1
|
Fernández-García M, Ares-Arroyo M, Wedel E, Montero N, Barbas C, Rey-Stolle MF, González-Zorn B, García A. Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules of Haemophilus influenzae Rd KW20. Int J Mol Sci 2023; 24:11150. [PMID: 37446331 DOI: 10.3390/ijms241311150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Haemophilus influenzae is a gram-negative bacterium of relevant clinical interest. H. influenzae Rd KW20 was the first organism to be sequenced and for which a genome-scale metabolic model (GEM) was developed. However, current H. influenzae GEMs are unable to capture several aspects of metabolome nature related to metabolite pools. To directly and comprehensively characterize the endometabolome of H. influenzae Rd KW20, we performed a multiplatform MS-based metabolomics approach combining LC-MS, GC-MS and CE-MS. We obtained direct evidence of 15-20% of the endometabolome present in current H. influenzae GEMs and showed that polar metabolite pools are interconnected through correlating metabolite islands. Notably, we obtained high-quality evidence of 18 metabolites not previously included in H. influenzae GEMs, including the antimicrobial metabolite cyclo(Leu-Pro). Additionally, we comprehensively characterized and evaluated the quantitative composition of the phospholipidome of H. influenzae, revealing that the fatty acyl chain composition is largely independent of the lipid class, as well as that the probability distribution of phospholipids is mostly related to the conditional probability distribution of individual acyl chains. This finding enabled us to provide a rationale for the observed phospholipid profiles and estimate the abundance of low-level species, permitting the expansion of the phospholipidome characterization through predictive probabilistic modelling.
Collapse
Affiliation(s)
- Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Mª Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Bruno González-Zorn
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Antonia García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| |
Collapse
|
2
|
López-López N, Gil-Campillo C, Díez-Martínez R, Garmendia J. Learning from -omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives. Comput Struct Biotechnol J 2021; 19:3042-3050. [PMID: 34136102 PMCID: PMC8178019 DOI: 10.1016/j.csbj.2021.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022] Open
Abstract
Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of -omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae-host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.
Collapse
Affiliation(s)
- Nahikari López-López
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Celia Gil-Campillo
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | | | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| |
Collapse
|
3
|
Southworth T, Higham A, Kolsum U, Li J, Scott T, Dungwa J, Sridhar S, Pham TH, Newbold P, Singh D. The relationship between airway immunoglobulin activity and eosinophils in COPD. J Cell Mol Med 2020; 25:2203-2212. [PMID: 33369092 PMCID: PMC7882983 DOI: 10.1111/jcmm.16206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
In chronic obstructive pulmonary disease (COPD), the effects of inhaled corticosteroids are predicted by blood eosinophil counts. We previously briefly reported increased immunoglobulin (Ig)A and IgM levels in bronchoalveolar lavage (BAL) of COPD patients with higher (eosinophilhigh) compared to lower (eosinophillow) blood eosinophils (>250/μL versus < 150/μL), suggesting differences in adaptive immune function. An inverse relationship exists between eosinophil counts and airway pathogenic bacteria levels. The mechanistic reasons for these associations between eosinophils, corticosteroids and pathogenic bacteria are unclear. IgA, IgM and IgG levels were assessed in BAL, bronchial biopsies and epithelium collected from eosinophilhigh (n = 20) and eosinophillow (n = 21) patients. Bronchial B‐cell numbers were measured by immunohistochemistry. B‐cell activity was assessed in bronchial samples and following exposure to BAL from eosinophilhigh and eosinophillow patients. BAL levels of non‐typeable Haemophilus influenza (NTHi)‐specific immunoglobulins were quantified. Results showed airway expression of IgA, IgG1 and IgM were lower in eosinophillow compared to eosinophilhigh patients, with lower levels of NTHi‐specific IgA and IgM. Bronchial B‐cell numbers were similar in both groups, but B‐cell activity was lower in eosinophillow patients. In conclusion, COPD eosinophillow patients show differences in adaptive immune function compared to COPD eosinophilhigh patients. These differences may cause different microbiomes in these COPD phenotypes.
Collapse
Affiliation(s)
- Thomas Southworth
- Division of Infection, Immunity and Respiratory Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, UK.,Medicines Evaluation Unit, Manchester, UK
| | - Andrew Higham
- Division of Infection, Immunity and Respiratory Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Umme Kolsum
- Division of Infection, Immunity and Respiratory Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Jian Li
- Division of Infection, Immunity and Respiratory Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, UK
| | | | | | - Sriram Sridhar
- Translational Science, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Tuyet-Hang Pham
- Translational Science & Experimental Medicine, Early Respiratory & Immunology, Research & Early Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Paul Newbold
- BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, MD, USA
| | - Dave Singh
- Division of Infection, Immunity and Respiratory Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, UK.,Medicines Evaluation Unit, Manchester, UK
| |
Collapse
|
4
|
Bishai WR, Timmins GS. Potential for breath test diagnosis of urease positive pathogens in lung infections. J Breath Res 2019; 13:032002. [DOI: 10.1088/1752-7163/ab2225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
5
|
Moore PJ, Sesma J, Alexis NE, Tarran R. Tobacco exposure inhibits SPLUNC1-dependent antimicrobial activity. Respir Res 2019; 20:94. [PMID: 31113421 PMCID: PMC6530064 DOI: 10.1186/s12931-019-1066-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
Background Tobacco smoke exposure impairs the lung’s innate immune response, leading to an increased risk of chronic infections. SPLUNC1 is a secreted, multifunctional innate defense protein that has antimicrobial activity against Gram negative organisms. We hypothesize that tobacco smoke-induced SPLUNC1 dysfunction contributes to the observed defect in innate immunity in tobacco smokers and that this dysfunction can be used as a potential biomarker of harm. Methods We collected sputum from never-smokers and otherwise healthy smokers. We performed Western blotting to determine SPLUNC1 levels and determined antimicrobial activity against nontypeable Haemophilus influenzae. An in vitro exposure model was utilized to measure the effect of tobacco exposure on human bronchial epithelial culture (HBEC) antimicrobial activity against H. influenzae. The direct effects of cigarette and little cigar smoke exposure on SPLUNC1 function was determined using 24 h growth measurements and LPS binding assays. Results H. influenzae growth in cigarette smoker’s sputum was significantly greater compared to never-smokers sputum over 24 h. HBEC supernatants and lysates contained significantly higher numbers of H. influenzae following chronic cigarette and little cigar smoke exposure compared to air-exposed controls. Furthermore, SPLUNC1’s antimicrobial activity and LPS-binding capability against both H. influenzae and P. aeruginosa was attenuated following cigarette and little cigar exposure. Conclusions These data suggest that cigarette and little cigar exposure impairs SPLUNC1’s antimicrobial ability and that this inhibition may serve as a novel biomarker of harm that can be used to assess the toxicity of commercial tobacco products.
Collapse
Affiliation(s)
- Patrick J Moore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, 7118A Marsico Hall, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Juliana Sesma
- CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Neil E Alexis
- Center for Environmental Medicine, Asthma and Lung Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert Tarran
- Marsico Lung Institute, University of North Carolina at Chapel Hill, 7118A Marsico Hall, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Department of Cell Biology & Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
6
|
Su YC, Jalalvand F, Thegerström J, Riesbeck K. The Interplay Between Immune Response and Bacterial Infection in COPD: Focus Upon Non-typeable Haemophilus influenzae. Front Immunol 2018; 9:2530. [PMID: 30455693 PMCID: PMC6230626 DOI: 10.3389/fimmu.2018.02530] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a debilitating respiratory disease and one of the leading causes of morbidity and mortality worldwide. It is characterized by persistent respiratory symptoms and airflow limitation due to abnormalities in the lower airway following consistent exposure to noxious particles or gases. Acute exacerbations of COPD (AECOPD) are characterized by increased cough, purulent sputum production, and dyspnea. The AECOPD is mostly associated with infection caused by common cold viruses or bacteria, or co-infections. Chronic and persistent infection by non-typeable Haemophilus influenzae (NTHi), a Gram-negative coccobacillus, contributes to almost half of the infective exacerbations caused by bacteria. This is supported by reports that NTHi is commonly isolated in the sputum from COPD patients during exacerbations. Persistent colonization of NTHi in the lower airway requires a plethora of phenotypic adaptation and virulent mechanisms that are developed over time to cope with changing environmental pressures in the airway such as host immuno-inflammatory response. Chronic inhalation of noxious irritants in COPD causes a changed balance in the lung microbiome, abnormal inflammatory response, and an impaired airway immune system. These conditions significantly provide an opportunistic platform for NTHi colonization and infection resulting in a "vicious circle." Episodes of large inflammation as the consequences of multiple interactions between airway immune cells and NTHi, accumulatively contribute to COPD exacerbations and may result in worsening of the clinical status. In this review, we discuss in detail the interplay and crosstalk between airway immune residents and NTHi, and their effect in AECOPD for better understanding of NTHi pathogenesis in COPD patients.
Collapse
Affiliation(s)
- Yu-Ching Su
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Farshid Jalalvand
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - John Thegerström
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| |
Collapse
|
7
|
Shen S, An B, Wang X, Hilchey SP, Li J, Cao J, Tian Y, Hu C, Jin L, Ng A, Tu C, Qu M, Zand MS, Qu J. Surfactant Cocktail-Aided Extraction/Precipitation/On-Pellet Digestion Strategy Enables Efficient and Reproducible Sample Preparation for Large-Scale Quantitative Proteomics. Anal Chem 2018; 90:10350-10359. [PMID: 30078316 DOI: 10.1021/acs.analchem.8b02172] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
For quantitative proteomics, efficient, robust, and reproducible sample preparation with high throughput is critical yet challenging, especially when large cohorts are involved, as is often required by clinical/pharmaceutical studies. We describe a rapid and straightforward surfactant cocktail-aided extraction/precipitation/on-pellet digestion (SEPOD) strategy to address this need. Prior to organic solvent precipitation and on-pellet digestion, SEPOD treats samples with a surfactant cocktail (SC) containing multiple nonionic/anionic surfactants, which achieves (i) exhaustive/reproducible protein extraction, including membrane-bound proteins; (ii) effective removal of detrimental nonprotein matrix components (e.g., >94% of phospholipids); (iii) rapid/efficient proteolytic digestion owing to dual (surfactants + precipitation) denaturation. The optimal SC composition and concentrations were determined by Orthogonal-Array-Design investigation of their collective/individuals effects on protein extraction/denaturation. Key parameters for cleanup and digestion were experimentally identified as well. The optimized SEPOD procedures allowed a rapid 6 h digestion providing a clean digest with high peptide yields and excellent quantitative reproducibility (especially low-abundance proteins). Compared with filter-assisted sample preparation (FASP) and in-solution digestion, SEPOD showed superior performance by recovering substantially more peptide/proteins (including integral membrane proteins), yielding significantly higher peptide intensities and improving quantification for peptides with extreme physicochemical properties. SEPOD was further applied in a large-cohort temporal investigation of 44 IAV-infected mouse lungs, providing efficient and reproducible peptide yields (77.9 ± 4.6%) across all samples. With the IonStar pipeline, >6 400 unique protein groups were quantified (≥2 peptide/protein, peptide-FDR < 0.05%), ∼99% without missing data in any sample with <7% technical median-intragroup CV. Altered proteome patterns revealed interesting novel insights into pathophysiological changes by IAV infection. In summary, SEPOD offers a feasible solution for rapid, efficient, and reproducible preparation of biological samples, facilitating high-quality proteomic quantification of large sample cohorts.
Collapse
Affiliation(s)
- Shichen Shen
- Department of Pharmaceutical Sciences , SUNY at Buffalo , Buffalo , New York 14214 , United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States
| | - Bo An
- Department of Pharmaceutical Sciences , SUNY at Buffalo , Buffalo , New York 14214 , United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States
| | - Xue Wang
- New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States.,Roswell Park Cancer Institute , Buffalo , New York 14263 , United States
| | - Shannon P Hilchey
- Division of Nephrology , University of Rochester Medical Center , Rochester , New York 14642 , United States
| | - Jun Li
- Department of Pharmaceutical Sciences , SUNY at Buffalo , Buffalo , New York 14214 , United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States
| | - Jin Cao
- National Institute for Food and Drug Control , Beijing , 100050 , China
| | - Yu Tian
- AbbVie Bioresearch Center Inc. , Worcester , Massachusetts 01605 , United States
| | - Chenqi Hu
- AbbVie Bioresearch Center Inc. , Worcester , Massachusetts 01605 , United States
| | - Liang Jin
- AbbVie Bioresearch Center Inc. , Worcester , Massachusetts 01605 , United States
| | - Andrew Ng
- New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States.,School of Dental Medicine , SUNY at Buffalo , Buffalo , New York 14214 , United States
| | - Chengjian Tu
- Department of Pharmaceutical Sciences , SUNY at Buffalo , Buffalo , New York 14214 , United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States
| | - Miao Qu
- Department of Neurology, Xuan Wu Hospital , Capital University of Medicine , Beijing , 100053 , China
| | - Martin S Zand
- Division of Nephrology , University of Rochester Medical Center , Rochester , New York 14642 , United States
| | - Jun Qu
- Department of Pharmaceutical Sciences , SUNY at Buffalo , Buffalo , New York 14214 , United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo , New York 14203 , United States
| |
Collapse
|
8
|
Wang X, Niu J, Li J, Shen X, Shen S, Straubinger RM, Qu J. Temporal Effects of Combined Birinapant and Paclitaxel on Pancreatic Cancer Cells Investigated via Large-Scale, Ion-Current-Based Quantitative Proteomics (IonStar). Mol Cell Proteomics 2018; 17:655-671. [PMID: 29358341 PMCID: PMC5880105 DOI: 10.1074/mcp.ra117.000519] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Indexed: 01/05/2023] Open
Abstract
Despite decades of effort, pancreatic adenocarcinoma (PDAC) remains an intractable clinical challenge. An insufficient understanding of mechanisms underlying tumor cell responses to chemotherapy contributes significantly to the lack of effective treatment regimens. Here, paclitaxel, a first-line chemotherapeutic agent, was observed to interact synergistically with birinapant, a second mitochondrial-derived activator of caspases mimetic. Therefore, we investigated molecular-level drug interaction mechanisms using comprehensive, reproducible, and well-controlled ion-current-based MS1 quantification (IonStar). By analyzing 40 biological samples in a single batch, we compared temporal proteomic responses of PDAC cells treated with birinapant and paclitaxel, alone and combined. Using stringent criteria (e.g. strict false-discovery-rate (FDR) control, two peptides/protein), we quantified 4069 unique proteins confidently (99.8% without any missing data), and 541 proteins were significantly altered in the three treatment groups, with an FDR of <1%. Interestingly, most of these proteins were altered only by combined birinapant/paclitaxel, and these predominantly represented three biological processes: mitochondrial function, cell growth and apoptosis, and cell cycle arrest. Proteins responsible for activation of oxidative phosphorylation, fatty acid β-oxidation, and inactivation of aerobic glycolysis were altered largely by combined birinapant/paclitaxel compared with single drugs, suggesting the Warburg effect, which is critical for survival and proliferation of cancer cells, was alleviated by the combination treatment. Metabolic profiling was performed to confirm substantially greater suppression of the Warburg effect by the combined agents compared with either drug alone. Immunoassays confirmed proteomic data revealing changes in apoptosis/survival signaling pathways, such as inhibition of PI3K/AKT, JAK/STAT, and MAPK/ERK signal transduction, as well as induction of G2/M arrest, and showed the drug combination induced much more apoptosis than did single agents. Overall, this in-depth, large-scale proteomics study provided novel insights into molecular mechanisms underlying synergy of combined birinapant/paclitaxel and describes a proteomics/informatics pipeline that can be applied broadly to the development of cancer drug combination regimens.
Collapse
Affiliation(s)
- Xue Wang
- From the ‡Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
| | - Jin Niu
- ¶Department of Pharmaceutical Sciences
| | - Jun Li
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
| | - Xiaomeng Shen
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
- ‖Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, New York 14214
| | - Shichen Shen
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
- ‖Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, New York 14214
| | - Robert M Straubinger
- From the ‡Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263;
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
- ¶Department of Pharmaceutical Sciences
| | - Jun Qu
- From the ‡Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263;
- §New York State Center of Excellence in Bioinformatics and Life Sciences, New York 14203
- ¶Department of Pharmaceutical Sciences
| |
Collapse
|
9
|
Cáceres TB, Thakur A, Price OM, Ippolito N, Li J, Qu J, Acevedo O, Hevel JM. Phe71 in Type III Trypanosomal Protein Arginine Methyltransferase 7 (TbPRMT7) Restricts the Enzyme to Monomethylation. Biochemistry 2018; 57:1349-1359. [PMID: 29378138 DOI: 10.1021/acs.biochem.7b01265] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make monomethylarginine (MMA). Given its role in epigenetics, the mechanistic basis for the strict monomethylation activity is under investigation. It is thought that PRMT7 enzymes are unable to add a second methyl group because of steric hindrance in the active site that restricts them to monomethylation. To test this, we probed the active site of trypanosomal PRMT7 (TbPRMT7) using accelerated molecular dynamics, site-directed mutagenesis, kinetic, binding, and product analyses. Both the dynamics simulations and experimental results show that the mutation of Phe71 to Ile converts the enzyme from a type III methyltransferase into a mixed type I/II, that is, an enzyme that can now perform dimethylation. In contrast, the serine and alanine mutants of Phe71 preserve the type III behavior of the native enzyme. These results are inconsistent with a sterics-only model to explain product specificity. Instead, molecular dynamics simulations of these variants bound to peptides show hydrogen bonding between would-be substrates and Glu172 of TbPRMT7. Only in the case of the Phe71 to Ile mutation is this interaction between MMA and the enzyme maintained, and the geometry for optimal SN2 methyl transfer is obtained. The results of these studies highlight the benefit of combined computational and experimental methods in providing a better understanding for how product specificity is dictated by PRMTs.
Collapse
Affiliation(s)
- Tamar B Cáceres
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Abhishek Thakur
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Owen M Price
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Nicole Ippolito
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| |
Collapse
|
10
|
Zhang M, An B, Qu Y, Shen S, Fu W, Chen YJ, Wang X, Young R, Canty JM, Balthasar JP, Murphy K, Bhattacharyya D, Josephs J, Ferrari L, Zhou S, Bansal S, Vazvaei F, Qu J. Sensitive, High-Throughput, and Robust Trapping-Micro-LC-MS Strategy for the Quantification of Biomarkers and Antibody Biotherapeutics. Anal Chem 2018; 90:1870-1880. [PMID: 29276835 PMCID: PMC5960441 DOI: 10.1021/acs.analchem.7b03949] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For LC-MS-based targeted quantification of biotherapeutics and biomarkers in clinical and pharmaceutical environments, high sensitivity, high throughput, and excellent robustness are all essential but remain challenging. For example, though nano-LC-MS has been employed to enhance analytical sensitivity, it falls short because of its low loading capacity, poor throughput, and low operational robustness. Furthermore, high chemical noise in protein bioanalysis typically limits the sensitivity. Here we describe a novel trapping-micro-LC-MS (T-μLC-MS) strategy for targeted protein bioanalysis, which achieves high sensitivity with exceptional robustness and high throughput. A rapid, high-capacity trapping of biological samples is followed by μLC-MS analysis; dynamic sample trapping and cleanup are performed using pH, column chemistry, and fluid mechanics separate from the μLC-MS analysis, enabling orthogonality, which contributes to the reduction of chemical noise and thus results in improved sensitivity. Typically, the selective-trapping and -delivery approach strategically removes >85% of the matrix peptides and detrimental components, markedly enhancing sensitivity, throughput, and operational robustness, and narrow-window-isolation selected-reaction monitoring further improves the signal-to-noise ratio. In addition, unique LC-hardware setups and flow approaches eliminate gradient shock and achieve effective peak compression, enabling highly sensitive analyses of plasma or tissue samples without band broadening. In this study, the quantification of 10 biotherapeutics and biomarkers in plasma and tissues was employed for method development. As observed, a significant sensitivity gain (up to 25-fold) compared with that of conventional LC-MS was achieved, although the average run time was only 8 min/sample. No appreciable peak deterioration or loss of sensitivity was observed after >1500 injections of tissue and plasma samples. The developed method enabled, for the first time, ultrasensitive LC-MS quantification of low levels of a monoclonal antibody and antigen in a tumor and cardiac troponin I in plasma after brief cardiac ischemia. This strategy is valuable when highly sensitive protein quantification in large sample sets is required, as is often the case in typical biomarker validation and pharmaceutical investigations of antibody therapeutics.
Collapse
Affiliation(s)
- Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Bo An
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Wei Fu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
- Department of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuan-Ju Chen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Rebeccah Young
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - John M Canty
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Keeley Murphy
- Thermo Scientific, San Jose, California 95134, United States
| | | | | | - Luca Ferrari
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Shaolian Zhou
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Surendra Bansal
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| |
Collapse
|
11
|
Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Orsburn B, Wang J, Qu J. An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts. J Proteome Res 2017; 16:2445-2456. [PMID: 28412812 PMCID: PMC5914162 DOI: 10.1021/acs.jproteome.7b00061] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In-depth and reproducible protein measurement in many biological samples is often critical for pharmaceutical/biomedical proteomics but remains challenging. MS1-based quantification using quadrupole/ultrahigh-field Orbitrap (Q/UHF-Orbitrap) holds great promise, but the critically important experimental approaches enabling reliable large-cohort analysis have long been overlooked. Here we described an IonStar experimental strategy achieving excellent quantitative quality of MS1 quantification. Key features include: (i) an optimized, surfactant-aided sample preparation approach provides highly efficient (>75% recovery) and reproducible (<15% CV) peptide recovery across large cell/tissue cohorts; (ii) a long column with modest gradient length (2.5 h) yields the optimal balance of depth/throughput on a Q/UHF-Orbitrap; (iii) a large-ID trap not only enables highly reproducible gradient delivery as for the first time observed via real-time conductivity monitoring, but also increases quantitative loading capacity by >8-fold and quantified >25% more proteins; (iv) an optimized HCD-OT markedly outperforms HCD-IT when analyzing large cohorts with high loading amounts; (v) selective removal of hydrophobic/hydrophilic matrix components using a novel selective trapping/delivery approach enables reproducible, robust LC-MS analysis of >100 biological samples in a single set, eliminating batch effect; (vi) MS1 acquired at higher resolution (fwhm = 120 k) provides enhanced S/N and quantitative accuracy/precision for low-abundance species. We examined this pipeline by analyzing a 5 group, 20 samples biological benchmark sample set, and quantified 6273 unique proteins (≥2 peptides/protein) under stringent cutoffs without fractionation, 6234 (>99.4%) without missing data in any of the 20 samples. The strategy achieved high quantitative accuracy (3-6% media error), low intragroup variation (6-9% media intragroup CV) and low false-positive biomarker discovery rates (3-8%) across the five groups, with quantified protein abundances spanning >6.5 orders of magnitude. Finally, this strategy is straightforward, robust, and broadly applicable in pharmaceutical/biomedical investigations.
Collapse
Affiliation(s)
- Xiaomeng Shen
- Department of Pharmaceutical Science, SUNY at Buffalo, Buffalo, New York 14228, United States
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- Department of Biochemistry, SUNY at Buffalo, Buffalo, New York 14228, United States
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
| | - Jun Li
- Department of Pharmaceutical Science, SUNY at Buffalo, Buffalo, New York 14228, United States
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
| | - Qiang Hu
- Roswell Park Cancer Institute, Buffalo, New York 14263, United States
| | - Lei Nie
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
- Shandong University, Shandong Sheng 250000, China
| | - Chengjian Tu
- Department of Pharmaceutical Science, SUNY at Buffalo, Buffalo, New York 14228, United States
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- Roswell Park Cancer Institute, Buffalo, New York 14263, United States
| | - Benjamin Orsburn
- ThermoFisher Scientific, Pittsburgh, Pennsylvania 15275, United States
| | - Jianmin Wang
- Roswell Park Cancer Institute, Buffalo, New York 14263, United States
| | - Jun Qu
- Department of Pharmaceutical Science, SUNY at Buffalo, Buffalo, New York 14228, United States
- Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York 14203, United States
| |
Collapse
|
12
|
Ahearn CP, Gallo MC, Murphy TF. Insights on persistent airway infection by non-typeable Haemophilus influenzae in chronic obstructive pulmonary disease. Pathog Dis 2017; 75:3753446. [PMID: 28449098 PMCID: PMC5437125 DOI: 10.1093/femspd/ftx042] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) is the most common bacterial cause of infection of the lower airways in adults with chronic obstructive pulmonary disease (COPD). Infection of the COPD airways causes acute exacerbations, resulting in substantial morbidity and mortality. NTHi has evolved multiple mechanisms to establish infection in the hostile environment of the COPD airways, allowing the pathogen to persist in the airways for months to years. Persistent infection of the COPD airways contributes to chronic airway inflammation that increases symptoms and accelerates the progressive loss of pulmonary function, which is a hallmark of the disease. Persistence mechanisms of NTHi include the expression of multiple redundant adhesins that mediate binding to host cellular and extracellular matrix components. NTHi evades host immune recognition and clearance by invading host epithelial cells, forming biofilms, altering gene expression and displaying surface antigenic variation. NTHi also binds host serum factors that confer serum resistance. Here we discuss the burden of COPD and the role of NTHi infections in the course of the disease. We provide an overview of NTHi mechanisms of persistence that allow the pathogen to establish a niche in the hostile COPD airways.
Collapse
Affiliation(s)
- Christian P. Ahearn
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
- Clinical and Translational Research Center, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Mary C. Gallo
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
- Clinical and Translational Research Center, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Timothy F. Murphy
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
- Clinical and Translational Research Center, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
- Division of Infectious Disease, Department of Medicine, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| |
Collapse
|
13
|
Tu C, Mojica W, Straubinger RM, Li J, Shen S, Qu M, Nie L, Roberts R, An B, Qu J. Quantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients. Proteomics Clin Appl 2017; 11:10.1002/prca.201600155. [PMID: 27943637 PMCID: PMC5418098 DOI: 10.1002/prca.201600155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/03/2016] [Accepted: 12/06/2016] [Indexed: 12/31/2022]
Abstract
PURPOSE The heterogeneous structure in tumor tissues from colorectal cancer (CRC) patients excludes an informative comparison between tumors and adjacent normal tissues. Here, we develop and apply a strategy to compare paired cancerous (CEC) versus normal (NEC) epithelial cells enriched from patients and discover potential biomarkers and therapeutic targets for CRC. EXPERIMENTAL DESIGN CEC and NEC cells are respectively isolated from five different tumor and normal locations in the resected colon tissue from each patient (N = 12 patients) using an optimized epithelial cell adhesion molecule (EpCAM)-based enrichment approach. An ion current-based quantitative method is employed to perform comparative proteomic analysis for each patient. RESULTS A total of 458 altered proteins that are common among >75% of patients are observed and selected for further investigation. Besides known findings such as deregulation of mitochondrial function, tricarboxylic acid cycle, and RNA post-transcriptional modification, functional analysis further revealed RAN signaling pathway, small nucleolar ribonucleoproteins (snoRNPs), and infection by RNA viruses are altered in CEC cells. A selection of the altered proteins of interest is validated by immunohistochemistry analyses. CONCLUSION AND CLINICAL RELEVANCE The informative comparison between matched CEC and NEC enhances our understanding of molecular mechanisms of CRC development and provides biomarker candidates and new pathways for therapeutic intervention.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Wilfrido Mojica
- Department of Pathology, State University of New York at Buffalo, State University of New York, Buffalo, NY 14260 USA
| | - Robert M. Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Miao Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- Beijing University of Chinese Medicine, Beijing, China, 100029
| | - Lei Nie
- School of pharmaceutical sciences, Shandong University, 44 Wenhua West Road, Jinan, China, 250012
| | - Rick Roberts
- Department of Structural Biology, State University of New York at Buffalo, State University of New York, Buffalo, NY 14260 USA
| | - Bo An
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| |
Collapse
|
14
|
Haemophilus influenzae: recent advances in the understanding of molecular pathogenesis and polymicrobial infections. Curr Opin Infect Dis 2015; 27:268-74. [PMID: 24699388 DOI: 10.1097/qco.0000000000000056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW Non-typeable Haemophilus influenzae (NTHi) is a human-specific mucosal pathogen and one of the most common causes of bacterial infections in children and patients with chronic obstructive pulmonary disease. It is also frequently found in polymicrobial superinfections. Great strides have recently been made in the understanding of the molecular mechanisms underlying NTHi pathogenesis. RECENT FINDINGS By using new methodology, such as experimental human colonization models and whole-genome approaches, investigators have shed light upon the various strategies of NTHi that are involved in pathogenesis. These include the escape of the mucociliary elevator, evasion of host immunity, survival in environments with scarce nutrients, and finally participation in polymicrobial infections. Lipooligosaccharide branching, proteinous adhesins, metabolic adaption to nutrient availability and many scavenging systems are implicated in these processes. Interestingly, genome-based studies comparing virulent and commensal strains have identified many hypothetical proteins as virulence determinants, suggesting that much regarding the molecular pathogenesis of NTHi remains to be solved. SUMMARY NTHi is an opportunistic pathogen and highly specialized colonizer of the human respiratory tract that has developed intricate mechanisms to establish growth and survival in the human host. Continued research is needed to further elucidate NTHi host-pathogen and pathogen-pathogen interactions.
Collapse
|
15
|
Post DMB, Held JM, Ketterer MR, Phillips NJ, Sahu A, Apicella MA, Gibson BW. Comparative analyses of proteins from Haemophilus influenzae biofilm and planktonic populations using metabolic labeling and mass spectrometry. BMC Microbiol 2014; 14:329. [PMID: 25551439 PMCID: PMC4302520 DOI: 10.1186/s12866-014-0329-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background Non-typeable H. influenzae (NTHi) is a nasopharyngeal commensal that can become an opportunistic pathogen causing infections such as otitis media, pneumonia, and bronchitis. NTHi is known to form biofilms. Resistance of bacterial biofilms to clearance by host defense mechanisms and antibiotic treatments is well-established. In the current study, we used stable isotope labeling by amino acids in cell culture (SILAC) to compare the proteomic profiles of NTHi biofilm and planktonic organisms. Duplicate continuous-flow growth chambers containing defined media with either “light” (L) isoleucine or “heavy” (H) 13C6-labeled isoleucine were used to grow planktonic (L) and biofilm (H) samples, respectively. Bacteria were removed from the chambers, mixed based on weight, and protein extracts were generated. Liquid chromatography-mass spectrometry (LC-MS) was performed on the tryptic peptides and 814 unique proteins were identified with 99% confidence. Results Comparisons of the NTHi biofilm to planktonic samples demonstrated that 127 proteins showed differential expression with p-values ≤0.05. Pathway analysis demonstrated that proteins involved in energy metabolism, protein synthesis, and purine, pyrimidine, nucleoside, and nucleotide processes showed a general trend of downregulation in the biofilm compared to planktonic organisms. Conversely, proteins involved in transcription, DNA metabolism, and fatty acid and phospholipid metabolism showed a general trend of upregulation under biofilm conditions. Selected reaction monitoring (SRM)-MS was used to validate a subset of these proteins; among these were aerobic respiration control protein ArcA, NAD nucleotidase and heme-binding protein A. Conclusions The present proteomic study indicates that the NTHi biofilm exists in a semi-dormant state with decreased energy metabolism and protein synthesis yet is still capable of managing oxidative stress and in acquiring necessary cofactors important for biofilm survival. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0329-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Deborah M B Post
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | - Jason M Held
- Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | | | - Nancy J Phillips
- The University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Alexandria Sahu
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | | | - Bradford W Gibson
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA. .,The University of California San Francisco, San Francisco, CA, 94143, USA.
| |
Collapse
|
16
|
Cholewa B, Pellitteri-Hahn MC, Scarlett CO, Ahmad N. Large-scale label-free comparative proteomics analysis of polo-like kinase 1 inhibition via the small-molecule inhibitor BI 6727 (Volasertib) in BRAF(V600E) mutant melanoma cells. J Proteome Res 2014; 13:5041-50. [PMID: 24884503 PMCID: PMC4227549 DOI: 10.1021/pr5002516] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/11/2022]
Abstract
Polo-like kinase 1 (Plk1) is a serine/threonine kinase that plays a key role during the cell cycle by regulating mitotic entry, progression, and exit. Plk1 is overexpressed in a variety of human cancers and is essential to sustained oncogenic proliferation, thus making Plk1 an attractive therapeutic target. However, the clinical efficacy of Plk1 inhibition has not emulated the preclinical success, stressing an urgent need for a better understanding of Plk1 signaling. This study addresses that need by utilizing a quantitative proteomics strategy to compare the proteome of BRAF(V600E) mutant melanoma cells following treatment with the Plk1-specific inhibitor BI 6727. Employing label-free nano-LC-MS/MS technology on a Q-exactive followed by SIEVE processing, we identified more than 20 proteins of interest, many of which have not been previously associated with Plk1 signaling. Here we report the down-regulation of multiple metabolic proteins with an associated decrease in cellular metabolism, as assessed by lactate and NAD levels. Furthermore, we have also identified the down-regulation of multiple proteasomal subunits, resulting in a significant decrease in 20S proteasome activity. Additionally, we have identified a novel association between Plk1 and p53 through heterogeneous ribonucleoprotein C1/C2 (hnRNPC), thus providing valuable insight into Plk1's role in cancer cell survival.
Collapse
Affiliation(s)
- Brian
D. Cholewa
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Molly C. Pellitteri-Hahn
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Cameron O. Scarlett
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Nihal Ahmad
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
- William
S. Middleton Memorial VA Hospital, 2500 Overlook Terrace, Madison, Wisconsin 53705, United States
| |
Collapse
|
17
|
Finney LJ, Ritchie A, Pollard E, Johnston SL, Mallia P. Lower airway colonization and inflammatory response in COPD: a focus on Haemophilus influenzae. Int J Chron Obstruct Pulmon Dis 2014; 9:1119-32. [PMID: 25342897 DOI: 10.2147/copd.s54477] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacterial infection of the lower respiratory tract in chronic obstructive pulmonary disease (COPD) patients is common both in stable patients and during acute exacerbations. The most frequent bacteria detected in COPD patients is Haemophilus influenzae, and it appears this organism is uniquely adapted to exploit immune deficiencies associated with COPD and to establish persistent infection in the lower respiratory tract. The presence of bacteria in the lower respiratory tract in stable COPD is termed colonization; however, there is increasing evidence that this is not an innocuous phenomenon but is associated with airway inflammation, increased symptoms, and increased risk for exacerbations. In this review, we discuss host immunity that offers protection against H. influenzae and how disturbance of these mechanisms, combined with pathogen mechanisms of immune evasion, promote persistence of H. influenzae in the lower airways in COPD. In addition, we examine the role of H. influenzae in COPD exacerbations, as well as interactions between H. influenzae and respiratory virus infections, and review the role of treatments and their effect on COPD outcomes. This review focuses predominantly on data derived from human studies but will refer to animal studies where they contribute to understanding the disease in humans.
Collapse
Affiliation(s)
- Lydia J Finney
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Andrew Ritchie
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | | | - Sebastian L Johnston
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Patrick Mallia
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| |
Collapse
|
18
|
Nouri-Nigjeh E, Sukumaran S, Tu C, Li J, Shen X, Duan X, DuBois DC, Almon RR, Jusko WJ, Qu J. Highly multiplexed and reproducible ion-current-based strategy for large-scale quantitative proteomics and the application to protein expression dynamics induced by methylprednisolone in 60 rats. Anal Chem 2014; 86:8149-57. [PMID: 25072516 PMCID: PMC4139173 DOI: 10.1021/ac501380s] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
A proteome-level time-series study
of drug effects (i.e., pharmacodynamics)
is critical for understanding mechanisms of action and systems pharmacology,
but is challenging, because of the requirement of a proteomics method
for reliable quantification of many biological samples. Here, we describe a highly reproducible strategy, enabling a global,
large-scale investigation of the expression dynamics of corticosteroid-regulated
proteins in livers from adrenalectomized rats over 11 time points
after drug dosing (0.5–66 h, N = 5/point).
The analytical advances include (i) exhaustive tissue extraction with
a Polytron/sonication procedure in a detergent cocktail buffer, and
a cleanup/digestion procedure providing very consistent protein yields
(relative standard deviation (RSD%) of 2.7%–6.4%) and peptide
recoveries (4.1–9.0%) across the 60 animals; (ii) an ultrahigh-pressure
nano-LC setup with substantially improved temperature stabilization,
pump-noise suppression, and programmed interface cleaning, enabling
excellent reproducibility for continuous analyses of numerous samples;
(iii) separation on a 100-cm-long column (2-μm particles) with
high reproducibility for days to enable both in-depth profiling and
accurate peptide ion-current match; and (iv) well-controlled ion-current-based
quantification. To obtain high-quality quantitative data necessary
to describe the 11 time-points protein expression temporal profiles,
strict criteria were used to define “quantifiable proteins”.
A total of 323 drug-responsive proteins were revealed with confidence,
and the time profiles of these proteins provided new insights into
the diverse temporal changes of biological cascades associated with
hepatic metabolism, response to hormone stimuli, gluconeogenesis,
inflammatory responses, and protein translation processes. Most profile
changes persisted well after the drug was eliminated. The developed
strategy can also be broadly applied in preclinical and clinical research,
where the analysis of numerous biological replicates is crucial.
Collapse
Affiliation(s)
- Eslam Nouri-Nigjeh
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Buffalo, New York 14214, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Shen X, Young R, Canty JM, Qu J. Quantitative proteomics in cardiovascular research: global and targeted strategies. Proteomics Clin Appl 2014; 8:488-505. [PMID: 24920501 DOI: 10.1002/prca.201400014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/02/2014] [Accepted: 06/06/2014] [Indexed: 11/05/2022]
Abstract
Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here, we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation.
Collapse
Affiliation(s)
- Xiaomeng Shen
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | | | | | | |
Collapse
|
20
|
Qu J, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models. J Proteome Res 2014; 13:2571-84. [PMID: 24697261 PMCID: PMC4015685 DOI: 10.1021/pr5000472] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Hibernating
myocardium is an adaptive response to repetitive myocardial
ischemia that is clinically common, but the mechanism of adaptation
is poorly understood. Here we compared the proteomes of hibernating
versus normal myocardium in a porcine model with 24 biological replicates.
Using the ion-current-based proteomic strategy optimized in this study
to expand upon previous proteomic work, we identified differentially
expressed proteins in new molecular pathways of cardiovascular interest.
The methodological strategy includes efficient extraction with detergent
cocktail; precipitation/digestion procedure with high, quantitative
peptide recovery; reproducible nano-LC/MS analysis on a long, heated
column packed with small particles; and quantification based on ion-current
peak areas. Under the optimized conditions, high efficiency and reproducibility
were achieved for each step, which enabled a reliable comparison of
24 the myocardial samples. To achieve confident discovery of differentially
regulated proteins in hibernating myocardium, we used highly stringent
criteria to define “quantifiable proteins”. These included
the filtering criteria of low peptide FDR and S/N > 10 for peptide
ion currents, and each protein was quantified independently from ≥2
distinct peptides. For a broad methodological validation, the quantitative
results were compared with a parallel, well-validated 2D-DIGE analysis
of the same model. Excellent agreement between the two orthogonal
methods was observed (R = 0.74), and the ion-current-based
method quantified almost one order of magnitude more proteins. In
hibernating myocardium, 225 significantly altered proteins were discovered
with a low false-discovery rate (∼3%). These proteins are involved
in biological processes including metabolism, apoptosis, stress response,
contraction, cytoskeleton, transcription, and translation. This provides
compelling evidence that hibernating myocardium adapts to chronic
ischemia. The major metabolic mechanisms include a down-regulation
of mitochondrial respiration and an increase in glycolysis. Meanwhile,
cardioprotective and cytoskeletal proteins are increased, while cardiomyocyte
contractile proteins are reduced. These intrinsic adaptations to regional
ischemia maintain long-term cardiomyocyte viability at the expense
of contractile function.
Collapse
Affiliation(s)
- Jun Qu
- Department of Pharmaceutical Sciences, ‡Department of Biochemistry, §Department of Medicine, ∥Department of Physiology and Biophysics, ⊥The Center for Research in Cardiovascular Medicine, and #Center for Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo , Buffalo, New York 14214, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Nørskov-Lauritsen N. Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev 2014; 27:214-40. [PMID: 24696434 PMCID: PMC3993099 DOI: 10.1128/cmr.00103-13] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.
Collapse
|
22
|
Tu C, Mammen MJ, Li J, Shen X, Jiang X, Hu Q, Wang J, Sethi S, Qu J. Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients. J Proteome Res 2013; 13:627-639. [PMID: 24188068 DOI: 10.1021/pr4007602] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteomic analysis of bronchoalveolar lavage fluid (BALF) in chronic obstructive pulmonary disease (COPD) patients may provide new biomarkers and deeper understanding of the disease mechanisms but remains challenging. Here we describe an ion-current-based strategy for comparative analysis of BALF proteomes from patients with moderate and stable COPD versus healthy controls. The strategy includes an efficient preparation procedure providing quantitative recovery and a nano-LC/MS analysis with a long, heated column. Under optimized conditions, high efficiency and reproducibility were achieved for each step, enabling a "20-plex" comparison of clinical subjects (n = 10/group). Without depletion/fractionation, a total of 423 unique protein groups were quantified under stringent criteria with at least two quantifiable peptides. Seventy-six proteins were determined as significantly altered in COPD, which represent a diversity of biological processes such as alcohol metabolic process, gluconeogenesis/glycolysis, inflammatory response, proteolysis, and oxidation reduction. Interestingly, altered alcohol metabolism responding to oxidant stress is a novel observation in COPD. The prominently elevated key enzymes involved in alcohol metabolism (e.g., ADH1B, ALDH2, and ALDH3A1) may provide a reasonable explanation for a bewildering observation in COPD patients known for decades: the underestimation of the blood alcohol concentrations through breath tests. These discoveries could provide new insights for identifying novel biomarkers and pathological mediators in clinical studies.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | | | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Xiaomeng Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Xiaosheng Jiang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY14203
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY14203
| | - Sanjay Sethi
- University at Buffalo, SUNY.,WNY VA Healthcare System, NY 14203 USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| |
Collapse
|
23
|
Tu C, Li J, Jiang X, Sheflin LG, Pfeffer BA, Behringer M, Fliesler SJ, Qu J. Ion-current-based proteomic profiling of the retina in a rat model of Smith-Lemli-Opitz syndrome. Mol Cell Proteomics 2013; 12:3583-98. [PMID: 23979708 PMCID: PMC3861709 DOI: 10.1074/mcp.m113.027847] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 08/21/2013] [Indexed: 12/26/2022] Open
Abstract
Smith-Lemli-Opitz syndrome (SLOS) is one of the most common recessive human disorders and is characterized by multiple congenital malformations as well as neurosensory and cognitive abnormalities. A rat model of SLOS has been developed that exhibits progressive retinal degeneration and visual dysfunction; however, the molecular events underlying the degeneration and dysfunction remain poorly understood. Here, we employed a well-controlled, ion-current-based approach to compare retinas from the SLOS rat model to retinas from age- and sex-matched control rats (n = 5/group). Retinas were subjected to detergent extraction and subsequent precipitation and on-pellet-digestion procedures and then were analyzed on a long, heated column (75 cm, with small particles) with a 7-h gradient. The high analytical reproducibility of the overall proteomics procedure enabled reliable expression profiling. In total, 1,259 unique protein groups, ~40% of which were membrane proteins, were quantified under highly stringent criteria, including a peptide false discovery rate of 0.4%, with high quality ion-current data (e.g. signal-to-noise ratio ≥ 10) obtained independently from at least two unique peptides for each protein. The ion-current-based strategy showed greater quantitative accuracy and reproducibility over a parallel spectral counting analysis. Statistically significant alterations of 101 proteins were observed; these proteins are implicated in a variety of biological processes, including lipid metabolism, oxidative stress, cell death, proteolysis, visual transduction, and vesicular/membrane transport, consistent with the features of the associated retinal degeneration in the SLOS model. Selected targets were further validated by Western blot analysis and correlative immunohistochemistry. Importantly, although photoreceptor cell death was validated by TUNEL analysis, Western blot and immunohistochemical analyses suggested a caspase-3-independent pathway. In total, these results provide compelling new evidence implicating molecular changes beyond the initial defect in cholesterol biosynthesis in this retinal degeneration model, and they might have broader implications with respect to the pathobiological mechanism underlying SLOS.
Collapse
Affiliation(s)
- Chengjian Tu
- From the ‡Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- §New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203
| | - Jun Li
- From the ‡Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- §New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203
| | - Xiaosheng Jiang
- From the ‡Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- §New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203
| | - Lowell G. Sheflin
- ¶Research Service, Veterans Administration Western New York Healthcare System, Buffalo, New York 14215
| | - Bruce A. Pfeffer
- ‖Departments of Ophthalmology and Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- **SUNY Eye Institute, Buffalo, New York 14215
| | - Matthew Behringer
- ‖Departments of Ophthalmology and Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
| | - Steven J. Fliesler
- ¶Research Service, Veterans Administration Western New York Healthcare System, Buffalo, New York 14215
- ‖Departments of Ophthalmology and Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- **SUNY Eye Institute, Buffalo, New York 14215
| | - Jun Qu
- From the ‡Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
- §New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203
| |
Collapse
|
24
|
O'Connell K, Li J, Engler F, Hennessy K, O'Neill F, Straubinger RM, Qu J, O'Connor R. Determination of the Proteomic Response to Lapatinib Treatment using a comprehensive and reproducible ion-current-based proteomics strategy. ACTA ACUST UNITED AC 2013; 1:27-42. [PMID: 29046878 DOI: 10.14302/issn.2326-0793.jpgr-13-257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lapatinib, a small molecule tyrosine kinase inhibitor is currently used in the treatment of HER2-positive breast cancer. The aim of this study was to further understanding of lapatinib response for the development of novel treatment lapatinib-focussed treatment strategies. HER2-overexpressing SKBR3 breast cancer cells were treated with lapatinib for 12 hours and the resultant proteome analyzed by a comprehensive ion-current-based LC-MS strategy. Among the 1224 unique protein identified from SKBR3 cell lysates, 67 showed a significant change in protein abundance in response to lapatinib. Of these, CENPE a centromeric protein with increased abundance, was chosen for further validation. Knockdown and inhibition of CENPE demonstrated that CENPE enhances SKBR3 cell survival in the presence of lapatinib. Based on this study, CENPE inhibitors may warrant further investigation for use in combination with lapatinib.
Collapse
Affiliation(s)
- Kathleen O'Connell
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY
| | - Frank Engler
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY
| | - Kim Hennessy
- National Institute for Cellular Biotechnology, DCU, Glasnevin, Dublin 9
| | - Fiona O'Neill
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, DCU, Glasnevin, Dublin 9
| | | | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY
| | - Robert O'Connor
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, DCU, Glasnevin, Dublin 9.,School of Nursing and Human Sciences, DCU, Glasnevin, Dublin 9
| |
Collapse
|
25
|
Su YC, Jalalvand F, Mörgelin M, Blom AM, Singh B, Riesbeck K. Haemophilus influenzae acquires vitronectin via the ubiquitous Protein F to subvert host innate immunity. Mol Microbiol 2013; 87:1245-66. [PMID: 23387957 DOI: 10.1111/mmi.12164] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2013] [Indexed: 02/06/2023]
Abstract
Acquisition of the complement inhibitor vitronectin (Vn) is important for the respiratory tract pathogen nontypeable Haemophilus influenzae (NTHi) to escape complement-mediated killing. NTHi actively recruits Vn, and we previously showed that this interaction involves Protein E (PE). Here we describe a second Vn-binding protein, a 30 kDa Yersinia YfeA homologue designated as Protein F (PF). An isogenic NTHi 3655Δhpf mutant devoid of PF displayed a reduced binding of Vn, and was consequently more sensitive to killing by human serum compared with the wild type. Surface expression of PF on Escherichia coli conferred binding of Vn that resulted in a serum resistant phenotype. Molecular analyses revealed that the N-terminal of PF (Lys23-Glu48) bound to the C-terminal of Vn (Phe352-Ser374) without disrupting the inhibitory role of Vn on the membrane attack complex. The PF-Vn complex actively delayed C9 deposition on PF-expressing bacteria. Comparative studies of binding affinity and multiple mutants demonstrated that both PE and PF contribute individually to NTHi serum survival. PF was highly conserved and ubiquitously expressed in a series of randomly selected NTHi clinical isolates (n = 18). In conclusion, the multifaceted binding of Vn is beneficial for NTHi survival in serum and may contribute to successful colonization and consequently infection.
Collapse
Affiliation(s)
- Yu-Ching Su
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Skåne University Hospital, SE-205 02, Malmö, Sweden
| | | | | | | | | | | |
Collapse
|
26
|
Pereira-Medrano AG, Knighton M, Fowler GJ, Ler ZY, Pham TK, Ow SY, Free A, Ward B, Wright PC. Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode. J Proteomics 2013; 78:197-210. [DOI: 10.1016/j.jprot.2012.09.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/02/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
|
27
|
Jalalvand F, Su YC, Mörgelin M, Brant M, Hallgren O, Westergren-Thorsson G, Singh B, Riesbeck K. Haemophilus influenzae protein F mediates binding to laminin and human pulmonary epithelial cells. J Infect Dis 2012; 207:803-13. [PMID: 23230060 DOI: 10.1093/infdis/jis754] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mucosal pathogen nontypeable Haemophilus influenzae (NTHi) adheres to the respiratory epithelium or, in the case of epithelial damage, to the underlying basement membrane and extracellular matrix that, among other proteins, consists of laminin. We have recently identified protein F, an ABC transporter involved in NTHi immune evasion. Homology modeling of the protein F tertiary structure revealed a strong resemblance to the streptococcal laminin-binding proteins Lbp and Lmb. Here, we show that protein F promotes binding of NTHi to laminin and primary bronchial epithelial cells. Analyses with recombinant proteins and synthetic peptides revealed that the N-terminal part of protein F contains the host-interacting region. Moreover, protein F exists in all clinical isolates, and isogenic NTHi Δhpf mutants display significantly reduced binding to laminin and epithelial cells. We thus suggest protein F to be an important and ubiquitous NTHi adhesin.
Collapse
Affiliation(s)
- Farshid Jalalvand
- Medical Microbiology, Department of Laboratory Medicine Malmö, Skåne University Hospital, Malmö, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Haemophilus influenzae OxyR: characterization of its regulation, regulon and role in fitness. PLoS One 2012; 7:e50588. [PMID: 23226321 PMCID: PMC3511568 DOI: 10.1371/journal.pone.0050588] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/23/2012] [Indexed: 12/27/2022] Open
Abstract
To prevent damage by reactive oxygen species, many bacteria have evolved rapid detection and response systems, including the OxyR regulon. The OxyR system detects reactive oxygen and coordinates the expression of numerous defensive antioxidants. In many bacterial species the coordinated OxyR-regulated response is crucial for in vivo survival. Regulation of the OxyR regulon of Haemophilus influenzae was examined in vitro, and significant variation in the regulated genes of the OxyR regulon among strains of H. influenzae was observed. Quantitative PCR studies demonstrated a role for the OxyR-regulated peroxiredoxin/glutaredoxin as a mediator of the OxyR response, and also indicated OxyR self-regulation through a negative feedback loop. Analysis of transcript levels in H. influenzae samples derived from an animal model of otitis media demonstrated that the members of the OxyR regulon were actively upregulated within the chinchilla middle ear. H. influenzae mutants lacking the oxyR gene exhibited increased sensitivity to challenge with various peroxides. The impact of mutations in oxyR was assessed in various animal models of H. influenzae disease. In paired comparisons with the corresponding wild-type strains, the oxyR mutants were unaffected in both the chinchilla model of otitis media and an infant model of bacteremia. However, in weanling rats the oxyR mutant was significantly impaired compared to the wild-type strain. In contrast, in all three animal models when infected with a mixture of equal numbers of both wild-type and mutant strains the mutant strain was significantly out competed by the wild-type strain. These findings clearly establish a crucial role for OxyR in bacterial fitness.
Collapse
|
29
|
Tu C, Li J, Bu Y, Hangauer D, Qu J. An ion-current-based, comprehensive and reproducible proteomic strategy for comparative characterization of the cellular responses to novel anti-cancer agents in a prostate cell model. J Proteomics 2012; 77:187-201. [PMID: 22982362 DOI: 10.1016/j.jprot.2012.08.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/18/2012] [Accepted: 08/31/2012] [Indexed: 11/18/2022]
Abstract
Proteome-level investigation of the molecular targets in anticancer action of promising pharmaceutical candidates is highly desirable but remains challenging due to the insufficient proteome coverage, limited capacity for biological replicates, and largely unregulated false positive biomarker discovery of current methods. This study described a practical platform strategy to address these challenges, using comparison of drug response proteomic signatures by two promising anti-cancer agents (KX01/KX02) as the model system for method development/optimization. Drug-treated samples were efficiently extracted followed by precipitation/on-pellet-digestion procedure that provides high, reproducible peptide recovery. High-resolution separations were performed on a 75-cm-long, heated nano-LC column with a 7-h gradient, with a highly reproducible nano-LC/nanospray configuration. An LTQ Orbitrap hybrid mass spectrometer with a charge overfilling approach to enhance sensitivity was used for detection. Analytical procedures were optimized and well-controlled to achieve high run-to-run reproducibility that permits numerous replicates in one set, and an ion-current-based approach was utilized for quantification. The false positives of biomarker discovery arising from technical variability was controlled based on FBDR measurement by comparing biomarker numbers in each drug-treated group vs. "sham samples", which were analyzed in an order randomly interleaved with the analysis drug-treated samples. More than 1500 unique protein groups were quantified under stringent criteria, and of which about 30% displayed differential expression with FBDR of 0.3-2.1% across groups. Comparison of drug-response proteomic signatures and the subsequent immunoassay revealed that the action mechanisms of KX01/KX02 are similar but significantly different from vinblastine, which correlates well with clinical and pre-clinical observations. Furthermore, the results strongly supported the hypothesis that KX01/KX02 are dual-action agents (through inhibition of tubulin and Src). Moreover, informative insights into the drug-actions on cell cycle, growth/proliferation, and apoptosis were obtained. This platform technology provides extensive evaluation of drug candidates and facilitates in-depth mechanism studies.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Yahao Bu
- Kinex Pharmaceuticals LLC, New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - David Hangauer
- Kinex Pharmaceuticals LLC, New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| |
Collapse
|
30
|
Zhang L, Xie J, Patel M, Bakhtyar A, Ehrlich GD, Ahmed A, Earl J, Marrs CF, Clemans D, Murphy TF, Gilsdorf JR. Nontypeable Haemophilus influenzae genetic islands associated with chronic pulmonary infection. PLoS One 2012; 7:e44730. [PMID: 22970300 PMCID: PMC3435294 DOI: 10.1371/journal.pone.0044730] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae (Hi) colonizes the human respiratory tract and is an important pathogen associated with chronic obstructive pulmonary disease (COPD). Bacterial factors that interact with the human host may be important in the pathogenesis of COPD. These factors, however, have not been well defined. The overall goal of this study was to identify bacterial genetic elements with increased prevalence among H. influenzae strains isolated from patients with COPD compared to those isolated from the pharynges of healthy individuals. Methodology/Principal Findings Four nontypeable H. influenzae (NTHi) strains, two isolated from the airways of patients with COPD and two from a healthy individual, were subjected to whole genome sequencing using 454 FLX Titanium technology. COPD strain-specific genetic islands greater than 500 bp in size were identified by in silico subtraction. Open reading frames residing within these islands include known Hi virulence genes such as lic2b, hgbA, iga, hmw1 and hmw2, as well as genes encoding urease and other enzymes involving metabolic pathways. The distributions of seven selected genetic islands were assessed among a panel of 421 NTHi strains of both disease and commensal origins using a Library-on-a-Slide high throughput dot blot DNA hybridization procedure. Four of the seven islands screened, containing genes that encode a methyltransferase, a dehydrogenase, a urease synthesis enzyme, and a set of unknown short ORFs, respectively, were more prevalent in COPD strains than in colonizing strains with prevalence ratios ranging from 1.21 to 2.85 (p≤0.0002). Surprisingly, none of these sequences show increased prevalence among NTHi isolated from the airways of patients with cystic fibrosis. Conclusions/Significance Our data suggest that specific bacterial genes, many involved in metabolic functions, are associated with the ability of NTHi strains to survive in the lower airways of patients with COPD.
Collapse
Affiliation(s)
- Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Wong SMS, Akerley BJ. Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis. Front Cell Infect Microbiol 2012; 2:23. [PMID: 22919615 PMCID: PMC3417392 DOI: 10.3389/fcimb.2012.00023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/15/2012] [Indexed: 12/28/2022] Open
Abstract
Haemophilus influenzae is a Gram-negative bacterium that has no identified natural niche outside of the human host. It primarily colonizes the nasopharyngeal mucosa in an asymptomatic mode, but has the ability to disseminate to other anatomical sites to cause otitis media, upper, and lower respiratory tract infections, septicemia, and meningitis. To persist in diverse environments the bacterium must exploit and utilize the nutrients and other resources available in these sites for optimal growth/survival. Recent evidence suggests that regulatory factors that direct such adaptations also control virulence determinants required to resist and evade immune clearance mechanisms. In this review, we describe the recent application of whole-genome approaches that together provide insight into distinct survival mechanisms of H. influenzae in the context of different sites of pathogenesis.
Collapse
Affiliation(s)
- Sandy M S Wong
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School Worcester, MA, USA
| | | |
Collapse
|
32
|
Krishnatry AS, Kamei T, Wang H, Qu J, Fung HL. Identification of nitroglycerin-induced cysteine modifications of pro-matrix metalloproteinase-9. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2291-2298. [PMID: 21766372 DOI: 10.1002/rcm.5118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nitroglycerin (NTG), an important cardiovascular agent, has been shown recently to activate matrix metalloproteinase-9 (MMP-9) in biological systems, possibly leading to destabilization of atherosclerotic plaques. The chemical mechanism for this activation, particularly on the cysteine switch of the pro-form of MMP-9 (proMMP-9), has not been investigated and was examined here using nano-flow liquid chromatography coupled to mass spectrometry. In order to obtain high sequence coverage, two orthogonal enzymes (trypsin and GluC) were employed to digest the protein in parallel. Two complementary activation methods, collision-induced dissociation (CID) and electron-transfer dissociation (ETD), were employed for the identification of various modifications. A high-resolution Orbitrap analyzer was used to enable confident identification. Incubation of NTG with proMMP-9 resulted in the formation of an unstable thionitrate intermediate and oxidation of the cysteine switch to sulfinic and irreversible sulfonic acid derivatives. The unstable thionitrate modification was confirmed by both CID and ETD in the proteolytic peptides produced by both trypsin and GluC. Incubation of proMMP-9 with diethylenetriamine NONOate (a nitric oxide donor) led to sulfonic acid formation, but no observable sulfinic acid modification. Extensive tyrosine nitration by NTG was observed at Tyr-262, in close proximity to an oxidized Cys-256 of proMMP-9. The intramolecular interaction between these two residues toward NTG-induced oxidation was examined using a synthesized peptide representing the sequence in this domain, PWCSTTANYDTDDR, and the modification status was compared against an analog in which Cys was substituted by Ala. We observed a thionitrate product, extensive Cys oxidative modifications and enhanced tyrosine nitration with the Cys peptide but not with the Ala analog. Our results indicated that neighboring Cys and Tyr residues can facilitate each other's oxidation in the presence of NTG.
Collapse
Affiliation(s)
- Anu Shilpa Krishnatry
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | | | | | | | | |
Collapse
|
33
|
Murphy TF, Brauer AL. Expression of urease by Haemophilus influenzae during human respiratory tract infection and role in survival in an acid environment. BMC Microbiol 2011; 11:183. [PMID: 21843372 PMCID: PMC3166929 DOI: 10.1186/1471-2180-11-183] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 08/16/2011] [Indexed: 12/21/2022] Open
Abstract
Background Nontypeable Haemophilus influenzae is a common cause of otitis media in children and lower respiratory tract infection in adults with chronic obstructive pulmonary disease (COPD). Prior studies have shown that H. influenzae expresses abundant urease during growth in the middle ear of the chinchilla and in pooled human sputum, suggesting that expression of urease is important for colonization and infection in the hostile environments of the middle ear and in the airways in adults. Virtually nothing else is known about the urease of H. influenzae, which was characterized in the present study. Results Analysis by reverse transcriptase PCR revealed that the ure gene cluster is expressed as a single transcript. Knockout mutants of a urease structural gene (ureC) and of the entire ure operon demonstrated no detectable urease activity indicating that this operon is the only one encoding an active urease. The ure operon is present in all strains tested, including clinical isolates from otitis media and COPD. Urease activity decreased as nitrogen availability increased. To test the hypothesis that urease is expressed during human infection, purified recombinant urease C was used in ELISA with pre acquisition and post infection serum from adults with COPD who experienced infections caused by H. influenzae. A total of 28% of patients developed new antibodies following infection indicating that H. influenzae expresses urease during airway infection. Bacterial viability assays performed at varying pH indicate that urease mediates survival of H. influenzae in an acid environment. Conclusions The H. influenzae genome contains a single urease operon that mediates urease expression and that is present in all clinical isolates tested. Nitrogen availability is a determinant of urease expression. H. influenzae expresses urease during human respiratory tract infection and urease is a target of the human antibody response. Expression of urease enhances viability in an acid environment. Taken together, these observations suggest that urease is important for survival and replication of H. influenzae in the human respiratory tract.
Collapse
Affiliation(s)
- Timothy F Murphy
- Division of Infectious Diseases, Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY 14203, USA.
| | | |
Collapse
|
34
|
Tu C, Li J, Young R, Page BJ, Engler F, Halfon MS, Canty JM, Qu J. Combinatorial peptide ligand library treatment followed by a dual-enzyme, dual-activation approach on a nanoflow liquid chromatography/orbitrap/electron transfer dissociation system for comprehensive analysis of swine plasma proteome. Anal Chem 2011; 83:4802-13. [PMID: 21491903 DOI: 10.1021/ac200376m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plasma proteome holds enormous clinical potential, yet an in-depth analysis of the plasma proteome remains a daunting challenge due to its high complexity and the extremely wide dynamic range in protein concentrations. Furthermore, existing antibody-based approaches for depleting high-abundance proteins are not adaptable to the analysis of the animal plasma proteome, which is often essential for experimental pathology/pharmacology. Here we describe a highly comprehensive method for the investigation of the animal plasma proteome which employs an optimized combinatorial peptide ligand library (CPLL) treatment to reduce the protein concentration dynamic range and a dual-enzyme, dual-activation strategy to achieve high proteomic coverage. The CPLL treatment enriched the lower abundance proteins by >100-fold when the samples were loaded in moderately denaturing conditions with multiple loading-washing cycles. The native and the CPLL-treated plasma were digested in parallel by two enzymes (trypsin and GluC) carrying orthogonal specificities. By performing this differential proteolysis, the proteome coverage is improved where peptides produced by only one enzyme are poorly detectable. Digests were fractionated with high-resolution strong cation exchange chromatography and then resolved on a long, heated nano liquid chromatography column. MS analysis was performed on a linear triple quadrupole/orbitrap with two complementary activation methods (collisionally induced dissociation (CID) and electron transfer dissociation). We applied this optimized strategy to investigate the plasma proteome from swine, a prominent animal model for cardiovascular diseases (CVDs). This large-scale analysis results in identification of a total of 3421 unique proteins, spanning a concentration range of 9-10 orders of magnitude. The proteins were identified under a set of commonly accepted criteria, including a precursor mass error of <15 ppm, Xcorr cutoffs, and ≥2 unique peptides at a peptide probability of ≥95% and a protein probability of ≥99%, and the peptide false-positive rate of the data set was 1.8% as estimated by searching the reversed database. CPLL treatment resulted in 55% more identified proteins over those from native plasma; moreover, compared with using only trypsin and CID, the dual-enzyme/activation approach enabled the identification of 2.6-fold more proteins and substantially higher sequence coverage for most individual proteins. Further analysis revealed 657 proteins as significantly associated with CVDs (p < 0.05), which constitute five CVD-related pathways. This study represents the first in-depth investigation of a nonhuman plasma proteome, and the strategy developed here is adaptable to the comprehensive analysis of other highly complex proteomes.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | | | | | | | | | | | | | | |
Collapse
|