1
|
Dou DR, Zhao Y, Belk JA, Zhao Y, Casey KM, Chen DC, Li R, Yu B, Srinivasan S, Abe BT, Kraft K, Hellström C, Sjöberg R, Chang S, Feng A, Goldman DW, Shah AA, Petri M, Chung LS, Fiorentino DF, Lundberg EK, Wutz A, Utz PJ, Chang HY. Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell 2024; 187:733-749.e16. [PMID: 38306984 PMCID: PMC10949934 DOI: 10.1016/j.cell.2023.12.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/03/2023] [Accepted: 12/31/2023] [Indexed: 02/04/2024]
Abstract
Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
Collapse
Affiliation(s)
- Diana R Dou
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanding Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Derek C Chen
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Suhas Srinivasan
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian T Abe
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ceke Hellström
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Sarah Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ami A Shah
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorinda S Chung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - David F Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Emma K Lundberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden; Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Anton Wutz
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Zurich, Switzerland
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
2
|
Lyons-Abbott S, Abramov A, Chan CL, Deer JR, Fu G, Hassouneh W, Koch T, Misquith A, O'Neill J, Simon SA, Wolf A, Yeh R, Vernet E. Choice of fusion proteins, expression host, and analytics solves difficult-to-produce protein challenges in discovery research. Biotechnol J 2024; 19:e2300162. [PMID: 37802118 DOI: 10.1002/biot.202300162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
High quality biological reagents are a prerequisite for pharmacological research. Herein a protein production screening approach, including quality assessment methods, for protein-based discovery research is presented. Trends from 2895 expression constructs representing 253 proteins screened in mammalian and bacterial hosts-91% of which are successfully expressed and purified-are discussed. Mammalian expression combined with the use of solubility-promoting fusion proteins is deemed suitable for most targets. Furthermore, cases utilizing stable cell line generation and choice of fusion protein for higher yield and quality of difficult-to-produce proteins (Leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4) and Neurturin) are presented and discussed. In the case of Neurturin, choice of fusion protein impacted the target binding 80-fold. These results highlight the need for exploration of construct designs and careful Quality Control (QC) of difficult-to-produce protein reagents.
Collapse
Affiliation(s)
| | - Ariel Abramov
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Chung-Leung Chan
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jen Running Deer
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Guangsen Fu
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Wafa Hassouneh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Tyree Koch
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ayesha Misquith
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jason O'Neill
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | | | - Anitra Wolf
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ronald Yeh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Erik Vernet
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| |
Collapse
|
3
|
A Proof of Principle Proteomic Study Detects Dystrophin in Human Plasma: Implications in DMD Diagnosis and Clinical Monitoring. Int J Mol Sci 2023; 24:ijms24065215. [PMID: 36982290 PMCID: PMC10049465 DOI: 10.3390/ijms24065215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a rare neuromuscular disease caused by pathogenic variations in the DMD gene. There is a need for robust DMD biomarkers for diagnostic screening and to aid therapy monitoring. Creatine kinase, to date, is the only routinely used blood biomarker for DMD, although it lacks specificity and does not correlate with disease severity. To fill this critical gap, we present here novel data about dystrophin protein fragments detected in human plasma by a suspension bead immunoassay using two validated anti-dystrophin-specific antibodies. Using both antibodies, a reduction of the dystrophin signal is detected in a small cohort of plasma samples from DMD patients when compared to healthy controls, female carriers, and other neuromuscular diseases. We also demonstrate the detection of dystrophin protein by an antibody-independent method using targeted liquid chromatography mass spectrometry. This last assay detects three different dystrophin peptides in all healthy individuals analysed and supports our finding that dystrophin protein is detectable in plasma. The results of our proof-of-concept study encourage further studies in larger sample cohorts to investigate the value of dystrophin protein as a low invasive blood biomarker for diagnostic screening and clinical monitoring of DMD.
Collapse
|
4
|
Preger C, Notarnicola A, Hellström C, Wigren E, Fernandes-Cerqueira C, Kvarnström M, Wahren-Herlenius M, Idborg H, Lundberg IE, Persson H, Gräslund S, Jakobsson PJ. Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies. J Autoimmun 2023; 134:102951. [PMID: 36470210 DOI: 10.1016/j.jaut.2022.102951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 12/04/2022]
Abstract
OBJECTIVES Autoantibodies are thought to play a key role in the pathogenesis of idiopathic inflammatory myopathies (IIM). However, up to 40% of IIM patients, even those with clinical manifestations of anti-synthetase syndrome (ASSD), test seronegative to known myositis-specific autoantibodies. We hypothesized the existence of new potential autoantigens among human cytoplasmic aminoacyl tRNA synthetases (aaRS) in patients with IIM. METHODS Plasma samples from 217 patients with IIM according to 2017 EULAR/ACR criteria, including 50 patients with ASSD, 165 without, and two with unknown ASSD status were identified retrospectively, as well as age and gender-matched sera from 156 population controls, and 219 disease controls. Patients with previously documented ASSD had to test positive for at least one of the five most common anti-aaRS autoantibodies (anti-Jo1, -PL7, -PL12, -EJ, and -OJ) and present with one or more of the following clinical manifestations: interstitial lung disease, myositis, arthritis, Raynaud's phenomenon, fever, or mechanic's hands. Demographics, laboratory, and clinical data of the IIM cohort (ASSD and non-ASSD) were compared. Samples were screened using a multiplex bead array assay for presence of autoantibodies against a panel of 117 recombinant protein variants, representing 33 myositis-related proteins, including all nineteen cytoplasmic aaRS. Prospectively collected clinical data for the IIM cohort were retrieved and compared between groups within the IIM cohort and correlated with the results of the autoantibody screening. Principal component analysis was used to analyze clinical manifestations between ASSD, non-ASSD groups, and individuals with novel anti-aaRS autoantibodies. RESULTS We identified reactivity towards 16 aaRS in 72 of the 217 IIM patients. Twelve patients displayed reactivity against nine novel aaRS. The novel autoantibody specificities were detected in four previously seronegative patients for myositis-specific autoantibodies and eight with previously detected myositis-specific autoantibodies. IIM individuals with novel anti-aaRS autoantibodies (n = 12) all had signs of myositis, and they had either muscle weakness and/or muscle enzyme elevation, 2/12 had mechanic's hands, 3/12 had interstitial lung disease, and 2/12 had arthritis. The individuals with novel anti-aaRS and a pathological muscle biopsy all presented widespread up-regulation of major histocompatibility complex class I. The reactivities against novel aaRS could be confirmed in ELISA and western blot. Using the multiplex bead array assay, we could confirm previously known reactivities to four of the most common aaRS (Jo1, PL12, PL7, and EJ (n = 45)) and identified patients positive for anti-Zo, -KS, and -HA (n = 10) that were not previously tested. A low frequency of anti-aaRS autoantibodies was also detected in controls. CONCLUSION Our results suggest that most, if not all, cytoplasmic aaRS may become autoantigenic. Autoantibodies against new aaRS may be found in plasma of patients previously classified as seronegative with potential high clinical relevance.
Collapse
Affiliation(s)
- Charlotta Preger
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Antonella Notarnicola
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Hellström
- KTH Royal Institute of Technology, Department of Protein Science, SciLifeLab, Stockholm, Sweden
| | - Edvard Wigren
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | | | - Marika Kvarnström
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Academic Specialist Center, Center for Rheumatology, Stockholm Health Services, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Helena Idborg
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid E Lundberg
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Helena Persson
- KTH Royal Institute of Technology, Department of Protein Science, SciLifeLab, Stockholm, Sweden
| | - Susanne Gräslund
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
5
|
San Segundo-Acosta P, Montero-Calle A, Jernbom-Falk A, Alonso-Navarro M, Pin E, Andersson E, Hellström C, Sánchez-Martínez M, Rábano A, Solís-Fernández G, Peláez-García A, Martínez-Useros J, Fernández-Aceñero MJ, Månberg A, Nilsson P, Barderas R. Multiomics Profiling of Alzheimer's Disease Serum for the Identification of Autoantibody Biomarkers. J Proteome Res 2021; 20:5115-5130. [PMID: 34628858 DOI: 10.1021/acs.jproteome.1c00630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New biomarkers of Alzheimer's disease (AD) with a diagnostic value in preclinical and prodromal stages are urgently needed. AD-related serum autoantibodies are potential candidate biomarkers. Here, we aimed at identifying AD-related serum autoantibodies using protein microarrays and mass spectrometry-based methods. To this end, an untargeted complementary screening using high-density (42,100 antigens) and low-density (384 antigens) planar protein-epitope signature tag (PrEST) arrays and an immunoprecipitation protocol coupled to mass spectrometry analysis were used for serum autoantibody profiling. From the untargeted screening phase, 377 antigens corresponding to 338 proteins were selected for validation. Out of them, IVD, CYFIP1, and ADD2 seroreactivity was validated using 128 sera from AD patients and controls by PrEST-suspension bead arrays, and ELISA or luminescence Halotag-based bead immunoassay using full-length recombinant proteins. Importantly, IVD, CYFIP1, and ADD2 showed in combination a noticeable AD diagnostic ability. Moreover, IVD protein abundance in the prefrontal cortex was significantly two-fold higher in AD patients than in controls by western blot and immunohistochemistry, whereas CYFIP1 and ADD2 were significantly down-regulated in AD patients. The panel of AD-related autoantigens identified by a comprehensive multiomics approach may provide new insights of the disease and should help in the blood-based diagnosis of Alzheimer's disease. Mass spectrometry raw data are available in the ProteomeXchange database with the access number PXD028392.
Collapse
Affiliation(s)
- Pablo San Segundo-Acosta
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ana Montero-Calle
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - August Jernbom-Falk
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | - Miren Alonso-Navarro
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | - Eni Andersson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | - Cecilia Hellström
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | | | - Alberto Rábano
- Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid 28031, Spain
| | | | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), Madrid 28046, Spain
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute-Fundacion Jimenez Diaz University Hospital, Madrid 28040, Spain
| | - María Jesús Fernández-Aceñero
- Servicio de Anatomía Patológica Hospital Universitario Clínico San Carlos, Departamento de Anatomía Patológica, Facultad de Medicina, Complutense University of Madrid, Madrid 28040, Spain
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Solna, Stockholm 171 65, Sweden
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| |
Collapse
|
6
|
Alkharaan H, Bayati S, Hellström C, Aleman S, Olsson A, Lindahl K, Bogdanovic G, Healy K, Tsilingaridis G, De Palma P, Hober S, Månberg A, Nilsson P, Pin E, Sällberg Chen M. Persisting Salivary IgG Against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys. J Infect Dis 2021; 224:407-414. [PMID: 33978762 PMCID: PMC8244549 DOI: 10.1093/infdis/jiab256] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/07/2021] [Indexed: 01/06/2023] Open
Abstract
Background Declining humoral immunity in coronavirus disease 2019 (COVID-19) patients and possible reinfection have raised concern. Mucosal immunity, particularly salivary antibodies, may be short lived although long-term studies are lacking. Methods Using a multiplex bead-based array platform, we investigated antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in 256 saliva samples from convalescent patients 1–9 months after symptomatic COVID-19 (n = 74, cohort 1), undiagnosed individuals with self-reported questionnaires (n = 147, cohort 2), and individuals sampled prepandemic (n = 35, cohort 3). Results Salivary IgG antibody responses in cohort 1 (mainly mild COVID-19) were detectable up to 9 months postrecovery, with high correlations between spike and nucleocapsid specificity. At 9 months, IgG remained in blood and saliva in most patients. Salivary IgA was rarely detected at this time point. In cohort 2, salivary IgG and IgA responses were significantly associated with recent history of COVID-19–like symptoms. Salivary IgG tolerated temperature and detergent pretreatments. Conclusions Unlike SARS-CoV-2 salivary IgA that appeared short lived, specific saliva IgG appeared stable even after mild COVID-19, as for blood serology. This noninvasive saliva-based SARS-CoV-2 antibody test with home self-collection may be a complementary alternative to conventional blood serology.
Collapse
Affiliation(s)
- Hassan Alkharaan
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shaghayegh Bayati
- Department of Protein Science, Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Cecilia Hellström
- Department of Protein Science, Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annika Olsson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Lindahl
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gordana Bogdanovic
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Katie Healy
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Patricia De Palma
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, Division of Protein Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Månberg
- Department of Protein Science, Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Elisa Pin
- Department of Protein Science, Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | | |
Collapse
|
7
|
Hober S, Hellström C, Olofsson J, Andersson E, Bergström S, Jernbom Falk A, Bayati S, Mravinacova S, Sjöberg R, Yousef J, Skoglund L, Kanje S, Berling A, Svensson AS, Jensen G, Enstedt H, Afshari D, Xu LL, Zwahlen M, von Feilitzen K, Hanke L, Murrell B, McInerney G, Karlsson Hedestam GB, Lendel C, Roth RG, Skoog I, Svenungsson E, Olsson T, Fogdell-Hahn A, Lindroth Y, Lundgren M, Maleki KT, Lagerqvist N, Klingström J, Da Silva Rodrigues R, Muschiol S, Bogdanovic G, Arroyo Mühr LS, Eklund C, Lagheden C, Dillner J, Sivertsson Å, Havervall S, Thålin C, Tegel H, Pin E, Månberg A, Hedhammar M, Nilsson P. Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay. Clin Transl Immunology 2021; 10:e1312. [PMID: 34295471 PMCID: PMC8288725 DOI: 10.1002/cti2.1312] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Objective The COVID-19 pandemic poses an immense need for accurate, sensitive and high-throughput clinical tests, and serological assays are needed for both overarching epidemiological studies and evaluating vaccines. Here, we present the development and validation of a high-throughput multiplex bead-based serological assay. Methods More than 100 representations of SARS-CoV-2 proteins were included for initial evaluation, including antigens produced in bacterial and mammalian hosts as well as synthetic peptides. The five best-performing antigens, three representing the spike glycoprotein and two representing the nucleocapsid protein, were further evaluated for detection of IgG antibodies in samples from 331 COVID-19 patients and convalescents, and in 2090 negative controls sampled before 2020. Results Three antigens were finally selected, represented by a soluble trimeric form and the S1-domain of the spike glycoprotein as well as by the C-terminal domain of the nucleocapsid. The sensitivity for these three antigens individually was found to be 99.7%, 99.1% and 99.7%, and the specificity was found to be 98.1%, 98.7% and 95.7%. The best assay performance was although achieved when utilising two antigens in combination, enabling a sensitivity of up to 99.7% combined with a specificity of 100%. Requiring any two of the three antigens resulted in a sensitivity of 99.7% and a specificity of 99.4%. Conclusion These observations demonstrate that a serological test based on a combination of several SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.
Collapse
|
8
|
Tegel H, Dannemeyer M, Kanje S, Sivertsson Å, Berling A, Svensson AS, Hober A, Enstedt H, Volk AL, Lundqvist M, Moradi M, Afshari D, Ekblad S, Xu L, Westin M, Bidad F, Schiavone LH, Davies R, Mayr LM, Knight S, Göpel SO, Voldborg BG, Edfors F, Forsström B, von Feilitzen K, Zwahlen M, Rockberg J, Takanen JO, Uhlén M, Hober S. High throughput generation of a resource of the human secretome in mammalian cells. N Biotechnol 2020; 58:45-54. [DOI: 10.1016/j.nbt.2020.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/04/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023]
|
9
|
Chae YK, Kim SH, Um Y. Relationship between Protein Expression Pattern and Host Metabolome Perturbation as Monitored by Two‐Dimensional NMR Spectroscopy. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Young Kee Chae
- Department of ChemistrySejong University Seoul 05006 Korea
| | - Seol Hyun Kim
- Department of ChemistrySejong University Seoul 05006 Korea
| | - Yoonjin Um
- Department of ChemistrySejong University Seoul 05006 Korea
| |
Collapse
|
10
|
Edfors F, Forsström B, Vunk H, Kotol D, Fredolini C, Maddalo G, Svensson AS, Boström T, Tegel H, Nilsson P, Schwenk JM, Uhlen M. Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. J Proteome Res 2019; 18:2706-2718. [PMID: 31094526 DOI: 10.1021/acs.jproteome.8b00924] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.
Collapse
Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Björn Forsström
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Helian Vunk
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - David Kotol
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Gianluca Maddalo
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Anne-Sophie Svensson
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Tove Boström
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Atlas Antibodies AB , SE - 114 21 Stockholm , Sweden
| | - Hanna Tegel
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Department of Neuroscience - Karolinska Institute , SE - 171 65 Solna , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK - 2970 Hørsholm , Denmark
| |
Collapse
|
11
|
Mikus M, Johansson C, Acevedo N, Nilsson P, Scheynius A. The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients. Clin Transl Allergy 2019; 9:6. [PMID: 30728947 PMCID: PMC6354350 DOI: 10.1186/s13601-019-0240-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023] Open
Abstract
Background Atopic dermatitis (AD) is a complex heterogeneous chronic inflammatory skin disease. Specific IgE antibodies against autoantigens have been observed in a subgroup of AD patients, however, little is known about IgG-auto-reactivity in AD. To investigate the presence of autoreactive IgG antibodies, we performed autoantibody profiling of IgG in patients with AD of different severities and in healthy controls (HC). Methods First, we performed an untargeted screening in plasma samples from 40 severe AD (sAD) patients and 40 HC towards 1152 protein fragments on planar antigen microarrays. Next, based on the findings and addition of more fragments, a targeted antigen suspension bead array was designed to profile a cohort of 50 sAD patients, 123 patients with moderate AD (mAD), and 84 HC against 148 protein fragments representing 96 unique proteins. Results Forty-nine percent of the AD patients showed increased IgG-reactivity to any of the four antigens representing keratin associated protein 17-1 (KRTAP17-1), heat shock protein family A (Hsp70) member 4 (HSPA4), S100 calcium binding proteins A12 (S100A12), and Z (S100Z). The reactivity was more frequent in the sAD patients (66%) than in those with mAD (41%), whereas only present in 25% of the HC. IgG-reactivity to S100A12, a protein including an antimicrobial peptide, was only observed in AD patients (13/173). Conclusions Autoantibody profiling of IgG-reactivity using microarray technology revealed an autoantibody-based subgroup in patients with AD. The four identified autoantigens and especially S100A12 could, if characterized further, increase the understanding of different pathogenic mechanisms behind AD and thereby enable better treatment. Electronic supplementary material The online version of this article (10.1186/s13601-019-0240-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maria Mikus
- 1Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Catharina Johansson
- 2Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Nathalie Acevedo
- 2Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden.,3Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Peter Nilsson
- 1Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annika Scheynius
- 2Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden.,4Clinical Genomics, SciLifeLab, Stockholm, Sweden
| |
Collapse
|
12
|
Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics 2018; 33:2487-2495. [PMID: 28398465 DOI: 10.1093/bioinformatics/btx207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/05/2017] [Indexed: 01/21/2023] Open
Abstract
Motivation The Human Protein Atlas (HPA) enables the simultaneous characterization of thousands of proteins across various tissues to pinpoint their spatial location in the human body. This has been achieved through transcriptomics and high-throughput immunohistochemistry-based approaches, where over 40 000 unique human protein fragments have been expressed in E. coli. These datasets enable quantitative tracking of entire cellular proteomes and present new avenues for understanding molecular-level properties influencing expression and solubility. Results Combining computational biology and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide the selection of protein fragments based on these characteristics to optimize high-throughput experimentation. Availability and implementation We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template for analysis of further expression and solubility datasets. Contact ebrunk@ucsd.edu or johanr@biotech.kth.se. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Anand Sastry
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Jonathan Monk
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Hanna Tegel
- KTH - Royal Institute of Technology, Department of Proteomics and Nanobiotechnology, SE-106 91 Stockholm, Sweden
| | - Mathias Uhlen
- KTH - Royal Institute of Technology, Department of Proteomics and Nanobiotechnology, SE-106 91 Stockholm, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, CA, USA.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Johan Rockberg
- KTH - Royal Institute of Technology, Department of Proteomics and Nanobiotechnology, SE-106 91 Stockholm, Sweden
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego, CA, USA.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
13
|
Chae YK, Kim SH, Markley JL. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy. PLoS One 2017; 12:e0177233. [PMID: 28486539 PMCID: PMC5423636 DOI: 10.1371/journal.pone.0177233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/24/2017] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli has been the most widely used host to produce large amounts of heterologous proteins. However, given an input plasmid DNA, E. coli may produce soluble protein, produce only inclusion bodies, or yield little or no protein at all. Many efforts have been made to surmount these problems, but most of them have involved time-consuming and labor-intensive trial-and-error. We hypothesized that different metabolomic fingerprints might be associated with different protein production outcomes. If so, then it might be possible to change the expression pattern by manipulating the metabolite environment. As a first step in testing this hypothesis, we probed a subset of the intracellular metabolites by partially labeling it with 13C-glucose. We tested 71 genes and identified 17 metabolites by employing the two-dimensional NMR spectroscopy. The statistical analysis showed that there existed the metabolite compositions favoring protein production. We hope that this work would help devise a systematic and predictive approach to the recombinant protein production.
Collapse
Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, Seoul, Korea
- * E-mail:
| | - Seol Hyun Kim
- Department of Chemistry, Sejong University, Seoul, Korea
| | - John L. Markley
- Department of Biochemistry, University of Wisconsin – Madison, Wisconsin, United States of America
| |
Collapse
|
14
|
A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer. J Immunother 2017; 40:132-139. [PMID: 28338506 DOI: 10.1097/cji.0000000000000164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We examined the immunologic effects of allogeneic hematopoietic stem cell transplantation (HSCT) in the treatment of pancreatic ductal adenocarcinoma, a deadly disease with a median survival of 24 months for resected tumors and a 5-year survival rate of 6%. After adjuvant chemotherapy, 2 patients with resected pancreatic ductal adenocarcinoma underwent HSCT with HLA-identical sibling donors. Comparable patients who underwent radical surgery, but did not have a donor, served as controls (n=6). Both patients developed humoral and cellular (ie, HLA-A*01:01-restricted) immune responses directed against 2 novel tumor-associated antigens (TAAs), INO80E and UCLH3 after HSCT. Both TAAs were highly expressed in the original tumor tissue suggesting that HSCT promoted a clinically relevant, long-lasting cellular immune response. In contrast to untreated controls, who succumbed to progressive disease, both patients are tumor-free 9 years after diagnosis. Radical surgery combined with HSCT may cure pancreatic adenocarcinoma and change the cellular immune repertoire capable of responding to clinically and biologically relevant TAAs.
Collapse
|
15
|
Edfors F, Danielsson F, Hallström BM, Käll L, Lundberg E, Pontén F, Forsström B, Uhlén M. Gene-specific correlation of RNA and protein levels in human cells and tissues. Mol Syst Biol 2016; 12:883. [PMID: 27951527 PMCID: PMC5081484 DOI: 10.15252/msb.20167144] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/05/2016] [Accepted: 09/15/2016] [Indexed: 02/02/2023] Open
Abstract
An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.
Collapse
Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Frida Danielsson
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| |
Collapse
|
16
|
Sjöberg R, Mattsson C, Andersson E, Hellström C, Uhlen M, Schwenk JM, Ayoglu B, Nilsson P. Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling. N Biotechnol 2016; 33:582-92. [DOI: 10.1016/j.nbt.2015.09.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 12/01/2022]
|
17
|
Thelin EP, Just D, Frostell A, Häggmark-Månberg A, Risling M, Svensson M, Nilsson P, Bellander BM. Protein profiling in serum after traumatic brain injury in rats reveals potential injury markers. Behav Brain Res 2016; 340:71-80. [PMID: 27591967 DOI: 10.1016/j.bbr.2016.08.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 08/29/2016] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The serum proteome following traumatic brain injury (TBI) could provide information for outcome prediction and injury monitoring. The aim with this affinity proteomic study was to identify serum proteins over time and between normoxic and hypoxic conditions in focal TBI. MATERIAL AND METHODS Sprague Dawley rats (n=73) received a 3mm deep controlled cortical impact ("severe injury"). Following injury, the rats inhaled either a normoxic (22% O2) or hypoxic (11% O2) air mixture for 30min before resuscitation. The rats were sacrificed at day 1, 3, 7, 14 and 28 after trauma. A total of 204 antibodies targeting 143 unique proteins of interest in TBI research, were selected. The sample proteome was analyzed in a suspension bead array set-up. Comparative statistics and factor analysis were used to detect differences as well as variance in the data. RESULTS We found that complement factor 9 (C9), complement factor B (CFB) and aldolase c (ALDOC) were detected at higher levels the first days after trauma. In contrast, hypoxia inducing factor (HIF)1α, amyloid precursor protein (APP) and WBSCR17 increased over the subsequent weeks. S100A9 levels were higher in hypoxic-compared to normoxic rats, together with a majority of the analyzed proteins, albeit few reached statistical significance. The principal component analysis revealed a variance in the data, highlighting clusters of proteins. CONCLUSIONS Protein profiling of serum following TBI using an antibody based microarray revealed temporal changes of several proteins over an extended period of up to four weeks. Further studies are warranted to confirm our findings.
Collapse
Affiliation(s)
- Eric Peter Thelin
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - David Just
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden.
| | - Arvid Frostell
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Anna Häggmark-Månberg
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden.
| | - Mårten Risling
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Mikael Svensson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden.
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden.
| | - Bo-Michael Bellander
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
18
|
Kee Chae Y, Hyun Kim S, Seong Hyun J. Probing Metabolite Space of Escherichia coli via Growth Medium Composition as Monitored by Two-Dimensional NMR Spectroscopy. Chem Biodivers 2016; 12:925-36. [PMID: 26080738 DOI: 10.1002/cbdv.201400200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 11/08/2022]
Abstract
As for recombinant protein production, Escherichia coli is one of the most frequently employed hosts because it offers a simple and inexpensive, but rapid and high-yield system in addition to the vast information on its molecular genetics and biology. However, due to its prokaryotic nature, it often fails to produce eukaryotic proteins in a desired form. To devise a systematic way leading to a condition that produces a large amount of usable proteins, we attempted to monitor intracellular metabolites under various conditions, and to link them to recombinant protein production. With such an intention, we identified 31 metabolites from cells grown in different media by using two-dimensional (2D) NMR spectroscopy. Our results revealed that 1) the level of betaine was low, while that of glutamic acid was high when grown in minimal media; 2) the level of glycerol was constantly high in all cases; 3) the level of oxidized glutathione was lower in Luria broth (LB); and 4) the level of leucine was low in minimal media. We hope this work might shed light onto how to improve production of the target proteins by metabolite profiling.
Collapse
Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul 143 - 747, Korea, (phone: +82-2-3408-3748; fax: +82-2-3408-4317).
| | - Seol Hyun Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul 143 - 747, Korea, (phone: +82-2-3408-3748; fax: +82-2-3408-4317)
| | - Jin Seong Hyun
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul 143 - 747, Korea, (phone: +82-2-3408-3748; fax: +82-2-3408-4317)
| |
Collapse
|
19
|
Kanje S, Hober S. In vivo biotinylation and incorporation of a photo-inducible unnatural amino acid to an antibody-binding domain improve site-specific labeling of antibodies. Biotechnol J 2016; 10:564-74. [PMID: 25655274 DOI: 10.1002/biot.201400808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/23/2015] [Accepted: 03/03/2015] [Indexed: 02/04/2023]
Abstract
Antibodies are important molecules in many research fields, where they play a key role in various assays. Antibody labeling is therefore of great importance. Currently, most labeling techniques take advantage of certain amino acid side chains that commonly appear throughout proteins. This makes it hard to control the position and exact degree of labeling of each antibody. Hence, labeling of the antibody may affect the antibody-binding site. This paper presents a novel protein domain based on the IgG-binding domain C2 of streptococcal protein G, containing the unnatural amino acid BPA, that can cross-link other molecules. This novel domain can, with improved efficiency compared to previously reported similar domains, site-specifically cross-link to IgG at the Fc region. An efficient method for simultaneous in vivo incorporation of BPA and specific biotinylation in a flask cultivation of Escherichia coli is described. In comparison to a traditionally labeled antibody sample, the C2-labeled counterpart proved to have a higher proportion of functional antibodies when immobilized on a solid surface and the same limit of detection in an ELISA. This method of labeling is, due to its efficiency and simplicity, of high interest for all antibody-based assays where it is important that labeling does not interfere with the antibody-binding site.
Collapse
Affiliation(s)
- Sara Kanje
- AlbaNova University Centre, KTH - Royal Institute of Technology, Department of Protein Technology, Stockholm, Sweden
| | | |
Collapse
|
20
|
Boström T, Takanen JO, Hober S. Antibodies as means for selective mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1021:3-13. [PMID: 26565067 DOI: 10.1016/j.jchromb.2015.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023]
Abstract
For protein analysis of biological samples, two major strategies are used today; mass spectrometry (MS) and antibody-based methods. Each strategy offers advantages and drawbacks. However, combining the two using an immunoenrichment step with MS analysis brings together the benefits of each method resulting in increased sensitivity, faster analysis and possibility of higher degrees of multiplexing. The immunoenrichment can be performed either on protein or peptide level and quantification standards can be added in order to enable determination of the absolute protein concentration in the sample. The combination of immunoenrichment and MS holds great promise for the future in both proteomics and clinical diagnostics. This review describes different setups of immunoenrichment coupled to mass spectrometry and how these can be utilized in various applications.
Collapse
Affiliation(s)
- Tove Boström
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Jenny Ottosson Takanen
- School of Biotechnology, Division of Proteomics and Nanobiotechnology, KTH-Royal Institute ofTechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
| |
Collapse
|
21
|
Chae YK, Kim SH. Searching for Growth Conditions for Optimized Expression of Recombinant Proteins inEscherichia coliby Using Two-Dimensional NMR Spectroscopy. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Young Kee Chae
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| | - Seol Hyun Kim
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| |
Collapse
|
22
|
Edfors F, Boström T, Forsström B, Zeiler M, Johansson H, Lundberg E, Hober S, Lehtiö J, Mann M, Uhlen M. Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins. Mol Cell Proteomics 2014; 13:1611-24. [PMID: 24722731 DOI: 10.1074/mcp.m113.034140] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope-labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A-coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope-labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed.
Collapse
Affiliation(s)
- Fredrik Edfors
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Tove Boström
- ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Björn Forsström
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marlis Zeiler
- ‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Henrik Johansson
- **Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Emma Lundberg
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sophia Hober
- ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Janne Lehtiö
- **Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Matthias Mann
- ‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mathias Uhlen
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden; ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| |
Collapse
|
23
|
Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
24
|
Ayoglu B, Häggmark A, Khademi M, Olsson T, Uhlén M, Schwenk JM, Nilsson P. Autoantibody profiling in multiple sclerosis using arrays of human protein fragments. Mol Cell Proteomics 2013; 12:2657-72. [PMID: 23732997 PMCID: PMC3769337 DOI: 10.1074/mcp.m112.026757] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ∼38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.
Collapse
Affiliation(s)
- Burcu Ayoglu
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
25
|
Renes J, Mariman E. Application of proteomics technology in adipocyte biology. MOLECULAR BIOSYSTEMS 2013; 9:1076-91. [PMID: 23629546 DOI: 10.1039/c3mb25596d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Obesity and its associated complications have reached epidemic proportions in Western-type societies. Concomitantly, the obesity incidence in developing countries is increasing. One hallmark of obesity is the differentiation of pre-adipocytes into mature triglyceride-loaded adipocytes present in subcutaneous and visceral adipose tissue depots. This may ultimately lead to dysfunctional adipose tissue together with detrimental changes in the profiles of (pre-)adipocyte-secreted proteins, known as adipokines. Obesity-induced alterations in adipokine profiles contribute to the development of obesity-associated disorders. Consequently, the interest in the molecular events responsible for adipose tissue modifications during weight gain and weight loss as well as in the aetiology of obesity-associated disorders is growing. Molecular mechanisms involved in pre-adipocyte differentiation and alterations in adipokine profiles have been examined at the gene and protein level by high-throughput technologies. Independent proteomics studies have contributed significantly to further insight into adipocyte biology, particularly with respect to adipokine profiling. In this review novel findings obtained with adipo-proteomics studies are highlighted and the relevance of proteomics technologies to further understand molecular aspects of adipocyte biology is discussed.
Collapse
Affiliation(s)
- Johan Renes
- Department of Human Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | | |
Collapse
|
26
|
Chae YK, Kim SH, Ellinger JJ, Markley JL. Tracing Metabolite Footsteps of Escherichia coli Along the Time Course of Recombinant Protein Expression by Two-Dimensional NMR Spectroscopy. B KOREAN CHEM SOC 2012; 33:4041-4046. [PMID: 23794775 PMCID: PMC3686544 DOI: 10.5012/bkcs.2012.33.12.4041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The recombinant expression of proteins has been the method of choice to meet the demands from proteomics and structural genomics studies. Despite its successful production of many heterologous proteins, Escherichia coli failed to produce many other proteins in their native forms. This may be related to the fact that the stresses resulting from the overproduction interfere with cellular processes. To better understand the physiological change during the overproduction phase, we profiled the metabolites along the time course of the recombinant protein expression. We identified 32 metabolites collected from different time points in the protein production phase. The stress induced by protein production can be characterized by (A) the increased usage of aspartic acid, choline, glycerol, and N-acetyllysine; and (B) the accumulation of adenosine, alanine, oxidized glutathione, glycine, N-acetylputrescine, and uracil. We envision that this work can be used to create a strategy for the production of usable proteins in large quantities.
Collapse
Affiliation(s)
| | | | - James J. Ellinger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L. Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
27
|
Adler B, Boström T, Ekström S, Hober S, Laurell T. Miniaturized and Automated High-Throughput Verification of Proteins in the ISET Platform with MALDI MS. Anal Chem 2012; 84:8663-9. [DOI: 10.1021/ac3017983] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Belinda Adler
- Department of Measurement Technology
and Industrial Electrical Engineering, Division of Nanobiotechnology, Lund University, Box 118, SE-211 00 Lund, Sweden
| | - Tove Boström
- Division of Proteomics, School
of Biotechnology, AlbaNova University Center, KTH, SE-106 91 Stockholm, Sweden
| | - Simon Ekström
- Department of Measurement Technology
and Industrial Electrical Engineering, Division of Nanobiotechnology, Lund University, Box 118, SE-211 00 Lund, Sweden
| | - Sophia Hober
- Division of Proteomics, School
of Biotechnology, AlbaNova University Center, KTH, SE-106 91 Stockholm, Sweden
| | - Thomas Laurell
- Department of Measurement Technology
and Industrial Electrical Engineering, Division of Nanobiotechnology, Lund University, Box 118, SE-211 00 Lund, Sweden
| |
Collapse
|
28
|
Sjöberg R, Sundberg M, Gundberg A, Sivertsson Å, Schwenk JM, Uhlén M, Nilsson P. Validation of affinity reagents using antigen microarrays. N Biotechnol 2012; 29:555-63. [DOI: 10.1016/j.nbt.2011.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 01/31/2023]
|
29
|
Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
Collapse
Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
| | | | | | | |
Collapse
|
30
|
Tegel H, Yderland L, Boström T, Eriksson C, Ukkonen K, Vasala A, Neubauer P, Ottosson J, Hober S. Parallel production and verification of protein products using a novel high-throughput screening method. Biotechnol J 2011; 6:1018-25. [PMID: 21681961 DOI: 10.1002/biot.201000430] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/14/2011] [Accepted: 04/04/2011] [Indexed: 11/09/2022]
Abstract
Protein production and analysis in a parallel fashion is today applied in laboratories worldwide and there is a great need to improve the techniques and systems used for this purpose. In order to save time and money, a fast and reliable screening method for analysis of protein production and also verification of the protein product is desired. Here, a micro-scale protocol for the parallel production and screening of 96 proteins in plate format is described. Protein capture was achieved using immobilized metal affinity chromatography and the product was verified using matrix-assisted laser desorption ionization time-of-flight MS. In order to obtain sufficiently high cell densities and product yield in the small-volume cultivations, the EnBase® cultivation technology was applied, which enables cultivation in as small volumes as 150 μL. Here, the efficiency of the method is demonstrated by producing 96 human, recombinant proteins, both in micro-scale and using a standard full-scale protocol and comparing the results in regard to both protein identity and sample purity. The results obtained are highly comparable to those acquired through employing standard full-scale purification protocols, thus validating this method as a successful initial screening step before protein production at a larger scale.
Collapse
Affiliation(s)
- Hanna Tegel
- School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Francis DM, Page R. Strategies to optimize protein expression in E. coli. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2010; Chapter 5:5.24.1-5.24.29. [PMID: 20814932 PMCID: PMC7162232 DOI: 10.1002/0471140864.ps0524s61] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recombinant protein expression in Escherichia coli (E. coli) is simple, fast, inexpensive, and robust, with the expressed protein comprising up to 50 percent of the total cellular protein. However, it also has disadvantages. For example, the rapidity of bacterial protein expression often results in unfolded/misfolded proteins, especially for heterologous proteins that require longer times and/or molecular chaperones to fold correctly. In addition, the highly reductive environment of the bacterial cytosol and the inability of E. coli to perform several eukaryotic post-translational modifications results in the insoluble expression of proteins that require these modifications for folding and activity. Fortunately, multiple, novel reagents and techniques have been developed that allow for the efficient, soluble production of a diverse range of heterologous proteins in E. coli. This overview describes variables at each stage of a protein expression experiment that can influence solubility and offers a summary of strategies used to optimize soluble expression in E. coli.
Collapse
|
32
|
Junker B. Kaizen for improvement of rapid protein production for early reagent protein quantities. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
33
|
Listwan P, Pédelacq JD, Lockard M, Bell C, Terwilliger TC, Waldo GS. The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2010; 11:41-9. [PMID: 20069378 PMCID: PMC2855807 DOI: 10.1007/s10969-009-9077-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 12/30/2009] [Indexed: 11/26/2022]
Abstract
Protein production in Escherichia coli involves high-level expression in a culture, followed by harvesting of the cells and finally their disruption, or lysis, to release the expressed proteins. We compare three high-throughput chemical lysis methods to sonication, using a robotic platform and methodologies developed in our laboratory [1]. Under the same expression conditions, all lysis methods varied in the degree of released soluble proteins. With a set of 96 test proteins, we used our split GFP to quantify the soluble and insoluble protein fractions after lysis. Both the amount of soluble protein and the percentage recovered in the soluble fraction using SoluLyse were well correlated with sonication. Two other methods, Bugbuster and lysozyme, did not correlate well with sonication. Considering the effects of lysis methods on protein solubility is especially important when accurate protein solubility measurements are needed, for example, when testing adjuvants, growth media, temperature, or when establishing the effects of truncation or sequence variation on protein stability.
Collapse
Affiliation(s)
- Pawel Listwan
- Bioscience Division, MS-M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA.
| | | | | | | | | | | |
Collapse
|
34
|
Tegel H, Tourle S, Ottosson J, Persson A. Increased levels of recombinant human proteins with the Escherichia coli strain Rosetta(DE3). Protein Expr Purif 2009; 69:159-67. [PMID: 19733669 DOI: 10.1016/j.pep.2009.08.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/26/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
Abstract
The effect of two Escherichiacoli expression strains on the production of recombinant human protein fragments was evaluated. High-throughput protein production projects, such as the Swedish Human Protein Atlas project, are dependent on high protein yield and purity. By changing strain from E. coli BL21(DE3) to E. coli Rosetta(DE3) the overall success rate of the protein production has increased dramatically. The Rosetta(DE3) strain compensates for a number of rare codons. Here, we describe how the protein expression of human gene fragments in E. coli strains BL21(DE3) and Rosetta(DE3) was evaluated in two stages. Initially a test set of 68 recombinant proteins that previously had been expressed in BL21(DE3) was retransformed and expressed in Rosetta(DE3). The test set generated very positive results with an improved expression yield and a significantly better purity of the protein product which prompted us to implement the Rosetta(DE3) strain in the high-throughput protein production. Except for analysis of protein yield and purity the sequences were also analyzed regarding number of rare codons and rare codon clusters. The content of rare codons showed to have a significant effect on the protein purity. Based on the results of this study the atlas project permanently changed expression strain to Rosetta(DE3).
Collapse
Affiliation(s)
- Hanna Tegel
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | | | | | | |
Collapse
|
35
|
|