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1.
Adv Sci (Weinh) ; : e2307754, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38605600

ABSTRACT

Neoantigen peptides hold great potential as vaccine candidates for tumor immunotherapy. However, due to the limitation of antigen cellular uptake and cross-presentation, the progress with neoantigen peptide-based vaccines has obviously lagged in clinical trials. Here, a stapling peptide-based nano-vaccine is developed, comprising a self-assembly nanoparticle driven by the nucleic acid adjuvant-antigen conjugate. This nano-vaccine stimulates a strong tumor-specific T cell response by activating antigen presentation and toll-like receptor signaling pathways. By markedly improving the efficiency of antigen/adjuvant co-delivery to the draining lymph nodes, the nano-vaccine leads to 100% tumor prevention for up to 11 months and without tumor recurrence, heralding the generation of long-term anti-tumor memory. Moreover, the injection of nano-vaccine with signal neoantigen eliminates the established MC-38 tumor (a cell line of murine carcinoma of the colon without exogenous OVA protein expression) in 40% of the mice by inducing potent cytotoxic T lymphocyte infiltration in the tumor microenvironment without substantial systemic toxicity. These findings represent that stapling peptide-based nano-vaccine may serve as a facile, general, and safe strategy to stimulate a strong anti-tumor immune response for the neoantigen peptide-based personalized tumor immunotherapy.

2.
Comput Struct Biotechnol J ; 21: 5538-5543, 2023.
Article in English | MEDLINE | ID: mdl-38034402

ABSTRACT

Target selection of the personalized cancer neoantigen vaccine, which is highly dependent on computational prediction algorithms, is crucial for its clinical efficacy. Due to the limited number of experimentally validated immunogenic neoepitopes as well as the complexity of neoantigens in eliciting T cell response, the accuracy of neoepitope immunogenicity prediction methods requires persistent efforts for improvement. We present a deep learning framework for neoepitope immunogenicity prediction - SIGANEO by integrating GAN-like network with similarity network to address issues of missing values and limited data concerning neoantigen prediction. This framework exhibits superior performance over competing machine-learning-based neoantigen prediction algorithms over an independent test dataset from TESLA consortium. Particularly for the clinical setting of neoantigen vaccine where only the top 10 and 20 predictions are selected for vaccine production, SIGANEO achieves significantly better accuracy for predicting experimentally validated neoepitopes. Our work demonstrates that deep learning techniques can greatly boost the accuracy of target identification for cancer neoantigen vaccine.

3.
Immunity ; 56(11): 2523-2541.e8, 2023 Nov 14.
Article in English | MEDLINE | ID: mdl-37924812

ABSTRACT

Gasdermin D (GSDMD)-activated inflammatory cell death (pyroptosis) causes mitochondrial damage, but its underlying mechanism and functional consequences are largely unknown. Here, we show that the N-terminal pore-forming GSDMD fragment (GSDMD-NT) rapidly damaged both inner and outer mitochondrial membranes (OMMs) leading to reduced mitochondrial numbers, mitophagy, ROS, loss of transmembrane potential, attenuated oxidative phosphorylation (OXPHOS), and release of mitochondrial proteins and DNA from the matrix and intermembrane space. Mitochondrial damage occurred as soon as GSDMD was cleaved prior to plasma membrane damage. Mitochondrial damage was independent of the B-cell lymphoma 2 family and depended on GSDMD-NT binding to cardiolipin. Canonical and noncanonical inflammasome activation of mitochondrial damage, pyroptosis, and inflammatory cytokine release were suppressed by genetic ablation of cardiolipin synthase (Crls1) or the scramblase (Plscr3) that transfers cardiolipin to the OMM. Phospholipid scramblase-3 (PLSCR3) deficiency in a tumor compromised pyroptosis-triggered anti-tumor immunity. Thus, mitochondrial damage plays a critical role in pyroptosis.


Subject(s)
Gasdermins , Pyroptosis , Neoplasm Proteins/metabolism , Cardiolipins/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Inflammasomes/metabolism
4.
bioRxiv ; 2023 Oct 02.
Article in English | MEDLINE | ID: mdl-37873428

ABSTRACT

Tissue-resident memory T (T RM ) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive T RM differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 T RM across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus T RM signature of 60 genes across skin and siIEL that can effectively distinguish T RM from circulating T cell populations, providing a more specific T RM signature than what was previously generated by comparing bulk T RM to naïve or non-tissue resident memory populations. This updated T RM signature included the AP-1 transcription factor family members Fos, Fosb and Fosl2 . Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature T RM . CyCIF tissue imaging detected nuclear co-localization of AP-1 members Fosb and Junb in resting CD8 T RM >100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in T RM biology and suggests a novel mechanism for rapid reactivation of resting T RM in tissue upon antigen encounter.

5.
Proc Natl Acad Sci U S A ; 120(31): e2306399120, 2023 08.
Article in English | MEDLINE | ID: mdl-37487070

ABSTRACT

Toll-like receptor 4 (TLR4) sensing of lipopolysaccharide (LPS), the most potent pathogen-associated molecular pattern of gram-negative bacteria, activates NF-κB and Irf3, which induces inflammatory cytokines and interferons that trigger an intense inflammatory response, which is critical for host defense but can also cause serious inflammatory pathology, including sepsis. Although TLR4 inhibition is an attractive therapeutic approach for suppressing overexuberant inflammatory signaling, previously identified TLR4 antagonists have not shown any clinical benefit. Here, we identify disulfiram (DSF), an FDA-approved drug for alcoholism, as a specific inhibitor of TLR4-mediated inflammatory signaling. TLR4 cell surface expression, LPS sensing, dimerization and signaling depend on TLR4 binding to MD-2. DSF and other cysteine-reactive drugs, previously shown to block LPS-triggered inflammatory cell death (pyroptosis), inhibit TLR4 signaling by covalently modifying Cys133 of MD-2, a key conserved residue that mediates TLR4 sensing and signaling. DSF blocks LPS-triggered inflammatory cytokine, chemokine, and interferon production by macrophages in vitro. In the aggressive N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mouse model of Parkinson's disease (PD) in which TLR4 plays an important role, DSF markedly suppresses neuroinflammation and dopaminergic neuron loss, and restores motor function. Our findings identify a role for DSF in curbing TLR4-mediated inflammation and suggest that DSF and other drugs that target MD-2 might be useful for treating PD and other diseases in which inflammation contributes importantly to pathogenesis.


Subject(s)
Alcoholism , Disulfiram , Animals , Mice , Toll-Like Receptor 4 , Lipopolysaccharides , Signal Transduction , Cytokines
7.
Nature ; 602(7897): 496-502, 2022 02.
Article in English | MEDLINE | ID: mdl-35110732

ABSTRACT

Gasdermins, a family of five pore-forming proteins (GSDMA-GSDME) in humans expressed predominantly in the skin, mucosa and immune sentinel cells, are key executioners of inflammatory cell death (pyroptosis), which recruits immune cells to infection sites and promotes protective immunity1,2. Pore formation is triggered by gasdermin cleavage1,2. Although the proteases that activate GSDMB, C, D and E have been identified, how GSDMA-the dominant gasdermin in the skin-is activated, remains unknown. Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a major skin pathogen that causes substantial morbidity and mortality worldwide3. Here we show that the GAS cysteine protease SpeB virulence factor triggers keratinocyte pyroptosis by cleaving GSDMA after Gln246, unleashing an active N-terminal fragment that triggers pyroptosis. Gsdma1 genetic deficiency blunts mouse immune responses to GAS, resulting in uncontrolled bacterial dissemination and death. GSDMA acts as both a sensor and substrate of GAS SpeB and as an effector to trigger pyroptosis, adding a simple one-molecule mechanism for host recognition and control of virulence of a dangerous microbial pathogen.


Subject(s)
Exotoxins , Pyroptosis , Animals , Bacterial Proteins/metabolism , Exotoxins/genetics , Exotoxins/metabolism , Mice , Streptococcus pyogenes
8.
NPJ Vaccines ; 6(1): 1, 2021 Jan 04.
Article in English | MEDLINE | ID: mdl-33398010

ABSTRACT

Modified Vaccinia Ankara (MVA) was recently approved as a smallpox vaccine. Variola is transmitted by respiratory droplets and MVA immunization by skin scarification (s.s.) protected mice far more effectively against lethal respiratory challenge with vaccinia virus (VACV) than any other route of delivery, and at lower doses. Comparisons of s.s. with intradermal, subcutaneous, or intramuscular routes showed that MVAOVA s.s.-generated T cells were both more abundant and transcriptionally unique. MVAOVA s.s. produced greater numbers of lung Ova-specific CD8+ TRM and was superior in protecting mice against lethal VACVOVA respiratory challenge. Nearly as many lung TRM were generated with MVAOVA s.s. immunization compared to intra-tracheal immunization with MVAOVA and both routes vaccination protected mice against lethal pulmonary challenge with VACVOVA. Strikingly, MVAOVA s.s.-generated effector T cells exhibited overlapping gene transcriptional profiles to those generated via intra-tracheal immunization. Overall, our data suggest that heterologous MVA vectors immunized via s.s. are uniquely well-suited as vaccine vectors for respiratory pathogens, which may be relevant to COVID-19. In addition, MVA delivered via s.s. could represent a more effective dose-sparing smallpox vaccine.

9.
J Allergy Clin Immunol ; 147(5): 1764-1777, 2021 05.
Article in English | MEDLINE | ID: mdl-33516870

ABSTRACT

BACKGROUND: Natural killer T (NKT) cells are unconventional T cells that bridge innate and adaptive immunity. NKT cells have been implicated in the development of atopic dermatitis (AD). OBJECTIVE: We aimed to investigate the role of NKT cells in AD development, especially in skin. METHODS: Global proteomic and transcriptomic analyses were performed by using skin and blood from human healthy-controls and patients with AD. Levels of CXCR4 and CXCL12 expression in skin NKT cells were analyzed in human AD and mouse AD models. By using parabiosis and intravital imaging, the role of skin CXCR4+ NKT cells was further evaluated in models of mice with AD by using CXCR4-conditionally deficient or CXCL12 transgenic mice. RESULTS: CXCR4 and its cognate ligand CXCL12 were significantly upregulated in the skin of humans with AD by global transcriptomic and proteomic analyses. CXCR4+ NKT cells were enriched in AD skin, and their levels were consistently elevated in our models of mice with AD. Allergen-induced NKT cells participate in cutaneous allergic inflammation. Similar to tissue-resident memory T cells, the predominant skin NKT cells were CXCR4+ and CD69+. Skin-resident NKT cells uniquely expressed CXCR4, unlike NKT cells in the liver, spleen, and lymph nodes. Skin fibroblasts were the main source of CXCL12. CXCR4+ NKT cells preferentially trafficked to CXCL12-rich areas, forming an enriched CXCR4+ tissue-resident NKT cells/CXCL12+ cell cluster that developed in acute and chronic allergic inflammation in our models of mice with AD. CONCLUSIONS: CXCR4+ tissue-resident NKT cells may form a niche that contributes to AD, in which CXCL12 is highly expressed.


Subject(s)
Chemokine CXCL12/immunology , Dermatitis, Atopic/immunology , Natural Killer T-Cells/immunology , Receptors, CXCR4/immunology , Skin/immunology , Animals , Chemokine CXCL12/genetics , Dermatitis, Atopic/genetics , Female , Gene Expression Profiling , Humans , Mice , Proteomics , Receptors, CXCR4/genetics
10.
BMC Bioinformatics ; 22(1): 7, 2021 Jan 06.
Article in English | MEDLINE | ID: mdl-33407098

ABSTRACT

BACKGROUND: Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learning algorithms and mass spectrometry data have indeed showed improvement on the average predicting power for class I HLA-peptide interaction. However, their prediction performances show great variability over individual HLA alleles and peptides with different lengths, which is particularly the case for HLA-C alleles due to the limited amount of experimental data. To meet the increasing demand for attaining the most accurate HLA-peptide binding prediction for individual patient in the real-world clinical studies, more advanced deep learning framework with higher prediction accuracy for HLA-C alleles and longer peptides is highly desirable. RESULTS: We present a pan-allele HLA-peptide binding prediction framework-MATHLA which integrates bi-directional long short-term memory network and multiple head attention mechanism. This model achieves better prediction accuracy in both fivefold cross-validation test and independent test dataset. In addition, this model is superior over existing tools regarding to the prediction accuracy for longer ligand ranging from 11 to 15 amino acids. Moreover, our model also shows a significant improvement for HLA-C-peptide-binding prediction. By investigating multiple-head attention weight scores, we depicted possible interaction patterns between three HLA I supergroups and their cognate peptides. CONCLUSION: Our method demonstrates the necessity of further development of deep learning algorithm in improving and interpreting HLA-peptide binding prediction in parallel to increasing the amount of high-quality HLA ligandome data.


Subject(s)
Computational Biology/methods , Histocompatibility Antigens Class I , Neural Networks, Computer , Peptides , Protein Binding , Algorithms , Histocompatibility Antigens Class I/chemistry , Histocompatibility Antigens Class I/metabolism , Humans , Models, Statistical , Peptides/chemistry , Peptides/metabolism
11.
Science ; 372(6549)2021 06 25.
Article in English | MEDLINE | ID: mdl-35058659

ABSTRACT

Host cells initiate cell death programs to limit pathogen infection. Inhibition of transforming growth factor-ß-activated kinase 1 (TAK1) by pathogenic Yersinia in macrophages triggers receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-dependent caspase-8 cleavage of gasdermin D (GSDMD) and inflammatory cell death (pyroptosis). A genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen to uncover mediators of caspase-8-dependent pyroptosis identified an unexpected role of the lysosomal FLCN-FNIP2-Rag-Ragulator supercomplex, which regulates metabolic signalling and the mechanistic target of rapamycin complex 1 (mTORC1). In response to Yersinia infection, FADD, RIPK1 and caspase-8 were recruited to Rag-Ragulator, causing RIPK1 phosphorylation and caspase-8 activation. Pyroptosis activation depended on Rag GTPase activity and lysosomal tethering of Rag-Ragulator, but not mTORC1. Thus, the lysosomal metabolic regulator Rag-Ragulator instructs the inflammatory response to Yersinia.


Subject(s)
Caspase 8/metabolism , Lysosomes/metabolism , Macrophages/metabolism , Macrophages/microbiology , Pyroptosis , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Yersinia pseudotuberculosis/physiology , Animals , CRISPR-Cas Systems , Cells, Cultured , HEK293 Cells , Humans , Inflammasomes/metabolism , Intracellular Membranes/metabolism , MAP Kinase Kinase Kinases/antagonists & inhibitors , MAP Kinase Kinase Kinases/metabolism , Mice , Monomeric GTP-Binding Proteins/metabolism , Multiprotein Complexes/metabolism , Signal Transduction , Yersinia pseudotuberculosis/pathogenicity
12.
EBioMedicine ; 58: 102879, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32711257

ABSTRACT

BACKGROUND: While the incidence of patients with atopic dermatitis (AD) with atopic march (AM) showing respiratory allergy is steadily rising, the pathomechanism is still unknown. There are currently no biomarkers to predict progression of AM. METHODS: To explore the mechanism of AM, patients with AD and AM and healthy controls were recruited and RNA microarray, flow cytometry, quantitative real-time polymerase chain reaction, and immunofluorescence staining were performed. We also co-cultured dendritic cells and CD4+T cells with various Dermatophagoides farinae allergen fractions. Cytokine levels were evaluated using enzyme-linked immunosorbent assay. FINDINGS: Both fatty-acid-binding protein 5 (FABP5) and Th17-related genes were more highly expressed in AM. FABP5 knockdown significantly decreased Th17-inducing cytokines in keratinocytes and IL-17A in T cells from AM patients. Further confirmation was obtained using an AM mice model compared to mice without AM. Der f 1, a major D. farinae allergen, increased FABP5 and IL-17A expression in T cells from AM patients. Higher serum FABP5 levels from AM patients were positively correlated with serum IL-17A levels. INTERPRETATION: FABP5 expression, possibly enhanced by higher epicutaneous and respiratory sensitization to Der f 1, may directly promote Th17 responses in AD patients with AM. Thus, AM progression can be explained by Th17 reaction induced by FABP5. FABP5 was identified as a potential biomarker in AM. FUNDING: This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (Ministry of Science and ICT; No. NRF-2017R1A2B4009568), grants of the Korean Health Technology R&D Project, Ministry for Health, Welfare & Family Affairs, and the Republic of Korea (HI13C0010, HI14C1324, HI14C1799).


Subject(s)
Antigens, Dermatophagoides/immunology , Dermatitis, Atopic/immunology , Fatty Acid-Binding Proteins/genetics , Genetic Markers , Th17 Cells/metabolism , Adult , Animals , Antigens, Dermatophagoides/adverse effects , CD4-Positive T-Lymphocytes/cytology , CD4-Positive T-Lymphocytes/drug effects , CD4-Positive T-Lymphocytes/immunology , Case-Control Studies , Cell Polarity , Cells, Cultured , Coculture Techniques , Dendritic Cells/cytology , Dendritic Cells/drug effects , Dendritic Cells/immunology , Dermatitis, Atopic/chemically induced , Dermatitis, Atopic/genetics , Disease Models, Animal , Disease Progression , Female , Humans , Male , Mice , Middle Aged , Oligonucleotide Array Sequence Analysis , Up-Regulation , Young Adult
13.
BMC Biol ; 18(1): 64, 2020 06 10.
Article in English | MEDLINE | ID: mdl-32522281

ABSTRACT

BACKGROUND: ß7 integrins are responsible for the efficient recruitment of lymphocytes from the blood and their retention in gut-associated lymphoid tissues. Integrin α4ß7 binds MAdCAM-1, mediating rolling adhesion of lymphocytes on blood vessel walls when inactive and firm adhesion when activated, thereby controlling two critical steps of lymphocyte homing to the gut. By contrast, integrin αEß7 mediates the adhesion of lymphocytes to gut epithelial cells by interacting with E-cadherin. Integrin ß7 blocking antibodies have shown efficacy in clinical management of inflammatory bowel disease (IBD); however, fully blocking ß7 function leads to the depletion of colonic regulatory T (Treg) cells and exacerbates dextran sulfate sodium (DSS)-induced colitis by evoking aberrant innate immunity, implying its potential adverse effect for IBD management. Thus, a better therapeutic strategy targeting integrin ß7 is required to avoid this adverse effect. RESULTS: Herein, we inhibited integrin α4ß7 activation in vivo by creating mice that carry in their integrin ß7 gene a mutation (F185A) which from structural studies is known to lock α4ß7 in its resting state. Lymphocytes from ß7-F185A knock-in (KI) mice expressed α4ß7 integrins that could not be activated by chemokines and showed significantly impaired homing to the gut. The ß7-F185A mutation did not inhibit αEß7 activation, but led to the depletion of αEß7+ lymphocytes in the spleen and a significantly reduced population of αEß7+ lymphocytes in the gut of KI mice. ß7-F185A KI mice were resistant to T cell transfer-induced chronic colitis, but did not show an increased susceptibility to DSS-induced innate colitis, the adverse effect of fully blocking ß7 function. CONCLUSIONS: Our findings demonstrate that specific inhibition of integrin α4ß7 activation is a potentially better strategy than fully blocking α4ß7 function for IBD treatment.


Subject(s)
Adaptive Immunity , Colitis/genetics , Integrins/genetics , Mutation , Animals , Colitis/immunology , Female , Integrins/metabolism , Male , Mice , Mice, Transgenic
14.
Cancer Immunol Res ; 8(5): 660-671, 2020 05.
Article in English | MEDLINE | ID: mdl-32161110

ABSTRACT

We assessed the contribution of IL1 signaling molecules to malignant tumor growth using IL1ß-/-, IL1α-/-, and IL1R1-/- mice. Tumors grew progressively in IL1R-/- and IL1α-/- mice but were often absent in IL1ß-/- mice. This was observed whether tumors were implanted intradermally or injected intravenously and was true across multiple distinct tumor lineages. Antibodies to IL1ß prevented tumor growth in wild-type (WT) mice but not in IL1R1-/- or IL1α-/- mice. Antibodies to IL1α promoted tumor growth in IL1ß-/- mice and reversed the tumor-suppressive effect of anti-IL1ß in WT mice. Depletion of CD8+ T cells and blockade of lymphocyte mobilization abrogated the IL1ß-/- tumor suppressive effect, as did crossing IL1ß-/- mice to SCID or Rag1-/- mice. Finally, blockade of IL1ß synergized with blockade of PD-1 to inhibit tumor growth in WT mice. These results suggest that IL1ß promotes tumor growth, whereas IL1α inhibits tumor growth by enhancing T-cell-mediated antitumor immunity.


Subject(s)
Adaptive Immunity , Antibodies, Monoclonal/pharmacology , CD8-Positive T-Lymphocytes/immunology , Interleukin-1alpha/immunology , Interleukin-1beta/immunology , Neoplasms/therapy , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Animals , Cell Line, Tumor , Disease Models, Animal , Interleukin-1alpha/metabolism , Interleukin-1beta/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, SCID , Neoplasms/immunology , Tumor Microenvironment
15.
Nature ; 569(7758): E12, 2019 May.
Article in English | MEDLINE | ID: mdl-31081500

ABSTRACT

In this Letter, Supplementary Fig. 1 was missing. This error has been corrected online.

16.
Nature ; 566(7743): 259-263, 2019 02.
Article in English | MEDLINE | ID: mdl-30728498

ABSTRACT

Cytosolic DNA triggers innate immune responses through the activation of cyclic GMP-AMP synthase (cGAS) and production of the cyclic dinucleotide second messenger 2',3'-cyclic GMP-AMP (cGAMP)1-4. 2',3'-cGAMP is a potent inducer of immune signalling; however, no intracellular nucleases are known to cleave 2',3'-cGAMP and prevent the activation of the receptor stimulator of interferon genes (STING)5-7. Here we develop a biochemical screen to analyse 24 mammalian viruses, and identify poxvirus immune nucleases (poxins) as a family of 2',3'-cGAMP-degrading enzymes. Poxins cleave 2',3'-cGAMP to restrict STING-dependent signalling and deletion of the poxin gene (B2R) attenuates vaccinia virus replication in vivo. Crystal structures of vaccinia virus poxin in pre- and post-reactive states define the mechanism of selective 2',3'-cGAMP degradation through metal-independent cleavage of the 3'-5' bond, converting 2',3'-cGAMP into linear Gp[2'-5']Ap[3']. Poxins are conserved in mammalian poxviruses. In addition, we identify functional poxin homologues in the genomes of moths and butterflies and the baculoviruses that infect these insects. Baculovirus and insect host poxin homologues retain selective 2',3'-cGAMP degradation activity, suggesting an ancient role for poxins in cGAS-STING regulation. Our results define poxins as a family of 2',3'-cGAMP-specific nucleases and demonstrate a mechanism for how viruses evade innate immunity.


Subject(s)
Deoxyribonucleases/chemistry , Deoxyribonucleases/metabolism , Membrane Proteins/metabolism , Nucleotides, Cyclic/metabolism , Nucleotidyltransferases/metabolism , Signal Transduction/immunology , Vaccinia virus/enzymology , Animals , Baculoviridae/enzymology , Butterflies/enzymology , Cell Line , Conserved Sequence , Crystallography, X-Ray , DNA, Viral/immunology , Female , Genes, Viral/genetics , Humans , Immune Evasion , Immunity, Innate/immunology , Mice , Mice, Inbred C57BL , Models, Molecular , Moths/enzymology , Second Messenger Systems , Vaccinia virus/genetics , Vaccinia virus/growth & development , Vaccinia virus/immunology , Virus Replication/genetics
17.
Cancers (Basel) ; 10(9)2018 Sep 04.
Article in English | MEDLINE | ID: mdl-30181502

ABSTRACT

Cytolytic immune activity in solid tissue can be quantified by transcript levels of two genes, GZMA and PRF1, which is named the CYT score. A previous study has investigated the molecular and genetic properties of tumors associated CYT, but a systematic exploration of how co-expression networks across different tumors are shaped by anti-tumor immunity is lacking. Here, we examined the connectivity and biological themes of CYT-associated modules in gene co-expression networks of 14 tumor and 3 matched normal tissues constructed from the RNA-Seq data of the "The Cancer Genome Atlas" project. We first found that tumors networks have more diverse CYT-correlated modules than normal networks. We next identified and investigated tissue-specific CYT-associated modules across 14 tumor types. Finally, a common CYT-associated network across 14 tumor types was constructed. Two common modules have mixed signs of correlation with CYT in different tumors. Given the tumors and normal tissues surveyed, our study presents a systematic view of the regulation of cytolytic immune activity across multiple tumor tissues.

18.
Front Immunol ; 9: 1347, 2018.
Article in English | MEDLINE | ID: mdl-29967608

ABSTRACT

Tissue-resident memory T cells (TRM) persist in peripheral tissues for long periods of time in the absence of antigenic stimulation. Upon re-encounter with cognate antigen, TRM trigger an immediate immune response at the local tissue microenvironment and provide the first line of host defense. TRM have been reported to play significant roles in host antimicrobial infection, cancer immunotherapy, and pathogenesis of a number of human autoimmune diseases, such as psoriasis, vitiligo, and atopic dermatitis. TRM display a distinct gene transcriptome with unique gene expression profiles related to cellular metabolism that is different from naive T cells (TN), central memory T cells (TCM), and effector memory T cells (TEM). Skin CD8+ TRM upregulate expression of genes associated with lipid uptake and metabolism and utilize mitochondria fatty acid ß-oxidation to support their long-term survival (longevity) and function. In this review, we will summarize the recent progresses in the metabolic programming of TRM and will also discuss the potential to target the unique metabolic pathways of TRM to treat TRM-mediated diseases.

19.
Cell ; 174(1): 187-201.e12, 2018 06 28.
Article in English | MEDLINE | ID: mdl-29779946

ABSTRACT

Widespread mRNA decay, an unappreciated feature of apoptosis, enhances cell death and depends on mitochondrial outer membrane permeabilization (MOMP), TUTases, and DIS3L2. Which RNAs are decayed and the decay-initiating event are unknown. Here, we show extensive decay of mRNAs and poly(A) noncoding (nc)RNAs at the 3' end, triggered by the mitochondrial intermembrane space 3'-to-5' exoribonuclease PNPT1, released during MOMP. PNPT1 knockdown inhibits apoptotic RNA decay and reduces apoptosis, while ectopic expression of PNPT1, but not an RNase-deficient mutant, increases RNA decay and cell death. The 3' end of PNPT1 substrates thread through a narrow channel. Many non-poly(A) ncRNAs contain 3'-secondary structures or bind proteins that may block PNPT1 activity. Indeed, mutations that disrupt the 3'-stem-loop of a decay-resistant ncRNA render the transcript susceptible, while adding a 3'-stem-loop to an mRNA prevents its decay. Thus, PNPT1 release from mitochondria during MOMP initiates apoptotic decay of RNAs lacking 3'-structures.


Subject(s)
Apoptosis , Exoribonucleases/metabolism , Mitochondria/metabolism , RNA, Messenger/metabolism , 3' Untranslated Regions , Apoptosis/drug effects , Caspase 3/metabolism , Cytochromes c/metabolism , Exoribonucleases/antagonists & inhibitors , Exoribonucleases/genetics , HCT116 Cells , Humans , Mitochondrial Membranes/metabolism , Nucleic Acid Conformation , Permeability , Poly(A)-Binding Protein I/chemistry , Poly(A)-Binding Protein I/metabolism , Protein Binding , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/metabolism , RNA Interference , RNA Stability/drug effects , RNA, Messenger/chemistry , RNA, Small Interfering/metabolism , RNA, Untranslated/chemistry , RNA, Untranslated/metabolism , TNF-Related Apoptosis-Inducing Ligand/pharmacology
20.
J Allergy Clin Immunol ; 142(2): 647-662, 2018 08.
Article in English | MEDLINE | ID: mdl-29128674

ABSTRACT

BACKGROUND: Candida albicans is a dimorphic fungus to which human subjects are exposed early in life, and by adulthood, it is part of the mycobiome of skin and other tissues. Neonatal skin lacks resident memory T (TRM) cells, but in adults the C albicans skin test is a surrogate for immunocompetence. Young adult mice raised under specific pathogen-free conditions are naive to C albicans and have been shown recently to have an immune system resembling that of neonatal human subjects. OBJECTIVE: We studied the evolution of the adaptive cutaneous immune response to Candida species. METHODS: We examined both human skin T cells and the de novo and memory immune responses in a mouse model of C albicans skin infection. RESULTS: In mice the initial IL-17-producing cells after C albicans infection were dermal γδ T cells, but by day 7, αß TH17 effector T cells were predominant. By day 30, the majority of C albicans-reactive IL-17-producing T cells were CD4 TRM cells. Intravital microscopy showed that CD4 effector T cells were recruited to the site of primary infection and were highly motile 10 days after infection. Between 30 and 90 days after infection, these CD4 T cells became increasingly sessile, acquired expression of CD69 and CD103, and localized to the papillary dermis. These established TRM cells produced IL-17 on challenge, whereas motile migratory memory T cells did not. TRM cells rapidly clear an infectious challenge with C albicans more effectively than recirculating T cells, although both populations participate. We found that in normal human skin IL-17-producing CD4+ TRM cells that responded to C albicans in an MHC class II-restricted fashion could be identified readily. CONCLUSIONS: These studies demonstrate that C albicans infection of skin preferentially generates CD4+ IL-17-producing TRM cells, which mediate durable protective immunity.


Subject(s)
Candida albicans/physiology , Candidiasis/immunology , Skin/immunology , T-Lymphocyte Subsets/physiology , Th17 Cells/physiology , Adaptive Immunity , Adult , Animals , Cell Differentiation , Cell Movement , Cells, Cultured , Disease Models, Animal , Humans , Immunocompetence , Immunologic Memory , Infant, Newborn , Interleukin-17/metabolism , Mice , Mice, Inbred C57BL , Receptors, Antigen, T-Cell, alpha-beta/metabolism , Skin/microbiology
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