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Abdel-Haq H. Feasibility of Using a Type I IFN-Based Non-Animal Approach to Predict Vaccine Efficacy and Safety Profiles. Vaccines (Basel) 2024; 12:583. [PMID: 38932312 PMCID: PMC11209158 DOI: 10.3390/vaccines12060583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Animal-based tests are used for the control of vaccine quality. However, because highly purified and safe vaccines are now available, alternative approaches that can replace or reduce animal use for the assessment of vaccine outcomes must be established. In vitro tests for vaccine quality control exist and have already been implemented. However, these tests are specifically designed for some next-generation vaccines, and this makes them not readily available for testing other vaccines. Therefore, universal non-animal tests are still needed. Specific signatures of the innate immune response could represent a promising approach to predict the outcome of vaccines by non-animal methods. Type I interferons (IFNs) have multiple immunomodulatory activities, which are exerted through effectors called interferon stimulated genes (ISGs), and are one of the most important immune signatures that might provide potential candidate molecular biomarkers for this purpose. This paper will mainly examine if this idea might be feasible by analyzing all relevant published studies that have provided type I IFN-related biomarkers for evaluating the safety and efficacy profiles of vaccines using an advanced transcriptomic approach as an alternative to the animal methods. Results revealed that such an approach could potentially provide biomarkers predictive of vaccine outcomes after addressing some limitations.
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Affiliation(s)
- Hanin Abdel-Haq
- Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy
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2
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Zhang L, Zhou Y, Xing X, Li H, Zhang Z, Qian R, Hu X. Upregulation of IFNE in cervical biopsies of patients with high-risk human papillomavirus infections. Immun Inflamm Dis 2023; 11:e1111. [PMID: 38156399 PMCID: PMC10698813 DOI: 10.1002/iid3.1111] [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: 06/02/2023] [Revised: 10/31/2023] [Accepted: 11/18/2023] [Indexed: 12/30/2023] Open
Abstract
PROBLEM Interferon epsilon (IFN-ε) is constitutively expressed in the epithelium of female reproductive tract and confers vital protection against sexually transmitted pathogens in mouse models. However, there is limited insight into the role of IFN-ε in human sexually transmitted infections such as human papillomavirus (HPV). METHOD OF STUDY Cervical biopsies were obtained from high-risk (HR) HPV positive (n = 28) and HR-HPV negative (n = 10) women. mRNA expression of IFN-ε in cervical tissues was measured by qPCR. Expression of the IFN-ε protein was determined by Western blot analysis, immunohistochemistry and immunofluorescence staining. RESULTS mRNA expression of IFN-ε was higher in the ectocervix than that of other IFNs, and was further upregulated in HR-HPV positive women compared with HR-HPV negative women. Expression of the IFN-ε protein was comparable between HR-HPV infected patients and healthy controls. CONCLUSIONS These results reveal differential expression of IFN-ε mRNA between individuals with or without HR-HPV infection, and imply direct or indirect regulatory mechanisms for IFN-ε transcription by HPV. Expression of IFN-ε protein in HPV infections would require further validation.
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Affiliation(s)
- Lu Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical UniversityBeijingChina
- Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Yuechen Zhou
- School of MedicineTsinghua UniversityBeijingChina
| | - Xiaoyan Xing
- School of MedicineTsinghua UniversityBeijingChina
| | - Hua Li
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical UniversityBeijingChina
- Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Zhan Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical UniversityBeijingChina
- Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Ruiya Qian
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical UniversityBeijingChina
- Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Xiaoyu Hu
- School of MedicineTsinghua UniversityBeijingChina
- Institute for Immunology and School of MedicineTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
- Beijing Key Laboratory for Immunological Research on Chronic DiseasesBeijingChina
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3
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Zhao FR, Wang W, Zheng Q, Zhang YG, Chen J. The regulation of antiviral activity of interferon epsilon. Front Microbiol 2022; 13:1006481. [PMID: 36386666 PMCID: PMC9642105 DOI: 10.3389/fmicb.2022.1006481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 01/08/2023] Open
Abstract
Interferon epsilon (IFN-ε) is a type I IFN. Some biological properties has been identified in many species, such as antiproliferative, anti-tumor, and antiviral effects, of IFN-ε, which are much weaker than those of IFN-α, have also been revealed. It has been shown to play a role in mucosal immunity and bacterial infection and in the prevention of certain sexually transmitted diseases, such as human immunodeficiency virus (HIV). This paper reviews the known activity of IFN-ε, particularly in some viruses. In general, this review provides a better understanding of effective IFN-ε treatment in the future.
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4
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Taylor BD, Criscitiello MF, Hernandez T, Norwood B, Noah A, Bazer FW. Interferon epsilon and preterm birth subtypes; a new piece of the type I interferon puzzle during pregnancy? Am J Reprod Immunol 2022; 87:e13526. [PMID: 35147251 PMCID: PMC9978937 DOI: 10.1111/aji.13526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/06/2022] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
PROBLEM Interferon epsilon (IFNε) is a unique type I IFN that is expressed in response to sex steroids. Studies suggest that type I IFNs regulate inflammation-induced preterm birth (PTB), but no study has examined the role of IFNε in human pregnancy. METHOD OF STUDY We used stored vaginal swabs between 8 and 26 weeks of gestation from the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) biobank and measured IFNε by enzyme-linked immunosorbent assay (ELISA). A total of 29 women with spontaneous preterm births, 34 women with medically indicated preterm births, and 134 women with term births were included. Secondary outcomes included a preterm birth with chorioamnionitis and preeclampsia with a preterm birth. Logistic regression calculated odds ratios (OR) and 95% confidence intervals (CI) adjusting for maternal age, race, body mass index, prior pregnancy complications, lower genital tract infections, chronic health conditions, and gestational age at blood draw. RESULTS AND CONCLUSIONS There was no significant association between IFNε and spontaneous preterm birth (ORadj 1.0, 0.8-1.3) or chorioamnionitis (ORadj 1.6, 0.7-3.5). A trend toward increased odds of medically indicated preterm birth (ORadj . 1.3, 1.0-1.8) was observed. This was likely due to elevated IFNε among women with preterm preeclampsia (ORadj . 2.0, 95% CI 1.3-3.2). While exploratory, our novel findings suggest that larger longitudinal studies of IFNε across human pregnancy may be warranted.
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Affiliation(s)
- Brandie DePaoli Taylor
- Department of Obstetrics and Gynecology, Division of Basic and Translational Research, University of Texas Medical Branch, Galveston, TX, 77555,Department of Preventive Medicine and Population Health, University of Texas Medical Branch-Galveston, Galveston, Texas,Correspondence: Brandie DePaoli Taylor, PhD, MPH, Department of Obstetrics and Gynecology, Division of Basic and Translational Research, University of Texas Medical Branch ; phone: 409-772-7592
| | - Michael F. Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, College Station, Texas 77843
| | - Tyne Hernandez
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, PA, 19143
| | - Brooke Norwood
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Akawinyene Noah
- Department of Obstetrics and Gynecology, Division of Basic and Translational Research, University of Texas Medical Branch, Galveston, TX, 77555,Department of Preventive Medicine and Population Health, University of Texas Medical Branch-Galveston, Galveston, Texas
| | - Fuller W. Bazer
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
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5
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Li Z, Roy S, Ranasinghe C. IL-13Rα2 Regulates the IL-13/IFN-γ Balance during Innate Lymphoid Cell and Dendritic Cell Responses to Pox Viral Vector-Based Vaccination. Vaccines (Basel) 2021; 9:440. [PMID: 34062727 PMCID: PMC8147251 DOI: 10.3390/vaccines9050440] [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: 03/05/2021] [Revised: 04/08/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
We have shown that manipulation of IL-13 and STAT6 signaling at the vaccination site can lead to different innate lymphoid cell (ILC)/dendritic cell (DC) recruitment, resulting in high avidity/poly-functional T cells and effective antibody differentiation. Here we show that permanent versus transient blockage of IL-13 and STAT6 at the vaccination site can lead to unique ILC-derived IL-13 and IFN-γ profiles, and differential IL-13Rα2, type I and II IL-4 receptor regulation on ILC. Specifically, STAT6-/- BALB/c mice given fowl pox virus (FPV) expressing HIV antigens induced elevated ST2/IL-33R+ ILC2-derived IL-13 and reduced NKp46+/- ILC1/ILC3-derived IFN-γ expression, whilst the opposite (reduced IL-13 and elevated IFN-γ expression) was observed during transient inhibition of STAT6 signaling in wild type BALB/c mice given FPV-HIV-IL-4R antagonist vaccination. Interestingly, disruption/inhibition of STAT6 signaling considerably impacted IL-13Rα2 expression by ST2/IL-33R+ ILC2 and NKp46- ILC1/ILC3, unlike direct IL-13 inhibition. Consistently with our previous findings, this further indicated that inhibition of STAT6 most likely promoted IL-13 regulation via IL-13Rα2. Moreover, the elevated ST2/IL-33R+ IL-13Rα2+ lung ILC2, 24 h post FPV-HIV-IL-4R antagonist vaccination was also suggestive of an autocrine regulation of ILC2-derived IL-13 and IL-13Rα2, under certain conditions. Knowing that IL-13 can modulate IFN-γ expression, the elevated expression of IFN-γR on lung ST2/IL-33R+ ILC2 provoked the notion that there could also be inter-regulation of lung ILC2-derived IL-13 and NKp46- ILC1/ILC3-derived IFN-γ via their respective receptors (IFN-γR and IL-13Rα2) at the lung mucosae early stages of vaccination. Intriguingly, under different IL-13 conditions differential regulation of IL-13/IL-13Rα2 on lung DC was also observed. Collectively these findings further substantiated that IL-13 is the master regulator of, not only DC, but also different ILC subsets at early stages of viral vector vaccination, and responsible for shaping the downstream adaptive immune outcomes. Thus, thoughtful selection of vaccine strategies/adjuvants that can manipulate IL-13Rα2, and STAT6 signaling at the ILC/DC level may prove useful in designing more efficacious vaccines against different/chronic pathogens.
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Affiliation(s)
- Zheyi Li
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; (Z.L.); (S.R.)
| | - Sreeja Roy
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; (Z.L.); (S.R.)
- Department of Immunology & Microbial Disease, Albany Medical College, 47 New Scotland Ave, Albany, NY 12208-3479, USA
| | - Charani Ranasinghe
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; (Z.L.); (S.R.)
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6
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Nickodem C, Criscitiello MF, Bazer F, Abiodun-Ojo O, Taylor BD. Interferon epsilon in the reproductive tract of healthy and genital herpes simplex virus-infected pregnant women: Results of a pilot study. Am J Reprod Immunol 2018; 80:e12995. [PMID: 29905034 DOI: 10.1111/aji.12995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/23/2018] [Indexed: 12/31/2022] Open
Abstract
PROBLEM Recently characterized interferon epsilon (IFNe) protects against sexually transmitted infections, including genital herpes simplex virus (HSV), in animal models. There are no reports of IFNe in genital tract secretions of pregnant women, and data on IFNe in non-pregnant women are limited. This pilot study is the first to measure concentrations of IFNe in vaginal and cervical secretions during pregnancy and compare values between healthy and genital HSV-infected women. METHOD OF STUDY Vaginal or cervical specimens from 30 pregnant women were obtained from the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) repository. Cervical samples were collected during the first trimester and vaginal samples across pregnancy. Enzyme-linked immunosorbent assay determined concentrations of IFNe (pg/mL). Data for IFNe were log-transformed and compared by maternal demographics, clinical variables, and HSV status using t tests and linear regression. Repeated measures analysis explored trends across pregnancy. RESULTS Among the entire cohort, first trimester concentrations of IFNe in vaginal or cervical secretions decreased as body mass index increased (β = -0.14, P = .0466). Concentrations of vaginal IFNe increased across pregnancy in HSV-infected and healthy women (P = .009). Average vaginal IFNe across pregnancy was lower in women with HSV compared to healthy women (P = .0009). CONCLUSION Interferon epsilon increased across pregnancy, but was less abundant in women with HSV. This pilot investigation cannot make any definitive conclusions. However, animal models suggest that IFNe may protect against STIs. Thus, larger studies are required to validate expression of IFNe in the reproductive tract of pregnant women with and without genital infections.
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Affiliation(s)
- Colette Nickodem
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, College Station, TX, USA
| | - Fuller Bazer
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Olayinka Abiodun-Ojo
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
| | - Brandie D Taylor
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
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7
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Tan H, Zeng C, Xie J, Alghamdi NJ, Song Y, Zhang H, Zhou A, Jin D. Effects of interferons and double-stranded RNA on human prostate cancer cell apoptosis. Oncotarget 2016; 6:39184-95. [PMID: 26452032 PMCID: PMC4770765 DOI: 10.18632/oncotarget.5508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 09/18/2015] [Indexed: 11/25/2022] Open
Abstract
Prostate cancer is the second most commonly diagnosed cancer among men in the United States. Prostate cancer therapy is severely hampered by lack of response and development of resistance to conventional chemotherapeutic drugs in patients. Therefore, the development and discovery of new drugs have become an urgent clinical need. Interferons (IFNs), a family of pleiotropic cytokines, exert antitumor activities due to their anti-proliferative, immunomodulatory and proapoptotic functions. Here, we report that pretreatment of prostate cancer PC-3 cells with IFNs sensitized these cells to double-stranded RNAs (dsRNAs)-induced apoptosis. The enhancement effect of IFN treatment was dependent on IFN subtypes, in particular, IFN γ. In comparison with IFN α or β, IFN γ treatment remarkably augmented apoptosis in PC-3 cells induced with polyinosinic:polycytidylic acid (poly I:C), a synthesized form of dsRNA. We demonstrated that IFN-signaling was necessary for these effects by using mutant cell lines. Transfection of 2-5A, the activator of RNase L, or silencing of dsRNA-dependent protein kinase R (PKR) by siRNA did not have any significant impact on this event, suggesting that neither RNase L nor PKR was involved in poly I:C/IFN γ-induced apoptosis in the cells. Further investigation of the apoptotic pathway revealed that Bak, a pro-apoptotic member of the Bcl-2family, was synergistically up-regulated by IFN γ and poly I:C, whereas other members of the family were not affected. Knocking down of Bak demonstrated its contribution to poly I:C/IFN γ-induced apoptosis in the cells. We believeour findings will precipitate the design of novel therapeutic strategies for prostate cancer.
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Affiliation(s)
- Haiyan Tan
- Clinical Chemistry Program, Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Chun Zeng
- Clinical Chemistry Program, Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Junbo Xie
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Norah J Alghamdi
- Clinical Chemistry Program, Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ya Song
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hongbing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Aimin Zhou
- Clinical Chemistry Program, Department of Chemistry, Cleveland State University, Cleveland, OH, USA.,Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH, USA
| | - Di Jin
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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8
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Torrelo A, Noguera-Morel L, Hernández-Martín A, Clemente D, Barja J, Buzón L, Azorín D, de Jesús A, López-Robledillo J, Colmenero I, Kutzner H, Goldbach-Mansky R, Requena L. Recurrent lipoatrophic panniculitis of children. J Eur Acad Dermatol Venereol 2016; 31:536-543. [DOI: 10.1111/jdv.13858] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/08/2016] [Indexed: 12/28/2022]
Affiliation(s)
- A. Torrelo
- Department of Dermatology; Hospital del Niño Jesús; Madrid Spain
| | - L. Noguera-Morel
- Department of Dermatology; Hospital del Niño Jesús; Madrid Spain
| | | | - D. Clemente
- Department of Rheumatology; Hospital del Niño Jesús; Madrid Spain
| | - J.M. Barja
- Department of Dermatology; Hospital El Bierzo; León Spain
| | - L. Buzón
- Department of Microbiology; Hospital Gregorio Marañón; Madrid Spain
| | - D. Azorín
- Department of Pathology; Hospital del Niño Jesús; Madrid Spain
| | - A.A. de Jesús
- Translational Autoinflammatory Disease Section; NIAMS; NIH; Bethesda USA
| | | | - I. Colmenero
- Paediatric Histopathology Department; Birmingham Children's Hospital; Birmingham UK
| | - H. Kutzner
- Dermatohistopathologisches Gemeinschaftslabor; Friedrichshafen Germany
| | - R. Goldbach-Mansky
- Translational Autoinflammatory Disease Section; NIAMS; NIH; Bethesda USA
| | - L. Requena
- Department of Dermatology; Fundación Jiménez Díaz; Madrid Spain
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9
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Li H, Huang X, Zeng Z, Peng XX, Peng B. Identification of the interactome between fish plasma proteins and Edwardsiella tarda reveals tissue-specific strategies against bacterial infection. Int J Biochem Cell Biol 2016; 78:260-267. [PMID: 27458055 DOI: 10.1016/j.biocel.2016.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Elucidating the complex pathogen-host interaction is essential for a comprehensive understanding of how these remarkable agents invade their hosts and how the hosts defend against these invaders. During the infection, pathogens interact intensively with host to enable their survival, which can be revealed through their interactome. Edwardsiella tarda is a Gram-negative bacterial pathogen causing huge economic loss in aquaculture and a spectrum of intestinal and extraintestinal diseases in humans. E. tarda is an ideal model for host-pathogen investigation as it infects fish in three distinct steps: entering the host, circulating through the blood and establishing infection. We adopted a previous established proteomic approach that inactivated E. tarda cells and covalent crosslink fish plasma proteins were used to capture plasma proteins and bacterial outer membrane proteins, respectively. By the combinatorial use of proteomic and biochemical approaches, six plasma proteins and seven outer membrane proteins (OMPs) were identified. Interactions among these proteins were validated with protein-array, far-Western blotting and co-immunoprecipitation. At last, seventeen plasma protein-bacteria protein-protein interaction were confirmed to be involved in the interaction network, forming a complex interactome. Compared to our previous results, different host proteins were detected, whereas some of the bacterial proteins were similar, which indicates that hosts adopt tissue-specific strategies to cope with the same pathogen during infection. Thus, our results provide a robust demonstration of both bacterial initiators and host receptors or interacting proteins to further explore infection and anti-infective mechanisms between hosts and microbes.
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Affiliation(s)
- Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquat Food Safety, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, Peoples Republic of China
| | - Xiaoyan Huang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquat Food Safety, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, Peoples Republic of China
| | - Zaohai Zeng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquat Food Safety, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, Peoples Republic of China
| | - Xuan-Xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquat Food Safety, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, Peoples Republic of China
| | - Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquat Food Safety, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, Peoples Republic of China.
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10
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Nickerson ML, Witte N, Im KM, Turan S, Owens C, Misner K, Tsang SX, Cai Z, Wu S, Dean M, Costello JC, Theodorescu D. Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response. Oncogene 2016; 36:35-46. [PMID: 27270441 PMCID: PMC5140783 DOI: 10.1038/onc.2016.172] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/14/2022]
Abstract
The utility of tumor-derived cell lines is dependent on their ability to recapitulate underlying genomic aberrations and primary tumor biology. Here, we sequenced the exomes of 25 bladder cancer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug response to BCa patient profiles in The Cancer Genome Atlas (TCGA). We observed a mutation pattern associated with altered CpGs and APOBEC-family cytosine deaminases similar to mutation signatures derived from somatic alterations in muscle-invasive (MI) primary tumors, highlighting a major mechanism(s) contributing to cancer-associated alterations in the BCa cell line exomes. Non-silent sequence alterations were confirmed in 76 cancer-associated genes, including mutations that likely activate oncogenes TERT and PIK3CA, and alter chromatin-associated proteins (MLL3, ARID1A, CHD6 and KDM6A) and established BCa genes (TP53, RB1, CDKN2A and TSC1). We identified alterations in signaling pathways and proteins with related functions, including the PI3K/mTOR pathway, altered in 60% of lines; BRCA DNA repair, 44% and SYNE1–SYNE2, 60%. Homozygous deletions of chromosome 9p21 are known to target the cell cycle regulators CDKN2A and CDKN2B. This loci was commonly lost in BCa cell lines and we show the deletions extended to the polyamine enzyme methylthioadenosine (MTA) phosphorylase (MTAP) in 36% of lines, transcription factor DMRTA1 (27%) and antiviral interferon epsilon (IFNE, 19%). Overall, the BCa cell line genomic aberrations were concordant with those found in BCa patient tumors. We used gene expression and copy number data to infer pathway activities for cell lines, then used the inferred pathway activities to build a predictive model of cisplatin response. When applied to platinum-treated patients gathered from TCGA, the model predicted treatment-specific response. Together, these data and analysis represent a valuable community resource to model basic tumor biology and to study the pharmacogenomics of BCa.
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Affiliation(s)
- M L Nickerson
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - N Witte
- Computational Bioscience Program, University of Colorado, Aurora, CO, USA
| | - K M Im
- Data Science for Genomics, LLC, Ellicott City, MD, USA
| | - S Turan
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - C Owens
- Department of Surgery (Urology), University of Colorado, Aurora, CO, USA
| | - K Misner
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Z Cai
- Shenzhen Second People's Hospital, Shenzhen, China
| | - S Wu
- Shenzhen Second People's Hospital, Shenzhen, China
| | - M Dean
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - J C Costello
- Computational Bioscience Program, University of Colorado, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
| | - D Theodorescu
- Department of Surgery (Urology), University of Colorado, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
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11
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Lee A, Park SP, Park CH, Kang BH, Park SH, Ha SJ, Jung KC. IL-4 Induced Innate CD8+ T Cells Control Persistent Viral Infection. PLoS Pathog 2015; 11:e1005193. [PMID: 26452143 PMCID: PMC4599894 DOI: 10.1371/journal.ppat.1005193] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/06/2015] [Indexed: 12/20/2022] Open
Abstract
Memory-like CD8+ T cells expressing eomesodermin are a subset of innate T cells initially identified in a number of genetically modified mice, and also exist in wild mice and human. The acquisition of memory phenotype and function by these T cells is dependent on IL–4 produced by PLZF+ innate T cells; however, their physiologic function is still not known. Here we found that these IL-4-induced innate CD8+ T cells are critical for accelerating the control of chronic virus infection. In CIITA-transgenic mice, which have a substantial population of IL-4-induced innate CD8+ T cells, this population facilitated rapid control of viremia and induction of functional anti-viral T-cell responses during infection with chronic form of lymphocytic choriomeningitis virus. Characteristically, anti-viral innate CD8+ T cells accumulated sufficiently during early phase of infection. They produced a robust amount of IFN-γ and TNF-α with enhanced expression of a degranulation marker. Furthermore, this finding was confirmed in wild-type mice. Taken together, the results from our study show that innate CD8+ T cells works as an early defense mechanism against chronic viral infection. Over the course of viral infection there may be a limited time period during which the host system can eliminate the virus. When viruses are not eliminated within this period of time, virus can establish persistent infection. Here, we show that IL-4-induced innate CD8+ T cells are able to effectively control chronic virus infection. Innate T cells are heterogeneous population of T cells that acquire effector/memory phenotype as a result of their maturation process in thymus, unlike conventional T cells that differentiate into memory cells after antigen encounter in periphery. Previous data suggest that innate T cells might serve as a first-line of defense against certain bacterial pathogens. IL-4-induced innate CD8+ T cells are a unique subset of innate T cells that were recently identified in both mouse and human. We found that IL-4-induced innate CD8+ T cells immediately accumulated after viral infection and produced a robust amount of effector cytokines. Thereby, IL-4-induced innate CD8+ T cells provide an effective barrier to the establishment of persistent infection via effective virus control during the early phase of viral infection. Collectively our data show that IL-4-induced innate CD8+ T cells works as an early defense mechanism against chronic viral infection.
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Affiliation(s)
- Ara Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Korea
| | - Seung Pyo Park
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Chan Hee Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Korea
| | - Byung Hyun Kang
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Seong Hoe Park
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Korea
- * E-mail: (SJH); (KCJ)
| | - Kyeong Cheon Jung
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- * E-mail: (SJH); (KCJ)
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12
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Capobianchi MR, Uleri E, Caglioti C, Dolei A. Type I IFN family members: similarity, differences and interaction. Cytokine Growth Factor Rev 2015; 26:103-11. [PMID: 25466633 PMCID: PMC7108279 DOI: 10.1016/j.cytogfr.2014.10.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 02/07/2023]
Abstract
Interferons (IFN) are key cytokines with multifaceted antiviral and cell-modulatory properties. Three distinct types of IFN are recognized (I-III) based on structural features, receptor usage, cellular source and biological activities. The action of IFNs is mediated by a complex, partially overlapping, transcriptional program initiated by the interaction with specific receptors. Genetic diversity, with polymorphisms and mutations, can modulate the extent of IFN responses and the susceptibility to infections. Almost all viruses developed mechanisms to subvert the IFN response, involving both IFN induction and effector mechanisms. Interactions between IFN types may occur, for both antiviral and cell-modulatory effects, in a complex interplay, involving both synergistic and antagonistic effects. Interferon-associated diseases, not related to virus infections may occur, some of them frequently observed in IFN-treated patients. On the whole, IFNs are pleiotropic biologic response modifiers, that, upon activation of thousands genes, induce a broad spectrum of activities, regulating cell cycle, differentiation, plasma membrane molecules, release of mediators, etc., that can be relevant for cell proliferation, innate and adaptive immunity, hematopoiesis, angiogenesis and other body functions.
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Affiliation(s)
- Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani", Via Portuense 292, Rome, Italy
| | - Elena Uleri
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Claudia Caglioti
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani", Via Portuense 292, Rome, Italy
| | - Antonina Dolei
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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13
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Hoffmann HH, Schneider WM, Rice CM. Interferons and viruses: an evolutionary arms race of molecular interactions. Trends Immunol 2015; 36:124-38. [PMID: 25704559 DOI: 10.1016/j.it.2015.01.004] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 12/24/2022]
Abstract
Over half a century has passed since interferons (IFNs) were discovered and shown to inhibit virus infection in cultured cells. Since then, researchers have steadily brought to light the molecular details of IFN signaling, catalogued their pleiotropic effects on cells, and harnessed their therapeutic potential for a variety of maladies. While advances have been plentiful, several fundamental questions have yet to be answered and much complexity remains to be unraveled. We explore the current knowledge surrounding four main questions: are type I IFN subtypes differentially produced in response to distinct pathogens? How are IFN subtypes distinguished by cells? What are the mechanisms and consequences of viral antagonism? Lastly, how can the IFN response be harnessed to improve vaccine efficacy?
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Affiliation(s)
- Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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14
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Furuya Y, Ludewick HP, Müllbacher A. Mysteries of type I IFN response: benefits versus detriments. Front Immunol 2015; 6:21. [PMID: 25674090 PMCID: PMC4309204 DOI: 10.3389/fimmu.2015.00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/09/2015] [Indexed: 01/08/2023] Open
Affiliation(s)
- Yoichi Furuya
- Center for Immunology and Microbial Disease, Albany Medical College , Albany, NY , USA
| | - Herbert P Ludewick
- Center for Immunology and Microbial Disease, Albany Medical College , Albany, NY , USA
| | - Arno Müllbacher
- Department of Immunology, The John Curtin School of Medical Research, Australian National University , Canberra, ACT , Australia
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15
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Wang X, Meng D. Innate endogenous adjuvants prime to desirable immune responses via mucosal routes. Protein Cell 2014; 6:170-84. [PMID: 25503634 PMCID: PMC4348248 DOI: 10.1007/s13238-014-0125-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 12/01/2022] Open
Abstract
Vaccination is an effective strategy to prevent infectious or immune related diseases, which has made remarkable contribution in human history. Recently increasing attentions have been paid to mucosal vaccination due to its multiple advantages over conventional ways. Subunit or peptide antigens are more reasonable immunogens for mucosal vaccination than live or attenuated pathogens, however adjuvants are required to augment the immune responses. Many mucosal adjuvants have been developed to prime desirable immune responses to different etiologies. Compared with pathogen derived adjuvants, innate endogenous molecules incorporated into mucosal vaccines demonstrate prominent adjuvanticity and safety. Nowadays, cytokines are broadly used as mucosal adjuvants for participation of signal transduction of immune responses, activation of innate immunity and polarization of adaptive immunity. Desired immune responses are promptly and efficaciously primed on basis of specific interactions between cytokines and corresponding receptors. In addition, some other innate molecules are also identified as potent mucosal adjuvants. This review focuses on innate endogenous mucosal adjuvants, hoping to shed light on the development of mucosal vaccines.
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Affiliation(s)
- Xiaoguang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China,
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16
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Tomasello E, Pollet E, Vu Manh TP, Uzé G, Dalod M. Harnessing Mechanistic Knowledge on Beneficial Versus Deleterious IFN-I Effects to Design Innovative Immunotherapies Targeting Cytokine Activity to Specific Cell Types. Front Immunol 2014; 5:526. [PMID: 25400632 PMCID: PMC4214202 DOI: 10.3389/fimmu.2014.00526] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/07/2014] [Indexed: 12/15/2022] Open
Abstract
Type I interferons (IFN-I) were identified over 50 years ago as cytokines critical for host defense against viral infections. IFN-I promote anti-viral defense through two main mechanisms. First, IFN-I directly reinforce or induce de novo in potentially all cells the expression of effector molecules of intrinsic anti-viral immunity. Second, IFN-I orchestrate innate and adaptive anti-viral immunity. However, IFN-I responses can be deleterious for the host in a number of circumstances, including secondary bacterial or fungal infections, several autoimmune diseases, and, paradoxically, certain chronic viral infections. We will review the proposed nature of protective versus deleterious IFN-I responses in selected diseases. Emphasis will be put on the potentially deleterious functions of IFN-I in human immunodeficiency virus type 1 (HIV-1) infection, and on the respective roles of IFN-I and IFN-III in promoting resolution of hepatitis C virus (HCV) infection. We will then discuss how the balance between beneficial versus deleterious IFN-I responses is modulated by several key parameters including (i) the subtypes and dose of IFN-I produced, (ii) the cell types affected by IFN-I, and (iii) the source and timing of IFN-I production. Finally, we will speculate how integration of this knowledge combined with advanced biochemical manipulation of the activity of the cytokines should allow designing innovative immunotherapeutic treatments in patients. Specifically, we will discuss how induction or blockade of specific IFN-I responses in targeted cell types could promote the beneficial functions of IFN-I and/or dampen their deleterious effects, in a manner adapted to each disease.
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Affiliation(s)
- Elena Tomasello
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Emeline Pollet
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Thien-Phong Vu Manh
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
| | - Gilles Uzé
- UMR 5235, Centre National de la Recherche Scientifique (CNRS), University Montpellier II , Montpellier , France
| | - Marc Dalod
- UM2, Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University , Marseille , France ; U1104, Institut National de la Santé et de la Recherche Médicale (INSERM) , Marseille , France ; UMR7280, Centre National de la Recherche Scientifique (CNRS) , Marseille , France
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