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Sun H, Han X, Du Z, Chen G, Guo T, Xie F, Gu W, Shi Z. Machine learning for the identification of neoantigen-reactive CD8 + T cells in gastrointestinal cancer using single-cell sequencing. Br J Cancer 2024; 131:387-402. [PMID: 38849478 PMCID: PMC11263575 DOI: 10.1038/s41416-024-02737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND It appears that tumour-infiltrating neoantigen-reactive CD8 + T (Neo T) cells are the primary driver of immune responses to gastrointestinal cancer in patients. However, the conventional method is very time-consuming and complex for identifying Neo T cells and their corresponding T cell receptors (TCRs). METHODS By mapping neoantigen-reactive T cells from the single-cell transcriptomes of thousands of tumour-infiltrating lymphocytes, we developed a 26-gene machine learning model for the identification of neoantigen-reactive T cells. RESULTS In both training and validation sets, the model performed admirably. We discovered that the majority of Neo T cells exhibited notable differences in the biological processes of amide-related signal pathways. The analysis of potential cell-to-cell interactions, in conjunction with spatial transcriptomic and multiplex immunohistochemistry data, has revealed that Neo T cells possess potent signalling molecules, including LTA, which can potentially engage with tumour cells within the tumour microenvironment, thereby exerting anti-tumour effects. By sequencing CD8 + T cells in tumour samples of patients undergoing neoadjuvant immunotherapy, we determined that the fraction of Neo T cells was significantly and positively linked with the clinical benefit and overall survival rate of patients. CONCLUSION This method expedites the identification of neoantigen-reactive TCRs and the engineering of neoantigen-reactive T cells for therapy.
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Affiliation(s)
- Hongwei Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao Han
- KangChen Bio-tech., Ltd, ShangHai, China
| | - Zhengliang Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Geer Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tonglei Guo
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Fei Xie
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Weiyue Gu
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China
| | - Zhiwen Shi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China.
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China.
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Tang Q, Yuan Y, Li L, Xu Y, Ji W, Xiao S, Han Y, Miao W, Cai J, You P, Chen M, Ding S, Li Z, Qi Z, Hou W, Luo H. Comprehensive analysis reveals that LTBR is a immune-related biomarker for glioma. Comput Biol Med 2024; 174:108457. [PMID: 38599071 DOI: 10.1016/j.compbiomed.2024.108457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Glioma is a common malignant brain tumor with great heterogeneity and huge difference in clinical outcomes. Although lymphotoxin (LT) beta receptor (LTBR) has been linked to immune system and response development for decades, the expression and function in glioma have not been investigated. To confirm the expression profile of LTBR, integrated RNA-seq data from glioma and normal brain tissues were analyzed. Functional enrichment analysis, TMEscore analysis, immune infiltration, the correlation of LTBR with immune checkpoints and ferroptosis, and scRNAseq data analysis in gliomas were in turn performed, which pointed out that LTBR was pertinent to immune functions of macrophages in gliomas. In addition, after being trained and validated in the tissue samples of the integrated dataset, an LTBR DNA methylation-based prediction model succeeded to distinguish gliomas from non-gliomas, as well as the grades of glioma. Moreover, by virtue of the candidate LTBR CpG sites, a prognostic risk-score model was finally constructed to guide the chemotherapy, radiotherapy, and immunotherapy for glioma patients. Taken together, LTBR is closely correlated with immune functions in gliomas, and LTBR DNA methylation could serve as a biomarker for diagnosis and prognosis of gliomas.
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Affiliation(s)
- Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Yifan Yuan
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Lingjuan Li
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Yue Xu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Department of General Dentistry, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi Province, China
| | - Wei Ji
- Department of Anesthesiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264000, Shandong Province, China
| | - Siyu Xiao
- Department of Rehabilitation, Gongan Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese Medicine, Jingzhou, 434300, Hubei Province, China
| | - Yi Han
- Naval Medical Center of PLA, Naval Medical University, Shanghai, 200052, China
| | - Wenrong Miao
- Naval Medical Center of PLA, Naval Medical University, Shanghai, 200052, China
| | - Jing Cai
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Pu You
- Shanghai QuietD Biotechnology Co., Ltd., Shanghai, 201210, China
| | - Ming Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Saineng Ding
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Zhen Li
- Shanghai QuietD Biotechnology Co., Ltd., Shanghai, 201210, China.
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
| | - Weiliang Hou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
| | - Hao Luo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
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3
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Stevens-Jones O, Mojzisova H, Elisak M, Constantinescu R, Hanzalova J, Axelsson M, Krysl D. Paraneoplastic or not? Sirtuin 2 in anti-N-methyl-d-aspartate receptor encephalitis. Eur J Neurol 2023; 30:3228-3235. [PMID: 37483157 DOI: 10.1111/ene.15987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND AND PURPOSE N-methyl-d-aspartate receptor (NMDAR) and leucine-rich glioma-inactivated protein 1 (LGI1) encephalitis are important types of autoimmune encephalitis (AE) with significant morbidity. In this study, we used a proteomic approach in search of novel clinically relevant biomarkers in these types of encephalitides. METHODS Swedish and Czech tertiary neuroimmunology centers collaborated in this retrospective exploratory study. Fifty-eight cerebrospinal fluid (CSF) samples of 28 patients with AE (14 definite NMDAR, 14 with definite LGI1 encephalitis) and 30 controls were included. CSF samples were analyzed using proximity extension assay technology (Olink Target 96 Inflammation panel). For each CSF sample, 92 proteins were measured. Clinical variables were retrospectively collected, and correlations with protein levels were statistically analyzed. RESULTS Patients and controls differed significantly in the following 18 biomarkers: TNFRSF9, TNFRSF12, TNFRSF14, TNFβ, TNFα, IL7, IL10, IL12B, IFNγ, CD5, CD6, CASP8, MMP1, CXCL8, CXCL10, CXCL11, IL20RA, and sirtuin 2 (SIRT2). In LGI1 encephalitis, no clinically useful association was found between biomarkers and clinical variables. In the NMDAR encephalitis group, SIRT2, TNFβ, and CD5 were significantly associated with ovarian teratoma. For SIRT2, this was true even for the first patients' CSF sample (SIRT2 without vs. with tumor, mean ± SD = 2.2 ± 0.29 vs. 2.88 ± 0.48; p = 0.007, 95% confidence interval = -1.15 to -0.22; r statistic in point-biserial correlation (rpb) = 0.66, p = 0.011). SIRT2 was positively correlated with age (rpb = 0.39, p = 0.018) and total hospital days (r = 0.55, p = <0.001). CONCLUSIONS SIRT2 should be investigated as a biomarker of paraneoplastic etiology in NMDAR encephalitis.
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Affiliation(s)
- Oskar Stevens-Jones
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - Hana Mojzisova
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Martin Elisak
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Radu Constantinescu
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - Jitka Hanzalova
- Department of Immunology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Markus Axelsson
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - David Krysl
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- Department of Clinical Neurophysiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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Rathmacher JA, Fuller JC, Abumrad NN, Flynn CR. Inflammation Biomarker Response to Oral 2-Hydroxybenzylamine (2-HOBA) Acetate in Healthy Humans. Inflammation 2023; 46:1343-1352. [PMID: 36935449 PMCID: PMC10025056 DOI: 10.1007/s10753-023-01801-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/21/2023]
Abstract
Inflammation is associated with the formation of reactive oxygen species (ROS) and the formation of lipid-derived compounds, such as isolevuglandins (IsoLGs), malondialdehyde, 4-hydroxy-nonenal, and 4-oxo-nonenal. The most reactive of these are the IsoLGs, which form covalent adducts with lysine residues and other cellular primary amines leading to changes in protein function, immunogenicity, and epigenetic alterations and have been shown to contribute to a number of inflammatory diseases. 2-Hydroxybenzylamine (2-HOBA) is a natural compound found in buckwheat seeds and reacts with all IsoLG adducts preventing adduct formation with proteins and DNA. Therefore, 2-HOBA is well positioned as an agent for the prevention of inflammatory-prone diseases. In this study, we examined the potential beneficial effects of 2-HOBA on oxidative stress and inflammatory biomarkers in two cohorts of healthy younger and older adults. We utilized the Olink® targeted inflammation panel before and after an oral 15-day treatment regimen with 2-HOBA. We found significant relative changes in the plasma concentration of 15 immune proteins that may reflect the in vivo immune targets of 2-HOBA. Treatment of 2-HOBA resulted in significant increased levels of CCL19, IL-12β, IL-20Rα, and TNFβ, whereas levels of TWEAK significantly decreased. Ingenuity Pathway Analysis identified canonical pathways regulated by the differentially secreted cytokines, chemokines, and growth factors upon 2-HOBA treatment and further points to biofunctions related to the recruitment, attraction, and movement of different immune cell types. In conclusion, 2-HOBA significantly altered the protein biomarkers CCL19, IL-12β, IL-20Rα, TNFβ, and TWEAK, and these may be responsible for the protective effects of 2-HOBA against reactive electrophiles, such as IsoLGs, commonly expressed in conditions of excessive oxidative stress. 2-HOBA has a role as a IsoLG scavenger to proactively improve immune health in a variety of conditions.
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Affiliation(s)
- John A Rathmacher
- MTI BioTech, Inc, Iowa State University Research Park, Ames, IA, USA
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Naji N Abumrad
- MTI BioTech, Inc, Iowa State University Research Park, Ames, IA, USA
- Metabolic Technologies, LLC, Missoula, MT, USA
- Department of Surgery, Vanderbilt University Medical Center, MRBIV Room 8465A, Nashville, TN, 37232, USA
| | - Charles R Flynn
- Department of Surgery, Vanderbilt University Medical Center, MRBIV Room 8465A, Nashville, TN, 37232, USA.
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Toyama T, Xu S, Kanemitsu Y, Hasegawa T, Noguchi T, Lee JY, Matsuzawa A, Naganuma A, Hwang GW. Methylmercury directly modifies the 105th cysteine residue in oncostatin M to promote binding to tumor necrosis factor receptor 3 and inhibit cell growth. Arch Toxicol 2023; 97:1887-1897. [PMID: 37193757 DOI: 10.1007/s00204-023-03520-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 05/18/2023]
Abstract
We previously found that methylmercury induces expression of oncostatin M (OSM), which is released extracellularly and binds to tumor necrosis factor receptor 3 (TNFR3), possibly enhancing its own toxicity. However, the mechanism by which methylmercury causes OSM to bind to TNFR3 rather than to its known receptors, OSM receptor and LIFR, is unknown. In this study, we aimed to elucidate the effect of methylmercury modification of cysteine residues in OSM on binding to TNFR3. Immunostaining of TNFR3-V5-expressing cells suggested that methylmercury promoted binding of OSM to TNFR3 on the cell membrane. In an in vitro binding assay, OSM directly bound to the extracellular domain of TNFR3, and this binding was promoted by methylmercury. Additionally, the formation of a disulfide bond in the OSM molecule was essential for the binding of both proteins, and LC/MS analysis revealed that methylmercury directly modified the 105th cysteine residue (Cys105) in OSM. Next, mutant OSM, in which Cys105 was replaced by serine or methionine, increased the binding to TNFR3, and a similar effect was observed in immunoprecipitation using cultured cells. Furthermore, cell proliferation was inhibited by treatment with Cys105 mutant OSMs compared with wildtype OSM, and this effect was cancelled by TNFR3 knockdown. In conclusion, we revealed a novel mechanism of methylmercury toxicity, in which methylmercury directly modifies Cys105 in OSM, thereby inhibiting cell proliferation via promoting binding to TNFR3. This indicates a chemical disruption in the interaction between the ligand and the receptor is a part of methylmercury toxicity.
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Affiliation(s)
- Takashi Toyama
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Sidi Xu
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Yoshitomi Kanemitsu
- Clinical and Translational Research Center, Niigata University Medical and Dental Hospital, 2-5274 Gakkochodori, Chuo-ku, Niigata, Niigata, 980-8574, Japan
| | - Takashi Hasegawa
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Takuya Noguchi
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Jin-Yong Lee
- Laboratory of Pharmaceutical Health Sciences, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, 951-8514, Japan
| | - Atsushi Matsuzawa
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Akira Naganuma
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Gi-Wook Hwang
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
- Laboratory of Environmental and Health Sciences, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan.
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Shin J, Piao Y, Bang D, Kim S, Jo K. DRPreter: Interpretable Anticancer Drug Response Prediction Using Knowledge-Guided Graph Neural Networks and Transformer. Int J Mol Sci 2022; 23:13919. [PMID: 36430395 PMCID: PMC9699175 DOI: 10.3390/ijms232213919] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Some of the recent studies on drug sensitivity prediction have applied graph neural networks to leverage prior knowledge on the drug structure or gene network, and other studies have focused on the interpretability of the model to delineate the mechanism governing the drug response. However, it is crucial to make a prediction model that is both knowledge-guided and interpretable, so that the prediction accuracy is improved and practical use of the model can be enhanced. We propose an interpretable model called DRPreter (drug response predictor and interpreter) that predicts the anticancer drug response. DRPreter learns cell line and drug information with graph neural networks; the cell-line graph is further divided into multiple subgraphs with domain knowledge on biological pathways. A type-aware transformer in DRPreter helps detect relationships between pathways and a drug, highlighting important pathways that are involved in the drug response. Extensive experiments on the GDSC (Genomics of Drug Sensitivity and Cancer) dataset demonstrate that the proposed method outperforms state-of-the-art graph-based models for drug response prediction. In addition, DRPreter detected putative key genes and pathways for specific drug-cell-line pairs with supporting evidence in the literature, implying that our model can help interpret the mechanism of action of the drug.
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Affiliation(s)
- Jihye Shin
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Yinhua Piao
- Department of Computer Science and Engineering, Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
| | - Dongmin Bang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- AIGENDRUG Co., Ltd., Seoul 08826, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- Department of Computer Science and Engineering, Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul 08826, Korea
- MOGAM Institute for Biomedical Research, Yongin-si 16924, Korea
| | - Kyuri Jo
- Department of Computer Engineering, Chungbuk National University, Cheongju 28644, Korea
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Card DC, Van Camp AG, Santonastaso T, Jensen-Seaman MI, Anthony NM, Edwards SV. Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes. Front Genet 2022; 13:979746. [PMID: 36425073 PMCID: PMC9679377 DOI: 10.3389/fgene.2022.979746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2β gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.
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Affiliation(s)
- Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
- *Correspondence: Daren C. Card,
| | - Andrew G. Van Camp
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
| | - Trenten Santonastaso
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | | | - Nicola M. Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
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The Molecular Quality and Mitochondrial Activity of Porcine Cumulus-Oocyte Complexes Are Affected by Their Exposure to Three Endocrine-Active Compounds under 3D In Vitro Maturation Conditions. Int J Mol Sci 2022; 23:ijms23094572. [PMID: 35562963 PMCID: PMC9100547 DOI: 10.3390/ijms23094572] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Abstract
Thus far, the potential short- and long-term detrimental effects of a variety of environmental chemicals designated as endocrine-active compounds (EACs) have been found to interfere with histo- and anatomo-physiological functions of the reproductive system in humans and wildlife species. For those reasons, this study sought to examine whether selected EACs, which encompass the fungicide vinclozolin (Vnz), the androgenic anabolic steroid nandrolone (Ndn) and the immunosuppressant cyclosporin A (CsA), affect the developmental competence and molecular quality (MQ) of porcine cumulus–oocyte complexes (COCs) subjected to in vitro maturation (IVM) under 3D culture conditions. The COCs underwent 3D-IVM in the presence of Vnz, Ndn or CsA for 48 h. To explore whether the selected EACs induce internucleosomal DNA fragmentation in cumulus cells (CCs), TUNEL-assisted detection of late apoptotic cells was performed. Additionally, for the detailed evaluation of pro- and antiapoptotic pathways in COCs, apoptosis proteome profiler arrays were used. To determine changes in intracellular metabolism in COCs, comprehensive assessments of mitochondrial ultrastructure and activity were carried out. Moreover, the relative abundances (RAs) of mRNAs transcribed from genes that are involved in scavenging reactive oxygen species (ROS), such as SIRT3 and FOXO3, and intramitochondrial bioenergetic balance, such as ATP synthase subunit (ATP5A1), were ascertained. Finally, to investigate the extent of progression of oocyte maturation, the intraooplasmic levels of cAMP and the RAs of mRNA transcripts encoding regulatory and biocatalytic subunits of a heterodimeric meiosis-promoting factor, termed cyclin B1 (CCNB1) and cyclin-dependent kinase 1 (CDC2), were also estimated. The obtained results provide, for the first time, strong evidence that both Vnz and Ndn decrease the developmental competence of oocytes and stimulate apoptosis processes in CCs. The present study is also the first to highlight that Vnz accelerates the maturation process in immature oocytes due to both increased ROS production and the augmented RA of the CCNB1 gene. Furthermore, Vnz was proven to trigger proapoptotic events in CCs by prompting the activity of the FOXO3 transcription factor, which regulates the mitochondrial apoptosis pathway. In turn, Ndn was shown to inhibit oocyte maturation by inducing molecular events that ultimately lead to an increase in the intraooplasmic cAMP concentration. However, due to the simultaneous enhancement of the expression of TNF-β and HSP27 proteins in CCs, Ndn might be responsible for the onset of their neoplastic transformation. Finally, our current investigation is the first to clearly demonstrate that although CsA did not interfere with the nuclear and cytoplasmic maturation of oocytes, by inducing mitophagy in CCs, it disrupted oocyte metabolism, consequently attenuating the parameters related to the MQ of COCs. Summing up, Vnz, Ndn and CsA reduced not only the processes of growth and IVM but also the MQ of porcine COCs, which might make them unsuitable for assisted reproductive technologies (ARTs) such as in vitro fertilization by either gamete co-incubation or intracytoplasmic sperm injection (ICSI) and cloning by somatic cell nuclear transfer (SCNT).
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Ko S, Lim J, Hong S. Functional characterization of a novel tumor necrosis factor gene (TNF-New) in rock bream (Oplegnathus fasciatus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104269. [PMID: 34600021 DOI: 10.1016/j.dci.2021.104269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/03/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
The novel tumor necrosis factor (TNF-New or TNFN) gene has been identified only in teleost such as zebrafish, medaka (Oryzias latipes), fugu (Takifugu rubripes), and rainbow trout (Oncorhynchus mykiss). In this study, a putative TNFN gene in rock bream (named RB-TNFN) was cloned and its functional expression in the immune system was analyzed. Although it was previously reported to share a high degree of homology with mammalian lymphotoxin (LT)-β, in silico analysis revealed that RB-TNFN differed slightly from mammalian LT-β in its genomic structure, phylogenetic relationship, and predicted protein tertiary structure, whereas the genomic location of TNFN (immediately behind TNF-α) was the same as that of LT-β. In healthy rock bream, RB-TNFN gene expression was the highest in the liver and the lowest in the head kidney. In vitro, it was significantly upregulated in head kidney cells following polyinosinic:polycytidylic acid, concanavalin A, phytohemagglutinin, or calcium ionophore (CI) stimulation and in spleen cells by lipopolysaccharide (LPS), CI, and rock bream iridovirus (RBIV). In vivo, it was upregulated in the spleen, liver, and gut on day 1 and in the blood on day 3 following LPS injection, and in the blood, head kidney, and liver following RBIV vaccination. Post-RBIV infection, the vaccinated group showed a significantly higher TNFN gene expression in the head kidney and blood than the unvaccinated group. Treatment with recombinant TNFN protein (RB-rTNFN) resulted in significantly upregulated interleukin-1β expression in the head kidney, spleen, blood, liver, and peritoneal cells. It also enhanced IL-8 gene expression in the head kidney, blood, and peritoneal cells, and interferon γ gene expression in the gut and gills on day 1. TNFN and cyclo-oxygenase-2 gene expression was upregulated in peritoneal cells on day 3. Flow cytometry analysis revealed a significant increase in the peritoneal lymphocyte population after the intraperitoneal (i.p.) injection of RB-rTNFN. These results suggest that RB-TNFN mediated innate and adaptive immunity in rock bream.
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Affiliation(s)
- Sungjae Ko
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Jongwon Lim
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Suhee Hong
- East Coast Research institute of Life Science, Gangneung-Wonju National University, South Korea.
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10
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Suo F, Zhou X, Setroikromo R, Quax WJ. Receptor Specificity Engineering of TNF Superfamily Ligands. Pharmaceutics 2022; 14:181. [PMID: 35057080 PMCID: PMC8781899 DOI: 10.3390/pharmaceutics14010181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
The tumor necrosis factor (TNF) ligand family has nine ligands that show promiscuity in binding multiple receptors. As different receptors transduce into diverse pathways, the study on the functional role of natural ligands is very complex. In this review, we discuss the TNF ligands engineering for receptor specificity and summarize the performance of the ligand variants in vivo and in vitro. Those variants have an increased binding affinity to specific receptors to enhance the cell signal conduction and have reduced side effects due to a lowered binding to untargeted receptors. Refining receptor specificity is a promising research strategy for improving the application of multi-receptor ligands. Further, the settled variants also provide experimental guidance for engineering receptor specificity on other proteins with multiple receptors.
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Affiliation(s)
- Fengzhi Suo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xinyu Zhou
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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11
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Hua X, Ge S, Zhang J, Xiao H, Tai S, Yang C, Zhang L, Liang C. A costimulatory molecule-related signature in regard to evaluation of prognosis and immune features for clear cell renal cell carcinoma. Cell Death Discov 2021; 7:252. [PMID: 34537809 PMCID: PMC8449780 DOI: 10.1038/s41420-021-00646-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Costimulatory molecules have been proven to enhance antitumor immune responses, but their roles in clear cell renal cell carcinoma (ccRCC) remain unexplored. In this study, we aimed to explore the gene expression profiles of costimulatory molecule genes in ccRCC and construct a prognostic signature to improve treatment decision-making and clinical outcomes. We performed the first comprehensive analysis of costimulatory molecules in patients with ccRCC and identified 13 costimulatory molecule genes with prognostic values and diagnostic values. Consensus clustering analysis based on these 13 costimulatory molecular genes showed different distribution patterns and prognostic differences for the two clusters identified. Then, a costimulatory molecule-related signature was constructed based on these 13 costimulatory molecular genes, and validated in an external dataset, showing good performance for predicting a patient’s prognosis. The signature was an independent risk factor for ccRCC patients and was significantly correlated with patients’ clinical factors, which could be used as a complement for clinical factors. In addition, the signature was associated with the tumor immune microenvironment and the response to immunotherapy. Patients identified as high-risk based on our signature exhibited a high mutation frequency, a high level of immune cell infiltration, and an immunosuppressive microenvironment. High-risk patients tended to have high cytolytic activity scores and immunophenoscore of CTLA4 and PD1/PD-L1/PD-L2 blocker than low-risk patients, suggesting these patients may be more suitable for immunotherapy. Therefore, our signature could provide clinicians with prognosis predictions and help guide treatment for ccRCC patients.
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Affiliation(s)
- Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Jiong Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Sheng Tai
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Cheng Yang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China. .,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China. .,The Institute of Urology, Anhui Medical University, Hefei, China.
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China. .,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China. .,The Institute of Urology, Anhui Medical University, Hefei, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China. .,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China. .,The Institute of Urology, Anhui Medical University, Hefei, China. .,Anhui Institute of translational medicine, Hefei, China.
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12
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Taxauer K, Hamway Y, Ralser A, Dietl A, Mink K, Vieth M, Singer BB, Gerhard M, Mejías-Luque R. Engagement of CEACAM1 by Helicobacterpylori HopQ Is Important for the Activation of Non-Canonical NF-κB in Gastric Epithelial Cells. Microorganisms 2021; 9:1748. [PMID: 34442827 PMCID: PMC8400456 DOI: 10.3390/microorganisms9081748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 01/01/2023] Open
Abstract
The gastric pathogen Helicobacter pylori infects half of the world's population and is a major risk factor for gastric cancer development. In order to attach to human gastric epithelial cells and inject the oncoprotein CagA into host cells, H. pylori utilizes the outer membrane protein HopQ that binds to the cell surface protein CEACAM, which can be expressed on the gastric mucosa. Once bound, H. pylori activates a number of signaling pathways, including canonical and non-canonical NF-κB. We investigated whether HopQ-CEACAM interaction is involved in activating the non-canonical NF-κB signaling pathway. Different gastric cancer cells were infected with the H. pylori wild type, or HopQ mutant strains, and the activation of non-canonical NF-κB was related to CEACAM expression levels. The correlation between CEACAM levels and the activation of non-canonical NF-κB was confirmed in human gastric tissue samples. Taken together, our findings show that the HopQ-CEACAM interaction is important for activation of the non-canonical NF-κB pathway in gastric epithelial cells.
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Affiliation(s)
- Karin Taxauer
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Youssef Hamway
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Anna Ralser
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Alisa Dietl
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Karin Mink
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Michael Vieth
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Klinikum Bayreuth, 95445 Bayreuth, Germany;
| | - Bernhard B. Singer
- Institute of Anatomy, Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
| | - Raquel Mejías-Luque
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich, 81675 Munich, Germany; (K.T.); (Y.H.); (A.R.); (A.D.); (K.M.); (M.G.)
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13
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Shou Y, Koroleva E, Spencer CM, Shein SA, Korchagina AA, Yusoof KA, Parthasarathy R, Leadbetter EA, Akopian AN, Muñoz AR, Tumanov AV. Redefining the Role of Lymphotoxin Beta Receptor in the Maintenance of Lymphoid Organs and Immune Cell Homeostasis in Adulthood. Front Immunol 2021; 12:712632. [PMID: 34335629 PMCID: PMC8320848 DOI: 10.3389/fimmu.2021.712632] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/29/2021] [Indexed: 02/04/2023] Open
Abstract
Lymphotoxin beta receptor (LTβR) is a promising therapeutic target in autoimmune and infectious diseases as well as cancer. Mice with genetic inactivation of LTβR display multiple defects in development and organization of lymphoid organs, mucosal immune responses, IgA production and an autoimmune phenotype. As these defects are imprinted in embryogenesis and neonate stages, the impact of LTβR signaling in adulthood remains unclear. Here, to overcome developmental defects, we generated mice with inducible ubiquitous genetic inactivation of LTβR in adult mice (iLTβRΔ/Δ mice) and redefined the role of LTβR signaling in organization of lymphoid organs, immune response to mucosal bacterial pathogen, IgA production and autoimmunity. In spleen, postnatal LTβR signaling is required for development of B cell follicles, follicular dendritic cells (FDCs), recruitment of neutrophils and maintenance of the marginal zone. Lymph nodes of iLTβRΔ/Δ mice were reduced in size, lacked FDCs, and had disorganized subcapsular sinus macrophages. Peyer`s patches were smaller in size and numbers, and displayed reduced FDCs. The number of isolated lymphoid follicles in small intestine and colon were also reduced. In contrast to LTβR-/- mice, iLTβRΔ/Δ mice displayed normal thymus structure and did not develop signs of systemic inflammation and autoimmunity. Further, our results suggest that LTβR signaling in adulthood is required for homeostasis of neutrophils, NK, and iNKT cells, but is dispensable for the maintenance of polyclonal IgA production. However, iLTβRΔ/Δ mice exhibited an increased sensitivity to C. rodentium infection and failed to develop pathogen-specific IgA responses. Collectively, our study uncovers new insights of LTβR signaling in adulthood for the maintenance of lymphoid organs, neutrophils, NK and iNKT cells, and IgA production in response to mucosal bacterial pathogen.
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Affiliation(s)
- Yajun Shou
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States,Department of Gastroenterology, Second Xiangya Hospital of Central South University, Changsha, China
| | - Ekaterina Koroleva
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | | | - Sergey A. Shein
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Anna A. Korchagina
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kizil A. Yusoof
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Raksha Parthasarathy
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Elizabeth A. Leadbetter
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Armen N. Akopian
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Amanda R. Muñoz
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Alexei V. Tumanov
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States,*Correspondence: Alexei V. Tumanov,
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14
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Aoyama S, Nakagawa R, Mulé JJ, Mailloux AW. Inducible Tertiary Lymphoid Structures: Promise and Challenges for Translating a New Class of Immunotherapy. Front Immunol 2021; 12:675538. [PMID: 34054863 PMCID: PMC8160316 DOI: 10.3389/fimmu.2021.675538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Tertiary lymphoid structures (TLS) are ectopically formed aggregates of organized lymphocytes and antigen-presenting cells that occur in solid tissues as part of a chronic inflammation response. Sharing structural and functional characteristics with conventional secondary lymphoid organs (SLO) including discrete T cell zones, B cell zones, marginal zones with antigen presenting cells, reticular stromal networks, and high endothelial venues (HEV), TLS are prominent centers of antigen presentation and adaptive immune activation within the periphery. TLS share many signaling axes and leukocyte recruitment schemes with SLO regarding their formation and function. In cancer, their presence confers positive prognostic value across a wide spectrum of indications, spurring interest in their artificial induction as either a new form of immunotherapy, or as a means to augment other cell or immunotherapies. Here, we review approaches for inducible (iTLS) that utilize chemokines, inflammatory factors, or cellular analogues vital to TLS formation and that often mirror conventional SLO organogenesis. This review also addresses biomaterials that have been or might be suitable for iTLS, and discusses remaining challenges facing iTLS manufacturing approaches for clinical translation.
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Affiliation(s)
- Shota Aoyama
- Department of Surgery, Institute of Gastroenterology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Ryosuke Nakagawa
- Department of Surgery, Institute of Gastroenterology, Tokyo Women’s Medical University, Tokyo, Japan
| | - James J. Mulé
- Immunology Program, Moffitt Cancer Center, Tampa, FL, United States
- Cutaneous Oncology Program, Moffitt Cancer Center, Tampa, FL, United States
| | - Adam W. Mailloux
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
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15
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Gubernatorova EO, Polinova AI, Petropavlovskiy MM, Namakanova OA, Medvedovskaya AD, Zvartsev RV, Telegin GB, Drutskaya MS, Nedospasov SA. Dual Role of TNF and LTα in Carcinogenesis as Implicated by Studies in Mice. Cancers (Basel) 2021; 13:1775. [PMID: 33917839 PMCID: PMC8068266 DOI: 10.3390/cancers13081775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Tumor necrosis factor (TNF) and lymphotoxin alpha (LTα) are two related cytokines from the TNF superfamily, yet they mediate their functions in soluble and membrane-bound forms via overlapping, as well as distinct, molecular pathways. Their genes are encoded within the major histocompatibility complex class III cluster in close proximity to each other. TNF is involved in host defense, maintenance of lymphoid tissues, regulation of cell death and survival, and antiviral and antibacterial responses. LTα, known for some time as TNFβ, has pleiotropic functions including control of lymphoid tissue development and homeostasis cross talk between lymphocytes and their environment, as well as lymphoid tissue neogenesis with formation of lymphoid follicles outside the lymph nodes. Along with their homeostatic functions, deregulation of these two cytokines may be associated with initiation and progression of chronic inflammation, autoimmunity, and tumorigenesis. In this review, we summarize the current state of knowledge concerning TNF/LTα functions in tumor promotion and suppression, with the focus on the recently uncovered significance of host-microbiota interplay in cancer development that may explain some earlier controversial results.
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Affiliation(s)
- Ekaterina O. Gubernatorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Almina I. Polinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail M. Petropavlovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Olga A. Namakanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexandra D. Medvedovskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ruslan V. Zvartsev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Georgij B. Telegin
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences (BIBCh, RAS), 142290 Pushchino, Russia;
| | - Marina S. Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei A. Nedospasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.I.P.); (M.M.P.); (O.A.N.); (A.D.M.); (R.V.Z.)
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Sirius University of Science and Technology, Federal Territory Sirius, 354340 Krasnodarsky Krai, Russia
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16
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Clathrin- and dynamin-dependent endocytosis limits canonical NF-κB signaling triggered by lymphotoxin β receptor. Cell Commun Signal 2020; 18:176. [PMID: 33148272 PMCID: PMC7640449 DOI: 10.1186/s12964-020-00664-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lymphotoxin β receptor (LTβR) is a member of tumor necrosis factor receptor (TNFR) superfamily which regulates the immune response. At the cellular level, upon ligand binding, the receptor activates the pro-inflammatory NF-κB and AP-1 pathways. Yet, the intracellular distribution of LTβR, the routes of its endocytosis and their connection to the signaling activation are not characterized. Here, we investigated the contribution of LTβR internalization to its signaling potential. Methods Intracellular localization of LTβR in unstimulated and stimulated cells was analyzed by confocal microscopy. Endocytosis impairment was achieved through siRNA- or CRISPR/Cas9-mediated depletion, or chemical inhibition of proteins regulating endocytic routes. The activation of LTβR-induced signaling was examined. The levels of effector proteins of the canonical and non-canonical branches of the NF-κB pathway, and the phosphorylation of JNK, Akt, ERK1/2, STAT1 and STAT3 involved in diverse signaling cascades, were measured by Western blotting. A transcriptional response to LTβR stimulation was assessed by qRT-PCR analysis. Results We demonstrated that LTβR was predominantly present on endocytic vesicles and the Golgi apparatus. The ligand-bound pool of the receptor localized to endosomes and was trafficked towards lysosomes for degradation. Depletion of regulators of different endocytic routes (clathrin-mediated, dynamin-dependent or clathrin-independent) resulted in the impairment of LTβR internalization, indicating that this receptor uses multiple entry pathways. Cells deprived of clathrin and dynamins exhibited enhanced activation of canonical NF-κB signaling represented by increased degradation of IκBα inhibitor and elevated expression of LTβR target genes. We also demonstrated that clathrin and dynamin deficiency reduced to some extent LTβR-triggered activation of the non-canonical branch of the NF-κB pathway. Conclusions Our work shows that the impairment of clathrin- and dynamin-dependent internalization amplifies a cellular response to LTβR stimulation. We postulate that receptor internalization restricts responsiveness of the cell to subthreshold stimuli. Video Abstract
Graphical abstract ![]()
Supplementary information Supplementary information accompanies this paper at 10.1186/s12964-020-00664-0.
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17
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Bergstrom CP, Beg MS, Ayers C, Gupta A, Neeland IJ. The association of lymphotoxin-beta receptor with the subsequent diagnosis of incident gastrointestinal cancer: results from the Dallas Heart Study. J Gastrointest Oncol 2020; 11:36-44. [PMID: 32175103 DOI: 10.21037/jgo.2020.01.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background Lymphotoxin-beta receptor (LTβR) is an immunological protein associated with inflammation, and from preclinical studies is implicated in tumorigenesis. The epidemiological relationships with cancer are unknown, hence this study investigated their associations. Methods From a multiethnic population-based cohort, 3,032 participants without a prevalent cancer (a diagnosis prior to or within one year of enrollment) at baseline underwent measurement of plasma LTβR. These participants were followed for incident cancer using the Texas Cancer Registry (TCR). Results Over a median follow-up of 12.1 years, 178 participants developed incident cancer, of which 30 participants developed incident gastrointestinal (GI) cancer. Median plasma LTβR (1.10 vs. 1.00 ng/mL, P<0.02) levels were higher in individuals with overall incident cancer compared to those without cancer. After adjustments for age, sex, and race/ethnicity, these relationships were no longer significant. When analyses were stratified by cancer type, LTβR was positively associated with GI cancer after adjustments: HR, 95% CI per 1-standard deviation increase in concentration 2.64 (1.23-5.68), P=0.013. LTβR stratified by quartiles was significantly associated temporally with the risk of incident GI cancer, log-rank: P=0.011. The median interval to incident GI cancer diagnosis was 5.9 years. Conclusions Increased plasma levels of LTβR are associated with the development of GI cancer. The antecedent findings years prior to a subsequent diagnosis of incident GI cancer suggest a role for LTβR in the pathogenesis of GI cancer. Further studies are needed to determine if LTβR can serve as an immune biomarker for GI cancer, in particular hepatocellular and colorectal cancers.
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Affiliation(s)
- Colin P Bergstrom
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Muhammad S Beg
- Division of Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Colby Ayers
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Arjun Gupta
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ian J Neeland
- Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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18
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Li N, Zhao Z, Bai J, Liu B, Mi H, Zhang L, Li G, Yang L. Characterization of the Th cytokines profile in ovine spleen during early pregnancy. JOURNAL OF APPLIED ANIMAL RESEARCH 2019. [DOI: 10.1080/09712119.2019.1634077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ning Li
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Zimo Zhao
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Jiachen Bai
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Baoliang Liu
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Hao Mi
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Leying Zhang
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
| | - Guiping Li
- Handan Animal Husbandry Technology Extension Station, Handan, People’s Republic of China
| | - Ling Yang
- Department of Animal Science, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, People’s Republic of China
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19
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Dimitrakopoulos FID, Kottorou AE, Antonacopoulou AG, Panagopoulos N, Scopa C, Kalofonou M, Dougenis D, Koutras A, Makatsoris T, Tzelepi V, Kalofonos HP. Expression of Immune System-Related Membrane Receptors CD40, RANK, BAFFR and LTβR is Associated with Clinical Outcome of Operated Non-Small-Cell Lung Cancer Patients. J Clin Med 2019; 8:jcm8050741. [PMID: 31137630 PMCID: PMC6572708 DOI: 10.3390/jcm8050741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/07/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
An increasing number of studies implicates the NF-κB (Nuclear Factor of kappa light chain gene enhancer in B cells) alternative pathway in non-small-cell lung cancer (NSCLC). We assessed the clinical significance of CD40 (Tumor necrosis factor receptor superfamily member 5, TNFRSF5), BAFFR (B-cell activating factor receptor), RANK (Receptor activator of NF-κB) and LTβR (lymphotoxin β receptor) receptors, which activate the alternative pathway of NF-κB, in NSCLC. Evaluation of CD40, BAFFR, RANK and LTβR expression was performed based on the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) datasets, while protein expression was assessed by immunohistochemistry in specimens from 119 operated NSCLC patients. CD40 gene overexpression was correlated with improved five-year overall survival (OS) (p < 0.001), while increased BAFFR and LTβR mRNA levels were associated with worse OS in patients with adenocarcinomas (p < 0.001 and p < 0.001, respectively). Similarly, patients with adenocarcinomas exhibited a negative correlation between membranous BAFFR protein expression in carcinoma cells and three- and five-year survival (p = 0.021; HR, 4.977 and p = 0.030; HR, 3.358, respectively) as well as between BAFFR protein overexpression in cancer-associated fibroblasts (CAFs) and two-year survival (p = 0.036; HR, 1.983). Patients with increased LTβR nuclear protein staining or stage II patients with lower cytoplasmic LTβR protein expression had worse five-year OS (p = 0.039 and p = 0.008, respectively). Moreover, CD40 protein expression in tumor infiltrating lymphocytes (TILs) and CAFs was positively associated with metastatic spread while BAFFR protein expression in CAFs was negatively associated with bone metastasis (p = 0.041). Our data suggests that CD40, BAFFR, RANK and LTβR play an important role in NSCLC and further supports the role of NF-κB alternative pathway in NSCLC.
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Affiliation(s)
- Foteinos-Ioannis D Dimitrakopoulos
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
| | - Anastasia E Kottorou
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
| | - Anna G Antonacopoulou
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
| | - Nikolaos Panagopoulos
- Department of Cardiothoracic Surgery, Medical School, University of Patras, 26504 Patras, Greece.
| | - Chrisoula Scopa
- Department of Pathology, Medical School, University of Patras, 26504 Patras, Greece.
| | - Melpomeni Kalofonou
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK.
| | - Dimitrios Dougenis
- Department of Cardiothoracic Surgery, Medical School, University of Patras, 26504 Patras, Greece.
| | - Angelos Koutras
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
| | - Thomas Makatsoris
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
| | - Vassiliki Tzelepi
- Department of Pathology, Medical School, University of Patras, 26504 Patras, Greece.
| | - Haralabos P Kalofonos
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, Medical School, University of Patras, 26504 Patras, Greece.
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20
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Gong K, Guo G, Gerber DE, Gao B, Peyton M, Huang C, Minna JD, Hatanpaa KJ, Kernstine K, Cai L, Xie Y, Zhu H, Fattah FJ, Zhang S, Takahashi M, Mukherjee B, Burma S, Dowell J, Dao K, Papadimitrakopoulou VA, Olivas V, Bivona TG, Zhao D, Habib AA. TNF-driven adaptive response mediates resistance to EGFR inhibition in lung cancer. J Clin Invest 2018; 128:2500-2518. [PMID: 29613856 DOI: 10.1172/jci96148] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/16/2018] [Indexed: 01/07/2023] Open
Abstract
Although aberrant EGFR signaling is widespread in cancer, EGFR inhibition is effective only in a subset of non-small cell lung cancer (NSCLC) with EGFR activating mutations. A majority of NSCLCs express EGFR wild type (EGFRwt) and do not respond to EGFR inhibition. TNF is a major mediator of inflammation-induced cancer. We find that a rapid increase in TNF level is a universal adaptive response to EGFR inhibition in NSCLC, regardless of EGFR status. EGFR signaling actively suppresses TNF mRNA levels by inducing expression of miR-21, resulting in decreased TNF mRNA stability. Conversely, EGFR inhibition results in loss of miR-21 and increased TNF mRNA stability. In addition, TNF-induced NF-κB activation leads to increased TNF transcription in a feed-forward loop. Inhibition of TNF signaling renders EGFRwt-expressing NSCLC cell lines and an EGFRwt patient-derived xenograft (PDX) model highly sensitive to EGFR inhibition. In EGFR-mutant oncogene-addicted cells, blocking TNF enhances the effectiveness of EGFR inhibition. EGFR plus TNF inhibition is also effective in NSCLC with acquired resistance to EGFR inhibition. We suggest concomitant EGFR and TNF inhibition as a potentially new treatment approach that could be beneficial for a majority of lung cancer patients.
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Affiliation(s)
- Ke Gong
- Department of Neurology and Neurotherapeutics
| | - Gao Guo
- Department of Neurology and Neurotherapeutics
| | - David E Gerber
- Internal Medicine, Division of Hematology-Oncology.,Harold C. Simmons Comprehensive Cancer Center
| | - Boning Gao
- Department of Pharmacology.,Hamon Center for Therapeutic Oncology Research
| | - Michael Peyton
- Department of Pharmacology.,Hamon Center for Therapeutic Oncology Research
| | - Chun Huang
- Department of Pharmacology.,Hamon Center for Therapeutic Oncology Research
| | - John D Minna
- Internal Medicine, Division of Hematology-Oncology.,Department of Pharmacology.,Hamon Center for Therapeutic Oncology Research
| | | | | | - Ling Cai
- Quantitative Biomedical Research Center
| | - Yang Xie
- Quantitative Biomedical Research Center
| | - Hong Zhu
- Harold C. Simmons Comprehensive Cancer Center.,Department of Clinical Sciences
| | | | | | | | - Bipasha Mukherjee
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sandeep Burma
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jonathan Dowell
- Internal Medicine, Division of Hematology-Oncology.,VA North Texas Health Care System, Dallas, Texas, USA
| | - Kathryn Dao
- Baylor Research Institute, Dallas, Texas, USA
| | | | - Victor Olivas
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Trever G Bivona
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Dawen Zhao
- Departments of Biomedical Engineering and Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Amyn A Habib
- Department of Neurology and Neurotherapeutics.,Harold C. Simmons Comprehensive Cancer Center.,VA North Texas Health Care System, Dallas, Texas, USA
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