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He J, Cao Y, Zhu Q, Wang X, Cheng G, Wang Q, He R, Lu H, Weng Y, Mao G, Bao Y, Wang J, Liu X, Han F, Shi P, Shen XZ. Renal macrophages monitor and remove particles from urine to prevent tubule obstruction. Immunity 2024; 57:106-123.e7. [PMID: 38159573 DOI: 10.1016/j.immuni.2023.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 07/17/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
When the filtrate of the glomerulus flows through the renal tubular system, various microscopic sediment particles, including mineral crystals, are generated. Dislodging these particles is critical to ensuring the free flow of filtrate, whereas failure to remove them will result in kidney stone formation and obstruction. However, the underlying mechanism for the clearance is unclear. Here, using high-resolution microscopy, we found that the juxtatubular macrophages in the renal medulla constitutively formed transepithelial protrusions and "sampled" urine contents. They efficiently sequestered and phagocytosed intraluminal sediment particles and occasionally transmigrated to the tubule lumen to escort the excretion of urine particles. Mice with decreased renal macrophage numbers were prone to developing various intratubular sediments, including kidney stones. Mechanistically, the transepithelial behaviors of medulla macrophages required integrin β1-mediated ligation to the tubular epithelium. These findings indicate that medulla macrophages sample urine content and remove intratubular particles to keep the tubular system unobstructed.
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Affiliation(s)
- Jian He
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yangyang Cao
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian Zhu
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinge Wang
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guo Cheng
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiang Wang
- Department of Laboratory Medicine, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rukun He
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haoran Lu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, Zhejiang, China
| | - Yuancheng Weng
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Genxiang Mao
- Zhejiang Provincial Key Lab of Geriatrics, Department of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yizhong Bao
- Zhejiang Provincial Key Lab of Geriatrics, Department of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jing Wang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoli Liu
- Department of Neurology, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Han
- Kidney Disease Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Peng Shi
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Xiao Z Shen
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Jang H, Choudhury S, Yu Y, Sievers BL, Gelbart T, Singh H, Rawlings SA, Proal A, Tan GS, Qian Y, Smith D, Freire M. Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19. Heliyon 2023; 9:e17958. [PMID: 37483779 PMCID: PMC10362241 DOI: 10.1016/j.heliyon.2023.e17958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
A growing number of studies indicate that coronavirus disease 2019 (COVID-19) is associated with inflammatory sequelae, but molecular signatures governing the normal versus pathologic convalescence process have not been well-delineated. Here, we characterized global immune and proteome responses in matched plasma and saliva samples obtained from COVID-19 patients collected between 20 and 90 days after initial clinical symptoms resolved. Convalescent subjects showed robust total IgA and IgG responses and positive antibody correlations in saliva and plasma samples. Shotgun proteomics revealed persistent inflammatory patterns in convalescent samples including dysfunction of salivary innate immune cells, such as neutrophil markers (e.g., myeloperoxidase), and clotting factors in plasma (e.g., fibrinogen), with positive correlations to acute COVID-19 disease severity. Saliva samples were characterized by higher concentrations of IgA, and proteomics showed altered myeloid-derived pathways that correlated positively with SARS-CoV-2 IgA levels. Beyond plasma, our study positions saliva as a viable fluid to monitor normal and aberrant immune responses including vascular, inflammatory, and coagulation-related sequelae.
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Affiliation(s)
- Hyesun Jang
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
| | | | - Yanbao Yu
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE, USA, 19716
| | - Benjamin L Sievers
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
| | - Terri Gelbart
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
| | - Harinder Singh
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
| | - Stephen A Rawlings
- MMP Adult Infectious Disease, Maine Medical Center, South Portland, ME, 04106, USA
| | - Amy Proal
- PolyBio Research Foundation. Mercer Island, WA, USA
| | - Gene S Tan
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
- Division of Infectious Diseases and Global Public Health Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yu Qian
- Informatics, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marcelo Freire
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA
- Division of Infectious Diseases and Global Public Health Department of Medicine, University of California San Diego, La Jolla, CA, USA
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3
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Pan X, Liu Y, Bao Y, Wei L, Gao Y. Changes in the urinary proteome before and after quadrivalent influenza vaccine and COVID-19 vaccination. Front Immunol 2022; 13:946791. [PMID: 36275736 PMCID: PMC9585259 DOI: 10.3389/fimmu.2022.946791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
The proteome of urine samples from quadrivalent influenza vaccine cohort were analyzed with self-contrasted method. Significantly changed urine protein at 24 hours after vaccination was enriched in immune-related pathways, although each person’s specific pathways varied. We speculate that this may be because different people have different immunological backgrounds associated with influenza. Then, urine samples were collected from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. The differential proteins compared between after the second dose (24h) and before the second dose were enriched in pathways involving in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating no first exposure to antigen. Surprisingly, the pathways enriched by the differential urinary protein before and after the first dose were similar to those before and after the second dose. It is inferred that although the volunteers were not infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. Two to four hours after the third vaccination, the differentially expressed protein were also enriched in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating that the immune response has been triggered in a short time after vaccination. Multicellular organismal process and regulated exocytosis after vaccination may be a new indicator to evaluate the immune effect of vaccines. Urinary proteome is a terrific window to monitor the changes in human immune function.
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Affiliation(s)
- Xuanzhen Pan
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yongtao Liu
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yijin Bao
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lilong Wei
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Youhe Gao
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
- *Correspondence: Youhe Gao,
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Liu Y, Pan X, Bao Y, Wei L, Gao Y. Many kinds of oxidized proteins are present more in the urine of the elderly. Clin Proteomics 2022; 19:22. [PMID: 35733114 PMCID: PMC9214981 DOI: 10.1186/s12014-022-09360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Many studies have shown an association between aging and oxidation. To our knowledge, there have been no studies exploring aging-related urine proteome modifications. The purpose of this study was to explore differences in global chemical modifications of urinary protein at different ages. Methods Discovery (n=38) cohort MS data including children, young and old groups were downloaded from three published studies, and this data was analyzed using open-pFind for identifying modifications. Verification cohort human samples (n=28) including young, middle-aged, and old groups, rat samples (n=7) at three-time points after birth, adulthood, and old age were collected and processed in the laboratory simultaneously based on label-free quantification combined with pFind. Results Discovery cohort: there were 28 kinds of differential oxidations in the old group that were higher than those in the young or children group in. Verification cohort: there were 17 kinds of differential oxidations of 49 oxidized proteins in the middle and old groups, which were significantly higher than those in the young group. Both oxidations and oxidized proteins distinguished different age groups well. There were also 15 kinds of differential oxidations in old age higher than others in the rat cohort. The results showed that the validation experiment was basically consistent with the results of the discovery experiment, showing that the level of oxidized proteins in urine increased significantly with age. Conclusions Our study is the first to show that oxidative proteins occur in urine and that oxidations are higher in older than younger ages. Perhaps improving the degree of excretion of oxidative protein in vivo through the kidney is helpful for maintaining the homeostasis of the body’s internal environment, delaying aging and the occurrence of senile diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09360-2.
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Affiliation(s)
- Yongtao Liu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Xuanzhen Pan
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Yijin Bao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Lilong Wei
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China.
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5
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He Y, Wang X, Lu W, Zhang D, Huang L, Luo Y, Xiong L, Li H, Zhang P, Li Q, Liang S. PGK1 contributes to tumorigenesis and sorafenib resistance of renal clear cell carcinoma via activating CXCR4/ERK signaling pathway and accelerating glycolysis. Cell Death Dis 2022; 13:118. [PMID: 35121728 PMCID: PMC8816910 DOI: 10.1038/s41419-022-04576-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/05/2022] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
Abstract
Phosphoglycerate kinase 1 (PGK1) has complicated and multiple functions in cancer occurrence, tumor progression and drug resistance. Sorafenib is the first-line treatment targeted drug for patients with kidney renal clear cell carcinoma (KIRC) as a tyrosine kinase inhibitor, but sorafenib resistance is extremely common to retard therapy efficiency. So far, it is unclear whether and how PGK1 is involved in the pathogenesis and sorafenib resistance of KIRC. Herein, the molecular mechanisms of PGK1-mediated KIRC progression and sorafenib resistance have been explored by comprehensively integrative studies using biochemical approaches, mass spectrometry (MS) identification, microarray assay, nude mouse xenograft model and bioinformatics analysis. We have confirmed PGK1 is specifically upregulated in KIRC based on the transcriptome data generated by our own gene chip experiment, proteomics identification and the bioinformatics analysis for five online transcriptome datasets, and PGK1 upregulation in tumor tissues and serum is indicative with poor prognosis of KIRC patients. In the KIRC tissues, a high expression of PGK1 is often accompanied with an increase of glycolysis-related enzymes and CXCR4. PGK1 exhibits pro-tumorigenic properties in vitro and in a xenograft tumor model by accelerating glycolysis and inducing CXCR4-mediated phosphorylation of AKT and ERK. Moreover, PGK1 promotes sorafenib resistance via increasing CXCR4-mediated ERK phosphorylation. In conclusion, PGK1-invovled metabolic reprogramming and activation of CXCR4/ERK signaling pathway contributes to tumor growth and sorafenib resistance of KIRC.
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6
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Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE. Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. MICROBIAL ECOLOGY 2021; 82:1030-1046. [PMID: 33155101 PMCID: PMC8551143 DOI: 10.1007/s00248-020-01596-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/01/2020] [Indexed: 05/14/2023]
Abstract
The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.
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Affiliation(s)
- Manolito G Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Kelvin Jens Moncera
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yi-Han Lin
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yanbao Yu
- Department of Genomic Medicine, J. Craig Venter Institute, 9605 Medical Center Drive Suite 150, Rockville, MD, 20850, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Central Florida Blvd, Orlando, FL, 32827, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Podgórna 50, 65-246, Zielona Góra, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland
| | - Anna Edlund
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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7
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Yu Y, Singh H, Tsitrin T, Bekele S, Lin YH, Sikorski P, Moncera KJ, Torralba MG, Morrow L, Wolcott R, Nelson KE, Pieper R. Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment. Front Med (Lausanne) 2021; 8:667462. [PMID: 34249966 PMCID: PMC8260951 DOI: 10.3389/fmed.2021.667462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022] Open
Abstract
Biofilms composed of multiple microorganisms colonize the surfaces of indwelling urethral catheters that are used serially by neurogenic bladder patients and cause chronic infections. Well-adapted pathogens in this niche are Escherichia coli, Proteus, and Enterococcus spp., species that cycle through adhesion and multilayered cell growth, trigger host immune responses, are starved off nutrients, and then disperse. Viable microbial foci retained in the urinary tract recolonize catheter surfaces. The molecular adaptations of bacteria in catheter biofilms (CBs) are not well-understood, promising new insights into this pathology based on host and microbial meta-omics analyses from clinical specimens. We examined catheters from nine neurogenic bladder patients longitudinally over up to 6 months. Taxonomic analyses from 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed that 95% of all catheter and corresponding urinary pellet (UP) samples contained bacteria. CB biomasses were dominated by Enterobacteriaceae spp. and often accompanied by lactic acid and anaerobic bacteria. Systemic antibiotic drug treatments of patients resulted in either transient or lasting microbial community perturbations. Neutrophil effector proteins were abundant not only in UP but also CB samples, indicating their penetration of biofilm surfaces. In the context of one patient who advanced to a kidney infection, Proteus mirabilis proteomic data suggested a combination of factors associated with this disease complication: CB biomasses were high; the bacteria produced urease alkalinizing the pH and triggering urinary salt deposition on luminal catheter surfaces; P. mirabilis utilized energy-producing respiratory systems more than in CBs from other patients. The NADH:quinone oxidoreductase II (Nqr), a Na+ translocating enzyme not operating as a proton pump, and the nitrate reductase A (Nar) equipped the pathogen with electron transport chains promoting growth under hypoxic conditions. Both P. mirabilis and E. coli featured repertoires of transition metal ion acquisition systems in response to human host-mediated iron and zinc sequestration. We discovered a new drug target, the Nqr respiratory system, whose deactivation may compromise P. mirabilis growth in a basic pH milieu. Animal models would not allow such molecular-level insights into polymicrobial biofilm metabolism and interactions because the complexity cannot be replicated.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Yi-Han Lin
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Lisa Morrow
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Randall Wolcott
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, MD, United States
- J. Craig Venter Institute, La Jolla, CA, United States
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HaileMariam M, Yu Y, Singh H, Teklu T, Wondale B, Worku A, Zewude A, Mounaud S, Tsitrin T, Legesse M, Gobena A, Pieper R. Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort. Front Cell Infect Microbiol 2021; 11:595554. [PMID: 34150670 PMCID: PMC8212885 DOI: 10.3389/fcimb.2021.595554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 01/01/2023] Open
Abstract
Differential diagnosis of tuberculosis (TB) and latent TB infection (LTBI) remains a public health priority in high TB burden countries. Pulmonary TB is diagnosed by sputum smear microscopy, chest X-rays, and PCR tests for distinct Mycobacterium tuberculosis (Mtb) genes. Clinical tests to diagnose LTBI rely on immune cell stimulation in blood plasma with TB-specific antigens followed by measurements of interferon-γ concentrations. The latter is an important cytokine for cellular immune responses against Mtb in infected lung tissues. Sputum smear microscopy and chest X-rays are not sufficiently sensitive while both PCR and interferon-γ release assays are expensive. Alternative biomarkers for the development of diagnostic tests to discern TB disease states are desirable. This study's objective was to discover sputum diagnostic biomarker candidates from the analysis of samples from 161 human subjects including TB patients, individuals with LTBI, negative community controls (NCC) from the province South Omo, a pastoral region in Ethiopia. We analyzed 16S rRNA gene-based bacterial taxonomies and proteomic profiles. The sputum microbiota did not reveal statistically significant differences in α-diversity comparing the cohorts. The genus Mycobacterium, representing Mtb, was only identified for the TB group which also featured reduced abundance of the genus Rothia in comparison with the LTBI and NCC groups. Rothia is a respiratory tract commensal and may be sensitive to the inflammatory milieu generated by infection with Mtb. Proteomic data supported innate immune responses against the pathogen in subjects with pulmonary TB. Ferritin, an iron storage protein released by damaged host cells, was markedly increased in abundance in TB sputum compared to the LTBI and NCC groups, along with the α-1-acid glycoproteins ORM1 and ORM2. These proteins are acute phase reactants and inhibit excessive neutrophil activation. Proteomic data highlight the effector roles of neutrophils in the anti-Mtb response which was not observed for LTBI cases. Less abundant in the sputum of the LTBI group, compared to the NCC group, were two immunomodulatory proteins, mitochondrial TSPO and the extracellular ribonuclease T2. If validated, these proteins are of interest as new biomarkers for diagnosis of LTBI.
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Affiliation(s)
- Milkessa HaileMariam
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, United States
| | - Harinder Singh
- J. Craig Venter Institute, Rockville, MD, United States
| | - Takele Teklu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia
| | - Biniam Wondale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Adane Worku
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Tamara Tsitrin
- J. Craig Venter Institute, Rockville, MD, United States
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ameni Gobena
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Rembert Pieper
- J. Craig Venter Institute, Rockville, MD, United States
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9
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Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R. Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort. GeroScience 2021. [PMID: 32974878 DOI: 10.1007/s11357-020-00269-y/figures/10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023] Open
Abstract
Key processes characterizing human aging are immunosenescence and inflammaging. The capacity of the immune system to adequately respond to external perturbations (e.g., pathogens, injuries, and biochemical irritants) and to repair somatic mutations that may cause cancers or cellular senescence declines. An important goal remains to identify genetic or biochemical, predictive biomarkers for healthy aging. We recruited two cohorts in the age range 70 to 82, one afflicted by chronic illnesses (non-healthy aging, NHA) and the other in good health (healthy aging, HA). NHA criteria included major cardiovascular, neurodegenerative, and chronic pulmonary diseases, diabetes, and cancers. Quantitative analysis of forty proinflammatory cytokines in blood plasma and more than 500 proteins in urine was performed to identify candidate biomarkers for and biological pathway implications of healthy aging. Nine cytokines revealed lower quantities in blood plasma for the NHA compared with the HA groups (fold change > 1.5; p value < 0.025) including IL-12p40 and IL-12p70. We note that, sampling at two timepoints, intra-individual cytokine abundance patterns clustered in 86% of all 60 cases, indicative of person-specific, highly controlled multi-cytokine signatures in blood plasma. Twenty-three urinary proteins were differentially abundant (HA versus NHA; fold change > 1.5; p value < 0.01). Among the proteins increased in abundance in the HA cohort were glycoprotein MUC18, ephrin type-B receptor 4, matrix remodeling-associated protein 8, angiopoietin-related protein 2, K-cadherin, and plasma protease C1 inhibitor. These proteins have been linked to the extracellular matrix, cell adhesion, and vascular remodeling and repair processes. In silico network analysis identified the regulation of coagulation, antimicrobial humoral immune responses, and the IL-12 signaling pathway as enriched GO terms. To validate links of these preliminary biomarkers and IL-12 signaling with healthy aging, clinical studies using larger cohorts and functional characterization of the genes/proteins in cellular models of aging need to be conducted.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Keehwan Kwon
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Tamara Tsitrin
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Joann Petrini
- Western Connecticut Health Network, 24 Hospital Avenue, Danbury, CT, 06810, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Rembert Pieper
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.
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10
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Lin YH, Platt MP, Gilley RP, Brown D, Dube PH, Yu Y, Gonzalez-Juarbe N. Influenza Causes MLKL-Driven Cardiac Proteome Remodeling During Convalescence. Circ Res 2021; 128:570-584. [PMID: 33501852 DOI: 10.1161/circresaha.120.318511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RATIONALE Patients with and without cardiovascular diseases have been shown to be at risk of influenza-mediated cardiac complications. Recent clinical reports support the notion of a direct link between laboratory-confirmed influenza virus infections and adverse cardiac events. OBJECTIVE Define the molecular mechanisms underlying influenza virus-induced cardiac pathogenesis after resolution of pulmonary infection and the role of necroptosis in this process. METHODS AND RESULTS Hearts from wild-type and necroptosis-deficient (MLKL [mixed lineage kinase domain-like protein]-KO) mice were dissected 12 days after initial influenza A virus (IAV) infection when viral titers were undetectable in the lungs. Immunofluorescence microscopy and plaque assays showed presence of viable IAV particles in the myocardium without generation of interferon responses. Global proteome and phosphoproteome analyses using high-resolution accurate mass-based LC-MS/MS and label-free quantitation showed that the global proteome as well as the phosphoproteome profiles were significantly altered in IAV-infected mouse hearts in a strain-independent manner. Necroptosis-deficient mice had increased survival and reduced weight loss post-IAV infection, as well as increased antioxidant and mitochondrial function, indicating partial protection to IAV infection. These findings were confirmed in vitro by pretreatment of human and rat myocytes with antioxidants or necroptosis inhibitors, which blunted oxidative stress and mitochondrial damage after IAV infection. CONCLUSIONS This study provides the first evidence that the cardiac proteome and phosphoproteome are significantly altered post-pulmonary influenza infection. Moreover, viral particles can persist in the heart after lung clearance, altering mitochondrial function and promoting cell death without active replication and interferon responses. Finally, our findings show inhibition of necroptosis or prevention of mitochondrial damage as possible therapeutic interventions to reduce cardiac damage during influenza infections. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Yi-Han Lin
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD (Y.-H.L., M.P.P., D.B., Y.Y., N.G.-J.)
| | - Maryann P Platt
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD (Y.-H.L., M.P.P., D.B., Y.Y., N.G.-J.)
| | - Ryan P Gilley
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, TX (R.P.G., P.H.D.)
| | - David Brown
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD (Y.-H.L., M.P.P., D.B., Y.Y., N.G.-J.)
| | - Peter H Dube
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, TX (R.P.G., P.H.D.)
| | - Yanbao Yu
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD (Y.-H.L., M.P.P., D.B., Y.Y., N.G.-J.)
| | - Norberto Gonzalez-Juarbe
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD (Y.-H.L., M.P.P., D.B., Y.Y., N.G.-J.)
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Teklu T, Wondale B, Taye B, Hailemariam M, Bekele S, Tamirat M, Zewude A, Mohamed T, Medhin G, Legesse M, Yu Y, Ameni G, Pieper R. Differences in plasma proteomes for active tuberculosis, latent tuberculosis and non-tuberculosis mycobacterial lung disease patients with and without ESAT-6/CFP10 stimulation. Proteome Sci 2020; 18:10. [PMID: 33292280 PMCID: PMC7603755 DOI: 10.1186/s12953-020-00165-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is one of the world's most problematic infectious diseases. The pathogen Mycobacterium tuberculosis (Mtb) is contained by the immune system in people with latent TB infection (LTBI). No overt disease symptoms occur. The environmental and internal triggers leading to reactivation of TB are not well understood. Non-tuberculosis Mycobacteria (NTM) can also cause TB-like lung disease. Comparative analysis of blood plasma proteomes from subjects afflicted by these pathologies in an endemic setting may yield new differentiating biomarkers and insights into inflammatory and immunological responses to Mtb and NTM. METHODS Blood samples from 40 human subjects in a pastoral region of Ethiopia were treated with the ESAT-6/CFP-10 antigen cocktail to stimulate anti-Mtb and anti-NTM immune responses. In addition to those of active TB, LTBI, and NTM cohorts, samples from matched healthy control (HC) subjects were available. Following the generation of sample pools, proteomes were analyzed via LC-MS/MS. These experiments were also performed without antigen stimulation steps. Statistically significant differences using the Z-score method were determined and interpreted in the context of the proteins' functions and their contributions to biological pathways. RESULTS More than 200 proteins were identified from unstimulated and stimulated plasma samples (UPSs and SPSs, respectively). Thirty-four and 64 proteins were differentially abundant with statistical significance (P < 0.05; Benjamini-Hochberg correction with an FDR < 0.05) comparing UPS and SPS proteomic data of four groups, respectively. Bioinformatics analysis of such proteins via the Gene Ontology Resource was indicative of changes in cellular and metabolic processes, responses to stimuli, and biological regulations. The m7GpppN-mRNA hydrolase was increased in abundance in the LTBI group compared to HC subjects. Charged multivesicular body protein 4a and platelet factor-4 were increased in abundance in NTM as compared to HC and decreased in abundance in NTM as compared to active TB. C-reactive protein, α-1-acid glycoprotein 1, sialic acid-binding Ig-like lectin 16, and vitamin K-dependent protein S were also increased (P < 0.05; fold changes≥2) in SPSs and UPSs comparing active TB with LTBI and NTM cases. These three proteins, connected in a STRING functional network, contribute to the acute phase response and influence blood coagulation. CONCLUSION Plasma proteomes are different comparing LTBI, TB, NTM and HC cohorts. The changes are augmented following prior blood immune cell stimulation with the ESAT-6/CFP-10 antigen cocktail. The results encourage larger-cohort studies to identify specific biomarkers to diagnose NTM infection, LTBI, and to predict the risk of TB reactivation.
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Affiliation(s)
- Takele Teklu
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia.
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Biniam Wondale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Biruhalem Taye
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- European Molecular Biology Laboratory, Notkestraβe 85, 22607, Hamburg, Germany
| | | | | | - Mesfin Tamirat
- Laboratory department, Jinka General Hospital, Jinka, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public health Institute, P.O box 1242, Addis Ababa, Ethiopia
| | - Temesgen Mohamed
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, USA
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
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12
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Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R. Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort. GeroScience 2020; 43:593-606. [PMID: 32974878 PMCID: PMC8110643 DOI: 10.1007/s11357-020-00269-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/14/2020] [Indexed: 01/02/2023] Open
Abstract
Key processes characterizing human aging are immunosenescence and inflammaging. The capacity of the immune system to adequately respond to external perturbations (e.g., pathogens, injuries, and biochemical irritants) and to repair somatic mutations that may cause cancers or cellular senescence declines. An important goal remains to identify genetic or biochemical, predictive biomarkers for healthy aging. We recruited two cohorts in the age range 70 to 82, one afflicted by chronic illnesses (non-healthy aging, NHA) and the other in good health (healthy aging, HA). NHA criteria included major cardiovascular, neurodegenerative, and chronic pulmonary diseases, diabetes, and cancers. Quantitative analysis of forty proinflammatory cytokines in blood plasma and more than 500 proteins in urine was performed to identify candidate biomarkers for and biological pathway implications of healthy aging. Nine cytokines revealed lower quantities in blood plasma for the NHA compared with the HA groups (fold change > 1.5; p value < 0.025) including IL-12p40 and IL-12p70. We note that, sampling at two timepoints, intra-individual cytokine abundance patterns clustered in 86% of all 60 cases, indicative of person-specific, highly controlled multi-cytokine signatures in blood plasma. Twenty-three urinary proteins were differentially abundant (HA versus NHA; fold change > 1.5; p value < 0.01). Among the proteins increased in abundance in the HA cohort were glycoprotein MUC18, ephrin type-B receptor 4, matrix remodeling-associated protein 8, angiopoietin-related protein 2, K-cadherin, and plasma protease C1 inhibitor. These proteins have been linked to the extracellular matrix, cell adhesion, and vascular remodeling and repair processes. In silico network analysis identified the regulation of coagulation, antimicrobial humoral immune responses, and the IL-12 signaling pathway as enriched GO terms. To validate links of these preliminary biomarkers and IL-12 signaling with healthy aging, clinical studies using larger cohorts and functional characterization of the genes/proteins in cellular models of aging need to be conducted.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Keehwan Kwon
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Tamara Tsitrin
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Joann Petrini
- Western Connecticut Health Network, 24 Hospital Avenue, Danbury, CT, 06810, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.,J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Rembert Pieper
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.
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13
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Yu Y, O'Rourke A, Lin YH, Singh H, Eguez RV, Beyhan S, Nelson KE. Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes. ACS Infect Dis 2020; 6:2120-2129. [PMID: 32673475 DOI: 10.1021/acsinfecdis.0c00196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Identifying the mode of action (MOA) of antibacterial compounds is the fundamental basis for the development of new antibiotics, and the challenge increases with the emerging secondary and indirect effect from antibiotic stress. Although various omics-based system biology approaches are currently available, enhanced throughput, accuracy, and comprehensiveness are still desirable to better define antibiotic MOA. Using label-free quantitative proteomics, we present here a comprehensive reference map of proteomic signatures of Escherichia coli under challenge of 19 individual antibiotics. Applying several machine learning techniques, we derived a panel of 14 proteins that can be used to classify the antibiotics into different MOAs with nearly 100% accuracy. These proteins tend to mediate diverse bacterial cellular and metabolic processes. Transcriptomic level profiling correlates well with protein expression changes in discriminating different antibiotics. The reported expression signatures will aid future studies in identifying MOA of unknown compounds and facilitate the discovery of novel antibiotics.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Aubrie O'Rourke
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Yi-Han Lin
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rodrigo Vargas Eguez
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Sinem Beyhan
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, Maryland 20850, United States
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
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14
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Zakharova NB, Pastyshkova LK, Goncharova AG, Orlova KD, Kashirina DN, Goncharov IN, Brzhozovsky AG, Ponomarev SA, Morozova OL, Larina IM. [Chromato-mass spectrometric analysis of urine proteins associated with the functions of Toll-receptors in a healthy person under conditions of 17-day isolation.]. Klin Lab Diagn 2020; 65:469-473. [PMID: 32762187 DOI: 10.18821/0869-2084-2020-65-8-469-473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Under controlled conditions of 17-day isolation (Sirius-17 experiment), the protein composition of urine was studied in 6 healthy test volunteers-3 women and 3 men. Collection of samples in the form of a second freely separated morning urine fraction was carried out in the background (seven days before the experiment), as well as 1 day after the end of exposure. Chromatographic-mass-spectrometric semi-quantitative analysis of the protein composition of samples was performed on a system consisting of an Agilent 1100 chromatograph and an LTQ-FT Ultra hybrid mass spectrometer using bioinformatics resources UniProtKB, GeneOntology. An asymptomatic change in the immune defense system of kidney tissue after isolation in a closed hermetic object is associated with a change in the content of 7 proteins that provide functional activity of the TLR tubules of the kidneys - FcRIII, MUC1, Galectin-3, Ficolin-2, APOA1, FLNA, FCGR3A and Clusterin. These proteins are found to be useful biomarkers in the study of physiology and kidney diseases. They can be attributed to candidates for protein markers of the initial stages of impaired recognition by the epithelium of renal tubules of bacteria with known pathogenic potential.
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Affiliation(s)
- N B Zakharova
- V. Razumovsky State medical University of Saratov Ministry of health of Russia, 410012, Saratov, Russia
| | | | - A G Goncharova
- Institute of biomedical problems RAN 123007, Moscow, Russia
| | - K D Orlova
- Institute of biomedical problems RAN 123007, Moscow, Russia
| | - D N Kashirina
- Institute of biomedical problems RAN 123007, Moscow, Russia
| | - I N Goncharov
- Institute of biomedical problems RAN 123007, Moscow, Russia
| | | | - S A Ponomarev
- Institute of biomedical problems RAN 123007, Moscow, Russia
| | - O L Morozova
- Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia
| | - I M Larina
- Institute of biomedical problems RAN 123007, Moscow, Russia
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15
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Na Nakorn P, Pannengpetch S, Isarankura-Na-Ayudhya P, Thippakorn C, Lawung R, Sathirapongsasuti N, Kitiyakara C, Sritara P, Vathesatogkit P, Isarankura-Na-Ayudhya C. Roles of kininogen-1, basement membrane specific heparan sulfate proteoglycan core protein, and roundabout homolog 4 as potential urinary protein biomarkers in diabetic nephropathy. EXCLI JOURNAL 2020; 19:872-891. [PMID: 32665774 PMCID: PMC7355151 DOI: 10.17179/excli2020-1396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022]
Abstract
Diabetic nephropathy, a major complication of diabetes mellitus (DM), is increasing worldwide and the large majority of patients have type 2 DM. Microalbuminuria has been used as a diagnostic marker of diabetic nephropathy. But owing to its insufficient sensitivity and specificity, other biomarkers are being sought. In addition, the pathophysiology of diabetic nephropathy is not fully understood and declines in renal function occur even without microalbuminuria. In this study, we investigated urinary proteins from three study groups (controls, and type 2 diabetic subjects with or without microalbuminuria). Non-targeted label-free Nano-LC QTOF analysis was conducted to discover underlying mechanisms and protein networks, and targeted label-free Nano-LC QTOF with SWATH was performed to qualify discovered protein candidates. Twenty-eight proteins were identified as candidates and functionally analyzed via String DB, gene ontology and pathway analysis. Four predictive mechanisms were analyzed: i) response to stimulus, ii) platelet activation, signaling and aggregation, iii) ECM-receptor interaction, and iv) angiogenesis. These mechanisms can provoke kidney dysfunction in type 2 diabetic patients via endothelial cell damage and glomerulus structural alteration. Based on these analyses, three proteins (kininogen-1, basement membrane-specific heparan sulfate proteoglycan core protein, and roundabout homolog 4) were proposed for further study as potential biomarkers. Our findings provide insights that may improve methods for both prevention and diagnosis of diabetic nephropathy.
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Affiliation(s)
- Piyada Na Nakorn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Supitcha Pannengpetch
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakornpathom, Thailand
| | | | - Chadinee Thippakorn
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakornpathom, Thailand
| | - Ratana Lawung
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nuankanya Sathirapongsasuti
- Section for Translational Medicine, Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Piyamitr Sritara
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prin Vathesatogkit
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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16
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Oros D, Ceprnja M, Zucko J, Cindric M, Hozic A, Skrlin J, Barisic K, Melvan E, Uroic K, Kos B, Starcevic A. Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry. Clin Proteomics 2020; 17:25. [PMID: 32581661 PMCID: PMC7310424 DOI: 10.1186/s12014-020-09289-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample. Methods In total, 16 urine samples having more than 105 CFU/mL were collected from clinical outpatients. These samples were analysed using standard urine culture methods, followed by 16S rRNA gene sequencing serving as control and here described culture-independent MALDI-TOF/TOF MS method being tested. Results Here we present advantages and disadvantages of bottom-up proteomics, using MALDI-TOF/TOF tandem mass spectrometry, for culture-independent identification of uropathogens (e.g. directly from urine samples). The direct approach provided reliable identification of bacteria at the genus level in monobacterial samples. Taxonomic identifications obtained by proteomics were compared both to standard urine culture test used in clinics and genomic test based on 16S rRNA sequencing. Conclusions Our findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in order to identify pathogens in polymicrobial urine samples.
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Affiliation(s)
- Damir Oros
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Marina Ceprnja
- Biochemical Laboratory, Special Hospital Agram, Polyclinic Zagreb, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Mario Cindric
- Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Amela Hozic
- Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Jasenka Skrlin
- Department for Clinical Microbiology and Hospital Infection, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Karmela Barisic
- Faculty of Pharmacy and Biochemistry, Zagreb University, Zagreb, Croatia
| | - Ena Melvan
- Department of Biological Science, Faculty of Science, Macquarie University, Sydney, Australia
| | - Ksenija Uroic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Blazenka Kos
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Antonio Starcevic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
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17
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Hulikova A, Kramer H, Khan H, Swietach P. Detection of Intravascular Hemolysis in Newborn Infants Using Urinary Carbonic Anhydrase I Immunoreactivity. J Appl Lab Med 2020; 5:921-934. [PMID: 32529247 DOI: 10.1093/jalm/jfaa051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/14/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND Mild hemolysis occurs physiologically in neonates, but more severe forms can lead to life-threatening anemia. Newborns in developing regions are particularly at-risk due to the higher incidence of triggers (protozoan infections, sepsis, certain genetic traits). In advanced healthcare facilities, hemolysis is monitored indirectly using resource-intensive methods that probe downstream ramifications. These approaches could potentially delay critical decisions in early-life care, and are not suitable for point-of-care testing. Rapid and cost-effective testing could be based on detecting red blood cell (RBC)-specific proteins, such as carbonic anhydrase I (CAI), in accessible fluids (e.g., urine). METHODS Urine was collected from 26 full-term male neonates and analyzed for CAI using immunoassays (ELISA, western blot) and proteomics (mass spectrometry). The cohort included a range of hemolytic states, including admissions with infection, ABO incompatibility, and receiving phototherapy. Data were paired with hemoglobin, serum bilirubin (SBR), and C-reactive protein (CRP) measurements. RESULTS Urine from a control cohort (CRP < 20 mg/L, SBR < 125µmol/L) had no detectable CAI, in line with results from healthy adults. CAI excretion was elevated in neonates with raised SBR (>125 µmol/L), including those qualifying for phototherapy. Newborns with low SBR (<125 µmol/L) but elevated CRP (>20 mg/L) produced urine with strong CAI immunoreactivity. Proteomics showed that CAI was the most abundant RBC-specific protein in CAI-immunopositive samples, and did not associate with other RBC-derived peptides, indicating an intravascular hemolytic source followed by CAI-selective excretion. CONCLUSIONS CAI is a direct biomarker of intravascular hemolysis that can be measured routinely in urine using non-invasive methods under minimal-laboratory conditions.
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Affiliation(s)
- Alzbeta Hulikova
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Holger Kramer
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Hammad Khan
- Evelina London Children's Hospital, Neonatal Unit 6th Floor, North Wing, St Thomas' Hospital, London, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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18
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Xu C, Zhou X, Xie T, Zhou Y, Zhang Q, Jiang S, Zhang R, Liao L, Dong J. Renal tubular Bim mediates the tubule-podocyte crosstalk via NFAT2 to induce podocyte cytoskeletal dysfunction. Theranostics 2020; 10:6806-6824. [PMID: 32550905 PMCID: PMC7295056 DOI: 10.7150/thno.43145] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/03/2020] [Indexed: 12/17/2022] Open
Abstract
Diabetic nephropathy (DN) is mainly regarded as diabetic glomerulopathy, and its progression is tightly correlated with tubular epithelial lesions. However, the underlying molecular mechanisms linking tubular damage and glomerulopathy are poorly understood. Methods: We previously reported that the upregulation of Bim mediated proximal tubular epithelial cell (PTEC) apoptosis and was crucial in the early stages of DN. Herein we modulated Bim expression in PTECs and subsequently determined podocyte (PC) cytoskeletal arrangement by building a Transwell co-culture system in high glucose (HG). Results: Compared to normal glucose, exposure to 40 mM of HG for 48 h induced significant expression of Bim in PTECs and disorganization in the PC cytoskeleton. When cocultured with PTECs in HG, exacerbated filamentous actin (F-actin) rearrangement and reduced synaptopodin levels were detected in PCs. In contrast, gene knockdown of Bim in PTECs was correlated with the absence of PC cytoskeletal disorganization. NFAT2 level and its nuclear translocation in PTECs were decreased by suppressing Bim expression. Upregulating NFAT2 disrupted the beneficial effects on F-actin organization in PCs obtained by inhibiting Bim. LncRNA microarray analysis identified NONHSAT179542.1, which was implicated in Bim-mediated PC cytoskeletal disorder. Conclusion: Our study clarified the functional role of Bim, a pro-apoptotic factor, which is involved in the crosstalk between PTECs and PCs. Bim promotes NFAT2 activation in PTECs, inducing the downregulation of lncRNA NONHSAT179542.1 in PCs, contributing to the cytoskeletal damage. Identification of the role of the Bim/NFAT2 pathway may represent a promising research direction for a better understanding of DN development.
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19
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Wang P, Yan F, Li Z, Yu Y, Parnell SE, Xiong Y. Impaired plasma membrane localization of ubiquitin ligase complex underlies 3-M syndrome development. J Clin Invest 2019; 129:4393-4407. [PMID: 31343991 DOI: 10.1172/jci129107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
3-M primordial dwarfism is an inherited disease characterized by severe pre- and postnatal growth retardation and by mutually exclusive mutations in three genes, CUL7, OBSL1, and CCDC8. The mechanism underlying 3-M dwarfism is not clear. We showed here that CCDC8, derived from a retrotransposon Gag protein in placental mammals, exclusively localized on the plasma membrane and was phosphorylated by CK2 and GSK3. Phosphorylation of CCDC8 resulted in its binding first with OBSL1, and then CUL7, leading to the membrane assembly of the 3-M E3 ubiquitin ligase complex. We identified LL5β, a plasma membrane protein that regulates cell migration, as a substrate of 3-M ligase. Wnt inhibition of CCDC8 phosphorylation or patient-derived mutations in 3-M genes disrupted membrane localization of the 3-M complex and accumulated LL5β. Deletion of Ccdc8 in mice impaired trophoblast migration and placental development, resulting in intrauterine growth restriction and perinatal lethality. These results identified a mechanism regulating cell migration and placental development that underlies the development of 3-M dwarfism.
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Affiliation(s)
- Pu Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Feng Yan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Zhijun Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Scott E Parnell
- Bowles Center for Alcohol Studies.,Department of Cell Biology and Physiology
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA.,Department of Biochemistry and Biophysics, and.,Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, North Carolina, USA
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20
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Cassatella MA, Östberg NK, Tamassia N, Soehnlein O. Biological Roles of Neutrophil-Derived Granule Proteins and Cytokines. Trends Immunol 2019; 40:648-664. [PMID: 31155315 DOI: 10.1016/j.it.2019.05.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Neutrophils, the most abundant white blood cells in human circulation, entertain intense interactions with other leukocyte subsets, platelets, and stromal cells. Molecularly, such interactions are typically communicated through proteins generated during granulopoiesis, stored in granules, or produced on demand. Here, we provide an overview of the mammalian regulation of granule protein production in the bone marrow and the de novo synthesis of cytokines by neutrophils recruited to tissues. In addition, we discuss some of the known biological roles of these protein messengers, and how neutrophil-borne granule proteins and cytokines can synergize to modulate inflammation and tumor development. Decoding the neutrophil interactome is important for therapeutically neutralizing individual proteins to putatively dampen inflammation, or for delivering modified neutrophil-borne proteins to boost host defense.
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Affiliation(s)
| | - Nataliya K Östberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Oliver Soehnlein
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden; Institute for Cardiovascular Prevention (IPEK), Klinikum der LMU, München, Germany; German Centre for Cardiovascular Research (DZHK), Partner site, Munich, Germany.
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21
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Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections. Conventional approaches to diagnose these infections rely on microbial urine culture, urine sediment microscopy and basic molecular urinalysis tests, in combination with assessments of patient symptoms that are indicative of UTI. The last decade has seen a more widespread clinical use of standardized MALDI-TOF methods to identify UTI-causing microbial agents. Shotgun proteomics methods to determine the extent of inflammation and types of immune cell effectors in urine have not become part of routine clinical tests. However, such methods are useful to investigate UTI pathogenesis, identify difficult-to-culture pathogens and understand antimicrobial effector mechanisms. The present chapter describes these approaches in order to gain quantitative and qualitative insights into inflammation and immune responses in patients with UTI and simultaneously profile the causative agents. The methods are also applicable to examine catheter-associated UTIs and vaginal infections from urine samples. Protocols provided here pertain to direct analyses of clinical specimens including urine sediments and urethral catheter biofilms.
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22
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Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. ProteoStorm: An Ultrafast Metaproteomics Database Search Framework. Cell Syst 2018; 7:463-467.e6. [PMID: 30268435 DOI: 10.1016/j.cels.2018.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/22/2018] [Accepted: 08/13/2018] [Indexed: 12/15/2022]
Abstract
Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies high-confidence peptide-spectrum matches (PSMs) while achieving a two-to-three orders-of-magnitude speedup over popular tools. A reanalysis of a urinary tract infection (UTI) dataset of 110 individuals revealed a complex pattern of polymicrobial expression, including sub-types of UTIs, cases of bacterial vaginosis, and evidence of no underlying disease. Importantly, compared to the initial UTI study that restricted the search database to a manually curated list of 20 genera, ProteoStorm identified additional genera that were previously unreported, including a case of infection with the rare pathogen Propionimicrobium.
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Affiliation(s)
- Doruk Beyter
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Miin S Lin
- Graduate Program in Bioinformatics & Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | | | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
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23
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HaileMariam M, Eguez RV, Singh H, Bekele S, Ameni G, Pieper R, Yu Y. S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics. J Proteome Res 2018; 17:2917-2924. [PMID: 30114372 DOI: 10.1021/acs.jproteome.8b00505] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The success of shotgun proteomic analysis depends largely on how samples are prepared. Current approaches (such as those that are gel-, solution-, or filter-based), although being extensively employed in the field, are time-consuming and less effective with respect to the repetitive sample processing, recovery, and overall yield. As an alternative, the suspension trapping (S-Trap) filter has been commercially available very recently in the format of a single or 96-well filter plate. In contrast to the conventional filter-aided sample preparation (FASP) approach, which utilizes a molecular weight cut-off (MWCO) membrane as the filter and requires hours of processing before digestion-ready proteins can be obtained, the S-Trap employs a three-dimensional porous material as filter media and traps particulate protein suspensions with the subsequent depletion of interfering substances and in-filter digestion. Due to the large (submicron) pore size, each centrifugation cycle of the S-Trap filter only takes 1 min, which significantly reduces the total processing time from approximately 3 h by FASP to less than 15 min, suggesting an ultrafast sample-preparation approach for shotgun proteomics. Here, we comprehensively evaluate the performance of the individual S-Trap filter and 96-well filter plate in the context of global protein identification and quantitation using whole-cell lysate and clinically relevant sputum samples.
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Affiliation(s)
- Milkessa HaileMariam
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States.,Aklilu Lemma Institute of Pathobiology , Addis Ababa University , Addis Ababa , Ethiopia
| | - Rodrigo Vargas Eguez
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Harinder Singh
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Shiferaw Bekele
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology , Addis Ababa University , Addis Ababa , Ethiopia
| | - Rembert Pieper
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Yanbao Yu
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
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24
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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25
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Yu Y, Bekele S, Pieper R. Quick 96FASP for high throughput quantitative proteome analysis. J Proteomics 2017; 166:1-7. [PMID: 28669814 DOI: 10.1016/j.jprot.2017.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/19/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter. To address this limitation, we now present a quick 96FASP (named q96FASP) approach that, relying on the use of filter membranes with a large MWCO size (~30kDa), significantly reduces centrifugal times. We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method. Processing a sample in multiple wells in parallel, we observed excellent experimental repeatability by label-free quantitation approach. We conclude that the q96FASP approach promises to be a promising cost- and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies. SIGNIFICANCE High throughput sample processing is of particular interests for quantitative proteomics. The previously developed 96FASP is high throughput and appealing, however it is time-consuming in the context of centrifugation-based liquid transfer (~1.5h per spin). This study presents a truly high throughput sample preparation method based on large cut-off 96-well filter plate, which shortens the spin time to ~20min. To our knowledge, this is the first multi-well method that is entirely comparable with conventional FASP. This study thoroughly examined two types of filter plates and performed side-by-side comparisons with single FASP. Two types of samples, whole cell lysate of a UTI (urinary tract infection)-associated Klebsiella pneumoniae cell and human urine, were tested which demonstrated its capability for quantitative proteomics. The q96FSAP approach makes the filter plate-based approach more appealing for protein biomarker discovery projects, and could be broadly applied to large scale proteomics analysis.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States.
| | - Shiferaw Bekele
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States
| | - Rembert Pieper
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States
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26
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Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R. Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections. PLoS Pathog 2017; 13:e1006151. [PMID: 28129394 PMCID: PMC5298345 DOI: 10.1371/journal.ppat.1006151] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 02/08/2017] [Accepted: 12/24/2016] [Indexed: 12/15/2022] Open
Abstract
Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs. The effector proteins were further enriched in DNA-protein complexes isolated in native PAGE gels. Immunofluorescence microscopy revealed a flattened morphology of neutrophils associated with decondensed chromatin, remnants of granules in the cell periphery, and myeloperoxidase co-localized with extracellular DNA, features consistent with early-phase NETs. Nuclear staining revealed that a considerable fraction of bacterial cells in these structures were dead. The proteomes of two pathogens, Staphylococcus aureus and Escherichia coli, were indicative of adaptive responses to early-phase NETs, specifically the release of virulence factors and arrest of ribosomal protein synthesis. Finally, we discovered patterns of proteolysis consistent with widespread cleavage of proteins by neutrophil elastase, proteinase 3 and cathepsin G and evidence of citrullination in many nuclear proteins. Urinary tract infections (UTIs) are one of the world’s most widespread infectious diseases, with an estimated number of 150 million cases per year. Neutrophils play an important role in the defense of human patients against microbes causing UTIs. Molecules produced by neutrophils that migrate into the urinary tract can kill the invading microbes and resolve an infection, often without a need to treat patients with an antibiotic. Our work shows strong support for a mechanism called the formation of neutrophil extracellular traps (NETs), previously described for other infections and autoimmune conditions, which are involved in killing pathogens that have invaded the urinary tract. We show evidence of extracellular chromatin-containing structures using immunofluorescence microscopy and identified proteins that bind to the chromatin DNA and have functions to damage and kill bacterial cells or stop their growth.
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Affiliation(s)
- Yanbao Yu
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Keehwan Kwon
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Tamara Tsitrin
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Shiferaw Bekele
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Patricia Sikorski
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Karen E. Nelson
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Rembert Pieper
- The J. Craig Venter Institute, Rockville, MD, United States of America
- * E-mail:
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