1
|
Beutgen VM, Shinkevich V, Pörschke J, Meena C, Steitz AM, Pogge von Strandmann E, Graumann J, Gómez-Serrano M. Secretome analysis using Affinity Proteomics and Immunoassays: a focus on Tumor Biology. Mol Cell Proteomics 2024:100830. [PMID: 39147028 DOI: 10.1016/j.mcpro.2024.100830] [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: 02/29/2024] [Revised: 07/20/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
The study of the cellular secretome using proteomic techniques continues to capture the attention of the research community across a broad range of topics in biomedical research. Due to their untargeted nature, independence from the model system employed, historically superior depth of analysis, as well as comparative affordability, mass spectrometry-based approaches traditionally dominate such analyses. More recently, however, affinity-based proteomic assays have massively gained in analytical depth, which together with their high sensitivity, dynamic range coverage as well as high throughput capabilities render them exquisitely suited to secretome analysis. In this review, we revisit the analytical challenges implied by secretomics and provide an overview of affinity-based proteomic platforms currently available for such analyses, using the study of the tumor secretome as an example for basic and translational research.
Collapse
Affiliation(s)
- Vanessa M Beutgen
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Veronika Shinkevich
- Institute of Pharmacology, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Johanna Pörschke
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Celina Meena
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Anna M Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany.
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany.
| |
Collapse
|
2
|
Scharbaai-Vázquez R, J. López Font F, A. Zayas Rodríguez F. Persistence in Chlamydia. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.109299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chlamydia spp. are important causes of acute and persistent/chronic infections. All Chlamydia spp. display a unique biphasic developmental cycle alternating between an infectious elementary body (EB) and a replicative form, the reticulate body (RB), followed by the multiplication of RBs by binary fission and progressive differentiation back into EBs. During its intracellular life, Chlamydia employs multiple mechanisms to ensure its persistence inside the host. These include evasion of diverse innate immune responses, modulation of host cell structure and endocytosis, inhibition of apoptosis, activation of pro-signaling pathways, and conversion to enlarged, non-replicative but viable “aberrant bodies” (ABs). Early research described several systems for Chlamydial persistence with a significant number of variables that make a direct comparison of results difficult. Now, emerging tools for genetic manipulations in Chlamydia and advances in global microarray, transcriptomics, and proteomics have opened new and exciting opportunities to understand the persistent state of Chlamydia and link the immune and molecular events of persistence with the pathogenesis of recurrent and chronic Chlamydial infections. This chapter reviews our current understanding and advances in the molecular biology of Chlamydia persistence.
Collapse
|
3
|
Brindl N, Boekhoff H, Bauer AS, Gaida MM, Dang HT, Kaiser J, Hoheisel JD, Felix K. Use of Autoreactive Antibodies in Blood of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasms (IPMN) for Grade Distinction and Detection of Malignancy. Cancers (Basel) 2022; 14:cancers14153562. [PMID: 35892825 PMCID: PMC9332220 DOI: 10.3390/cancers14153562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: A reliable non-invasive distinction between low- and high-risk pancreatic intraductal papillary mucinous neoplasms (IPMN) is needed to effectively detect IPMN with malignant potential. This would improve preventative care and reduce the risk of developing pancreatic cancer and overtreatment. The present study aimed at exploring the presence of autoreactive antibodies in the blood of patients with IPMN of various grades of dysplasia. (2) Methods: A single-center cohort was studied composed of 378 serum samples from patients with low-grade IPMN (n = 91), high-grade IPMN (n = 66), IPMN with associated invasive cancer (n = 30), pancreatic ductal adenocarcinoma (PDAC) stages T1 (n = 24) and T2 (n = 113), and healthy controls (n = 54). A 249 full-length recombinant human protein microarray was used for profiling the serum samples. (3) Results: 14 proteins were identified as potential biomarkers for grade distinction in IPMN, yielding high specificity but mediocre sensitivity. (4) Conclusions: The identified autoantibodies are potential biomarkers that may assist in the detection of malignancy in IPMN patients.
Collapse
Affiliation(s)
- Niall Brindl
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
- Correspondence: (N.B.); (K.F.); Tel.: +49-163-638-1860 (N.B.)
| | - Henning Boekhoff
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Andrea S. Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Matthias M. Gaida
- Institute of Pathology, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany;
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
- TRON, Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Hien T. Dang
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19144, USA;
| | - Jörg Kaiser
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Klaus Felix
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Correspondence: (N.B.); (K.F.); Tel.: +49-163-638-1860 (N.B.)
| |
Collapse
|
4
|
Liu C, Hufnagel K, O'Connell CM, Goonetilleke N, Mokashi N, Waterboer T, Tollison TS, Peng X, Wiesenfeld HC, Hillier SL, Zheng X, Darville T. Reduced Endometrial Ascension and Enhanced Reinfection Associated with IgG Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia. J Infect Dis 2021; 225:846-855. [PMID: 34610131 DOI: 10.1093/infdis/jiab496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Previous research revealed antibodies targeting Chlamydia trachomatis (CT) elementary bodies was not associated with reduced endometrial or incident infection in CT-exposed women. However, data on the role of CT protein-specific antibodies in protection are limited. METHODS A whole-proteome CT array screening serum pools from CT-exposed women identified 121 immunoprevalent proteins. Individual sera were probed using a focused array. IgG antibody frequencies and endometrial or incident infection relationships were examined using Wilcoxon Rank sum test. The impact of breadth and magnitude of protein-specific IgGs on ascension and incident infection were examined using multivariable stepwise logistic regression. Complementary RNA-sequencing quantified CT gene transcripts in cervical swabs from infected women. RESULTS IgG to Pgp3 and CT005 were associated with reduced endometrial infection; anti-CT443, -CT486 and -CT123 were associated with increased incident infection. Increased breadth of protein recognition did not however predict protection from endometrial or incident infection. mRNAs for immunoprevalent CT proteins were highly abundant in the cervix. CONCLUSIONS Protein-specific CT antibodies are not sufficient to protect against ascending or incident infection but broad recognition of CT proteins by IgG correlates with cervical CT gene transcript abundance, suggesting CT protein abundance correlates with immunogenicity and signifies their potential as vaccine candidates.
Collapse
Affiliation(s)
- Chuwen Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrin Hufnagel
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Neha Mokashi
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Tammy S Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Xiaojing Zheng
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
5
|
Horner PJ, Flanagan H, Horne AW. Is There a Hidden Burden of Disease as a Result of Epigenetic Epithelial-to-Mesenchymal Transition Following Chlamydia trachomatis Genital Tract Infection? J Infect Dis 2021; 224:S128-S136. [PMID: 34396405 DOI: 10.1093/infdis/jiab088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chlamydia trachomatis (CT), the most common bacterial sexually transmitted infection worldwide, has been widely researched for its involvement in many disease pathologies in the reproductive tract, including pelvic inflammatory disease, ectopic pregnancy, and tubal factor infertility. Recent findings, through the efforts to understand the pathogenesis of CT, suggest that CT can induce the process of epithelial-to-mesenchymal transition (EMT) through epigenetic changes in the epithelium of the female reproductive tract. This literature review aims to analyze the evidence for CT's ability to promote EMT and to pinpoint the areas that merit further investigation.
Collapse
Affiliation(s)
- Patrick J Horner
- Population Health Sciences, University of Bristol, Bristol, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, United Kingdom
| | - Heather Flanagan
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew W Horne
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
6
|
Jeske R, Reininger D, Turgu B, Brauer A, Harmel C, Fernández de Larrea-Baz N, Martín V, Moreno V, Kogevinas M, Pollán M, Hoheisel JD, Waterboer T, Butt J, Aragonés N, Hufnagel K. Development of Helicobacter pylori Whole-Proteome Arrays and Identification of Serologic Biomarkers for Noncardia Gastric Cancer in the MCC-Spain Study. Cancer Epidemiol Biomarkers Prev 2020; 29:2235-2242. [PMID: 32998950 DOI: 10.1158/1055-9965.epi-20-0348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 09/04/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Helicobacter pylori (H. pylori) is a bacterial carcinogen and the leading risk factor for noncardia gastric cancer (NCGC). Detecting antibodies against specific H. pylori proteins in peripheral blood can be applied to characterize infection and determine disease associations. Most studies analyzing the association between H. pylori infection and gastric cancer have focused on previously identified antigens, predominantly the virulence factor cytotoxin-associated gene A (CagA). Selecting antigens in an unbiased approach may, however, allow the identification of novel biomarkers. METHODS Using a combination of multiple spotting technique and cell-free, on-chip protein expression, we displayed the H. pylori genome (strain 26695) on high-density microarrays. Immunogenic proteins were identified by serum pool incubations and henceforth analyzed in individual samples. To test its applicability, we used sera from a multicase-control (MCC)-Spain study. Serologic responses between NCGC cases and controls were assessed by conditional logistic regression estimating ORs and 95% confidence intervals. RESULTS We successfully expressed 93% of the 1,440 H. pylori open reading frames in situ. Of these, 231 (17%) were found to be immunogenic. By comparing 58 NCGC cases with 58 matched controls, we confirmed a higher seroprevalence of CagA among cases (66%) than controls (31%). We further identified a potential novel marker, the Helicobacter outer membrane protein A (HopA). CONCLUSIONS In this study, we provide evidence that our H. pylori whole-proteome microarray offers a platform for unbiased de novo identification of serologic biomarkers. IMPACT Given its versatile workflow, antibody responses against other H. pylori strains and possible associations with diverse H. pylori-related outcomes can be systematically analyzed.
Collapse
Affiliation(s)
- Rima Jeske
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Dennis Reininger
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Busra Turgu
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amber Brauer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Harmel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nerea Fernández de Larrea-Baz
- Environmental and Cancer Epidemiology Area, National Center of Epidemiology, Carlos III Health Institute (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Vicente Martín
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,The Research Group in Gene-Environment and Health Interactions, University of León, León, Spain
| | - Victor Moreno
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
| | - Manolis Kogevinas
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Marina Pollán
- Environmental and Cancer Epidemiology Area, National Center of Epidemiology, Carlos III Health Institute (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Jörg D Hoheisel
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Butt
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nuria Aragonés
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)-CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,Epidemiology Section, Division of Public Health, Department of Health, Madrid, Spain
| | - Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
7
|
McQueen BE, Kiatthanapaiboon A, Fulcher ML, Lam M, Patton K, Powell E, Kollipara A, Madden V, Suchland RJ, Wyrick P, O'Connell CM, Reidel B, Kesimer M, Randell SH, Darville T, Nagarajan UM. Human Fallopian Tube Epithelial Cell Culture Model To Study Host Responses to Chlamydia trachomatis Infection. Infect Immun 2020; 88:e00105-20. [PMID: 32601108 PMCID: PMC7440757 DOI: 10.1128/iai.00105-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Chlamydia trachomatis infection of the human fallopian tubes can lead to damaging inflammation and scarring, ultimately resulting in infertility. To study the human cellular responses to chlamydial infection, researchers have frequently used transformed cell lines that can have limited translational relevance. We developed a primary human fallopian tube epithelial cell model based on a method previously established for culture of primary human bronchial epithelial cells. After protease digestion and physical dissociation of excised fallopian tubes, epithelial cell precursors were expanded in growth factor-containing medium. Expanded cells were cryopreserved to generate a biobank of cells from multiple donors and cultured at an air-liquid interface. Culture conditions stimulated cellular differentiation into polarized mucin-secreting and multiciliated cells, recapitulating the architecture of human fallopian tube epithelium. The polarized and differentiated cells were infected with a clinical isolate of C. trachomatis, and inclusions containing chlamydial developmental forms were visualized by fluorescence and electron microscopy. Apical secretions from infected cells contained increased amounts of proteins associated with chlamydial growth and replication, including transferrin receptor protein 1, the amino acid transporters SLC3A2 and SLC1A5, and the T-cell chemoattractants CXCL10, CXCL11, and RANTES. Flow cytometry revealed that chlamydial infection induced cell surface expression of T-cell homing and activation proteins, including ICAM-1, VCAM-1, HLA class I and II, and interferon gamma receptor. This human fallopian tube epithelial cell culture model is an important tool with translational potential for studying cellular responses to Chlamydia and other sexually transmitted pathogens.
Collapse
Affiliation(s)
- Bryan E McQueen
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amy Kiatthanapaiboon
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - M Leslie Fulcher
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mariam Lam
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kate Patton
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Emily Powell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Avinash Kollipara
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Victoria Madden
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert J Suchland
- University of Washington, Division of Allergy and Infectious Diseases, Department of Medicine, Seattle, Washington, USA
| | - Priscilla Wyrick
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Catherine M O'Connell
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Boris Reidel
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mehmet Kesimer
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Uma M Nagarajan
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| |
Collapse
|
8
|
Ghassem-Zadeh S, Hufnagel K, Bauer A, Frossard JL, Yoshida M, Kutsumi H, Acha-Orbea H, Neulinger-Muñoz M, Vey J, Eckert C, Strobel O, Hoheisel JD, Felix K. Novel Autoantibody Signatures in Sera of Patients with Pancreatic Cancer, Chronic Pancreatitis and Autoimmune Pancreatitis: A Protein Microarray Profiling Approach. Int J Mol Sci 2020; 21:E2403. [PMID: 32244327 PMCID: PMC7177860 DOI: 10.3390/ijms21072403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of disease-associated autoantibodies is of high importance. Their assessment could complement current diagnostic modalities and assist the clinical management of patients. We aimed at developing and validating high-throughput protein microarrays able to screen patients' sera to determine disease-specific autoantibody-signatures for pancreatic cancer (PDAC), chronic pancreatitis (CP), autoimmune pancreatitis and their subtypes (AIP-1 and AIP-2). In-house manufactured microarrays were used for autoantibody-profiling of IgG-enriched preoperative sera from PDAC-, CP-, AIP-1-, AIP-2-, other gastrointestinal disease (GID) patients and healthy controls. As a top-down strategy, three different fluorescence detection-based protein-microarrays were used: large with 6400, intermediate with 345, and small with 36 full-length human recombinant proteins. Large-scale analysis revealed 89 PDAC, 98 CP and 104 AIP immunogenic antigens. Narrowing the selection to 29 autoantigens using pooled sera first and individual sera afterwards allowed a discrimination of CP and AIP from PDAC. For validation, predictive models based on the identified antigens were generated which enabled discrimination between PDAC and AIP-1 or AIP-2 yielded high AUC values of 0.940 and 0.925, respectively. A new repertoire of autoantigens was identified and their assembly as a multiplex test will provide a fast and cost-effective tool for differential diagnosis of pancreatic diseases with high clinical relevance.
Collapse
Affiliation(s)
- Sahar Ghassem-Zadeh
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
- Department of Biochemistry, University of Lausanne, 1066 Epalinges-Lausanne, Switzerland;
| | - Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Andrea Bauer
- Department of Functional Genomics, DKFZ, 69120 Heidelberg, Germany; (A.B.); (J.D.H.)
| | - Jean-Louis Frossard
- Department of Medical Specialties, Division of Gastroenterology, University Hospital of Geneva, 1205 Geneva, Switzerland;
| | - Masaru Yoshida
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Hiromu Kutsumi
- Center for Clinical Research and Advanced Medicine Shiga University of Medical Science Seta Tsukinowa-cho, Otsu 520-2192, Japan;
| | - Hans Acha-Orbea
- Department of Biochemistry, University of Lausanne, 1066 Epalinges-Lausanne, Switzerland;
| | - Matthias Neulinger-Muñoz
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
| | - Johannes Vey
- Institute of Medical Biometry and Informatics, University Medical Center Ruprecht-Karls University Heidelberg, 69120 Heidelberg, Germany;
| | - Christoph Eckert
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
| | - Jörg D. Hoheisel
- Department of Functional Genomics, DKFZ, 69120 Heidelberg, Germany; (A.B.); (J.D.H.)
| | - Klaus Felix
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
| |
Collapse
|
9
|
Mazraani R, Timms P, Hill PC, Suaalii-Sauni T, Niupulusu T, Temese SVA, Iosefa-Siitia L, Auvaa L, Tapelu SA, Motu MF, Righarts A, Walsh MS, Rombauts L, Allan JA, Horner P, Huston WM. Evaluation of a PGP3 ELISA for surveillance of the burden of Chlamydia infection in women from Australia and Samoa. Pathog Dis 2020; 77:5519228. [PMID: 31201421 PMCID: PMC6607412 DOI: 10.1093/femspd/ftz031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 06/10/2019] [Indexed: 01/10/2023] Open
Abstract
Serological assays can be used to investigate the population burden of infection and potentially sequelae from Chlamydia. We investigated the PGP3 ELISA as a sero-epidemiological tool for infection or sub-fertility in Australian and Samoan women. The PGP3 ELISA absorbance levels were compared between groups of women with infertility, fertile, and current chlamydial infections. In the Australian groups, women with chlamydial tubal factor infertility had significantly higher absorbance levels in the PGP3 ELISA compared to fertile women (P < 0.0001), but not when compared to women with current chlamydial infection (P = 0.44). In the Samoan study, where the prevalence of chlamydial infections is much higher there were significant differences in the PGP3 ELISA absorbance levels between chlamydial sub-fertile women and fertile women (P = 0.003). There was no difference between chlamydial sub-fertile women and women with a current infection (P = 0.829). The results support that the PGP3 assay is effective for sero-epidemiological analysis of burden of infection, but not for evaluation of chlamydial pathological sequelae such as infertility.
Collapse
Affiliation(s)
- Rami Mazraani
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, 9016, New Zealand
| | - Tamaailau Suaalii-Sauni
- School of Languages and Cultures, Victoria University of Wellington, Wellington, 2820, New Zealand
| | | | - Seiuli V A Temese
- Centre for Samoa Studies, National University of Samoa, Le Papaigalagala Campus, To'omatagi, Samoa
| | | | | | | | | | - Antoinette Righarts
- Preventive and Social Medicine, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand
| | - Michael S Walsh
- Planning, Funding and Health Outcomes, Waitemata and Auckland District Health Boards, Auckland, New Zealand
| | - Luk Rombauts
- MIMR-PH Institute of Medical Research, Monash, Australia
| | - John A Allan
- UC Health Clinical School, The Wesley Hospital, Auchenflower, Queensland, 4066, Australia
| | - Patrick Horner
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|
10
|
Moritz CP, Paul S, Stoevesandt O, Tholance Y, Camdessanché JP, Antoine JC. Autoantigenomics: Holistic characterization of autoantigen repertoires for a better understanding of autoimmune diseases. Autoimmun Rev 2020; 19:102450. [DOI: 10.1016/j.autrev.2019.102450] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
|
11
|
Köhler T, Heida T, Hoefgen S, Weigel N, Valiante V, Thiele J. Cell-free protein synthesis and in situ immobilization of deGFP-MatB in polymer microgels for malonate-to-malonyl CoA conversion. RSC Adv 2020; 10:40588-40596. [PMID: 35520868 PMCID: PMC9057574 DOI: 10.1039/d0ra06702d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
We describe a bottom-up approach towards functional enzymes utilizing microgels as carriers for genetic information that enable cell-free protein synthesis, in situ immobilization, and utilization of functional deGFP-MatB.
Collapse
Affiliation(s)
- Tony Köhler
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Thomas Heida
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Sandra Hoefgen
- Biobricks of Microbial Natural Product Syntheses
- Department of Molecular and Applied Microbiology
- Leibniz Institute for Natural Product Research and Infection Biology
- 07745 Jena
- Germany
| | - Niclas Weigel
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Vito Valiante
- Biobricks of Microbial Natural Product Syntheses
- Department of Molecular and Applied Microbiology
- Leibniz Institute for Natural Product Research and Infection Biology
- 07745 Jena
- Germany
| | - Julian Thiele
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| |
Collapse
|
12
|
Chlamydia trachomatis Whole-Proteome Microarray Analysis of The Netherlands Chlamydia Cohort Study. Microorganisms 2019; 7:microorganisms7120703. [PMID: 31888186 PMCID: PMC6956083 DOI: 10.3390/microorganisms7120703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022] Open
Abstract
Chlamydia trachomatis (Ct) whole-proteome microarrays were utilized to identify antibody patterns associated with infection; pelvic inflammatory disease (PID), tubal factor infertility, chronic pelvic pain (CPP) and ectopic pregnancy in a subsample of the Netherlands Chlamydia cohort study. Serum pools were analyzed on whole-proteome arrays. The 121 most reactive antigens identified during whole-proteome arrays were selected for further analysis with minimized microarrays that allowed for single sera analysis. From the 232 single sera; 145 (62.5%) serum samples were reactive for at least one antigen. To discriminate between positive and negative serum samples; we created a panel of in total 18 antigens which identified 96% of all microarray positive samples. Antigens CT_858; CT_813 and CT_142 were most reactive. Comparison of antibody reactivity's among women with and without Ct related sequelae revealed that the reactivity of CT_813 and CT_142 was less common among women with PID compared to women without (29.0% versus 58.6%, p = 0.005 and 25.8% versus 50.6%, p = 0.017 respectively). CT_858 was less common among CPP cases compared to controls (33.3% versus 58.6; p = 0.028). Using a whole-proteome array to select antigens for minimized arrays allows for the identification of novel informative antigens as general infection markers or disease associated antigens.
Collapse
|
13
|
Hoenderboom BM, van Willige ME, Land JA, Pleijster J, Götz HM, van Bergen JEAM, Dukers-Muijrers NHTM, Hoebe CJPA, van Benthem BHB, Morré SA. Antibody Testing in Estimating Past Exposure to C hlamydia trachomatis in the Netherlands Chlamydia Cohort Study. Microorganisms 2019; 7:microorganisms7100442. [PMID: 31614620 PMCID: PMC6843155 DOI: 10.3390/microorganisms7100442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 01/22/2023] Open
Abstract
The asymptomatic course of Chlamydia trachomatis (CT) infections can result in underestimated CT lifetime prevalence. Antibody testing might improve this estimate. We assessed CT antibody positivity and predictive factors thereof in the Netherlands Chlamydia Cohort Study. Women who had ≥1 CT Nucleic Acid Amplification Test (NAAT) in the study (2008–2011) and who provided self-reported information on NAATs were tested for CT major outer membrane protein specific IgG in serum (2016). CT antibody positivity was assessed and predictive factors were identified using multivariable logistic regressions, separately for CT-positive women (≥1 positive NAAT or ≥1 self-reported positive CT test) and CT-negative women (negative by study NAAT and self-report). Of the 3,613 women studied, 833 (23.1%) were CT -positive. Among the CT-negative women, 208 (7.5%, 95% CI 6.5–8.5) tested positive for CT antibodies. This increased CT lifetime prevalence with 5.8% (95% CI 5.0–6.5). Among women with a CT-positive history, 338 (40.6%, 95% CI 38.5–44.1) tested positive. Predictive factors for antibody positivity related to lower social economic status, sexual risk behavior, multiple infections, higher body mass index, and non-smoking. CT antibody testing significantly increased the lifetime prevalence. Combining NAAT outcomes, self-reported positive tests, and antibody testing reduced misclassification in CT prevalence estimates.
Collapse
Affiliation(s)
- Bernice M Hoenderboom
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
- Laboratory of Immunogenetics, department Medical Microbiology and Infection Control, Location VU University Medical Center, Amsterdam University Medical Centre (UMC), De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
| | - Michelle E van Willige
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
| | - Jolande A Land
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Universiteitssingel 40, 6229 ET Maastricht, The Netherlands.
| | - Jolein Pleijster
- Laboratory of Immunogenetics, department Medical Microbiology and Infection Control, Location VU University Medical Center, Amsterdam University Medical Centre (UMC), De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
| | - Hannelore M Götz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
- Department Infectious Disease Control, Municipal Public Health Service Rotterdam-Rijnmond (GGD Rotterdam), Schiedamsedijk 95, 3011 EN Rotterdam, The Netherlands.
- Department of Public Health, Erasmus MC-University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.
| | - Jan E A M van Bergen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
- Department of General Practice, Division Clinical Methods and Public Health, location Academic Medical Center, Amsterdam University Medical Centre (UMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands.
- STI AIDS Netherlands (SOA AIDS Nederland), Keizersgracht 392, 1016 GB Amsterdam, The Netherlands.
| | - Nicole H T M Dukers-Muijrers
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Het Overloon 2, 6411 TE Heerlen, The Netherlands.
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), P. Debyelaan 25, 6229 HX Maastricht, The Netherlands.
| | - Christian J P A Hoebe
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Het Overloon 2, 6411 TE Heerlen, The Netherlands.
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), P. Debyelaan 25, 6229 HX Maastricht, The Netherlands.
| | - Birgit H B van Benthem
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
| | - Servaas A Morré
- Laboratory of Immunogenetics, department Medical Microbiology and Infection Control, Location VU University Medical Center, Amsterdam University Medical Centre (UMC), De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Universiteitssingel 40, 6229 ET Maastricht, The Netherlands.
| |
Collapse
|
14
|
Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
Collapse
Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
15
|
Darville T, Albritton HL, Zhong W, Dong L, O'Connell CM, Poston TB, Quayle AJ, Goonetilleke N, Wiesenfeld HC, Hillier SL, Zheng X. Anti-chlamydia IgG and IgA are insufficient to prevent endometrial chlamydia infection in women, and increased anti-chlamydia IgG is associated with enhanced risk for incident infection. Am J Reprod Immunol 2019; 81:e13103. [PMID: 30784128 DOI: 10.1111/aji.13103] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
PROBLEM Chlamydia infections in women can ascend to the upper genital tract, and repeated infections are common, placing women at risk for sequelae. The protective role of anti-chlamydia antibodies to surface exposed antigens in ascending and incident infection is unclear. METHOD OF STUDY A whole-bacterial ELISA was used to quantify chlamydia-specific IgG and IgA in serum and cervical secretions of 151 high-risk women followed longitudinally. Correlations were determined between antibody and cervical burden, and causal mediation analysis investigated the effect of antibody on ascension. We examined the relationship of antibody to incident infection using the marginal Cox model. RESULTS Serum and cervical anti-chlamydia IgG and cervical IgA levels correlated inversely with cervical burden. While lower burden was associated with reduced ascension, causal mediation analysis revealed that the indirect effects of antibody mediated through reductions in bacterial burden were insufficient to prevent ascension. Analysis of women uninfected at enrollment revealed that serum and cervical anti-chlamydia IgG were associated with increased risk of incident infection; hazard ratio increased 3.6-fold (95% CI, 1.3-10.3), and 22.6-fold (95% CI, 3.1-165.2) with each unit of serum and cervical IgG, respectively. CONCLUSION Although anti-chlamydia IgG and IgA correlated with reduced cervical chlamydia burden, they failed to prevent ascension and increased levels of anti-chlamydia IgG were associated with increased risk for incident infection.
Collapse
Affiliation(s)
- Toni Darville
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina
| | - Hannah L Albritton
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Wujuan Zhong
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Li Dong
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | | | - Taylor B Poston
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina
| | - Alison J Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Nilu Goonetilleke
- Departments of Microbiology & Immunology and Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Xiaojing Zheng
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina
| |
Collapse
|
16
|
Hufnagel K, Reininger D, Ng SW, Gassert N, Rohland JK, Shahryarhesami S, Bauer AS, Waterboer T, Hoheisel JD. In situ, Cell-free Protein Expression on Microarrays and Their Use for the Detection of Immune Responses. Bio Protoc 2019; 9:e3152. [PMID: 33654961 DOI: 10.21769/bioprotoc.3152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 11/02/2022] Open
Abstract
Until recently, whole-proteome microarrays for comprehensive studies of protein interactions were mostly produced by individual cloning and cellular expression of very many open reading frames, followed by protein isolation and purification as well as array production. To overcome this cumbersome process, we have developed a method to generate microarrays representing entire proteomes by a combination of multiple spotting and on-chip, cell-free protein expression. Here, we describe the protocol for the production of bacterial protein microarrays. With slight adaptations, however, the procedure can be applied to the proteome of any organism. Expression constructs of each gene are generated by PCR on bacterial genomic DNA followed by a common secondary amplification that is adding relevant regulative elements to either end of the constructs. The unpurified PCR-products are spotted onto the microarray surface. Full-length proteins are directly expressed in situ in a cell-free manner and stay attached to the surface without further action. As an example of a typical application, we describe here the proteome-wide analysis of the immune response to a bacterial infectious agent by characterizing the binding profiles of the antibodies in patient sera.
Collapse
Affiliation(s)
- Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Dennis Reininger
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siu Wang Ng
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadine Gassert
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane K Rohland
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Soroosh Shahryarhesami
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
17
|
Woodhall SC, Gorwitz RJ, Migchelsen SJ, Gottlieb SL, Horner PJ, Geisler WM, Winstanley C, Hufnagel K, Waterboer T, Martin DL, Huston WM, Gaydos CA, Deal C, Unemo M, Dunbar JK, Bernstein K. Advancing the public health applications of Chlamydia trachomatis serology. THE LANCET. INFECTIOUS DISEASES 2018; 18:e399-e407. [PMID: 29983342 DOI: 10.1016/s1473-3099(18)30159-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 02/04/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022]
Abstract
Genital Chlamydia trachomatis infection is the most commonly diagnosed sexually transmitted infection. Trachoma is caused by ocular infection with C trachomatis and is the leading infectious cause of blindness worldwide. New serological assays for C trachomatis could facilitate improved understanding of C trachomatis epidemiology and prevention. C trachomatis serology offers a means of investigating the incidence of chlamydia infection and might be developed as a biomarker of scarring sequelae, such as pelvic inflammatory disease. Therefore, serological assays have potential as epidemiological tools to quantify unmet need, inform service planning, evaluate interventions including screening and treatment, and to assess new vaccine candidates. However, questions about the performance characteristics and interpretation of C trachomatis serological assays remain, which must be addressed to advance development within this field. In this Personal View, we explore the available information about C trachomatis serology and propose several priority actions. These actions involve development of target product profiles to guide assay selection and assessment across multiple applications and populations, establishment of a serum bank to facilitate assay development and evaluation, and development of technical and statistical methods for assay evaluation and analysis of serological findings. The field of C trachomatis serology will benefit from collaboration across the public health community to align technological developments with their potential applications.
Collapse
Affiliation(s)
- Sarah C Woodhall
- Blood Safety, Hepatitis, Sexually Transmitted Infections (STI) and HIV Service, Public Health England, London, UK; National Institute for Health Research Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, UK; National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, University College London, London, UK.
| | - Rachel J Gorwitz
- Division of STD Prevention, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie J Migchelsen
- Blood Safety, Hepatitis, Sexually Transmitted Infections (STI) and HIV Service, Public Health England, London, UK; Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Sami L Gottlieb
- Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Patrick J Horner
- National Institute for Health Research Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, UK; Population Health Sciences, University of Bristol, Bristol, UK
| | - William M Geisler
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Katrin Hufnagel
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana L Martin
- Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
| | - Carolyn Deal
- Division of Microbiology and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Örebro University, Örebro, Sweden
| | - J Kevin Dunbar
- Blood Safety, Hepatitis, Sexually Transmitted Infections (STI) and HIV Service, Public Health England, London, UK; National Institute for Health Research Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, UK; National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Kyle Bernstein
- Division of STD Prevention, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|