Genes and immunity最新文献

{"title":"Macrophage inhibition in the alleviation of nonalcoholic steatohepatitis caused by bariatric surgery","authors":"Qianwen Zheng, Shizhou Deng, Xiyu Chen, Yayun Wang, Yanling Yang","doi":"10.1038/s41435-025-00334-6","DOIUrl":"10.1038/s41435-025-00334-6","url":null,"abstract":"The incidence of nonalcoholic steatohepatitis (NASH) is increasing worldwide, and effective treatment is urgently needed. To understand the molecular mechanisms behind the effectiveness of bariatric surgery in treating NASH, we integrated single-cell and bulk RNA sequencing data to identify the role of liver macrophage polarization in alleviating NASH and screen possible drugs for treatment. Analysis revealed that bariatric surgery alleviates NASH by inhibiting liver M1 macrophage polarization with 12 differentially expressed M1 macrophage-related genes. Additionally, 56 potentially effective drugs were predicted for NASH treatment. These findings shed light on the effectiveness of bariatric surgery in treating NASH and offer potential drug candidates for further exploration.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 4","pages":"297-311"},"PeriodicalIF":4.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12353787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077436","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}

{"title":"The role of B cell immunity in lung adenocarcinoma","authors":"Long Shu, Tania Tao, Desheng Xiao, Shuang Liu, Yongguang Tao","doi":"10.1038/s41435-025-00331-9","DOIUrl":"10.1038/s41435-025-00331-9","url":null,"abstract":"Lung cancer is the deadliest cancer globally. Non-small cell lung cancer (NSCLC), including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma, constitutes a significant portion of cases. Adenocarcinoma, the most prevalent type, has seen a rising incidence. Immune checkpoint inhibitors (ICIs) have improved outcomes in lung adenocarcinoma (LUAD), yet response rates remain unsatisfactory. PD-1/PD-L1 inhibitors are primary ICIs for LUAD, targeting the PD-1/PD-L1 pathway between CD8+ T cells and tumor cells. However, LUAD presents a “cold tumor” phenotype with fewer CD8+ T cells and lower PD-1 expression, leading to resistance to ICIs. Thus, understanding the function of other immune cell in tumor microenvironment is crucial for developing novel immunotherapies for LUAD. B cells, which is part of the adaptive immune system, have gained attention for its role in cancer immunology. While research on B cells lags behind T cells, recent studies reveal their close correlation with prognosis and immunotherapy effectiveness in various solid tumors, including lung cancer. B cells show higher abundance, activity, and prognostic significance in LUAD than that in LUSC. This review summarizes the difference of B cell immunity between LUAD and other lung cancers, outlines the role of B cell immunity in LUAD.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"253-265"},"PeriodicalIF":4.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975313","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":"A Golgi apparatus-related signature predicts the immune microenvironment and prognosis of gastric cancer","authors":"Changlei Wu, Liang Sun, Wenjie Zhu, Chao Huang, Zhengming Zhu, Zitao Liu","doi":"10.1038/s41435-025-00332-8","DOIUrl":"10.1038/s41435-025-00332-8","url":null,"abstract":"In recent years, numerous studies have provided evidence of the involvement of the Golgi apparatus (GA) in various stages of cancer development. Nonetheless, the specific impact of GA-related characteristics on gastric cancer (GC) progression remains ambiguous. We utilized LASSO and multivariate COX regression methods to develop a GA-associated risk score (GARS). The GARS is constructed from seven signature genes, which are highly expressed in tumors. In our research, we have found that GARS is an effective indicator for predicting the prognosis of GC, chemotherapy sensitivity, and immune therapy response. Patients in the low GARS group exhibit characteristics such as a good prognosis, increased sensitivity to immune therapy, 5-fluorouracil, and paclitaxel. Finally, our experimental results confirm that knocking down F2R significantly reduces the proliferation and migration abilities of GC cells. This study highlights the importance of GA characteristics in predicting the prognosis of GC and in developing personalized treatment strategies. The experimental findings on F2R offer valuable theoretical insights for the diagnosis and management of GC.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"242-252"},"PeriodicalIF":4.5,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994000","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":"Novel modulation of T effector memory cells-expressing CD45RA by prednisone in inoperable advanced type B thymoma patients","authors":"Xin-tao Yu, Jian Cui, Xing-guo Yang, Xiang Gao, Lei Yu","doi":"10.1038/s41435-025-00329-3","DOIUrl":"10.1038/s41435-025-00329-3","url":null,"abstract":"Due to the covert onset of thymoma, nearly 30% of patients are diagnosed at stage III or IV, losing the opportunity for surgical treatment. We have initiated the application of prednisone in treating refractory thymoma and explored biomarkers to identify potential cases that might benefit from prednisone treatment. In a study involving 96 patients with thymoma, we confirmed a significant tumor shrinkage with prednisone acetate treatment. A reduced diameter ratio indicated that type B1 and B2 thymomas exhibited the most obvious response to prednisone acetate, especially type B2 thymoma. However, the reduced diameter ratio was < 30% in type A, AB, and B3 thymomas. Immunofluorescence and flow cytometry of tumor tissues indicated that TEMRA (T Effector Memory-Expressing CD45RA) cells primarily exist in type B thymoma. However, the percentage of interleukin-8 + TEMRA cells decreased only in B1 and B2 thymoma tissues after prednisone acetate treatment. These findings are particularly significant for patients with type B thymoma with stage III or IV.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"222-228"},"PeriodicalIF":4.5,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983988","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}

{"title":"Characterizing the immune landscape of tumor-infiltrating lymphocytes in non-small cell lung cancer","authors":"Jin-Guo Liu, Lin Yu, Xian-Ling Guo, Xue-Min He, Man Li, Ren-Yuan Gao, Bing-Hui Zhao, Qian-Yu Li, Wen-Jing Zhu, Ping Xu, Xiao-Hua Gu, Yong-An Chen, Xiao-Lan Yin, Yan Shang, Zhen-Hong Guo, Jia-Hao Mao, Yang-Xi Hu, Li-Ming Lu, Jian Hua, Hua Zhang, Yue Li","doi":"10.1038/s41435-025-00330-w","DOIUrl":"10.1038/s41435-025-00330-w","url":null,"abstract":"Tumor-Infiltrating Lymphocytes (TILs) immunotherapy is a highly promising treatment for Non-small Cell Lung Cancer (NSCLC), which is responsible for 18% of all cancer-related deaths. The heterogeneity of TILs remains poorly understood. Here, we utilized combined single-cell RNA (scRNA)/T cell receptor sequencing (scTCR-seq) data from lung adenocarcinoma (LUAD) patients. Naïve CD4+ and effector memory CD8+ T cells were increased in tumor tissue compared with circulating blood samples. Activated signaling pathways were detected, and GZMA was identified as a potential novel diagnostic biomarker. During the transitional phase, macrophages (FTL) and dendritic (AIF1) cells transported the most CD3 TCR clones to T cells, while cytotoxicity CD8+ T (NKG7) cells transported to terminal exhausted CD8+ T cells. In both transition and expansion phases, T helper cells (CXCL13) are transported to regulatory T cells (Tregs). Additionally, we investigated the expression profiles of key cytokines, checkpoint receptors, and their ligands. Cytotoxicity CD8+ T cells (CCL5 and IFNG), T helper cells (FTL, TNFRSF4, and TIGIT), and regulatory T cells (CTLA4, TIGIT and FTL) exhibited functional roles in both primary and metastatic tumor stages. Taken together, our study provides a single-cell resolution of the TIL immune landscape and suggests potential treatment strategies to overcome drug resistance.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"229-241"},"PeriodicalIF":4.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983864","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":"Association between HLA genetics and SARS-CoV-2 infection in a large real-world cohort","authors":"Stanley I. Letovsky, Xia Cao, Jill A. Hollenbach, Steven J. Mack, Martin Maiers","doi":"10.1038/s41435-025-00328-4","DOIUrl":"10.1038/s41435-025-00328-4","url":null,"abstract":"Genetic variation in the human leukocyte antigen (HLA) region is thought to influence susceptibility to and severity of a variety of infectious diseases. Several studies have explored a possible relationship between HLA genetics and SARS-CoV-2 infection, although mixed results, small sample sizes, and difficulty controlling for exposure risk have made it difficult to draw firm conclusions. Here, a dataset of 419,234 subjects with HLA genotype data and COVID-19 PCR test results was studied. A baseline analysis was performed to examine the association of non-HLA factors on COVID-19 positivity. Then, multivariate logistic regressions, incorporating single and paired HLA alleles, were performed and then corrected for significant factors from the baseline analysis. Proxies for socioeconomic status and exposure risk were significantly associated with COVID-19 positivity across all ancestry groups studied. Forty-one single HLA alleles displayed significant association with COVID-19 positivity; after controlling for socioeconomic status and exposure risk, only eight significant associations remained. Additionally, two HLA allele pairs were associated with test positivity after correction. Of all variables, socioeconomic status showed the greatest effect size. The results from this study suggest that many, if not all, of the reported associations between HLA alleles and SARS-CoV-2 infection may be spurious, owing to confounding factors.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"213-221"},"PeriodicalIF":4.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005552","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}

{"title":"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, Rajalingam Raja, 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/s41435-025-00325-7","DOIUrl":"10.1038/s41435-025-00325-7","url":null,"abstract":"Hemophilia-A (HA) is the X-linked bleeding disorder caused by heterogeneous factor (F)VIII gene (F8)-mutations and deficiencies in plasma-FVIII-activity that prevent intrinsic-pathway mediated coagulation-amplification. Severe-HA patients (HAPs) require life-long infusions of therapeutic-FVIII-proteins (tFVIIIs) but ~30% develop neutralizing-tFVIII-antibodies called “FVIII-inhibitors (FEIs)”. We investigated the genetics underlying the variable risk of FEI-development in 450 North American HAPs (206 and 244 respectively self-reporting black-African- or white-European-ancestry) by analyzing the genotypes of single-nucleotide-variations (SNVs) in candidate immune-mediated-disease (IMD)-genes using a binary linear-mixed model of genetic association with baseline-FEI-status, the dependent variable, while simultaneously accounting for their genetic relationships and heterogeneous-F8-mutations to prevent the statistical problem of non-independence. We a priori selected gene-centric-association-scans of pleiotropic-IMD-genes implicated in the development of either ≥2 autoimmune-/autoinflammatory-disorders (AADs) or FEIs and ≥1 AAD. We found that baseline-FEI-status was significantly associated with NOS2A (rs117382854; p = 3.2 × 10−6) and B3GNT2 (rs10176009; p = 5.1 × 10−6)—pleiotropic-IMD-genes known previously to function in anti-microbial-/-tumoral-immunity but not in the development of FEIs—and confirmed associations with CTLA4 (rs231780; p = 2.2 × 10−5). We also found that baseline-FEI-status has a substantial heritability (~55%) that involves (i) a F8-mutation-specific component of ~8%, (ii) an additive-genetic contribution from SNVs in IMD-genes of ~47%, and (iii) race, which is a significant determinant independent of F8-mutation-types and non-F8-genetics.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"179-189"},"PeriodicalIF":4.5,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967698","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":"Comprehensive analysis of heat shock proteins in glioma revealed the association with glioma-associated myeloid cells","authors":"Jiacheng Xu, Yuduo Guo, Weihai Ning, Jun Wang, Yujia Chen, Deshan Liu, Jingjing Yang, Yongmei Song, Hongwei Zhang","doi":"10.1038/s41435-025-00327-5","DOIUrl":"10.1038/s41435-025-00327-5","url":null,"abstract":"In the central nervous system, glioma stands as the predominant primary brain tumor. Heat shock proteins exerted a critical influence on tumor progression and tumor immune microenvironment. However, research on heat shock proteins in glioma remained ambiguous. We analyzed data from the CPTAC, TCGA, and GTEx databases, identifying seven heat shock protein genes critical to glioma prognosis. Subsequently, through Lasso regression, a model based on heat shock protein genes (DNAJC7, DNAJC12, HSPB2, HSP90B1, HSPA5) was constructed. And the risk score showed a positive correlation to the immune score. Further investigation into immune cells revealed that HSPA5 and HSP90B1 were expressed at higher levels in glioma and significantly linked to M2 macrophage infiltration. Considering the limited research on HSP90B1 in glioma, we further revealed that HSP90B1 might have a connection with two crucial signaling pathways within tumors: PI3K/AKT and Wnt/β-catenin. Given that lactate could promote the M2 polarization of macrophages, we further found that HSP90B1 could enhance the transcription of glycolysis-related genes, including LDHA. Overall, our study demonstrated that heat shock protein genes were significantly linked to glioma patient prognosis. Additionally, we observed that HSP90B1 had a significant relationship with M2 macrophage infiltration and potentially regulated LDHA level in glioma.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"200-212"},"PeriodicalIF":4.5,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990073","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}

{"title":"Transcript-targeted antigen mapping reveals the potential of POSTN splicing junction epitopes in glioblastoma immunotherapy","authors":"Zujian Xiong, Chaim T. Sneiderman, Chloe R. Kuminkoski, Jared Reinheimer, Lance Schwegman, ReidAnn E. Sever, Ahmed Habib, Baoli Hu, Sameer Agnihotri, Dhivyaa Rajasundaram, Pascal O. Zinn, Thomas G. Forsthuber, Ian F. Pollack, Xuejun Li, Itay Raphael, Gary Kohanbash","doi":"10.1038/s41435-025-00326-6","DOIUrl":"10.1038/s41435-025-00326-6","url":null,"abstract":"Tumor antigens are crucial for T-cell mediated immunotherapy, but identified antigens for gliomas remain limited. Aberrant splicing variants are commonly expressed in tumors, resulting in unique tumor isoforms with potential antigenic properties. Herein, we analyzed multi-omics data from 587 glioma patients and assembled a library of putative tumor-enriched isoform antigens (TIA) and corresponding peptides presented on each HLA-I allele. We constructed an individual-specific TIA peptide candidate repertoire for each patient based on their TIA expression and HLA-I haplotypes. TIAs were highly expressed, enriched with glioma malignancy, and demonstrated strong HLA-binding affinity. We focused on periostin isoform-203 (POSTN-203), which was associated with poor survival of patients and contained multiple predicted HLA-restricted peptide epitopes. A selected HLA-A11-restricted peptide from POSTN-203 (POSTN-203A11) induced antigen-specific T-cell responses against both peptide-pulsed and POSTN-203-expressing glioma cells in an HLA-specific manner. Our findings highlight TIAs as a promising source of immunogenic antigens and POSTN-203 as a potential promising target for glioma immunotherapy.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 3","pages":"190-199"},"PeriodicalIF":4.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779786","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":"Age-dependent gene expression trajectories during early childhood in children at increased risk for type 1 diabetes","authors":"Ivo Zeller, Andreas Weiss, Sandra Hummel, Anette-Gabriele Ziegler, Ezio Bonifacio","doi":"10.1038/s41435-025-00324-8","DOIUrl":"10.1038/s41435-025-00324-8","url":null,"abstract":"Early childhood is a period of rapid growth and immune system development. It is also critical for type 1 diabetes (T1D) autoimmunity, which has a peak incidence between 1 and 2 years of age. Here, we investigated age-related longitudinal gene expression changes in peripheral blood mononuclear cells from children aged 3 months to 3 years who had an increased genetic risk for T1D, aiming to delineate gene expression trajectories and identify patterns potentially linked to the development of islet autoimmunity. We found 2 432 genes (12.5% of analyzed genes) to exhibit significant temporal dynamics in the first 3 years of life. These genes were grouped into six major clusters each demonstrating distinct expression trajectories of consistent increase or decrease with age, as well as U-shaped, and inverted U-shaped age-related patterns. Notably, genes in clusters with U-shaped expression trajectories, which mirrored the incidence of islet autoantibodies, were enriched for T1D susceptibility genes, particularly within the Major Histocompatibility Complex (MHC) region. This study underscores the dynamic nature of gene expression in early childhood and its potential connection to T1D risk.","PeriodicalId":12691,"journal":{"name":"Genes and immunity","volume":"26 2","pages":"173-177"},"PeriodicalIF":4.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12006016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669636","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}