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Bennett SJ, Yalcin D, Privatt SR, Ngalamika O, Lidenge SJ, West JT, Wood C. Antibody profiling and predictive modeling discriminate between Kaposi sarcoma and asymptomatic KSHV infection. PLoS Pathog 2024; 20:e1012023. [PMID: 38381773 PMCID: PMC10911871 DOI: 10.1371/journal.ppat.1012023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/04/2024] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Protein-level immunodominance patterns against Kaposi sarcoma-associated herpesvirus (KSHV), the aetiologic agent of Kaposi sarcoma (KS), have been revealed from serological probing of whole protein arrays, however, the epitopes that underlie these patterns have not been defined. We recently demonstrated the utility of phage display in high-resolution linear epitope mapping of the KSHV latency-associated nuclear antigen (LANA/ORF73). Here, a VirScan phage immunoprecipitation and sequencing approach, employing a library of 1,988 KSHV proteome-derived peptides, was used to quantify the breadth and magnitude of responses of 59 sub-Saharan African KS patients and 22 KSHV-infected asymptomatic individuals (ASY), and ultimately to support an application of machine-learning-based predictive modeling using the peptide-level responses. Comparing anti-KSHV antibody repertoire revealed that magnitude, not breadth, increased in KS. The most targeted epitopes in both KS and ASY were in the immunodominant proteins, notably, K8.129-56 and ORF65140-168, in addition to LANA. Finally, using unbiased machine-learning-based predictive models, reactivity to a subset of 25 discriminative peptides was demonstrated to successfully classify KS patients from asymptomatic individuals. Our study provides the highest resolution mapping of antigenicity across the entire KSHV proteome to date, which is vital to discern mechanisms of viral pathogenesis, to define prognostic biomarkers, and to design effective vaccine and therapeutic strategies. Future studies will investigate the diagnostic, prognostic, and therapeutic potential of the 25 discriminative peptides.
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Affiliation(s)
- Sydney J. Bennett
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Sara R. Privatt
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Owen Ngalamika
- Dermatology and Venereology Section, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | - Salum J. Lidenge
- Ocean Road Cancer Institute, Dar es Salaam, Tanzania
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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2
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Bennett SJ, Yalcin D, Privatt SR, Ngalamika O, Lidenge SJ, West JT, Wood C. Antibody epitope profiling of the KSHV LANA protein using VirScan. PLoS Pathog 2022; 18:e1011033. [PMID: 36534707 PMCID: PMC9810164 DOI: 10.1371/journal.ppat.1011033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/03/2023] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The humoral antibody response against Kaposi sarcoma-associated herpesvirus (KSHV) in infected individuals has been characterized demonstrating the latency-associated nuclear antigen (LANA) as the most antigenic KSHV protein. Despite the antigenicity of the protein, specific LANA epitopes have not been systematically characterized. Here, we utilized a bacteriophage T7 library, which displays 56-amino acid KSHV LANA peptides with 28-amino acid overlap (VirScan), to define those epitopes in LANA targeted by antibodies from a cohort of 62 sub-Saharan African Kaposi sarcoma (KS) patients and 22 KSHV-infected asymptomatic controls. Intra- and inter-patient breadth and magnitude of the anti-LANA responses were quantified at the peptide and amino acid levels. From these data, we derived a detailed epitope annotation of the entire LANA protein, with a high-resolution focus on the N- and C-termini. Overall, the central repeat region was highly antigenic, but the responses to this region could not be confidently mapped due to its high variability. The highly conserved N-terminus was targeted with low breadth and magnitude. In a minority of individuals, antibodies specific to the nuclear localization sequence and a portion of the proline-rich regions of the N-terminus were evident. In contrast, the first half of the conserved C-terminal domain was consistently targeted with high magnitude. Unfortunately, this region was not included in LANA partial C-terminal crystal structures, however, it was predicted to adopt predominantly random-coil structure. Coupled with functional and secondary structure domain predictions, VirScan revealed fine resolution epitope mapping of the N- and C-terminal domains of LANA that is consistent with previous antigenicity studies and may prove useful to correlate KSHV humoral immunity with pathogenesis.
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Affiliation(s)
- Sydney J. Bennett
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Sara R. Privatt
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Owen Ngalamika
- Dermatology and Venereology Section, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | - Salum J. Lidenge
- Ocean Road Cancer Institute, Dar es Salaam, Tanzania
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- * E-mail:
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3
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Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis. Adv Virus Res 2020; 109:201-254. [PMID: 33934828 DOI: 10.1016/bs.aivir.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The DNA viruses, Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), are members of the gammaherpesvirus subfamily, a group of viruses whose infection is associated with multiple malignancies, including cancer. The primary host for these viruses is humans and, like all herpesviruses, infection with these pathogens is lifelong. Due to the persistence of gammaherpesvirus infection and the potential for cancer formation in infected individuals, there is a driving need to understand not only the biology of these viruses and how they remain undetected in host cells but also the mechanism(s) by which tumorigenesis occurs. One of the methods that has provided much insight into these processes is proteomics. Proteomics is the study of all the proteins that are encoded by a genome and allows for (i) identification of existing and novel proteins derived from a given genome, (ii) interrogation of protein-protein interactions within a system, and (iii) discovery of druggable targets for the treatment of malignancies. In this chapter, we explore how proteomics has contributed to our current understanding of gammaherpesvirus biology and their oncogenic processes, as well as the clinical applications of proteomics for the detection and treatment of gammaherpesvirus-associated cancers.
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Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
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Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Camargo MC, Kim KM, Matsuo K, Torres J, Liao LM, Morgan D, Michel A, Waterboer T, Song M, Gulley ML, Dominguez RL, Yatabe Y, Kim S, Cortes-Martinez G, Lissowska J, Zabaleta J, Pawlita M, Rabkin CS. Circulating Antibodies against Epstein-Barr Virus (EBV) and p53 in EBV-Positive and -Negative Gastric Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:414-419. [PMID: 31719065 PMCID: PMC8272980 DOI: 10.1158/1055-9965.epi-19-0790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 11/04/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV)-positive gastric cancers have clinicopathologic differences from EBV-negative tumors and lack TP53 mutation. Serologic profiles may inform viral contribution to carcinogenesis. METHODS We compared humoral responses of EBV-positive (n = 67) and EBV-negative (n = 137) patients with gastric cancer from the International EBV-Gastric Cancer Consortium. Serum antibodies against four EBV proteins, nuclear (EBNA), viral capsid (VCA), early-diffuse (EA-D), and Zta replication activator (ZEBRA), and to p53 were assessed by multiplex assays. OR of antibody level tertiles (T1-T3) were adjusted by logistic regression. We also conducted a meta-analysis of reported anti-p53 seropositivity in gastric cancer. RESULTS Consistent with EBV's ubiquity, 99% of patients were seropositive for anti-EBNA and 98% for anti-VCA, without difference by tumor EBV status. Seropositivity varied between patients with EBV-positive and EBV-negative tumors for anti-EA-D (97% vs. 67%, respectively, P < 0.001) and anti-ZEBRA (97% vs. 85%, respectively, P = 0.009). Adjusted ORs (vs. T1) for patients with EBV-positive versus EBV-negative tumors were significantly elevated for higher antibodies against EBNA (2.6 for T2 and 13 for T3), VCA (1.8 for T2 and 2.4 for T3), EA-D (6.0 for T2 and 44 for T3), and ZEBRA (4.6 for T2 and 12 for T3). Antibodies to p53 were inversely associated with EBV positivity (3% vs. 15%; adjusted OR = 0.16, P = 0.021). Anti-p53 prevalence from the literature was 15%. CONCLUSIONS These serologic patterns suggest viral reactivation in EBV-positive cancers and identify variation of p53 seropositivity by subtype. IMPACT Anti-EBV and anti-p53 antibodies are differentially associated with tumor EBV positivity. Serology may identify EBV-positive gastric cancer for targeted therapies.
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Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center, Nagoya, Japan
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México City, México
| | - Linda M Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Douglas Morgan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Angelika Michel
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Minkyo Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ricardo L Dominguez
- Department of Medicine, Western Regional Hospital, Santa Rosa de Copan, Honduras
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Gustavo Cortes-Martinez
- Servicio de Cirugía, Hospital de Oncología, CMN SXXI, Instituto Mexicano del Seguro Social, México City, México
| | - Jolanta Lissowska
- Division of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Michael Pawlita
- Infections and Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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6
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Liu Z, Coghill AE, Pfeiffer RM, Proietti C, Hsu WL, Chien YC, Lekieffre L, Krause L, Yu KJ, Lou PJ, Wang CP, Mulvenna J, Middeldorp JM, Bethony J, Chen CJ, Doolan DL, Hildesheim A. Patterns of Interindividual Variability in the Antibody Repertoire Targeting Proteins Across the Epstein-Barr Virus Proteome. J Infect Dis 2019; 217:1923-1931. [PMID: 29509907 DOI: 10.1093/infdis/jiy122] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/01/2018] [Indexed: 12/25/2022] Open
Abstract
Background Little is known about variation in antibody responses targeting the full spectrum of Epstein-Barr virus (EBV) proteins and how such patterns inform disease risk. Methods We used a microarray to measure immunoglobulin G (IgG) and immunoglobulin A (IgA) antibody responses against 199 EBV protein sequences from 5 EBV strains recovered from 289 healthy adults from Taiwan. We described positivity patterns, estimated the correlation between antibodies, and investigated the associations between environmental and genetic risk factors and variations in antibody responses. Results Healthy adults were more likely to mount IgG antibody responses to EBV proteins (median positivity frequency, 46.5% for IgG and 17.3% for IgA; P = 1.6 × 10-46, by the Wilcoxon rank sum test). Responses against glycoproteins were particularly prevalent. The correlations between antibody responses of the same class were higher than correlations across classes. The mucosal exposure to proteins involved in EBV reactivation (as determined by the IgA response) was associated with smoking (P = .002, by the sequence kernel association test-combined), and approximately one quarter of adults displayed antibody responses associated with EBV-related cancer risk. Conclusions These data comprehensively define the variability in human IgG and IgA antibody responses to the EBV proteome. Patterns observed can serve as the foundation for elucidating which individuals are at highest risk of EBV-associated clinical conditions and for identifying targets for effective immunodiagnostic tests.
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Affiliation(s)
- Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Anna E Coghill
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Carla Proietti
- QIMR Berghofer Medical Research Institute, Brisbane, Cairns, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Wan-Lun Hsu
- Genomics Research Center, Academia Sinica, Taipei.,Graduate Institute of Epidemiology and Prevention Medicine, College of Public Health, National Taiwan University, Taipei
| | - Yin-Chu Chien
- Genomics Research Center, Academia Sinica, Taipei.,National Institute of Cancer Research, National Health Research Institute, Miaoli, Taiwan
| | - Lea Lekieffre
- QIMR Berghofer Medical Research Institute, Brisbane, Cairns, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Brisbane, Cairns, Australia
| | - Kelly J Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Pei-Jen Lou
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei
| | - Cheng-Ping Wang
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei
| | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Brisbane, Cairns, Australia
| | - Jaap M Middeldorp
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Jeff Bethony
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University Medical Center, Washington, D. C
| | - Chien-Jen Chen
- Genomics Research Center, Academia Sinica, Taipei.,Graduate Institute of Epidemiology and Prevention Medicine, College of Public Health, National Taiwan University, Taipei
| | - Denise L Doolan
- QIMR Berghofer Medical Research Institute, Brisbane, Cairns, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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7
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Abstract
The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new, and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent progress in genomics and mass spectrometry have led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel-based, array-based, mass spectrometry-based, DNA-based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of protein antigens targeted by the immune system during disease.
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Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabel Baltat
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada.
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8
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Lv H, Ye L, Liu Q, Li SG, Li T, Huang NL, Gao Y, Fan LB, Du WD. S-S-PEG-COOH Self-Assembled Monolayer on Gold Surface Enabled a Combined Assay for Serological EBV Antibody Isotypes. Proteomics Clin Appl 2018; 13:e1800067. [PMID: 30311429 DOI: 10.1002/prca.201800067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/13/2018] [Indexed: 11/09/2022]
Abstract
PURPOSE Epstein-Barr virus (EBV) is a ubiquitous human gamma herpes virus that infects human epithelial cells and B lymphocytes. It would be potentially valuable to develop novel combined assays to benefit screening for large panels of samples of EBV infectious diseases. EXPERIMENTAL DESIGN A simple antigen-probed biochip that is modified with S-S-PEG-COOH and is used as a label-free high-throughput screening method for a combined detection of EBV capsid antigen IgM antibody, capsid antigen IgG antibody, and nuclear antigen IgG antibody. RESULTS This protein biochip has similar feasibility, sensitivity, and specificity in comparison with Liaison chemiluminescent immunoassay (CLIA). Detection limit of the EBV antibodies by the biochip is almost identical to that by CLIA-L (2.91 U mL-1 vs 3.00 U mL-1 for EBNA-1 IgG, 8 U mL-1 vs10 U mL-1 for EBV-VCA IgG, and 3.5 U mL-1 vs 10 U mL-1 for EBV-VCA IgM). Tests of the three serological antibodies against EBV by the biochip are consistent with the CLIA-L method in 274 clinical sera, respectively. Finally, the combined biochip is successfully utilized for diagnostic identification of EBV infection in 14 patients with infectious mononucleosis (IM) and 25 patients with systemic lupus erythematosus SLE, as well as additional 10 known real-time PCR positive patients. CONCLUSIONS AND CLINICAL RELEVANCE This biochip format will enable concurrent detection of antibodies against EBV infection and confirm infection status of EBV. It will be a versatile tool for large-scale epidemiological screening in view of its miniaturization and high throughput.
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Affiliation(s)
- Hui Lv
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Lei Ye
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Qian Liu
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Song-Guo Li
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Tao Li
- Department of Clinical Laboratory, The First Affiliated Hospital, Anhui Medical University, Hefei, 230022, China
| | - Na-Li Huang
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yi Gao
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Li-Bin Fan
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Wei-Dong Du
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
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9
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Feng Y, Chen CS, Ho J, Pearce D, Hu S, Wang B, Desai P, Kim KS, Zhu H. High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology). Anal Chem 2018; 90:10958-10966. [PMID: 30106562 DOI: 10.1021/acs.analchem.8b02513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial meningitis in neonates and infants is an acute lethal disease and occurs in response to microbial exploitation of the blood-brain barrier (BBB), resulting in the intracranial inflammation. Several pathogens, such as Escherichia coli ( E. coli), can cause this devastating disease; however, the underlying molecular mechanisms by which these pathogens exploit the BBB remain incompletely understood. To identify important players on both the pathogen and host sides that govern the E. coli-BBB cell interactions, we took advantage of the E. coli and human proteome microarrays (i.e., HuProt) as an unbiased, proteome-wide tool for identification of important players on both sides. Using the E. coli proteome microarrays, we developed a unique high throughput chip-based cell probing assay to probe with fluorescent live human brain microvascular endothelial cells (HBMEC, which constitute the BBB). We identified several transmembrane proteins, which effectively bound to live HBMEC. We focused on YojI protein for further study. By probing the HuProt arrays with YojI, interferon-alpha receptor (IFNAR2) was identified as one of its binding proteins. The importance of YojI and IFNAR2 involved in E. coli-HBMEC interactions was characterized using the YojI knockout bacteria and IFNAR2-knock down HBMEC and further confirmed by E. coli binding assay in HBMEC. This study represents a new paradigm (dual-microarray technology) that enables rapid, unbiased discovery of both pathogen and host players that are involved in pathogen-host interactions for human infectious diseases in a high throughput manner.
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Affiliation(s)
- Yingzhu Feng
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management , Tainan City 701 , Taiwan.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Biomedical Science and Engineering , National Central University , Taoyuan City 32001 , Taiwan
| | - Jessica Ho
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Donna Pearce
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Shaohui Hu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Bochu Wang
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China
| | - Prashant Desai
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21231 , United States
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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10
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Goswami R, Shair KHY, Gershburg E. Molecular diversity of IgG responses to Epstein-Barr virus proteins in asymptomatic Epstein-Barr virus carriers. J Gen Virol 2017; 98:2343-2350. [PMID: 28795661 DOI: 10.1099/jgv.0.000891] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Epstein-Barr virus (EBV) is a ubiquitous pathogen that infects over 90 % of adults. EBV is the primary etiological agent of infectious mononucleosis and is closely associated with nasopharyngeal carcinoma, gastric carcinoma, Hodgkin lymphoma and Burkitt lymphoma. Clinical serological assays for EBV diagnosis only survey a small portion of the viral proteome, which does not represent the total antigenic breadth presented to the immune system during viral infection. In this study, we have generated an expression library containing the majority of EBV ORFs, and have systematically evaluated IgG responses to those EBV proteins in sera from EBV carriers. In addition to confirming previously recognized dominant EBV antigens, this study has identified additional immunodominant antigens, and has revealed a more expansive antigenic profile of the humoral responses to EBV in asymptomatic carriers. This EBV expression library will be deposited in a public repository with the goal of disseminating this new research tool for the application of identifying potential new biomarkers for EBV-associated diseases.
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Affiliation(s)
- Ria Goswami
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62794-9626, USA.,Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL 62702, USA.,Present address: Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kathy Ho Yen Shair
- Cancer Virology Program, University of Pittsburgh Cancer Institute Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Edward Gershburg
- Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL 62702, USA.,Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62794-9626, USA.,Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
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11
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Zhang L, Jia X, Jin JO, Lu H, Tan Z. Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:110-120. [PMID: 28391008 PMCID: PMC5415375 DOI: 10.1016/j.gpb.2016.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/03/2016] [Accepted: 11/24/2016] [Indexed: 12/24/2022]
Abstract
Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications. Furthermore, we reviewed the applications of proteomics in the discovery of HIV-related diseases and HIV infection mechanisms. Proteins identified by proteomic studies might offer new avenues for the diagnosis and treatment of HIV infection and the related diseases.
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Affiliation(s)
- Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jun-O Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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12
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Rapid Multiplexed Immunoassay for Detection of Antibodies to Kaposi's Sarcoma-Associated Herpesvirus. PLoS One 2016; 11:e0163616. [PMID: 27669509 PMCID: PMC5036886 DOI: 10.1371/journal.pone.0163616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/12/2016] [Indexed: 11/29/2022] Open
Abstract
Diagnosis of KSHV-infected individuals remains a challenge. KSHV prevalence is high in several populations with high prevalence of HIV, leading to increased risk of development of Kaposi’s sarcoma (KS). While current assays are reliable for detecting antibodies to KSHV, none are routinely utilized to identify individuals with KSHV infection and thus at increased risk for KS due to assay complexity, lack of access to testing, and cost, particularly in resource-limited settings. Here we describe the addition of KSHV proteins LANA and K8.1 to a previously evaluated HIV/co-infection multiplexed fluorescence immunoassay system. This study demonstrates assay performance by measuring antibody reactivity for KSHV and HIV-1 in a collection of clinical specimens from patients with biopsy-proven KS and sourced negative controls. The KSHV assay correctly identified 155 of 164 plasma samples from patients with biopsy-proven KS and 85 of 93 KSHV antibody (Ab)-negative samples for a sensitivity of 95.1% and specificity of 91.4%. Assay performance for HIV-1 detection was also assessed with 100% agreement with independently verified HIV-1 Ab-positive and Ab-negative samples. These results demonstrate good sensitivity and specificity for detection of antibody to KSHV antigens, and demonstrate the potential for multiplexed co-infection testing in resource-limited settings to identify those at increased risk for HIV-1-related complications.
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Stutzman-Rodriguez K, Rovnak J, VandeWoude S, Troyer RM. Domestic cats seropositive for Felis catus gammaherpesvirus 1 are often qPCR negative. Virology 2016; 498:23-30. [PMID: 27540873 DOI: 10.1016/j.virol.2016.07.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/13/2016] [Accepted: 07/26/2016] [Indexed: 12/01/2022]
Abstract
Felis catus gammaherpesvirus 1 (FcaGHV1) is a newly described virus that infects domestic cats. To identify FcaGHV1 antigens, we developed an immunofluorescent antibody assay by expressing FcaGHV1 open reading frames (ORFs) in feline cells and incubating fixed cells with sera from FcaGHV1-positive cats. Of the seven ORFs tested, ORF52 and ORF38 had the strongest, most consistent antibody responses. We used recombinant ORF52 and ORF38 proteins to develop two FcaGHV1 ELISAs. These assays were used to detect reactivity in cats previously tested by qPCR for FcaGHV1 in blood cell DNA. Results indicated 32%FcaGHV1seroprevalence, compared to 15%qPCR-evaluated prevalence (n=133);all but one qPCR positive animal was seropositive. ELISA results confirmed infection risk factors previously identified by qPCR: geographic location, male sex, and adult age. These data suggest that FcaGHV1is a common infection of domestic cats that has a seropositive but often qPCR negative state characteristic of herpesviral latency.
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Affiliation(s)
- Kathryn Stutzman-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Ryan M Troyer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA; Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA.
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Wu JJ, Avey D, Li W, Gillen J, Fu B, Miley W, Whitby D, Zhu F. ORF33 and ORF38 of Kaposi's Sarcoma-Associated Herpesvirus Interact and Are Required for Optimal Production of Infectious Progeny Viruses. J Virol 2016; 90:1741-56. [PMID: 26637455 PMCID: PMC4734004 DOI: 10.1128/jvi.02738-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/23/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED We recently showed that the interaction between Kaposi's sarcoma-associated herpesvirus (KSHV) tegument proteins ORF33 and ORF45 is crucial for progeny virion production, but the exact functions of KSHV ORF33 during lytic replication were unknown (J. Gillen, W. Li, Q. Liang, D. Avey, J. Wu, F. Wu, J. Myoung, and F. Zhu, J Virol 89:4918-4931, 2015, http://dx.doi.org/10.1128/JVI.02925-14). Therefore, here we investigated the relationship between ORF33 and ORF38, whose counterparts in both alpha- and betaherpesviruses interact with each other. Using specific monoclonal antibodies, we found that both proteins are expressed during the late lytic cycle with similar kinetics and that both are present in mature virions as components of the tegument. Furthermore, we confirmed that ORF33 interacts with ORF38. Interestingly, we observed that ORF33 tightly associates with the capsid, whereas ORF38 associates with the envelope. We generated ORF33-null, ORF38-null, and double-null mutants and found that these mutants apparently have identical phenotypes: the mutations caused no apparent effect on viral gene expression but reduced the yield of progeny virion by about 10-fold. The progeny virions also lack certain virion component proteins, including ORF45. During viral lytic replication, the virions associate with cytoplasmic vesicles. We also observed that ORF38 associates with the membranes of vesicles and colocalizes with the Golgi membrane or early endosome membrane. Further analyses of ORF33/ORF38 mutants revealed the reduced production of virion-containing vesicles, suggesting that ORF33 and ORF38 are involved in the transport of newly assembled viral particles into cytoplasmic vesicles, a process important for viral maturation and egress. IMPORTANCE Herpesvirus assembly is an essential step in virus propagation that leads to the generation of progeny virions. It is a complicated process that depends on the delicate regulation of interactions among virion proteins. We previously revealed an essential role of ORF45-ORF33 binding for virus assembly. Here, we report that ORF33 and its binding partner, ORF38, are required for infectious virus production due to their important role in the tegumentation process. Moreover, we found that both ORF33 and ORF38 are involved in the transportation of virions through vesicles during maturation and egress. Our results provide new insights into the important roles of ORF33 and ORF38 during viral assembly, a process critical for virus propagation that is intimately linked to KSHV pathobiology.
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Affiliation(s)
- Jian-Jun Wu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Denis Avey
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Wenwei Li
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Joseph Gillen
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Bishi Fu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Wendell Miley
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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15
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Burbelo PD, Lebovitz EE, Notkins AL. Luciferase immunoprecipitation systems for measuring antibodies in autoimmune and infectious diseases. Transl Res 2015; 165:325-35. [PMID: 25241936 PMCID: PMC4306608 DOI: 10.1016/j.trsl.2014.08.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/26/2014] [Accepted: 08/26/2014] [Indexed: 12/22/2022]
Abstract
Antibody profiles have the potential to revolutionize personalized medicine by providing important information related to autoimmunity against self-proteins and exposure to infectious agents. One immunoassay technology, luciferase immunoprecipitation systems (LIPS), harnesses light-emitting recombinant proteins to generate robust, high-quality antibody data often spanning a large dynamic range of detection. Here, we describe the general format of LIPS and discuss studies using the technology to measure autoantibodies in several human autoimmune diseases including type 1 diabetes, Sjögren's syndrome, systemic lupus erythematosus, and immunodeficiencies secondary to anticytokine autoantibodies. We also describe the usefulness of evaluating antibodies against single or multiple antigens from infectious agents for diagnosis, pathogen discovery, and for obtaining individual exposure profiles. These diverse findings support the notion that the LIPS is a useful technology for generating antibody profiles for personalized diagnosis and monitoring of human health.
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Key Words
- ards, acute respiratory distress syndrome
- dntm, disseminated nontuberculous mycobacterial
- ebv, epstein-barr virus
- elisa, enzyme-linked immunoassay
- hcv, hepatitis c virus
- hiv, human immunodeficiency virus
- htlv, human t-lymphotropic virus
- il, interleukin
- kshv, kaposi sarcoma-associated herpes virus
- lips, luciferase immunoprecipitation systems
- mers, middle east respiratory virus
- nphv, nonprimate hepatitis c-like virus
- rip, radioimmunoprecipitation assay
- ruc, renilla luciferase
- sle, systemic lupus erythematosus
- ss, sjögren's syndrome
- t1d, type i diabetes
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Affiliation(s)
- Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD.
| | - Evan E Lebovitz
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Abner L Notkins
- Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
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16
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Coghill AE, Hildesheim A. Epstein-Barr virus antibodies and the risk of associated malignancies: review of the literature. Am J Epidemiol 2014; 180:687-95. [PMID: 25167864 DOI: 10.1093/aje/kwu176] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV), a ubiquitous herpes virus that infects 90% of humans by adulthood, is linked to the development of various cancers, including nasopharyngeal carcinoma, gastric cancer, Burkitt lymphoma, non-Hodgkin lymphoma (NHL), and Hodgkin lymphoma. We reviewed the literature published since 1980 regarding an association between antibodies against EBV proteins and the risk of EBV-associated malignancies. Immunoglobulin A antibody levels that are elevated before diagnosis have consistently been associated with the risk of nasopharyngeal carcinoma, and patients with Hodgkin lymphoma have significantly higher immunoglobulin G antibody levels than disease-free controls. However, the link between the immune response to EBV and other EBV-associated malignancies was less clear. Although evidence of an association between the risk of Burkitt lymphoma and immunoglobulin G antibodies was consistent for available studies, the sample sizes were limited. Evidence for a link between antibodies against EBV and risk of either gastric cancer or NHL was inconsistent. Future investigations should account for tumor EBV status because only 7%-10% of gastric tumors and select NHL subtypes are related to EBV infection. Comparing differences in the associations between the humoral immune response to EBV and disease risk across cancers may help elucidate how this ubiquitous virus contributes to distinct tumors globally.
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Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV; also known as human herpesvirus 8) is the etiologic agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. These cancers often occur in the context of immunosuppression, which has made KSHV-associated malignancies an increasing global health concern with the persistence of the AIDS epidemic. KSHV has also been linked to several acute inflammatory diseases. KSHV exists between a lytic and latent lifecycle, which allows the virus to transition between active replication and quiescent infection. KSHV encodes a number of proteins and small RNAs that are thought to inadvertently transform host cells while performing their functions of helping the virus persist in the infected host. KSHV also has an arsenal of components that aid the virus in evading the host immune response, which help the virus establish a successful lifelong infection. In this comprehensive chapter, we will discuss the diseases associated with KSHV infection, the biology of latent and lytic infection, and individual proteins and microRNAs that are known to contribute to host cell transformation and immune evasion.
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Affiliation(s)
- Louise Giffin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Blossom Damania
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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18
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Labo N, Miley W, Marshall V, Gillette W, Esposito D, Bess M, Turano A, Uldrick T, Polizzotto MN, Wyvill KM, Bagni R, Yarchoan R, Whitby D. Heterogeneity and breadth of host antibody response to KSHV infection demonstrated by systematic analysis of the KSHV proteome. PLoS Pathog 2014; 10:e1004046. [PMID: 24675986 PMCID: PMC3968157 DOI: 10.1371/journal.ppat.1004046] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/17/2014] [Indexed: 01/15/2023] Open
Abstract
The Kaposi sarcoma associated herpesvirus (KSHV) genome encodes more than 85 open reading frames (ORFs). Serological evaluation of KSHV infection now generally relies on reactivity to just one latent and/or one lytic protein (commonly ORF73 and K8.1). Most of the other polypeptides encoded by the virus have unknown antigenic profiles. We have systematically expressed and purified products from 72 KSHV ORFs in recombinant systems and analyzed seroreactivity in US patients with KSHV-associated malignancies, and US blood donors (low KSHV seroprevalence population). We identified several KSHV proteins (ORF38, ORF61, ORF59 and K5) that elicited significant responses in individuals with KSHV-associated diseases. In these patients, patterns of reactivity were heterogeneous; however, HIV infection appeared to be associated with breadth and intensity of serological responses. Improved antigenic characterization of additional ORFs may increase the sensitivity of serologic assays, lead to more rapid progresses in understanding immune responses to KSHV, and allow for better comprehension of the natural history of KSHV infection. To this end, we have developed a bead-based multiplex assay detecting antibodies to six KSHV antigens.
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Affiliation(s)
- Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Wendell Miley
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - William Gillette
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dominic Esposito
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Matthew Bess
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Alexandra Turano
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mark N. Polizzotto
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kathleen M. Wyvill
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Rachel Bagni
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Ghesquières H, Dogan A, Link BK, Maurer MJ, Cunningham JM, Novak AJ, Larrabee BR, Slager SL, Allmer C, Habermann TM, Ansell SM, Cerhan JR. FCGR2A and FCGR3A polymorphisms in classical Hodgkin lymphoma by Epstein-Barr virus status. Leuk Lymphoma 2013; 54:2571-3. [PMID: 23597143 DOI: 10.3109/10428194.2013.796048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Hervé Ghesquières
- Onco-Hematology, Centre Léon Bérard, Université Claude Bernard , UMR CNRS 5239, Lyon , France
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20
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Gogineni E, Marshall V, Miley W, Bayat A, Whitby D, Kovacs JA, Burbelo PD. Quantitative determinations of anti-Kaposi sarcoma-associated herpesvirus antibody levels in men who have sex with men. Diagn Microbiol Infect Dis 2013; 76:56-60. [PMID: 23541691 PMCID: PMC3634905 DOI: 10.1016/j.diagmicrobio.2013.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/26/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Infection with Kaposi sarcoma-associated herpesvirus (KSHV; also called human herpesvirus-8) is common among men who have sex with men (MSM). Here, quantitative anti-KSHV antibody levels were measured using luciferase immunoprecipitation systems (LIPS) in an MSM cohort with and without HIV from the NIH Clinical Center. Antibodies were detected using a mixture of 4 KSHV antigens in the MSM cohort and in Kaposi sarcoma (KS) patients. Along with HIV status, these results were compared with K8.1 and ORF73 ELISA, PCR virus detection, and additional LIPS testing. LIPS revealed that 25% (76/307) of the MSM cohort were KSHV seropositive, including 59 HIV+ and 17 HIV- subjects. The anti-KSHV antibody levels detected by LIPS were not statistically different between the KSHV+/HIV+ and KSHV+/HIV- subgroups but were lower than the KS patients (P < 0.0001). ELISA analysis of the MSM cohort detected a 35.5% frequency of KSHV infection and showed agreement with 81% of the samples evaluated by LIPS. Further LIPS testing with v-cyclin, a second ORF73 fragment and ORF38 reconciled some of the differences observed between LIPS and the ELISA immunoassays, and the revised LIPS seroprevalence in the MSM cohort was increased to 31%. Additional quantitative antibody analysis demonstrated statistically lower KSHV antibody levels in MSM compared to KS patients, but no difference was found between KSHV infected with and without HIV coinfection. These findings also suggest that antibodies against v-cyclin and ORF38 are useful for identifying patients with asymptomatic KSHV infection.
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Affiliation(s)
- Emile Gogineni
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
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21
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Development of whole-virus multiplex luminex-based serological assays for diagnosis of infections with kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 homologs in macaques. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:409-19. [PMID: 23345584 DOI: 10.1128/cvi.00673-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV)/human herpesvirus 8 is a tumorigenic rhadinovirus that is associated with all forms of Kaposi's sarcoma. Current serological detection of KSHV is based on enzyme-linked immunosorbent or immunofluorescence assays that suffer from a variety of problems, including the lack of defined standards for test comparison. While KSHV is the only known human rhadinovirus, two lineages of KSHV-like rhadinoviruses are found in Old World primates: the RV1 lineage includes KSHV and retroperitoneal fibromatosis herpesvirus (RFHV) in macaques, and the RV2 lineage includes RRV and MneRV2 from different macaque species. To develop animal models of KSHV-associated diseases, we developed quantitative multiplex bead-based serological assays to detect antibodies against rhadinovirus antigens. Proteins from KSHV (RV1) and MneRV2 (RV2) virions were coupled to spectrally distinct fluorescent beads and used in Luminex flow cytometry-based assays to detect immune responses in macaques. Both assays showed large dynamic ranges with high levels of seroreactivity to both KSHV and MneRV2 proteins. A large set of macaque serum samples from the Washington National Primate Research Center was screened, and most of the samples (82%) were positive in both assays, consistent with the high level of RV1-RV2 coinfection detected by PCR. The macaque sera showed broad, variable, and unique serological responses to the different viral antigens, allowing an initial seroprevalence to be determined for the macaque viruses. The Luminex assays offer a novel multiplexed approach to assess rhadinovirus infection patterns in both humans and nonhuman primates. This will help advance our understanding of rhadinovirus biology and associated host immunological responses.
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22
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Lindsey J, Khan U, Ansari W, Powell T, Wang Y, Guirguis M. The antibody response to Epstein–Barr virions is altered in multiple sclerosis. J Neuroimmunol 2013; 254:146-53. [DOI: 10.1016/j.jneuroim.2012.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/22/2022]
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Abstract
The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent advances in genomics and proteomics, has led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel based, array based, mass spectrometry, DNA based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of antigens targeted by the immune system during disease.
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Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada
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24
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Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012; 6:548-62. [PMID: 23027439 PMCID: PMC3600421 DOI: 10.1002/prca.201200041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
Abstract
Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology.
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Affiliation(s)
- Heng Zhu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, MD, USA.
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25
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The Cancer-Associated Virus Landscape in HIV Patients with Oral Hairy Leukoplakia, Kaposi's Sarcoma, and Non-Hodgkin Lymphoma. AIDS Res Treat 2012; 2012:634523. [PMID: 22924124 PMCID: PMC3423820 DOI: 10.1155/2012/634523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/13/2012] [Accepted: 07/01/2012] [Indexed: 12/25/2022] Open
Abstract
Although HIV-positive patients are at higher risk for developing a variety of infection-related cancers, the prevalence of infections with the seven known cancer-associated viruses has not been studied. Luciferase immunoprecipitation systems were used to evaluate antiviral antibodies in four 23-person groups: healthy blood donors and HIV-infected patients with oral hairy leukoplakia (OLP), Kaposi's sarcoma (KS), or non-Hodgkin lymphoma (NHL). Antibody profiling revealed that all HIV-positive individuals were strongly seropositive for anti-gp41 and antireverse transcriptase antibodies. However, anti-p24 HIV antibody levels were highly variable and some OLP and KS patients demonstrated weak or negative responses. Profiling two EBV antigens revealed no statistical difference in antibody levels among the three HIV-infected groups. A high frequency of KSHV infection was detected in HIV patients including 100% of KS, 78% of OLP, and 57% of NHL patients. Most HIV-infected subjects (84%) showed anti-HBV core antibodies, but only a few showed antibodies against HCV. MCV seropositivity was also common (94%) in the HIV-infected individuals and KS patients showed statistically higher antibody levels compared to the OLP and NHL patients. Overall, 68% of the HIV-infected patients showed seropositivity with at least four cancer-associated viruses. Antibody profiles against these and other infectious agents could be useful for enhancing the clinical management of HIV patients.
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Application of proteomics to soft tissue sarcomas. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:876401. [PMID: 22778956 PMCID: PMC3388341 DOI: 10.1155/2012/876401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/21/2012] [Indexed: 01/27/2023]
Abstract
Soft tissue sarcomas are rare and account for less than 1% of all malignant cancers. Other than development of intensive therapies, the clinical outcome of patients with soft tissue sarcoma remains very poor, particularly when diagnosed at a late stage. Unique mutations have been associated with certain soft tissue sarcomas, but their etiologies remain unknown. The proteome is a functional translation of a genome, which directly regulates the malignant features of tumors. Thus, proteomics is a promising approach for investigating soft tissue sarcomas. Various proteomic approaches and clinical materials have been used to address clinical and biological issues, including biomarker development, molecular target identification, and study of disease mechanisms. Several cancer-associated proteins have been identified using conventional technologies such as 2D-PAGE, mass spectrometry, and array technology. The functional backgrounds of proteins identified were assessed extensively using in vitro experiments, thus supporting expression analysis. These observations demonstrate the applicability of proteomics to soft tissue sarcoma studies. However, the sample size in each study was insufficient to allow conclusive results. Given the low frequency of soft tissue sarcomas, multi-institutional collaborations are required to validate the results of proteomic approaches.
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