1
|
Kruk ME, Mehta S, Murray K, Higgins L, Do K, Johnson JE, Wagner R, Wendt CH, O'Connor JB, Harris JK, Laguna TA, Jagtap PD, Griffin TJ. An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems 2024:e0092923. [PMID: 38934598 DOI: 10.1128/msystems.00929-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., Pseudomonas), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.
Collapse
Affiliation(s)
- Monica E Kruk
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Kevin Murray
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katherine Do
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chris H Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - John B O'Connor
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - J Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Theresa A Laguna
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| |
Collapse
|
2
|
Sheng G, Chu H, Duan H, Sun H, Xie Z, Sun Z, Cao T. A novel enzyme-linked ligand-sorbent assay (ELLSA) to screening pulmonary tuberculosis: a retrospective cross-sectional study. Microbes Infect 2024; 26:105332. [PMID: 38537770 DOI: 10.1016/j.micinf.2024.105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Little knowledge of antigen existence in the pulmonary tuberculosis (PTB) patient serum impeded its development in antigen detection technology, despite its considerable potential. METHODS Human ligand proteins and their adsorbent Mycobacterium tuberculosis (M.tb) proteins in the serum of PTB patients were identified using human protein chip (HuProt™) and LC-MS/MS, successively. The monoclonal antibody of ligand proteins, C5orf24, and polyclonal antibody of 9 M.tb proteins were prepared on mice and rabbits which were used to develop a novel enzyme-linked ligand-sorbent assay (ELLSA). The 412 volunteers were divided into the PTB group (n = 250) and the healthy control (n = 162). The PTB group was further divided into ATB (n = 131), LTBI (n = 18), Clinical diagnosis (n = 18), and Suspected (n = 73). All samples were tested by ELLSA to evaluate the diagnostic performance of ELLSA in PTB patients. RESULTS Nine ligand proteins specific to PTB patients were identified on chips, with Chromosome 5 Open Reading Frame 24 (C5orf24) and kinocilin (KNCN) showing significantly higher signals. Proteomic analysis of the C5orf24-and KNCN-adsorbent protein complexes revealed 10 and 10 of the M.tb proteins, respectively. According to the composition reference of standard, the ELLSA based on C5orf24 ligand demonstrated a higher sensitivity of 69.6% and specificity of 90.18% in ATB patients and had a sensitivity of 64.22% in bacterial negative pulmonary tuberculosis, whereas the sensitivity of MGIT 960 and Xpert M.tb/RIF were 0%, respectively. CONCLUSIONS M.tb proteins in serum can be enriched by ligand proteins and detected by ELLSA which proved to have excellent diagnostic performance for PTB.
Collapse
Affiliation(s)
- Gang Sheng
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Hongqian Chu
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Huijuan Duan
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Hong Sun
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Zhongyao Xie
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Zhaogang Sun
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
| | - Tingming Cao
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
| |
Collapse
|
3
|
Ma G, Wang P, Yang Y, Wang W, Ma J, Zhou L, Ouyang J, Li R, Zhang S. emPAI-assisted strategy enhances screening and assessment of Mycobacterium tuberculosis infection serological markers. Microb Biotechnol 2021; 14:1827-1838. [PMID: 34173722 PMCID: PMC8313264 DOI: 10.1111/1751-7915.13829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/12/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023] Open
Abstract
Discovering new serological markers of Mycobacterium tuberculosis (MTB) infection and establishing a rapid and efficient detection technology is of great significance for the prevention and control of tuberculosis. In this study, we established an exponentially modified protein abundance index (emPAI) value-assisted strategy to investigate and improve the screening efficiency of serological biomarkers of tuberculosis. First, we used LC-MS/MS to analyse MTB culture filtrate proteins (MTB-CFPs), and 632 MTB proteins were identified. Then, the characteristic values of MTB-CFPs - including emPAI value, molecular weight (Mw), isoelectric point (pI), grand average of hydropathy (GRAVY), transmembrane domain (TMD) and functional groups were calculated. Next, we successfully prepared 10 MTB proteins with emPAI value > 1.0 and recombinantly expressed these proteins in Escherichia coli. At the same time, 3 MTB proteins with emPAI between 0.1 and 0.5 were randomly selected as the control groups, and the immunogenicity of the recombinant MTB proteins was detected using ELISA. The sensitivity and receiver operating characteristic (ROC) curves were calculated for each recombinant MTB protein. The results showed that the areas under the curve (AUC) value of Rv2031c, Rv0577, Rv0831c, Rv0934 and Rv3248c were all higher than those of Rv3875 (AUC, 0.6643). Further analysis of the relationship between emPAI value and antibody sensitivity, AUC value and antibody affinity in mice immunized with recombinant MTB protein showed that emPAI values were positively correlated with them, and R-squared value ranged from 0.64 to 0.79. The only exception was ESAT-6 (encoded by the Rv3875 gene), which AUC value was relatively low owing to its strong immunosuppressive properties. This study provides a rationale for the serological marker screening of emPAI-assisted tuberculosis clinical test. The results also provide new technical support for the screening of candidate serological markers of infectious diseases in the future.
Collapse
Affiliation(s)
- Guorong Ma
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesNingxia Medical UniversityYinchuan750004China
| | - Pei Wang
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Yanhui Yang
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesNingxia Medical UniversityYinchuan750004China
| | - Wei Wang
- College of Biological Science and EngineeringNorthern University for NationalitiesYinchuan750021China
| | - Jinhua Ma
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesNingxia Medical UniversityYinchuan750004China
| | - Lin Zhou
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesNingxia Medical UniversityYinchuan750004China
| | - Junlin Ouyang
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Prevention and Control of Common Infectious DiseasesNingxia Medical UniversityYinchuan750004China
| | - Rongxiu Li
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Shulin Zhang
- Department of Immunology and MicrobiologySchool of MedicineShanghai Jiao Tong UniversityShanghai200025China
- Tuberculosis Research CenterSchool of MedicineShanghai Public Health Clinical CenterShanghai201508China
| |
Collapse
|
4
|
Poeta P, Silva V, Guedes A, Eduardo Pereira J, Cláudia Coelho A, Igrejas G. Tuberculosis in the 21th century: Current status of diagnostic methods. Exp Lung Res 2019; 44:352-360. [PMID: 30663432 DOI: 10.1080/01902148.2018.1545880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.
Collapse
Affiliation(s)
- Patrícia Poeta
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Vanessa Silva
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| | - Andreia Guedes
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal
| | - José Eduardo Pereira
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Ana Cláudia Coelho
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Gilberto Igrejas
- b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| |
Collapse
|