHEJ gene, Lig4, is transcriptionally controlled to support stage-specific function concurrent with programmed DSBs. Moreover, we provide an example of how DNA cis-regulatory elements very close to a promoter can have substantial transcriptional effects.
{"title":"Transcriptional regulation of Ligase IV by an intronic regulatory element directs thymocyte development","authors":"Matthew D. Estrada, Christopher J. Gebhardt, Mariam A. Salem, Christina N. Rau, Kruthika Sharma, Rebecca A. Glynn, Craig H. Bassing, Eugene M. Oltz, Patrick L. Collins","doi":"10.1038/s41435-025-00353-3","DOIUrl":"10.1038/s41435-025-00353-3","url":null,"abstract":"Double-strand breaks represent the most dangerous form of DNA damage, and in resting cells, these breaks are sealed via the non-homologous end joining (NHEJ) factor Ligase IV (LIG4). Excessive NHEJ may be genotoxic, necessitating multiple mechanisms to control NHEJ activity. However, a clear mechanism of transcriptional control for them has not yet been identified. Here, we examine mechanisms governing Lig4 transcription in mammals, finding that most tissues maintain very low levels of LIG4 production. Select tissues upregulate LIG4, employing different strategies for genomic regulation. In developing lymphocytes, the Lig4 locus is devoid of long-range chromatin contacts; instead, its expression and role in immune development depend upon a promoter-proximal intronic regulatory element. Deletion of the Lig4 intronic regulatory element results in thymocyte-specific loss of Lig4 upregulation, defects in lymphocyte development, and altered antigen receptor rearrangement. Our findings show the NHEJ gene, Lig4, is transcriptionally controlled to support stage-specific function concurrent with programmed DSBs. Moreover, we provide an example of how DNA cis-regulatory elements very close to a promoter can have substantial transcriptional effects.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"509-518"},"PeriodicalIF":4.5,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00353-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-03DOI: 10.1038/s41435-025-00352-4
Andrii Iakovliev, Olivia Castellini-Pérez, Buddhiprabha Erabadda, PRECISESADS Clinical Consortium, PRECISESADS Flow Cytometry Consortium, Javier Martín, Guillermo Barturen, Paul M. McKeigue, Elena Carnero-Montoro, Marta E. Alarcón-Riquelme, Athina Spiliopoulou
The “omnigenic” hypothesis postulates that the polygenic effects of common variants on a typical complex trait coalesce on relatively few core genes through trans-effects on their expression. Our aim was to identify core genes for systemic lupus erythematosus (SLE) by testing for association with genome-wide aggregated trans-effects (GATE) scores for gene expression in a large genetic dataset (5267/4909 SLE cases/controls). SLE was strongly associated with upregulation of expression of eight interferon-stimulated genes driven by shared trans-effects. We estimate that trans-effects on interferon signaling account for 9% of the total genetic effect on SLE risk. Outside this pathway, GATE analysis detected twenty putative core genes for SLE. Direct protein measurements for these genes were strongly associated with SLE in UK Biobank. Two putative core genes (TNFRSF17, TNFRSF13B) encode receptors (BCMA, TACI) expressed on B cells; their ligands (BAFF, APRIL) are targeted by drugs licensed or in development for SLE. Four genes (PDCD1, LAG3, TNFRSF9, CD27) encode receptors that have been characterized as immune checkpoints, and three (CD5L, SIGLEC1, CXCL13) are biomarkers of SLE disease activity. These results provide genetic support for existing drug targets in SLE (interferon signaling, BAFF/APRIL signaling) and identify other possible therapeutic targets including immune checkpoint receptors.
{"title":"Discovery of core genes for systemic lupus erythematosus via genome-wide aggregated trans-effects analysis","authors":"Andrii Iakovliev, Olivia Castellini-Pérez, Buddhiprabha Erabadda, PRECISESADS Clinical Consortium, PRECISESADS Flow Cytometry Consortium, Javier Martín, Guillermo Barturen, Paul M. McKeigue, Elena Carnero-Montoro, Marta E. Alarcón-Riquelme, Athina Spiliopoulou","doi":"10.1038/s41435-025-00352-4","DOIUrl":"10.1038/s41435-025-00352-4","url":null,"abstract":"The “omnigenic” hypothesis postulates that the polygenic effects of common variants on a typical complex trait coalesce on relatively few core genes through trans-effects on their expression. Our aim was to identify core genes for systemic lupus erythematosus (SLE) by testing for association with genome-wide aggregated trans-effects (GATE) scores for gene expression in a large genetic dataset (5267/4909 SLE cases/controls). SLE was strongly associated with upregulation of expression of eight interferon-stimulated genes driven by shared trans-effects. We estimate that trans-effects on interferon signaling account for 9% of the total genetic effect on SLE risk. Outside this pathway, GATE analysis detected twenty putative core genes for SLE. Direct protein measurements for these genes were strongly associated with SLE in UK Biobank. Two putative core genes (TNFRSF17, TNFRSF13B) encode receptors (BCMA, TACI) expressed on B cells; their ligands (BAFF, APRIL) are targeted by drugs licensed or in development for SLE. Four genes (PDCD1, LAG3, TNFRSF9, CD27) encode receptors that have been characterized as immune checkpoints, and three (CD5L, SIGLEC1, CXCL13) are biomarkers of SLE disease activity. These results provide genetic support for existing drug targets in SLE (interferon signaling, BAFF/APRIL signaling) and identify other possible therapeutic targets including immune checkpoint receptors.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"497-508"},"PeriodicalIF":4.5,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00352-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-02DOI: 10.1038/s41435-025-00354-2
Marie Bourdon, Caroline Manet, Xavier Montagutelli
Interferon regulatory factor 3 (IRF3) is the first transcription factor activating the expression of type I interferons (IFN-I). It is present in the cytoplasm of most cell types under basal conditions and its activation by phosphorylation allows a rapid triggering of the IFN-I pathway in response to viral infection. This activation of IFN-I is amplified by IRF7, the other major IFN-I transcription factor which expression is induced, in most cell types, by the interferon response. However, recent data have shown that the role of IRF3 in viral infection extends beyond the IFN-I pathway. Here, we review the studies investigating the impact of IRF3 deficiencies in infected cells and in vivo, in mice and in humans. We discuss the discrepancies between and within studies, between isolated cells and whole organisms. While IRF3 is also involved in other pathological processes, we highlight how the newly discovered functions of IRF3 deepen our understanding of its multiple roles in viral infections, which could stimulate the development of pharmacological manipulation of its biological activities.
{"title":"IRF3 in viral infections: more than just triggering the interferon response","authors":"Marie Bourdon, Caroline Manet, Xavier Montagutelli","doi":"10.1038/s41435-025-00354-2","DOIUrl":"10.1038/s41435-025-00354-2","url":null,"abstract":"Interferon regulatory factor 3 (IRF3) is the first transcription factor activating the expression of type I interferons (IFN-I). It is present in the cytoplasm of most cell types under basal conditions and its activation by phosphorylation allows a rapid triggering of the IFN-I pathway in response to viral infection. This activation of IFN-I is amplified by IRF7, the other major IFN-I transcription factor which expression is induced, in most cell types, by the interferon response. However, recent data have shown that the role of IRF3 in viral infection extends beyond the IFN-I pathway. Here, we review the studies investigating the impact of IRF3 deficiencies in infected cells and in vivo, in mice and in humans. We discuss the discrepancies between and within studies, between isolated cells and whole organisms. While IRF3 is also involved in other pathological processes, we highlight how the newly discovered functions of IRF3 deepen our understanding of its multiple roles in viral infections, which could stimulate the development of pharmacological manipulation of its biological activities.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"419-428"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-18DOI: 10.1038/s41435-025-00351-5
Hongya Zhu, Divya Ganapathi Sankaran, Norah L. Smith, Ciarán W. P. Daly, Kristel Yee Mon, Cybelle Tabilas, Erin M. Wissink, Brian D. Rudd, Andrew Grimson
Naïve CD8 + T cells are heterogenous, with subsets exhibiting divergent kinetics and functions post-activation. MicroRNAs, important mediators of post-transcriptional regulation, contribute to specification of different naïve T cell subsets. However, the microRNA regulatory circuits mediating functional specialization of naïve subsets are poorly understood. Here, we profiled microRNA expression in diverse subsets of naïve CD8 + T cells, revealing significant differences in their microRNA expression landscapes. We developed a novel framework, miR-Inf, to decipher microRNA regulatory programs. miR-Inf features two innovative attributes: (i) an efficient approach based on intron-exon ratios to estimate gene decay rates from a compendium of RNA-seq profiles, in order to better capture microRNA regulatory effects, and (ii) identification of cell-type-specific microRNA targets by integrating decay rate data and microRNA expression data. We applied this framework to identify consequential miRNAs in naïve CD8 + T cell subsets and predicted their subset-specific targets. Our analyses revealed that miR-29, a microRNA known to be important in CD8 + T cells, likely functions by modulating transcripts encoding epigenetic factors, thereby pre-programming different naïve T cell subsets to exhibit different immune responses post-activation. Collectively, our data and broadly applicable framework defined microRNA regulatory circuits across a variety of naïve CD8 + T cell subsets.
{"title":"An efficient framework to decipher microRNA regulatory programs applied to T cells","authors":"Hongya Zhu, Divya Ganapathi Sankaran, Norah L. Smith, Ciarán W. P. Daly, Kristel Yee Mon, Cybelle Tabilas, Erin M. Wissink, Brian D. Rudd, Andrew Grimson","doi":"10.1038/s41435-025-00351-5","DOIUrl":"10.1038/s41435-025-00351-5","url":null,"abstract":"Naïve CD8 + T cells are heterogenous, with subsets exhibiting divergent kinetics and functions post-activation. MicroRNAs, important mediators of post-transcriptional regulation, contribute to specification of different naïve T cell subsets. However, the microRNA regulatory circuits mediating functional specialization of naïve subsets are poorly understood. Here, we profiled microRNA expression in diverse subsets of naïve CD8 + T cells, revealing significant differences in their microRNA expression landscapes. We developed a novel framework, miR-Inf, to decipher microRNA regulatory programs. miR-Inf features two innovative attributes: (i) an efficient approach based on intron-exon ratios to estimate gene decay rates from a compendium of RNA-seq profiles, in order to better capture microRNA regulatory effects, and (ii) identification of cell-type-specific microRNA targets by integrating decay rate data and microRNA expression data. We applied this framework to identify consequential miRNAs in naïve CD8 + T cell subsets and predicted their subset-specific targets. Our analyses revealed that miR-29, a microRNA known to be important in CD8 + T cells, likely functions by modulating transcripts encoding epigenetic factors, thereby pre-programming different naïve T cell subsets to exhibit different immune responses post-activation. Collectively, our data and broadly applicable framework defined microRNA regulatory circuits across a variety of naïve CD8 + T cell subsets.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"486-496"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41435-025-00351-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Excessive neutrophil extracellular traps (NETs) induce an intense inflammatory response in periodontitis. Recently, Tregs were shown to be essential for attenuating inflammation-driven bone resorption. However, the regulation of Tregs differentiation by NETs in periodontitis is still unclear and needs further investigation. In this study, a murine experimental periodontitis model was established either without or with NETs depletion via DNase I. Firstly, we revealed that NETs accumulated significantly in both periodontal tissues and sera of mice models with periodontitis, while the depletion of NETs alleviated alveolar bone resorption. Moreover, RNA sequencing and bioinformatics analysis revealed that NETs depletion regulated the immune response of gingival tissue, especially affecting T-cell differentiation, and identified potential regulatory pathways. Subsequently, we verified that inhibition of NETs promoted the infiltration of Tregs and increased expression levels of IL-10 and TGF-β in periodontal tissue. Furthermore, in vitro studies demonstrated that NETs produced by P. g-LPS-stimulated neutrophils impeded the differentiation of co-cultured naive CD4+ T cells into Tregs, which could be restored by DNase I-mediated digestion of NETs. In conclusion, excessive NETs could exacerbate alveolar bone resorption in periodontitis by interfering with the differentiation of Tregs, and DNase I provides a novel targeted strategy for the immunotherapy of periodontitis.
{"title":"Neutrophil extracellular traps aggravate periodontitis by disturbing regulatory T-cell differentiation","authors":"Beibei Chen, Danni Song, Tianfan Cheng, Lijian Jin, Yongming Li, Chongshan Liao","doi":"10.1038/s41435-025-00350-6","DOIUrl":"10.1038/s41435-025-00350-6","url":null,"abstract":"Excessive neutrophil extracellular traps (NETs) induce an intense inflammatory response in periodontitis. Recently, Tregs were shown to be essential for attenuating inflammation-driven bone resorption. However, the regulation of Tregs differentiation by NETs in periodontitis is still unclear and needs further investigation. In this study, a murine experimental periodontitis model was established either without or with NETs depletion via DNase I. Firstly, we revealed that NETs accumulated significantly in both periodontal tissues and sera of mice models with periodontitis, while the depletion of NETs alleviated alveolar bone resorption. Moreover, RNA sequencing and bioinformatics analysis revealed that NETs depletion regulated the immune response of gingival tissue, especially affecting T-cell differentiation, and identified potential regulatory pathways. Subsequently, we verified that inhibition of NETs promoted the infiltration of Tregs and increased expression levels of IL-10 and TGF-β in periodontal tissue. Furthermore, in vitro studies demonstrated that NETs produced by P. g-LPS-stimulated neutrophils impeded the differentiation of co-cultured naive CD4+ T cells into Tregs, which could be restored by DNase I-mediated digestion of NETs. In conclusion, excessive NETs could exacerbate alveolar bone resorption in periodontitis by interfering with the differentiation of Tregs, and DNase I provides a novel targeted strategy for the immunotherapy of periodontitis.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 5","pages":"475-485"},"PeriodicalIF":4.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144821274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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