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Van Gompel E, Demirdal D, Fernandes-Cerqueira C, Horuluoglu B, Galindo-Feria A, Wigren E, Gräslund S, De Langhe E, Benveniste O, Notarnicola A, Chemin K, Lundberg IE. Autoantibodies against the melanoma differentiation-associated protein 5 in patients with dermatomyositis target the helicase domains. Rheumatology (Oxford) 2024; 63:1466-1473. [PMID: 37572295 PMCID: PMC11065437 DOI: 10.1093/rheumatology/kead400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 08/14/2023] Open
Abstract
OBJECTIVES Clinical observations in patients with dermatomyositis (DM) and autoantibodies against the melanoma differentiation-associated protein 5 (MDA5) suggest that the autoantibodies contribute to the pathogenesis of MDA5(+) DM. To gain insight into the role of the anti-MDA5 autoantibodies, we aimed to identify their binding sites on the different domains of the MDA5 protein. METHODS We developed an in-house ELISA to assess the reactivity against the MDA5 domains (conformational epitopes) in plasma (n = 8) and serum (n = 24) samples from MDA5(+) patients with varying clinical manifestations and disease outcomes. The reactivities were also assessed using western blot (linearized epitopes). An ELISA-based depletion assay was developed to assess cross-reactivity among the different MDA5 domains. RESULTS All eight plasma samples consistently showed reactivity towards conformational and linearized epitopes on the helicase domains of the MDA5 protein. The ELISA-based depletion assay suggests that anti-MDA5 autoantibodies specifically target each of the three helicase domains. Twenty-two of the 24 serum samples showed reactivity in the in-house ELISA and all 22 displayed reactivity towards the helicase domains of the MDA5 protein. CONCLUSIONS Our data revealed that the main immunogenic targets of anti-MDA5 autoantibodies from MDA5(+) patients are the helicase domains. Considering that the helicase domains are responsible for the enzymatic activity and subsequent triggering of an inflammatory response, our findings suggest that binding of anti-MDA5 autoantibodies could alter the canonical activity of the MDA5 protein and potentially affect the downstream induction of a pro-inflammatory cascade.
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Affiliation(s)
- Eveline Van Gompel
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Deniz Demirdal
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Gastro, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Catia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angeles Galindo-Feria
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Gastro, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Edvard Wigren
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ellen De Langhe
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Division of Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Olivier Benveniste
- Centre de Recherche en Myologie, Unité Mixte de Recherche Scientifique 974, Sorbonne Université, INSERM, Paris, France
- Département de Médecine Interne et Immunologie Clinique, Centre de Référence Maladies Neuro-Musculaires, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Antonella Notarnicola
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Gastro, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Karine Chemin
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Gastro, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Demirdal D, Van Gompel E, Wigren E, Dastmalchi M, Horuluoglu B, Galindo-Feria AS, Gräslund S, Chemin K, Lundberg IE, Notarnicola A. POS0905 CHARACTERISATION OF SWEDISH MYOSITIS PATIENTS WITH ANTI-MDA5 AUTOANTIBODIES AND CORRELATION OF CLINICAL FEATURES WITH AUTOANTIBODY LEVELS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundThe association between anti-melanoma differentiation association protein 5 autoantibodies (aMDA5) and rapidly progressive interstitial lung disease (RP-ILD) in clinically amyopathic dermatomyositis is well established in Asian population cohorts. In western cohorts, ILD has been strongly associated with aMDA5 but data regarding RP-ILD have been more conflicting. It is also suggested that western cohorts have more pronounced myopathic features than Asian.ObjectivesTo characterise the disease manifestations of a Swedish aMDA5 positive idiopathic inflammatory myositis (IIM) cohort and to explore antigen reactivity of the MDA5 protein.MethodsFirst available serum samples collected from 28 consecutive patients with IIM and positive aMDA5 ever tested by ELISA, Line Blot (LB) or Immunoprecipitation, attending Karolinska University Hospital between 1999 and 2021, were included. Clinical data including presence of anti-SSA autoantibodies by ELISA or LB was retrieved retrospectively. An in-house ELISA was used to screen serum samples for reactivity against a recombinant MDA5 protein (rMDA5, aa A110-D1025, UniProt ID Q9BYX4) and seven MDA5-derived constructs containing different domains. Correlations between aMDA5 reactivity levels and clinical data were explored.ResultsNine patients showed no reactivity to any of the rMDA5 constructs by ELISA and were excluded from further analysis.Reactivity against rMDA5 was confirmed by ELISA in 19 patients (median 184.7 µg/mL (interquartile range (IQR) 277.07). The cohort included 13 male and 6 female patients, 94% Caucasian, with mean age at diagnosis of 41.05 years (standard deviation (SD) 10.5). Median disease duration at time of sampling was 0 months (IQR 1). All patients except one had signs of muscle involvement (muscle weakness, elevated muscle enzymes, muscle oedema or muscle biopsy consistent with myositis). At diagnosis 63.2% of patients reported muscle weakness (21.1 % had a manual muscle test 8 score <75). Dermatological findings were observed in 17/19 (89.7 %). During disease course nine patients (47.4%) had confirmed arthritis.ILD was diagnosed in 16/19 patients (84.2%), four of these (25%) developed a RP-ILD. One patient passed away due to RP-ILD and one required a lung transplant. Patients with ILD had a statistically significant higher mean age at diagnosis than those without (42.8.5 (SD 10.3) vs 31.3 (SD 4.7) years, p=0.02). Patients developing RP-ILD were not significantly older than patients with chronic ILD. Respiratory symptoms were reported by 75% of patients with ILD at time of diagnosis. The mean total lung capacity (TLC) of the ILD cohort was 68% (SD 17), mean diffusion capacity of carbon monoxide (DLCO) was 59% (SD 15) and mean forced vital capacity (FVC) was 62% (SD 19). There was a higher proportion of patients with CRP ≥ 3 times the reference range at diagnosis amongst patients with FVC <70 % than patients with FVC >70 % (88.9 % vs 16.7 %, p= 0.01).Ten patients (52.6%) had anti-SSA autoantibodies, all had ILD. Anti-SSA positive patients had a statistically significant lower TLC than those without (62% vs 79% respectively, p=0.04) and a lower FVC (57% vs 76% respectively, p=0.05).We found a weak non-statistically significant negative correlation between titres of aMDA5 and TLC, DLCO and FVC (Pearson coefficients -0.187, -0.289, -0.130 respectively). Frequency of ILD was higher in patients with aMDA5 titres >100 µg/mL than those with titers <100, but not statistically significant (81.3% vs 18.8%, respectively).ConclusionIn this Caucasian cohort of aMDA5 positive IIM patients, ILD was present in over 80% of patients, of these, one quarter had RP-ILD. Older patients were more likely to present with ILD. Anti-SSA positivity and higher CRP levels were associated with worse lung function. We found a weak negative correlation between aMDA5 titres and lung function tests, as well as a trend of higher frequency of ILD in patients with higher aMDA5 titres. Muscle and skin involvement were found in a high proportion of patients.AcknowledgementsD. Demirdal & E. Van Gompel contributed equally to this abstract.Disclosure of InterestsDeniz Demirdal: None declared, Eveline Van Gompel: None declared, Edvard Wigren: None declared, Maryam Dastmalchi: None declared, Begum Horuluoglu: None declared, Angeles Shunashy Galindo-Feria: None declared, Susanne Gräslund: None declared, Karine Chemin: None declared, Ingrid E. Lundberg Shareholder of: Roche and Novartis., Consultant of: Consulting fees from Corbus Pharmaceuticals Inc, Astra Zeneca, Bristol Myer´s Squibb, Corbus Pharmaceutical, EMD Serono Research & Development Institute, Argenx, Octapharma, Kezaar, Orphazyme, and Janssen, Grant/research support from: Research grants from Astra Zeneca, Antonella Notarnicola Speakers bureau: compensation for lecture at conference sponsored by Boehringer Ingelheim.
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Preger C, Notarnicola A, Hellström C, Wigren E, Lundberg IE, Jakobsson PJ, Persson H, Gräslund S. POS0053 ABUNDANT AUTOANTIBODY ISOTYPES IN IDIOPATHIC INFLAMMATORY MYOPATHIES. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.1980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundAnti-synthetase syndrome (ASSD), a sub-group of idiopathic inflammatory myopathies (IIM) is characterized by the presence of autoantibodies targeting aminoacyl tRNA synthetases (aaRS) and specific clinical manifestations such as myositis and interstitial lung disease (ILD) [1]. Some of the most common anti-aaRS autoantibodies in ASSD are anti-Jo1, -PL7, -PL12 and-EJ. In addition, many anti-aaRS positive patients are also positive for anti-Ro52. Having the combination of anti-Jo1 and anti-Ro52 increases the risk of developing ILD [2]. The presence of autoantibodies is an important part of the classification of ASSD, however only autoantibodies of IgG isotype are usually analyzed in the clinical setting. In rheumatoid arthritis there is evidence that anti-citrullinated protein/peptide antibodies (ACPA) can be found as IgG, IgA and IgM, and importantly, specific isotypes might correlate with disease activity [3, 4].ObjectivesTo verify if other autoantibody isotypes, besides IgG, might be present in sera of patients with IIM/ASSD and to compare with the corresponding frequencies in population controls (PC).MethodsStored sera collected from consecutive 366 IIM patients and 156 age/gender matched PC at Karolinska University Hospital were retrospectively selected. The serum samples were screened for the presence of autoantibodies of isotypes IgG, IgA and IgM, against a panel of 20 antigens representing Jo1 (HisRS), PL7 (ThrRS), PL12 (AlaRS), EJ (GlyRS), and Ro52 (TRIM21) using a multiplex bead array assay.ResultsWe identified IIM patients with autoantibodies of different isotypes, and a low frequency in PC (Figure 1). For anti-Jo1 autoantibodies we could detect IIM patients with only IgG (n=13), only IgM (n=8) and only IgA (n=4), but the majority had a combination of two (n=32) or three isotypes (n=16). For the other anti-aaRS autoantibodies the distribution was more equal to each of the three isotypes with anti-PL12 and anti-PL7 being represented by a slightly higher frequency of IgG and only a few patients had antibodies of more than one isotype targeting PL12, PL7 or EJ. The majority of anti-Ro52 positive IIM patients (n=52) only harbored IgG isotype. The combination of anti-Ro52 and anti-aaRS autoantibodies was identified in 28 patients (anti-Jo1 (n=19), -PL12 (n=2), -PL7 (n=3), and -EJ (n=4)). Most patients with such combination had anti-Ro52 IgG together with anti-aaRS IgG or IgG in combination with IgA and/or IgM. The exception was observed for three anti-Jo1 positive patients who had the combination anti-Ro52 IgG with only anti-Jo1 IgM and one anti-PL7 positive patient who had anti-Ro52 IgA together with anti-PL7 IgA and IgG.Figure 1.Venn diagrams showing reactivity in idiopathic inflammatory myopathies (IIM) (top) and population controls (PC) (bottom) for the three autoantibody isotypes IgG, IgA and IgM against five myositis antigens: Jo1 (HisRS), PL12 (AlaRS), ThrRS (PL7), EJ (GlyRS) and Ro52 (TRIM21).ConclusionThe frequency of the different autoantibody isotypes seems to be autoantigen dependent. Our results suggest that for anti-aaRS autoantibodies it could be important to investigate additional autoantibody isotypes, as some patients only harbor autoantibodies of IgM or IgA isotypes but not IgG. The clinical relevance of the different antibody isotypes still needs to be determined.References[1]Mahler, M., et al., Rev, 2014. 13(4-5): p. 367-71.[2]Huang, H.L., et al., J Clin Neurosci, 2020.[3]Arlestig, L., et al., Ann Rheum Dis, 2012. 71(6): p. 825-9.[4]Roos Ljungberg, K., et al., Arthritis Res Ther, 2020. 22(1): p. 274.Table 1.Total number of individuals and percentage (n (%)) in each group for each of the isotypes and antigens.anti-Jo1anti-PL12anti-PL7anti-EJanti-Ro52IIMPCIIMPCIIMPCIIMPCIIMPCIgG61 (16.7)1 (0.6)7 (1.9)0 (0.0)7 (1.9)0 (0.0)3 (0.8)0 (0.0)54 (14.8)5 (3.2)IgA20 (5.5)0 (0.0)2 (1.2)1 (0.6)3 (0.8)2 (1.3)1 (0.3)1 (0.6)3 (0.8)1 (0.6)IgM56 (15.3)1 (0.6)1 (0.3)2 (1.3)7 (1.9)0 (0.0)1 (0.3)0 (0.0)3 (0.8)2 (1.3)AcknowledgementsSciLifeLab facilities Autoimmunity and Serology Profiling and Human Antibody Therapeutics (Drug Discovery and Development). IMI project EUbOPEN, This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 875510. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA and Ontario Institute for Cancer Research, Royal Institution for the Advancement of Learning McGill University, Kungliga Tekniska Hoegskolan, Diamond Light Source Limited.Disclosure of InterestsCharlotta Preger Grant/research support from: IMI project EUbOPEN, Grant no 875510, Antonella Notarnicola: None declared, Cecilia Hellström: None declared, Edvard Wigren Grant/research support from: IMI project EUbOPEN, Grant no 875510, Ingrid E. Lundberg Shareholder of: Roche and Novartis, Consultant of: Corbus Pharmaceuticals Inc, Astra Zeneca, Bristol Myer´s Squibb, Corbus Pharmaceutical, EMD Serono Research & Development Institute, Argenx, Octapharma, Kezaar, Orphazyme, and Janssen, Grant/research support from: Astra Zeneca, Per-Johan Jakobsson Shareholder of: Gesynta Pharma, Consultant of: UCB, Grant/research support from: Gesynta Pharma, Helena Persson Employee of: Affibody AB, Susanne Gräslund Grant/research support from: IMI project EUbOPEN, Grant no 875510
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Notarnicola A, Preger C, Lundström SL, Renard N, Wigren E, Van Gompel E, Galindo-Feria AS, Persson H, Fathi M, Grunewald J, Jakobsson PJ, Gräslund S, Lundberg IE, Fernandes-Cerqueira C. Longitudinal assessment of reactivity and affinity profile of anti-Jo1 autoantibodies to distinct HisRS domains and a splice variant in a cohort of patients with myositis and anti-synthetase syndrome. Arthritis Res Ther 2022; 24:62. [PMID: 35236390 PMCID: PMC8889758 DOI: 10.1186/s13075-022-02745-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 02/13/2022] [Indexed: 02/08/2023] Open
Abstract
Background To address the reactivity and affinity against histidyl-transfer RNA synthetase (HisRS) autoantigen of anti-Jo1 autoantibodies from serum and bronchoalveolar lavage fluid (BALF) in patients with idiopathic inflammatory myopathies/anti-synthetase syndrome (IIM/ASSD). To investigate the associations between the reactivity profile and clinical data over time. Methods Samples and clinical data were obtained from (i) 25 anti-Jo1+ patients (19 sera with 16 longitudinal samples and 6 BALF/matching sera at diagnosis), (ii) 29 anti-Jo1− patients (25 sera and 4 BALF/matching sera at diagnosis), and (iii) 27 age/gender-matched healthy controls (24 sera and 3 BALF/matching sera). Reactivity towards HisRS full-length (HisRS-FL), three HisRS domains (WHEP, antigen binding domain (ABD), and catalytic domain (CD)), and the HisRS splice variant (SV) was tested. Anti-Jo1 IgG reactivity was evaluated by ELISA and western blot using IgG purified from serum by affinity chromatography. In paired serum-BALF, anti-Jo1 IgG and IgA reactivity was analyzed by ELISA. Autoantibody affinity was measured by surface plasmon resonance using IgG purified from sera. Correlations between autoantibody reactivity and clinical data were evaluated at diagnosis and longitudinally. Results Anti-Jo1 IgG from serum and BALF bound HisRS-FL, WHEP, and SV with high reactivity at the time of diagnosis and recognized both conformation-dependent and conformation-independent HisRS epitopes. Anti-HisRS-FL IgG displayed high affinity early in the disease. At the time of IIM/ASSD diagnosis, the highest autoantibody levels against HisRS-FL were found in patients ever developing interstitial lung disease (ILD) and arthritis, but with less skin involvement. Moreover, the reactivity of anti-WHEP IgG in BALF correlated with poor pulmonary function. Levels of autoantibodies against HisRS-FL, HisRS domains, and HisRS splice variant generally decreased over time. With some exceptions, longitudinal anti-HisRS-FL antibody levels changed in line with ILD activity. Conclusion High levels and high-affinity anti-Jo1 autoantibodies towards HisRS-FL were found early in disease in sera and BALF. In combination with the correlation of anti-HisRS-FL antibody levels with ILD and ILD activity in longitudinal samples as well as of anti-WHEP IgG in BALF with poor pulmonary function, this supports the previously raised hypothesis that the lung might have a role in the immune reaction in anti-Jo1-positive patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02745-6.
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Affiliation(s)
- Antonella Notarnicola
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden. .,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Charlotta Preger
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Structural Genomics Consortium, Toronto, Canada
| | - Susanna L Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
| | - Nuria Renard
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edvard Wigren
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Structural Genomics Consortium, Toronto, Canada
| | - Eveline Van Gompel
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, KULeuven, Leuven, Belgium
| | - Angeles S Galindo-Feria
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Maryam Fathi
- Department of Respiratory Medicine and Allergy, J7:30, Bioclinicum, Karolinska University Hospital, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Johan Grunewald
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Respiratory Medicine and Allergy, J7:30, Bioclinicum, Karolinska University Hospital, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Structural Genomics Consortium, Toronto, Canada
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Cátia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-171 64, Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,4Dcell, 14 rue de la Beaune, 93100, Montreuil, France
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Galindo-Feria AS, Horuluoglu B, Day J, Fernandes-Cerqueira C, Wigren E, Gräslund S, Proudman S, Lundberg IE, Limaye V. Autoantibodies against Four-and-a-Half-LIM Domain 1 (FHL1) in Inflammatory Myopathies: Results from an Australian Single-Center Cohort. Rheumatology (Oxford) 2022; 61:4145-4154. [PMID: 35022656 PMCID: PMC9536793 DOI: 10.1093/rheumatology/keac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives To determine the prevalence and associations of autoantibodies targeting a muscle-specific autoantigen, four-and-a-half-LIM-domain 1 (FHL1), in South Australian patients with histologically-confirmed idiopathic inflammatory myopathies (IIM) and in patients with SSc. Material and methods Sera from patients with IIM (n = 267) from the South Australian Myositis Database (SAMD), SSc (n = 174) from the Australian Scleroderma Cohort Study (ASCS) and healthy controls (HC, n = 100) were analysed for anti-FHL1 autoantibodies by Enzyme-Linked ImmunoSorbent Assay (ELISA). Results Autoantibodies to FHL1 were more frequent in patients with IIM (37/267, 13.8%) compared with SSc (12/174, 7%) (P < 0.02) and HC (2/100, 2%) (P < 0.001). The most common IIM subtypes among FHL1+ IIM patients were (32%) and IBM (2/37, 32%). No statistically significant differences in muscular or extra-muscular manifestations of IIM were found when comparing patients who were anti-FHL1+ with their anti-FHL1– counterparts. In 29/37 (78%) anti-FHL1+ patients, no myositis-specific autoantibodies (MSA) were present. In FHL1+ muscle biopsies, there was less frequent infiltration by CD45+ cells (P = 0.04). There was a trend for HLA alleles DRB1*07 and DRB1*15 to be more frequent in anti-FHL1+ compared with anti-FHL1– patients (9/25 vs 19/113, P = 0.09 and 8/25 vs 15/114, P = 0.09, respectively). Conclusions We report a substantial prevalence (13.8%) of anti-FHL1 autoantibodies in a large cohort of patients with histologically confirmed IIM; 75% of these cases did not have a detectable myositis-specific autoantibody. Anti-FHL1 autoantibodies were also detected in a subgroup of patients with SSc (7%), indicating that anti-FHL1 autoantibodies may not be myositis-specific. The trend towards an HLA-DR association might indicate a specific immune response to the FHL1 protein.
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Affiliation(s)
- Angeles S Galindo-Feria
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden, Karolinska Institutet
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden, Karolinska Institutet
| | - Jessica Day
- Rheumatology Unit, Royal Adelaide Hospital, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Catia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden, Karolinska Institutet.,4Dcell, Montreuil, France
| | - Edvard Wigren
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Structural Genomics Consortium, Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Structural Genomics Consortium, Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Proudman
- Rheumatology Unit, Royal Adelaide Hospital, Adelaide, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden, Karolinska Institutet
| | - Vidya Limaye
- Rheumatology Unit, Royal Adelaide Hospital, Adelaide, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, Australia
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Szykowska A, Chen Y, Smith TB, Preger C, Yang J, Qian D, Mukhopadhyay SM, Wigren E, Neame SJ, Gräslund S, Persson H, Atkinson PJ, Di Daniel E, Mead E, Wang J, Davis JB, Burgess-Brown NA, Bullock AN. Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain. Structure 2021; 29:1241-1252.e5. [PMID: 34233201 PMCID: PMC8575122 DOI: 10.1016/j.str.2021.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/11/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022]
Abstract
Mutations in TREM2, a receptor expressed by microglia in the brain, are associated with an increased risk of neurodegeneration, including Alzheimer's disease. Numerous studies support a role for TREM2 in sensing damaging stimuli and triggering signaling cascades necessary for neuroprotection. Despite its significant role, ligands and regulators of TREM2 activation, and the mechanisms governing TREM2-dependent responses and its cleavage from the membrane, remain poorly characterized. Here, we present phage display generated antibody single-chain variable fragments (scFvs) to human TREM2 immunoglobulin-like domain. Co-crystal structures revealed the binding of two scFvs to an epitope on the TREM2 domain distal to the putative ligand-binding site. Enhanced functional activity was observed for oligomeric scFv species, which inhibited the production of soluble TREM2 in a HEK293 cell model. We hope that detailed characterization of their epitopes and properties will facilitate the use of these renewable binders as structural and functional biology tools for TREM2 research.
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Affiliation(s)
- Aleksandra Szykowska
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Yu Chen
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Thomas B Smith
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK; Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Charlotta Preger
- Structural Genomics Consortium (SGC), Karolinska Institutet, Karolinska University Hospital, Division of Rheumatology, Department of Medicine Solna, 171 76 Stockholm, Sweden
| | - Jingjing Yang
- Viva Biotech Ltd., 334 Aidisheng Road, Zhangjiang High-Tech Park, Shanghai 201203, China
| | - Dongming Qian
- Viva Biotech Ltd., 334 Aidisheng Road, Zhangjiang High-Tech Park, Shanghai 201203, China
| | - Shubhashish M Mukhopadhyay
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Edvard Wigren
- Structural Genomics Consortium (SGC), Karolinska Institutet, Karolinska University Hospital, Division of Rheumatology, Department of Medicine Solna, 171 76 Stockholm, Sweden
| | | | - Susanne Gräslund
- Structural Genomics Consortium (SGC), Karolinska Institutet, Karolinska University Hospital, Division of Rheumatology, Department of Medicine Solna, 171 76 Stockholm, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development & School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Stockholm, Sweden
| | | | - Elena Di Daniel
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK; Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Emma Mead
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK; Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - John Wang
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - John B Davis
- Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK; Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
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Van Gompel E, Cerqueira C, Wigren E, Gräslund S, Chemin K, Horuluoglu B, De Langhe E, Benveniste O, Lundberg IE. OP0321 DELINEATING THE IMMUNOGENIC DOMAINS OF MDA5 USING PATIENT DERIVED AUTOANTIBODIES. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.4264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The presence of myositis specific anti-melanoma differentiation associated protein 5 (MDA5) autoantibodies is associated with mucocutaneous ulcerations, rapidly progressing interstitial lung disease (RPILD), arthritis and mild muscle involvement in patients. RPILD is the major cause of mortality. At present it is unknown which domain of the MDA5 protein is the main elicitor of an immunogenic response.Objectives:The aim of this study is to delineate the domains in the MDA5 protein that are the target of autoantibodies.Methods:Anti-MDA5 IgG were isolated from MDA5(+) patient plasma (7 UPMC, 1 KI and 1 KULeuven) by affinity chromatography using an in-house affinity column as described earlier in Ossipova et al, 2014(1). 8 constructs covering different regions of the MDA5 protein were recombinantly produced in E.coli (Uniprot ID Q9BYX4, Figure 1). An in-house ELISA was developed to identify the domains with the main epitope(s) by measuring the reactivity of the plasma samples and purified autoantibodies against these MDA5 protein constructs, similar to what was reported by Fernandes-Cerqueira et al, 2018(2). The biotinylated MDA5 proteins were immobilized on streptavidin coated plates and subsequently incubated with primary antibodies (purified autoantibodies(2) or original plasma) and a HRP-conjugated secondary antibody. The ELISA was developed by the addition of TMB substrate and the optical density (OD) was measured at 450 nm.Figure 1.Graphical presentation of the constructs representing different (combinations of) domains of the MDA5 protein.Results:The preliminary data suggest the main reactivity of the plasma samples and the corresponding purified autoantibodies is directed towards the helicase domains and that there is variability between the patients in the reactivity towards domains located at the end of the protein.Conclusion:The study aims to resolve the main immunogenic domain of the MDA5 protein, which will lead to more insight in the disease mechanisms. The preliminary results suggest this domain is in the center of the MDA5 protein, but further experiments are necessary. We will use this set up to study differences in reactivity between patients (from different cohorts) and assess if differences in antibody reactivity could be linked to clinical features such as RPILD. Such correlations might be beneficial to predict the disease progression and to apply personal treatment approaches.References:[1]Ossipova E, Cerqueira CF, Reed E, Kharlamova N, Israelsson L, et al. Affinity purified anti-citrullinated protein/peptide antibodies target antigens expressed in the rheumatoid joint. Arthritis Res Ther. 2014;16(4):R167.[2]Fernandes-Cerqueira C, Renard N, Notarnicola A, Wigren E, Gräslund S, et al. Patients with anti-Jo1 antibodies display a characteristic IgG Fc-glycan profile which is further enhanced in anti-Jo1 autoantibodies. Scientific reports. 2018;8(1):17958.Disclosure of Interests:Eveline Van Gompel: None declared, Catia Cerqueira: None declared, Edvard Wigren: None declared, Susanne Gräslund: None declared, Karine Chemin: None declared, Begum Horuluoglu: None declared, Ellen De Langhe: None declared, Olivier Benveniste: None declared, Ingrid E. Lundberg Consultant of: Consulting fees from Corbus Pharmaceuticals, Inc, Grant/research support from: Research grants from Bristol Myers Squibb and AstraZeneca.
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Preger C, Wigren E, Ossipova E, Marks C, Lengqvist J, Hofström C, Andersson O, Jakobsson PJ, Gräslund S, Persson H. Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases. J Biol Chem 2020; 295:13981-13993. [PMID: 32817337 DOI: 10.1074/jbc.ra120.012893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/10/2020] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) have long been viewed as mere housekeeping proteins and have therefore often been overlooked in drug discovery. However, recent findings have revealed that many aaRSs have noncanonical functions, and several of the aaRSs have been linked to autoimmune diseases, cancer, and neurological disorders. Deciphering these roles has been challenging because of a lack of tools to enable their study. To help solve this problem, we have generated recombinant high-affinity antibodies for a collection of thirteen cytoplasmic and one mitochondrial aaRSs. Selected domains of these proteins were produced recombinantly in Escherichia coli and used as antigens in phage display selections using a synthetic human single-chain fragment variable library. All targets yielded large sets of antibody candidates that were validated through a panel of binding assays against the purified antigen. Furthermore, the top-performing binders were tested in immunoprecipitation followed by MS for their ability to capture the endogenous protein from mammalian cell lysates. For antibodies targeting individual members of the multi-tRNA synthetase complex, we were able to detect all members of the complex, co-immunoprecipitating with the target, in several cell types. The functionality of a subset of binders for each target was also confirmed using immunofluorescence. The sequences of these proteins have been deposited in publicly available databases and repositories. We anticipate that this open source resource, in the form of high-quality recombinant proteins and antibodies, will accelerate and empower future research of the role of aaRSs in health and disease.
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Affiliation(s)
- Charlotta Preger
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Edvard Wigren
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elena Ossipova
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Carolyn Marks
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Camilla Hofström
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Oskar Andersson
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden .,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
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Preger C, Notarnicola A, Hellström C, Wigren E, Cerqueira C, Nilsson P, Lundberg IE, Persson H, Gräslund S, Jakobsson PJ. SAT0288 CHARACTERIZATION OF ANTI-AMINOACYL TRNA SYNTHETASE AUTOANTIBODIES IN PATIENTS WITH IDIOPATHIC INFLAMMATORY MYOPATHIES. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.1414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Idiopathic inflammatory myopathies (IIM) are rare chronic inflammatory diseases associated with high mortality and morbidity [1]. One sub-group of IIM, anti-synthetase syndrome (ASS), is characterized by the presence of autoantibodies that target aminoacyl transfer(t) RNA synthetases (aaRS), together with specific clinical manifestations such as myositis, interstitial lung disease (ILD), arthritis, mechanic’s hand, Raynaud’s syndrome and fever [2]. The most common anti-aaRS autoantibody, anti-Jo1 targeting histidyl tRNA synthetase (HisRS), is present in up to 20-30% of patients with IIM, and up to 90% of patients with myositis and ILD [3, 4]. Besides Jo1, there are today seven other identified autoantigens within the aaRS family.Objectives:A large part of patients with IIM, including individuals with clinical manifestations indicating ASS, test seronegative to all known myositis specific autoantibodies. However, these patients could potentially harbor autoantibodies against targets not tested for in clinic. In this study, we aimed at extending the detection of autoantibodies by including all cytoplasmic aaRS in the analysis of patients with IIM. We hypothesized the existence of new potential autoantigens within this protein family.Methods:The presence of anti-aaRS autoantibodies was determined using a multiplex suspension bead array assay on 242 IIM patients from the Karolinska University Hospital myositis cohort. A panel of 186 recombinant constructs, representing 57 proteins that included full-length or partial sequence overlaps between constructs of all cytoplasmic aaRS as well as other myositis related proteins, were coupled to magnetic color-coded beads and each plasma sample was tested against the complete antigen panel.Results:By the use of this multiplex method we identified patients with autoantibodies against many of the tested aaRS. Autoantibodies binding to HisRS have previously been shown to bind with higher reactivity to the WHEP domain of HisRS and this was also confirmed in this study. We confirmed reactivity against three of the other aaRS tested for in the clinic (PL-12, PL-7, and EJ). In addition, we identified patients positive for anti-Zo, -KS and -HA, autoantibodies usually not screened for in routine. Finally, our data indicates that there are autoantibodies binding to other aaRS than the previously known eight autoantigens, which will be presented.Conclusion:In this study, we could detect autoantibodies in plasma from patients with IIM, both against the most common aaRS autoantigens, but also against other aaRS that are usually not tested for in clinic. We conclude that it is important to continue the studies of anti-aaRS autoantibodies, and their correlation to clinical manifestations, and in the long run also include more aaRS autoantigens in clinical practice.References:[1]Dobloug, G.C., et al., Mortality in idiopathic inflammatory myopathy: results from a Swedish nationwide population-based cohort study. Ann Rheum Dis, 2018. 77(1): p. 40-47.[2]Barsotti, S. and I.E. Lundberg, Myositis an evolving spectrum of disease. Immunol Med, 2018. 41(2): p. 46-54.[3]Vencovsky, J., H. Alexanderson, and I.E. Lundberg, Idiopathic Inflammatory Myopathies. Rheum Dis Clin North Am, 2019. 45(4): p. 569-581.[4]Richards, T.J., et al., Characterization and peripheral blood biomarker assessment of anti-Jo-1 antibody-positive interstitial lung disease. Arthritis Rheum, 2009. 60(7): p. 2183-92.Disclosure of Interests:Charlotta Preger: None declared, Antonella Notarnicola: None declared, Cecilia Hellström: None declared, Edvard Wigren: None declared, Catia Cerqueira: None declared, Peter Nilsson: None declared, Ingrid E. Lundberg Grant/research support from: Bristol Meyer Squibb, Corbus Pharmaceuticals, Inc and Astra Zeneca, Helena Persson: None declared, Susanne Gräslund: None declared, Per-Johan Jakobsson Shareholder of: Gesynta Pharma, Grant/research support from: Gesynta Pharma, AstraZeneca,
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Notarnicola A, Preger C, Lundström S, Renard N, Wigren E, Van Gompel E, Galindo-Feria AS, Persson H, Fathi M, Grunewald J, Jakobsson PJ, Gräslund S, Lundberg IE, Cerqueira C. SAT0335 SERUM AND BALF-DERIVED ANTI-JO1 AUTOANTIBODIES EXHIBIT HIGH REACTIVITY TO DISTINCT HISRS DOMAINS AND ASSOCIATE WITH LUNG AND JOINT INVOLVEMENT IN PATIENTS WITH IIM/ASS. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.3266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Autoantibodies that target aminoacyl transfer(t) RNA synthetases (aaRS) represent the serological marker of the anti-synthetase syndrome (ASS), a major subgroup of the idiopathic inflammatory myopathies (IIM) (1). Among the anti-aaRS, anti-histidyl tRNA synthetase (HisRS) autoantibodies (anti-Jo1) are the most common. Up to 90% of IIM/ASS patients diagnosed with interstitial lung disease (ILD) harbor anti-Jo1 autoantibodies (2).Objectives:Reactivity and affinity of anti-Jo1 autoantibodies from serum and broncheoalveolar lavage fluid (BALF) were investigated against HisRS autoantigen. Associations with clinical data from patients IIM/ASS were addressed.Methods:Total IgGs were purified by affinity chromatography. Samples and clinical data were obtained from: i) 26 anti-Jo1+patients (19 at diagnosis, 16/19 at follow-up, 7 BALF/matching serum at baseline; ii) 29 anti-Jo1-(25 serum at diagnosis, 4 BALF/matching serum at baseline); iii) 24 age/gender matched healthy controls. Anti-Jo1 IgG and IgA response against HisRS was evaluated by ELISA and western blot. Affinity was measured by surface plasmon resonance. HisRS full-length (HisRS-FL), two HisRS domains (ABD and CD), and two HisRS splice variants (WHEP and WHEP + ABD splice variant (SV)) were tested. Correlations between autoantibody reactivity and clinical data, at baseline and over disease course, were evaluated.Results:Anti-Jo1 autoantibodies from serum and lung bound HisRS-FL, WHEP and SV with high reactivity and affinity already at diagnosis and recognized both conformational and linear HisRS epitopes (Fig. 1). Levels of autoantibodies (against HisRS-FL, -domains and -splice variants) varied among patients and overtime. Patients with ILD, arthritis and less skin involvement presented higher anti-Jo1 titers compared to those with lower anti-Jo1 titers and to the anti-Jo1 negative group (Fig. 2). Anti-WHEP reactivity in BALF strongly correlated with poor pulmonary function.Conclusion:High reactivity and affinity at time of diagnosis indicates that autoimmunity against HisRS is most likely initiated before IIM/ASS diagnosis. Reactivity to specific splice variants of HisRS may be employed as diagnostic and prognostic markers.References:[1]Marguerie C, Bunn CC, Beynon HL, Bernstein RM, Hughes JM, So AK, Walport MJ: Polymyositis, pulmonary fibrosis and autoantibodies to aminoacyl-tRNA synthetase enzymes. Q J Med 1990, 77(282):1019-1038[2]Richards TJ, Eggebeen A, Gibson K, Yousem S, Fuhrman C, Gochuico BR, Fertig N, Oddis CV, Kaminski N, Rosas IO et al: Characterization and peripheral blood biomarker assessment of anti-Jo-1 antibody-positive interstitial lung disease. Arthritis Rheum 2009, 60(7):2183-2192.Fig. 1.Anti-Jo1 reactivity in total IgG purified from the first available serum sampleFig. 2.Reactivity of total anti-Jo1+ IgG purified from the first available serum close to IIM/ASS diagnosis in relation to clinical dataDisclosure of Interests:Antonella Notarnicola: None declared, Charlotta Preger: None declared, Susanna Lundström: None declared, Nuria Renard: None declared, Edvard Wigren: None declared, Eveline Van Gompel: None declared, Angeles Shunashy Galindo-Feria: None declared, Helena Persson: None declared, Maryam Fathi: None declared, Johan Grunewald: None declared, Per-Johan Jakobsson Shareholder of: Gesynta Pharma, Grant/research support from: Gesynta Pharma, AstraZeneca,, Susanne Gräslund: None declared, Ingrid E. Lundberg Grant/research support from: Bristol Meyer Squibb, Corbus Pharmaceuticals, Inc and Astra Zeneca, Catia Cerqueira: None declared
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12
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Idborg H, Zandian A, Ossipova E, Wigren E, Preger C, Mobarrez F, Checa A, Sohrabian A, Pucholt P, Sandling JK, Fernandes-Cerqueira C, Rönnelid J, Oke V, Grosso G, Kvarnström M, Larsson A, Wheelock CE, Syvänen AC, Rönnblom L, Kultima K, Persson H, Gräslund S, Gunnarsson I, Nilsson P, Svenungsson E, Jakobsson PJ. Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients. Front Immunol 2019; 10:1029. [PMID: 31156624 PMCID: PMC6533644 DOI: 10.3389/fimmu.2019.01029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease, which currently lacks specific diagnostic biomarkers. The diversity within the patients obstructs clinical trials but may also reflect differences in underlying pathogenesis. Our objective was to obtain protein profiles to identify potential general biomarkers of SLE and to determine molecular subgroups within SLE for patient stratification. Plasma samples from a cross-sectional study of well-characterized SLE patients (n = 379) and matched population controls (n = 316) were analyzed by antibody suspension bead array targeting 281 proteins. To investigate the differences between SLE and controls, Mann–Whitney U-test with Bonferroni correction, generalized linear modeling and receiver operating characteristics (ROC) analysis were performed. K-means clustering was used to identify molecular SLE subgroups. We identified Interferon regulating factor 5 (IRF5), solute carrier family 22 member 2 (SLC22A2) and S100 calcium binding protein A12 (S100A12) as the three proteins with the largest fold change between SLE patients and controls (SLE/Control = 1.4, 1.4, and 1.2 respectively). The lowest p-values comparing SLE patients and controls were obtained for S100A12, Matrix metalloproteinase-1 (MMP1) and SLC22A2 (padjusted = 3 × 10−9, 3 × 10−6, and 5 × 10−6 respectively). In a set of 15 potential biomarkers differentiating SLE patients and controls, two of the proteins were transcription factors, i.e., IRF5 and SAM pointed domain containing ETS transcription factor (SPDEF). IRF5 was up-regulated while SPDEF was found to be down-regulated in SLE patients. Unsupervised clustering of all investigated proteins identified three molecular subgroups among SLE patients, characterized by (1) high levels of rheumatoid factor-IgM, (2) low IRF5, and (3) high IRF5. IRF5 expressing microparticles were analyzed by flow cytometry in a subset of patients to confirm the presence of IRF5 in plasma and detection of extracellular IRF5 was further confirmed by immunoprecipitation-mass spectrometry (IP-MS). Interestingly IRF5, a known genetic risk factor for SLE, was detected extracellularly and suggested by unsupervised clustering analysis to differentiate between SLE subgroups. Our results imply a set of circulating molecules as markers of possible pathogenic importance in SLE. We believe that these findings could be of relevance for understanding the pathogenesis and diversity of SLE, as well as for selection of patients in clinical trials.
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Affiliation(s)
- Helena Idborg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Arash Zandian
- SciLifeLab, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elena Ossipova
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Edvard Wigren
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Charlotta Preger
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Fariborz Mobarrez
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Akademiska Hospital, Uppsala University, Uppsala, Sweden
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Azita Sohrabian
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Cátia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Vilija Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Giorgia Grosso
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marika Kvarnström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development & School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Susanne Gräslund
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Nilsson
- SciLifeLab, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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13
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Favalli N, Biendl S, Hartmann M, Piazzi J, Sladojevich F, Gräslund S, Brown PJ, Näreoja K, Schüler H, Scheuermann J, Franzini R, Neri D. A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition. ChemMedChem 2018; 13:1303-1307. [PMID: 29856130 PMCID: PMC6126618 DOI: 10.1002/cmdc.201800193] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 11/06/2022]
Abstract
A DNA-encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5-bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a Kd value of 6 nm, while compounds with the same substituents on an equidistant but flexible l-lysine scaffold showed 140-fold lower affinity. A 18 nm tankyrase-1 binder featured l-lysine as linking moiety, while molecules based on d-Lysine or (2S,4S)-amino-l-proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.
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Affiliation(s)
- Nicholas Favalli
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Stefan Biendl
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Marco Hartmann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Filippo Sladojevich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La, Roche Ltd., Grenzacherstrasse 124, 4070 Basel (Switzerland)
| | - Susanne Gräslund
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Peter J. Brown
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
| | - Katja Näreoja
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Herwig Schüler
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Raphael Franzini
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
- University of Utah, College of Pharmacy, 30 South 2000 East, Salt Lake City, UT 84112 (801) 581-6731
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
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14
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Favalli N, Biendl S, Hartmann M, Piazzi J, Sladojevich F, Gräslund S, Brown PJ, Näreoja K, Schüler H, Scheuermann J, Franzini R, Neri D. Cover Feature: A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition (ChemMedChem 13/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nicholas Favalli
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Stefan Biendl
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Marco Hartmann
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Jacopo Piazzi
- Philochem AG; Liebernstrasse 3 8112 Otelfingen Switzerland
| | - Filippo Sladojevich
- Roche Pharma Research and Early Development; Roche Innovation Center Basel, F. Hoffmann-La, Roche Ltd.; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Susanne Gräslund
- Structural Genomics Consortium (SGC); University of Toronto; Toronto ON M5G 1L7 Canada
- Department of Structural Biology; Department of Medical Biochemistry and Biophysics (MBB); Karolinska Institutet; Scheeles väg 2 17177 Stockholm Sweden
| | - Peter J. Brown
- Structural Genomics Consortium (SGC); University of Toronto; Toronto ON M5G 1L7 Canada
| | - Katja Näreoja
- Department of Structural Biology; Department of Medical Biochemistry and Biophysics (MBB); Karolinska Institutet; Scheeles väg 2 17177 Stockholm Sweden
| | - Herwig Schüler
- Department of Structural Biology; Department of Medical Biochemistry and Biophysics (MBB); Karolinska Institutet; Scheeles väg 2 17177 Stockholm Sweden
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Raphael Franzini
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
- College of Pharmacy; University of Utah; 30 South 2000 East Salt Lake City UT 84112 USA
| | - Dario Neri
- Institute of Pharmaceutical Sciences; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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15
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Abstract
We describe a mass spectrometry-based approach for validation of antibody specificity. This method allows validation of antibodies or antibody fragments, against their endogenous targets. It can assess if the antibody is able to bind to its native antigen in cell lysates among thousands of other proteins, DNA, RNA, and other cellular components. In addition, it identifies other proteins the antibody is able to immunoprecipitate allowing for the assessment of antibody specificity and selectivity. This method is easily scalable, adaptable to different cell lines and conditions and has been shown to be reproducible between multiple laboratories.
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Affiliation(s)
- Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Tomtebodavägen 23A, 17165, Solna, Sweden.
| | - Charlotta Preger
- Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | - Johan Lengqvist
- Centre for Molecular Medicine, Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
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16
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Rechem CV, Black JC, Greninger P, Zhao Y, Boukhali M, Donado C, Aryee MJ, Burrowes PD, Ladd B, Gräslund S, Haas W, Christiani DC, Benes CH, Whetstine JR. Abstract NTOC-110: UNEXPECTED ROLES FOR KDM4A: PROTEIN SYNTHESIS AND MTOR INHIBITOR SENSITIVITY. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.ovcasymp16-ntoc-110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Single nucleotide polymorphisms (SNPs) occur within chromatin-modulating factors; however, little is known about how these variants within the coding sequence impact cancer progression or treatment. Therefore, there is a need to establish their biochemical and/or molecular contribution, their use in sub-classifying patients and their impact on therapeutic response. We demonstrate that coding SNP-A482 within the lysine tri-demethylase KDM4A/JMJD2A associates with differential outcome in cancer patients and promotes KDM4A protein turnover. Interestingly, homozygous SNP-482 cells have increased mTOR inhibitor sensitivity. mTOR inhibitors significantly reduce SNP-A482 protein levels, which parallels the increased drug sensitivity observed with KDM4A depletion. Furthermore, we demonstrate that KDM4A interacts with the translation initiation complex and impacts the distribution of translation initiation factors within polysome fractions. Upon KDM4A depletion, protein synthesis was reduced and there was enhanced protein synthesis suppression with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Lastly, we demonstrate that JIB-04, a JmjC demethylases inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected role for KDM4A in regulating protein synthesis, in modulating mTOR inhibitor sensitivity and suggest potential novel therapeutic applications for this class of enzyme.
Citation Format: Capucine Van Rechem, Joshua C. Black, Patricia Greninger, Yang Zhao, Myriam Boukhali, Carlos Donado, Martin J. Aryee, Paul d. Burrowes, Brendon Ladd, Susanne Gräslund, Wilhelm Haas, David C. Christiani, Cyril H. Benes and Johnathan R. Whetstine. UNEXPECTED ROLES FOR KDM4A: PROTEIN SYNTHESIS AND MTOR INHIBITOR SENSITIVITY [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr NTOC-110.
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Affiliation(s)
- Capucine Van Rechem
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Joshua C. Black
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Patricia Greninger
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Yang Zhao
- 2Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, MA 02115
- 3Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Myriam Boukhali
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Carlos Donado
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Martin J. Aryee
- 4MGH Cancer Center and Harvard Medical School, Department of Pathology and Department of Medicine, Charlestown, MA, 02129
| | - Paul d. Burrowes
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Brendon Ladd
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Susanne Gräslund
- 5Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Wilhelm Haas
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - David C. Christiani
- 2Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, MA 02115
- 6Pulmonary and Critical Care Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Cyril H. Benes
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
| | - Johnathan R. Whetstine
- 1MGH Cancer Center and Harvard Medical School, Department of Medicine, Charlestown, MA, 02129
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17
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Abstract
Site-specific biotinylation of proteins is often the method of choice to enable efficient immobilization of a protein on a surface without interfering with protein folding. The tight interaction of biotin and streptavidin is frequently used to immobilize an antigen during phage display selections of binders. Here we describe a method of in vivo biotinylation of proteins during expression in E. coli, by tagging the protein with the short biotin acceptor peptide sequence, Avi tag, and co-expression of the E. coli biotin ligase (BirA) resulting in precise biotinylation of a specific lysine residue in the tag.
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Affiliation(s)
- Susanne Gräslund
- Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23a, Gamma:6, 171 65, Solna, Sweden.
| | - Pavel Savitsky
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
| | - Susanne Müller-Knapp
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
- Goethe-University Frankfurt, Buchmann Institute for life Sciences, Riedberg Campus, 60438, Frankfurt am Main, Germany
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18
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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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19
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Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step. Int J Mol Sci 2015; 16:23587-603. [PMID: 26437402 PMCID: PMC4632715 DOI: 10.3390/ijms161023587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Kevin T Gorman
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Chris R Vinci
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
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20
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Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury ARM. Recombinant renewable polyclonal antibodies. MAbs 2015; 7:32-41. [PMID: 25530082 DOI: 10.4161/19420862.2015.989047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.
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21
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Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics 2015; 14:2833-47. [PMID: 26290498 PMCID: PMC4597156 DOI: 10.1074/mcp.o115.052209] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Antibodies are key reagents in biology and medicine, but commercial sources are rarely recombinant and thus do not provide a permanent and renewable resource. Here, we describe an industrialized platform to generate antigens and validated recombinant antibodies for 346 transcription factors (TFs) and 211 epigenetic antigens. We describe an optimized automated phage display and antigen expression pipeline that in aggregate produced about 3000 sequenced Fragment antigen-binding domain that had high affinity (typically EC50<20 nm), high stability (Tm∼80 °C), good expression in E. coli (∼5 mg/L), and ability to bind antigen in complex cell lysates. We evaluated a subset of Fabs generated to homologous SCAN domains for binding specificities. These Fragment antigen-binding domains were monospecific to their target SCAN antigen except in rare cases where they cross-reacted with a few highly related antigens. Remarkably, immunofluorescence experiments in six cell lines for 270 of the TF antigens, each having multiple antibodies, show that ∼70% stain predominantly in the cytosol and ∼20% stain in the nucleus which reinforces the dominant role that translocation plays in TF biology. These cloned antibody reagents are being made available to the academic community through our web site recombinant-antibodies.org to allow a more system-wide analysis of TF and chromatin biology. We believe these platforms, infrastructure, and automated approaches will facilitate the next generation of renewable antibody reagents to the human proteome in the coming decade.
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Affiliation(s)
- Michael Hornsby
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Marcin Paduch
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Shane Miersch
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Annika Sääf
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Tet Matsuguchi
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Brian Lee
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Karolina Wypisniak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Allison Doak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Daniel King
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Svitlana Usatyuk
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Kimberly Perry
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Vince Lu
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - William Thomas
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Judy Luke
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jay Goodman
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Robert J Hoey
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Darson Lai
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Carly Griffin
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Zhijian Li
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Franco J Vizeacoumar
- **Saskatchewan Cancer Agency, University of Saskatchewan, Saskatoon, S7N 4H4, Canada
| | - Debbie Dong
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Elliot Campbell
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Stephen Anderson
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Nan Zhong
- ‡‡Structural Genomics Consortium, Toronto, M5G Il7, Canada
| | | | - Shohei Koide
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jason Moffat
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Sachdev Sidhu
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada;
| | - Anthony Kossiakoff
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - James Wells
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158;
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22
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Trésaugues L, Lundbäck T, Welin M, Flodin S, Nyman T, Silvander C, Gräslund S, Nordlund P. Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate. PLoS One 2015; 10:e0131507. [PMID: 26121039 PMCID: PMC4485890 DOI: 10.1371/journal.pone.0131507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an “housecleaning” enzyme specialized in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. Here we present the crystal structure of human NUDT16 both in its apo-form and in complex with its product inosine monophosphate (IMP). NUDT16 appears as a dimer whose formation generates a positively charged trench to accommodate substrate-binding. Complementation of the structural data with detailed enzymatic and biophysical studies revealed the determinants of substrate recognition and particularly the importance of the substituents in position 2 and 6 on the purine ring. The affinity for the IMP product, harboring a carbonyl in position 6 on the base, compared to purine monophosphates lacking a H-bond acceptor in this position, implies a catalytic cycle whose rate is primarily regulated by the product-release step. Finally, we have also characterized a phenomenon of inhibition by the product of the reaction, IMP, which might exclude non-deleterious nucleotides from NUDT16-mediated hydrolysis regardless of their cellular concentration. Taken together, this study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (PN); (LT)
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PN); (LT)
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23
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Samain F, Ekblad T, Mikutis G, Zhong N, Zimmermann M, Nauer A, Bajic D, Decurtins W, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D, Franzini RM. Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library. J Med Chem 2015; 58:5143-9. [DOI: 10.1021/acs.jmedchem.5b00432] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Torun Ekblad
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | | | - Nan Zhong
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Mauro Zimmermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Angela Nauer
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Davor Bajic
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Willy Decurtins
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Susanne Gräslund
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Herwig Schüler
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | - Dario Neri
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Raphael M. Franzini
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
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24
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015; 54:3927-31. [DOI: 10.1002/anie.201410736] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Indexed: 11/10/2022]
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26
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Van Rechem C, Black JC, Boukhali M, Aryee MJ, Gräslund S, Haas W, Benes CH, Whetstine JR. Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Cancer Discov 2015; 5:255-63. [PMID: 25564516 DOI: 10.1158/2159-8290.cd-14-1326] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Chromatin-modifying enzymes are predominantly nuclear; however, these factors are also localized to the cytoplasm, and very little is known about their role in this compartment. In this report, we reveal a non-chromatin-linked role for the lysine-specific demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation complex and affects the distribution of translation initiation factors within polysome fractions. Furthermore, KDM4A depletion reduced protein synthesis and enhanced the protein synthesis suppression observed with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Finally, we demonstrate that JIB-04, a JmjC demethylase inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected cytoplasmic role for KDM4A in regulating protein synthesis and suggest novel potential therapeutic applications for this class of enzyme. SIGNIFICANCE This report documents an unexpected cytoplasmic role for the lysine demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation machinery, regulates protein synthesis and, upon coinhibition with mTOR inhibitors, enhances the translation suppression and cell sensitivity to these therapeutics.
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Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Martin J Aryee
- Massachusetts General Hospital Department of Pathology and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts.
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27
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Trésaugues L, Silvander C, Flodin S, Welin M, Nyman T, Gräslund S, Hammarström M, Berglund H, Nordlund P. Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases. Structure 2014; 22:744-55. [PMID: 24704254 DOI: 10.1016/j.str.2014.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/15/2022]
Abstract
SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Susanne Flodin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Hammarström
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Helena Berglund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
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28
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Allali-Hassani A, Kuznetsova E, Hajian T, Wu H, Dombrovski L, Li Y, Gräslund S, Arrowsmith CH, Schapira M, Vedadi M. A Basic Post-SET Extension of NSDs Is Essential for Nucleosome Binding In Vitro. ACTA ACUST UNITED AC 2014; 19:928-35. [PMID: 24595546 DOI: 10.1177/1087057114525854] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 02/04/2014] [Indexed: 11/16/2022]
Abstract
The nuclear receptor SET domain-containing family of proteins (NSD1, NSD2, and NSD3) is known to mono- and dimethylate lysine 36 of histone H3 (H3K36). Overexpression and translocation of NSDs have been widely implicated in a variety of diseases including cancers. Although the substrate specificity of NSDs has been a subject of many valuable studies, the activity of these proteins has never been fully characterized in vitro. In this study, we present full kinetic characterization of NSD1, NSD2, and NSD3 and provide robust in vitro assays suitable for screening these proteins in a 384-well format using nucleosome as a substrate. Through monitoring the changes in substrate specificity of a series of NSD constructs and using molecular modeling, we show that a basic post-SET extension common to all three NSDs (corresponding to residues 1209 to 1226 of NSD2) is essential for proper positioning on nucleosome substrates.
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Affiliation(s)
| | | | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada Ontario Cancer Institute, The Campbell Family Institute for Cancer Research and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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29
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Burgess-Brown NA, Mahajan P, Strain-Damerell C, Gileadi O, Gräslund S. Medium-throughput production of recombinant human proteins: protein production in E. coli. Methods Mol Biol 2014; 1091:73-94. [PMID: 24203325 DOI: 10.1007/978-1-62703-691-7_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In Chapter 4 we described the SGC process for generating multiple constructs of truncated versions of each protein using LIC. In this chapter we provide a step-by-step procedure of our E. coli system for test expressing intracellular (soluble) proteins in a 96-well format that enables us to identify which proteins or truncated versions are expressed in a soluble and stable form suitable for structural studies. In addition, we detail the process for scaling up cultures for large-scale protein purification. This level of production is required to obtain sufficient quantities (i.e., milligram amounts) of protein for further characterization and/or crystallization experiments. Our standard process is purification by immobilized metal affinity chromatography (IMAC) using nickel resin followed by size exclusion chromatography (SEC), with additional procedures arising from the complexity of the protein itself.
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30
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Welin M, Lehtiö L, Johansson A, Flodin S, Nyman T, Trésaugues L, Hammarström M, Gräslund S, Nordlund P. Substrate specificity and oligomerization of human GMP synthetase. J Mol Biol 2013; 425:4323-33. [PMID: 23816837 DOI: 10.1016/j.jmb.2013.06.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
Abstract
Guanine monophosphate (GMP) synthetase is a bifunctional two-domain enzyme. The N-terminal glutaminase domain generates ammonia from glutamine and the C-terminal synthetase domain aminates xanthine monophosphate (XMP) to form GMP. Mammalian GMP synthetases (GMPSs) contain a 130-residue-long insert in the synthetase domain in comparison to bacterial proteins. We report here the structure of a eukaryotic GMPS. Substrate XMP was bound in the crystal structure of the human GMPS enzyme. XMP is bound to the synthetase domain and covered by a LID motif. The enzyme forms a dimer in the crystal structure with subunit orientations entirely different from the bacterial counterparts. The inserted sub-domain is shown to be involved in substrate binding and dimerization. Furthermore, the structural basis for XMP recognition is revealed as well as a potential allosteric site. Enzymes in the nucleotide metabolism typically display an increased activity in proliferating cells due to the increased need for nucleotides. Many drugs used as immunosuppressants and for treatment of cancer and viral diseases are indeed nucleobase- and nucleoside-based compounds, which are acting on or are activated by enzymes in this pathway. The information obtained from the crystal structure of human GMPS might therefore aid in understanding interactions of nucleoside-based drugs with GMPS and in structure-based design of GMPS-specific inhibitors.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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31
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Egeblad L, Welin M, Flodin S, Gräslund S, Wang L, Balzarini J, Eriksson S, Nordlund P. Pan-pathway based interaction profiling of FDA-approved nucleoside and nucleobase analogs with enzymes of the human nucleotide metabolism. PLoS One 2012; 7:e37724. [PMID: 22662200 PMCID: PMC3360617 DOI: 10.1371/journal.pone.0037724] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022] Open
Abstract
To identify interactions a nucleoside analog library (NAL) consisting of 45 FDA-approved nucleoside analogs was screened against 23 enzymes of the human nucleotide metabolism using a thermal shift assay. The method was validated with deoxycytidine kinase; eight interactions known from the literature were detected and five additional interactions were revealed after the addition of ATP, the second substrate. The NAL screening gave relatively few significant hits, supporting a low rate of “off target effects.” However, unexpected ligands were identified for two catabolic enzymes guanine deaminase (GDA) and uridine phosphorylase 1 (UPP1). An acyclic guanosine prodrug analog, valaciclovir, was shown to stabilize GDA to the same degree as the natural substrate, guanine, with a ΔTagg around 7°C. Aciclovir, penciclovir, ganciclovir, thioguanine and mercaptopurine were also identified as ligands for GDA. The crystal structure of GDA with valaciclovir bound in the active site was determined, revealing the binding of the long unbranched chain of valaciclovir in the active site of the enzyme. Several ligands were identified for UPP1: vidarabine, an antiviral nucleoside analog, as well as trifluridine, idoxuridine, floxuridine, zidovudine, telbivudine, fluorouracil and thioguanine caused concentration-dependent stabilization of UPP1. A kinetic study of UPP1 with vidarabine revealed that vidarabine was a mixed-type competitive inhibitor with the natural substrate uridine. The unexpected ligands identified for UPP1 and GDA imply further metabolic consequences for these nucleoside analogs, which could also serve as a starting point for future drug design.
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Affiliation(s)
- Louise Egeblad
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Balzarini
- Rega Institute for Medical Research, Leuven, Belgium
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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32
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Buckle AM, Bate MA, Androulakis S, Cinquanta M, Basquin J, Bonneau F, Chatterjee DK, Cittaro D, Gräslund S, Gruszka A, Page R, Suppmann S, Wheeler JX, Agostini D, Taussig M, Taylor CF, Bottomley SP, Villaverde A, de Marco A. Recombinant protein quality evaluation: proposal for a minimal information standard. Stand Genomic Sci 2011; 5:195-7. [PMID: 22180821 PMCID: PMC3235516 DOI: 10.4056/sigs.1834511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Ashley M. Buckle
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
- Corresponding authors: Ario de Marco, University of Nova Gorica (UNG), Rožna Dolina (Nova Gorica), Slovenia. Tel. 0039.3493542056;
| | - Mark A. Bate
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
| | - Steve Androulakis
- Monash eResearch Centre, Monash University, Clayton, Victoria, Australia
| | | | - Jerome Basquin
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany
| | - Deb K. Chatterjee
- Protein Expression Laboratory, SAIC-Frederick Inc., National Cancer Institute, Frederick, MD USA
| | | | - Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, Department of Medical Biophysics and Biochemistry, Stockholm, Sweden
| | | | - Rebecca Page
- Brown University, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, USA
| | - Sabine Suppmann
- Max Planck Institute of Biochemistry, Microchemistry Core Facility, Martinsried, Germany
| | - Jun X. Wheeler
- National Institute for Biological Standards and Control, Health Protection Agency, Hertfordshire, UK
| | | | - Mike Taussig
- Protein Technologies Group, Babraham Bioscience Technologies, Cambridge UK
| | - Chris F. Taylor
- The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Stephen P. Bottomley
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
| | - Antonio Villaverde
- Institute for Biotechnology and Biomedicine and Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Ario de Marco
- Department Environmental Sciences, University of Nova Gorica, Nova Gorica, Slovenia
- Corresponding authors: Ario de Marco, University of Nova Gorica (UNG), Rožna Dolina (Nova Gorica), Slovenia. Tel. 0039.3493542056;
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33
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Keates T, Cooper CD, Savitsky P, Allerston CK, Phillips C, Hammarström M, Daga N, Berridge G, Mahajan P, Burgess-Brown NA, Müller S, Gräslund S, Gileadi O. Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation. N Biotechnol 2011; 29:515-25. [PMID: 22027370 PMCID: PMC3383991 DOI: 10.1016/j.nbt.2011.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 11/17/2022]
Abstract
The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome.
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Affiliation(s)
- Tracy Keates
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Christopher D.O. Cooper
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Pavel Savitsky
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Charles K. Allerston
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Claire Phillips
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Martin Hammarström
- The Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Neha Daga
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Georgina Berridge
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Pravin Mahajan
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Nicola A. Burgess-Brown
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Susanne Müller
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Susanne Gräslund
- The Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Opher Gileadi
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Corresponding author:
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Kotzsch A, Vernet E, Hammarström M, Berthelsen J, Weigelt J, Gräslund S, Sundström M. A secretory system for bacterial production of high-profile protein targets. Protein Sci 2011; 20:597-609. [PMID: 21308845 DOI: 10.1002/pro.593] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Escherichia coli represents a robust, inexpensive expression host for the production of recombinant proteins. However, one major limitation is that certain protein classes do not express well in a biologically relevant form using standard expression approaches in the cytoplasm of E. coli. To improve the usefulness of the E. coli expression platform we have investigated combinations of promoters and selected N-terminal fusion tags for the extracellular expression of human target proteins. A comparative study was conducted on 24 target proteins fused to outer membrane protein A (OmpA), outer membrane protein F (OmpF) and osmotically inducible protein Y (OsmY). Based on the results of this initial study, we carried out an extended expression screen employing the OsmY fusion and multiple constructs of a more diverse set of human proteins. Using this high-throughput compatible system, we clearly demonstrate that secreted biomedically relevant human proteins can be efficiently retrieved and purified from the growth medium.
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Affiliation(s)
- Alexander Kotzsch
- Facility for Protein Science and Technology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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35
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Colwill K, Gräslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods 2011; 8:551-8. [PMID: 21572409 DOI: 10.1038/nmeth.1607] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 04/11/2011] [Indexed: 12/16/2022]
Abstract
Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.
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Affiliation(s)
- Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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36
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Pershad K, Pavlovic J, Gräslund S, Nilsson P, Colwill K, Karatt-Vellatt A, Schofield D, Dyson M, Pawson T, Kay B, McCafferty J. Generating a panel of highly specific antibodies to 20 human SH2 domains by phage display. Protein Eng Des Sel 2010; 23:279-88. [PMID: 20164216 PMCID: PMC2841545 DOI: 10.1093/protein/gzq003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 12/31/2009] [Accepted: 01/05/2010] [Indexed: 12/02/2022] Open
Abstract
To demonstrate the utility of phage display in generating highly specific antibodies, affinity selections were conducted on 20 related Src Homology 2 (SH2) domains (ABL1, ABL2, BTK, BCAR3, CRK, FYN, GRB2, GRAP2, LYN, LCK, NCK1, PTPN11 C, PIK3R1 C, PLCgamma1 C, RASA1 C, SHC1, SH2D1A, SYK N, VAV1 and the tandem domains of ZAP70). The domains were expressed in Escherichia coli, purified and used in affinity selection experiments. In total, 1292/3800 of the resultant antibodies were shown to bind the target antigen. Of the 695 further evaluated in specificity ELISAs against all 20 SH2 domains, 379 antibodies were identified with unique specificity (i.e. monospecific). Sequence analysis revealed that there were at least 150 different clones with 1-19 different antibodies/antigen. This includes antibodies that distinguish between ABL1 and ABL2, despite their 89% sequence identity. Specificity was confirmed for many on protein arrays fabricated with 432 different proteins. Thus, even though the SH2 domains share a common three-dimensional structure and 20-89% identity at the primary structure level, we were able to isolate antibodies with exquisite specificity within this family of structurally related domains.
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Affiliation(s)
- K. Pershad
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - J.D. Pavlovic
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - S. Gräslund
- Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - P. Nilsson
- Department of Proteomics, School of Biotechnology, KTH-Royal Institute of Technology, Albanova University Centre, Stockholm SE-10691, Sweden
| | - K. Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, CanadaM5G 1X5
| | - A. Karatt-Vellatt
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - D.J. Schofield
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - M.R. Dyson
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - T. Pawson
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, CanadaM5S 1A8
| | - B.K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - J. McCafferty
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
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Mersmann M, Meier D, Mersmann J, Helmsing S, Nilsson P, Gräslund S, Colwill K, Hust M, Dübel S. Towards proteome scale antibody selections using phage display. N Biotechnol 2009; 27:118-28. [PMID: 19883803 DOI: 10.1016/j.nbt.2009.10.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 10/19/2009] [Accepted: 10/22/2009] [Indexed: 11/16/2022]
Abstract
In vitro antibody generation by panning a large universal gene library with phage display was employed to generate antibodies to more than 60 different antigens. Of particular interest was a comparison of pannings on 20 different SH2 domains provided by the Structural Genomics Consortium (SGC). Streamlined methods for high throughput antibody generation developed within the 'Antibody Factory' of the German National Genome Research Network (NGFN) were demonstrated to minimise effort and provide a reliable and robust source for antibodies. For the SH2 domains, in two successive series of selections, 2668 clones were analysed, resulting in 347 primary hits in ELISA. Half of these hits were further analysed, and more than 90 different scFv antibodies to all antigens were identified. The validation of selected antibodies by cross-reactivity ELISA, western blot and on protein microarrays demonstrated the versatility of the in vitro antibody selection pipeline to generate a renewable resource of highly specific monoclonal binders in proteome scale numbers with substantially reduced effort and time.
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Affiliation(s)
- Michael Mersmann
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, Braunschweig, Germany
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38
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Thorsell AG, Persson C, Gräslund S, Hammarström M, Busam RD, Hallberg BM. Crystal structure of human diphosphoinositol phosphatase 1. Proteins 2009; 77:242-6. [DOI: 10.1002/prot.22489] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Magnusdottir A, Stenmark P, Flodin S, Nyman T, Kotenyova T, Gräslund S, Ogg D, Nordlund P. The structure of the PP2A regulatory subunit B56 gamma: the remaining piece of the PP2A jigsaw puzzle. Proteins 2009; 74:212-21. [PMID: 18618707 DOI: 10.1002/prot.22150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The PP2A serine/threonine phosphatase regulates a plethora of cellular processes. In the cell the predominant form of the enzyme is a heterotrimer, formed by a core dimer composed of a catalytic and a scaffolding subunit, which assemble together with one of a range of different regulatory B subunits. Here, we present the first structure of a free non-complexed B subunit, B56 gamma. Comparison with the recent structures of a heterotrimeric complex and the core dimer reveals several significant conformational changes in the interface region between the B56 gamma and the core dimer. These allow for an assembly scheme of the PP2A holoenzyme to be put forth where B56 gamma first complexes with the scaffolding subunit and subsequently binds to the catalytic subunit and this induces the formation of a binding site for the invariant C-terminus of the catalytic subunit that locks in the complex as a last step of assembly.
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Affiliation(s)
- Audur Magnusdottir
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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40
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Trésaugues L, Stenmark P, Schüler H, Flodin S, Welin M, Nyman T, Hammarström M, Moche M, Gräslund S, Nordlund P. The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site. Proteins 2008; 73:1047-52. [PMID: 18767156 DOI: 10.1002/prot.22198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lionel Trésaugues
- Department of Medical Biochemistry and Biophysics, Structural Genomics Consortium, Karolinska Institute, Stockholm, Sweden
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41
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42
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Weigelt J, Nordlund P, Berglund H, Schuler H, Holmberg-Schiavone L, Hällberg M, Gräslund S, Wikström M. Structural genomic of protein families and pathways in human disease. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308095408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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43
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Thorsell AG, Persson C, Voevodskaya N, Busam RD, Hammarström M, Gräslund S, Gräslund A, Hallberg BM. Structural and biophysical characterization of human myo-inositol oxygenase. J Biol Chem 2008; 283:15209-16. [PMID: 18364358 DOI: 10.1074/jbc.m800348200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Altered inositol metabolism is implicated in a number of diabetic complications. The first committed step in mammalian inositol catabolism is performed by myo-inositol oxygenase (MIOX), which catalyzes a unique four-electron dioxygen-dependent ring cleavage of myo-inositol to D-glucuronate. Here, we present the crystal structure of human MIOX in complex with myo-inosose-1 bound in a terminal mode to the MIOX diiron cluster site. Furthermore, from biochemical and biophysical results from N-terminal deletion mutagenesis we show that the N terminus is important, through coordination of a set of loops covering the active site, in shielding the active site during catalysis. EPR spectroscopy of the unliganded enzyme displays a two-component spectrum that we can relate to an open and a closed active site conformation. Furthermore, based on site-directed mutagenesis in combination with biochemical and biophysical data, we propose a novel role for Lys(127) in governing access to the diiron cluster.
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Affiliation(s)
- Ann-Gerd Thorsell
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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44
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Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. Protein production and purification. Nat Methods 2008; 5:135-46. [PMID: 18235434 PMCID: PMC3178102 DOI: 10.1038/nmeth.f.202] [Citation(s) in RCA: 612] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
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45
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Gräslund S, Sagemark J, Berglund H, Dahlgren LG, Flores A, Hammarström M, Johansson I, Kotenyova T, Nilsson M, Nordlund P, Weigelt J. The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins. Protein Expr Purif 2007; 58:210-21. [PMID: 18171622 DOI: 10.1016/j.pep.2007.11.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/31/2007] [Accepted: 11/13/2007] [Indexed: 11/16/2022]
Abstract
Bacterial over-expression of proteins is a powerful tool to obtain soluble protein amenable to biochemical, biophysical and/or structural characterization. However, it is well established that many recombinant proteins cannot be produced in a soluble form. Several theoretical and empirical methods to improve soluble production have been suggested, although there is to date no universally accepted protocol. This report describes, and quantitatively analyses, a systematic multi-construct approach to obtain soluble protein. Although commonly used in several laboratories, quantitative analyses of the merits of the strategy applied to a larger number of target proteins are missing from the literature. In this study, typically 10 different protein constructs were tested for each targeted domain of nearly 400 human proteins. Overall, soluble expression was obtained for nearly 50% of the human target proteins upon over-expression in Escherichia coli. The chance of obtaining soluble expression was almost doubled using the multi-construct method as compared to more traditional approaches. Soluble protein constructs were subsequently subjected to crystallization trials and the multi-construct approach yielded a more than fourfold increase, from 15 proteins to 65, for the likelihood of obtaining well-diffracting crystals. The results also demonstrate the value of testing multiple constructs in crystallization trials. Finally, a retrospective analysis of gel filtration profiles indicates that these could be used with caution to prioritize protein targets for crystallization trials.
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Affiliation(s)
- Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, Department of Medical Biophysics and Biochemistry, 17177 Stockholm, Sweden.
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46
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Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H. In situ proteolysis for protein crystallization and structure determination. Nat Methods 2007; 4:1019-21. [PMID: 17982461 DOI: 10.1038/nmeth1118] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 10/03/2007] [Indexed: 11/09/2022]
Abstract
We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.
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Affiliation(s)
- Aiping Dong
- Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada
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47
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Walldén K, Stenmark P, Nyman T, Flodin S, Gräslund S, Loppnau P, Bianchi V, Nordlund P. Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition. J Biol Chem 2007; 282:17828-36. [PMID: 17405878 DOI: 10.1074/jbc.m700917200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.
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Affiliation(s)
- Karin Walldén
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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Stenmark P, Kursula P, Flodin S, Gräslund S, Landry R, Nordlund P, Schüler H. Crystal structure of human inosine triphosphatase. Substrate binding and implication of the inosine triphosphatase deficiency mutation P32T. J Biol Chem 2007; 282:3182-7. [PMID: 17138556 DOI: 10.1074/jbc.m609838200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inosine triphosphatase (ITPA) is a ubiquitous key regulator of cellular non-canonical nucleotide levels. It breaks down inosine and xanthine nucleotides generated by deamination of purine bases. Its enzymatic action prevents accumulation of ITP and reduces the risk of incorporation of potentially mutagenic inosine nucleotides into nucleic acids. Here we describe the crystal structure of human ITPA in complex with its prime substrate ITP, as well as the apoenzyme at 2.8 and 1.1A, respectively. These structures show for the first time the site of substrate and Mg2+ coordination as well as the conformational changes accompanying substrate binding in this class of enzymes. Enzyme substrate interactions induce an extensive closure of the nucleotide binding grove, resulting in tight interactions with the base that explain the high substrate specificity of ITPA for inosine and xanthine over the canonical nucleotides. One of the dimer contact sites is made up by a loop that is involved in coordinating the metal ion in the active site. We predict that the ITPA deficiency mutation P32T leads to a shift of this loop that results in a disturbed affinity for nucleotides and/or a reduced catalytic activity in both monomers of the physiological dimer.
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Affiliation(s)
- Pål Stenmark
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
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Abstract
This study documented the use of chemicals and biological products in marine and brackish water shrimp farming in Thailand, the world's top producer of farmed shrimp. Interviews were conducted with 76 shrimp farmers in three major shrimp producing regions, the eastern Gulf coast, the southern Gulf coast and the Andaman coast area. Farmers in the study used on average 13 different chemicals and biological products. The most commonly used products were soil and water treatment products, pesticides and disinfectants. Farmers in the southern Gulf coast area used a larger number of products than farmers in the other two areas. In the study, the use of more than 290 different chemicals and biological products was documented. Many of the pesticides, disinfectants and antibiotics used by the farmers could have negative effects on the cultured shrimps, cause a risk for food safety, occupational health, and/or have negative effects on adjacent ecosystems. Manufacturers and retailers of the products often neglected to provide farmers with necessary information regarding active ingredient and relevant instructions for safe and efficient use.
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Affiliation(s)
- S Gräslund
- Department of Systems Ecology, Stockholm University, SE-106 91 Stockholm, Sweden.
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Gräslund S, Eklund M, Falk R, Uhlén M, Nygren PA, Ståhl S. A novel affinity gene fusion system allowing protein A-based recovery of non-immunoglobulin gene products. J Biotechnol 2002; 99:41-50. [PMID: 12204556 DOI: 10.1016/s0168-1656(02)00158-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An expression vector system has been developed, taking advantage of a novel, Staphylococcus aureus protein A (SPA)-binding affinity tag Z(SPA-1), enabling straightforward affinity blotting procedures and efficient recovery by affinity purification of expressed gene products on readily available reagents and chromatography media. The 58 amino acid SPA-binding affinity tag Z(SPA-1), was previously selected from a library constructed by combinatorial mutagenesis of a protein domain from SPA. An Escherichia coli expression vector for intracellular T7 promoter (P(T7)) driven production was constructed with an N-terminal dual affinity tag, consisting of a hexahistidyl (His(6)) tag in frame with the Z(SPA-1) tag, thus allowing alternative affinity recovery methods. To evaluate the system, five cDNA clones from a mouse testis cDNA library were expressed, and two alternative blotting procedures were developed for convenient screening of expression efficiencies. The five produced fusion proteins were recovered on both immobilized metal-ion affinity chromatography (IMAC) columns and on Protein A-based chromatography media, to allow comparative studies. It was found that the Protein A-based recovery resulted in the highest degree of purity, and furthermore, gene products that were produced as inclusion bodies could after denaturation be efficiently affinity purified on Protein A-Sepharose in the presence of 0.5 M guanidine hydrochloride. The convenience and robustness of the presented expression system should make it highly suitable for various high-throughput protein expression efforts.
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Affiliation(s)
- Susanne Gräslund
- Division of Molecular Biotechnology, Department of Biotechnology, Royal Institute of Technology (KTH), SCFAB, SE-10691 Stockholm, Sweden
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