{"title":"Computational neoantigen prediction for cancer immunotherapy.","authors":"Lakshman Tejaswi, Poornima Ramesh, Shetty Aditya, Rajesh Raju, Thottethodi Subrahmanya Keshava Prasad","doi":"10.1038/s41435-025-00365-z","DOIUrl":"https://doi.org/10.1038/s41435-025-00365-z","url":null,"abstract":"<p><p>Cancer represents a significant global health concern, profoundly affecting morbidity and mortality rates worldwide. Due to cancer-associated genetic changes, cancer cells harbor neoantigens (Tumor-Specific Antigens). They are attractive targets for personalized and generalized cancer therapeutics, including cancer vaccines, T cell adoptive therapy, and immunomonitoring. Such antigens can arise at genomic, transcriptomic, and proteomic levels. The host immune system recognizes neoantigens through their presentation on Major Histocompatibility Complexes (MHC), leading to T cell activation and antitumor response, provided sufficient co-stimulatory signals are provided by antigen-presenting cells, including dendritic cells. Computational tools for neoantigen analysis are rapidly advancing, improving prediction accuracy. Bioinformatics tools aid in identifying somatic mutations and selecting neoantigens based on MHC binding and immunogenicity scores. Cost-efficient computational Human Leukocyte Antigen haplotyping uses sequencing data, while proteogenomic strategies, integrating immunopeptidomics, validate neoantigens by detecting peptides naturally presented by tumor cells. Integrating proteome-based validation provides experimental confirmation, strengthening confidence in predictions. Ongoing developments in bioinformatics and multi-omics integration contribute to neoantigen identification, enabling personalized cancer immunotherapies. This review discusses various computational tools/pipelines, their implementation, clinical trials on neoantigenic vaccines, and the limitations/prospects of neoantigen prediction.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318148","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}
Bo Cai, Yizheng You, Longbo Huang, Cheng Zhu, Haofeng Lin, Jinyang Chen, Ruitao Ye, Zhou Zhou, Yibin Huang, Longying Zha, Ligang Jie, Du Hongyan
{"title":"Abnormal activation of platelets and inflammation in smoking-induced rheumatoid arthritis is alleviated by 3,3'-diindolylmethane.","authors":"Bo Cai, Yizheng You, Longbo Huang, Cheng Zhu, Haofeng Lin, Jinyang Chen, Ruitao Ye, Zhou Zhou, Yibin Huang, Longying Zha, Ligang Jie, Du Hongyan","doi":"10.1038/s41435-025-00360-4","DOIUrl":"https://doi.org/10.1038/s41435-025-00360-4","url":null,"abstract":"<p><p>Rheumatoid arthritis (RA) is generally recognized as a complex disease initiated by environmental factors in the context of genetic susceptibility, among which smoking is one of the independent risk factors for RA. Smoking exposure would promote RA inflammation amplification probably because of platelet abnormal activation. This study aims to discover the preventive bioactivities of 3,3'-diindolylmethane (DIM) against RA with smoke exposure and explore the mechanisms by targeting platelet. The findings demonstrate that DIM can ameliorate smoking induced inflammation amplification in CIA mice through diverse of pathology analysis. Notably, the platelet abnormal activation was observed in CIA mice with smoke exposure and it was indeed inhibited by DIM treatment. Additionally, in vitro cigarette smoke extract (CSE) promoted platelet abnormal activation and aggregation characterizing by up-regulation of CD62p expression, Ca<sup>2+</sup> mobilization, ROS release and down-regulation of mitochondrial membrane potential (ΔΨm), while DIM could suppress these processes. We verified DIM could mitigate RA inflammation amplification induced by smoking and smoke exposure via inhibiting MAPK/NF-κB and PI3K/Akt/mTOR pathways phosphorylation during platelets abnormal activation. Our research provided a scientific basis for the rational use of DIM and other phytochemicals in the prevention and treatment of RA with smoking and smoke exposure from the perspective of nutrition.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274469","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}
Yunjie Li, Shuya Bai, Jichang Hu, Heli Li, Chen Hu, Jinzhu Zhao, Hong Qian, Zhouping Tang, Yangyang Feng
{"title":"Post-translational acylation modulates immunosuppression and immunotherapy efficacy in hepatocellular carcinoma.","authors":"Yunjie Li, Shuya Bai, Jichang Hu, Heli Li, Chen Hu, Jinzhu Zhao, Hong Qian, Zhouping Tang, Yangyang Feng","doi":"10.1038/s41435-025-00362-2","DOIUrl":"https://doi.org/10.1038/s41435-025-00362-2","url":null,"abstract":"<p><p>Acylation modification plays a crucial role in modulating hepatocellular carcinoma (HCC) progression, and their specific prognostic implications in HCC have not been thoroughly investigated. Eleven acylation modifications (crotonylation, lactylation, succinylation, benzoylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, palmitoylation, myristoylation, and prenylation) were generated consensus cluster. Then, WGCNA was utilized to identify module genes. Finally, machine learning approach was employed to create acylation modification related genes.score (AMRG.score). This analysis revealed two distinct subtypes of AMRG, each characterized by unique molecular signatures. Through the combination of DEGs, DEGs associated with prognosis, and WGCNA, a total of 21 key genes were identified, leading to the creation of AMRG.score. AMRG.score was rigorously validated across independent external cohorts (TCGA-LIHC, LIRI-JP, GSE10143, GSE14520, GSE27150, GSE36376, and GSE76427) and an in-house cohort, demonstrating its reliability and potential applicability. The AMRG.score serves a dual purpose in its application, as it encapsulates essential the clinical context and offers valuable insights regarding the immunotherapy. In particular, patients categorized with a high AMRG.score displayed an active TME and sensitive to immunotherapy. This novel acylation modification-related prognostic signature could effectively assess the prognosis and therapeutic responses of HCC patients, providing new perspectives for individualized treatment for the patient population.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145228387","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}
{"title":"αCGRP deficiency aggravates pulmonary fibrosis by promoting senescence in alveolar type 2 cells.","authors":"Xiaoting Lv, Qingquan Chen, Ziying Zhou, Weijing Wu, Xingliang Yu, Yiming Zeng","doi":"10.1038/s41435-025-00361-3","DOIUrl":"https://doi.org/10.1038/s41435-025-00361-3","url":null,"abstract":"<p><p>To investigate whether αCGRP (Calca) deficiency exacerbates pulmonary fibrosis (PF) by promoting alveolar type 2 (AT2) cell senescence, we retrospectively analyzed clinical data and lung biopsy samples from PF patients (n = 15). In vivo, lung tissues from Calca-knockout (KO) rats and D-galactose (D-gal)-induced senescence models were analyzed using immunohistochemistry, single-cell RNA sequencing (scRNA-seq), and label-free proteomics. PF patient samples showed low αCGRP expression, AT2 subtype differentiation, and high Calca promoter methylation. In Calca<sup>-/-</sup> rats, AT2 differentiation and oxidative lipid metabolism were enhanced, with increased senescence gene signatures. scRNA-seq revealed upregulation of linoleic, α-linolenic, and arachidonic acid metabolism, alongside suppression of oxidative stress responses in AT2 of the Calca<sup>-/-</sup> group. D-gal treatment induced alveolitis, fibrotic changes and AT2 subtype differentiation, and the most severe alveolar inflammation was found in Calca<sup>-/-</sup>+D-gal rats. Proteomics revealed distinct metabolic pathway alterations between WT + D-gal and Calca<sup>-/-</sup>+D-gal, and Calca<sup>-/-</sup> and WT + D-gal rats. Differences in metabolic and PPAR pathways were observed between Calca<sup>-/-</sup> and Calca<sup>-/-</sup>+D-gal rats. Additionally, both D-gal treatment and Calca<sup>-/-</sup> affect oxidative phosphorylation. Overall, αCGRP deficiency disrupts AT2 lipid metabolism, and accelerates AT2 inflammatory senescence, ultimately promoting pulmonary fibrosis.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191526","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}
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":"https://doi.org/10.1038/s41435-025-00345-3","url":null,"abstract":"","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ning Zhang, Tangbing Chen, Yintao Chang, Mingzhi Cao, Huan Wang, Chengli Wu, Hong Jiang
{"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":"https://doi.org/10.1038/s41435-025-00355-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"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}
{"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":"https://doi.org/10.1038/s41435-025-00357-z","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"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":"https://doi.org/10.1038/s41435-025-00358-y","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":" ","pages":""},"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}
Aarón D. Ramírez-Sánchez, Stephanie Zühlke, Raúl Aguirre-Gamboa, Martijn Vochteloo, Lude Franke, Knut E. A. Lundin, Sebo Withoff, Iris H. Jonkers
{"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}