1
|
Ferreira MV, Nogueira T, Rios RA, Lopes TJS. A graph-based machine learning framework identifies critical properties of FVIII that lead to hemophilia A. FRONTIERS IN BIOINFORMATICS 2023; 3:1152039. [PMID: 37235045 PMCID: PMC10206133 DOI: 10.3389/fbinf.2023.1152039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction: Blood coagulation is an essential process to cease bleeding in humans and other species. This mechanism is characterized by a molecular cascade of more than a dozen components activated after an injury to a blood vessel. In this process, the coagulation factor VIII (FVIII) is a master regulator, enhancing the activity of other components by thousands of times. In this sense, it is unsurprising that even single amino acid substitutions result in hemophilia A (HA)-a disease marked by uncontrolled bleeding and that leaves patients at permanent risk of hemorrhagic complications. Methods: Despite recent advances in the diagnosis and treatment of HA, the precise role of each residue of the FVIII protein remains unclear. In this study, we developed a graph-based machine learning framework that explores in detail the network formed by the residues of the FVIII protein, where each residue is a node, and two nodes are connected if they are in close proximity on the FVIII 3D structure. Results: Using this system, we identified the properties that lead to severe and mild forms of the disease. Finally, in an effort to advance the development of novel recombinant therapeutic FVIII proteins, we adapted our framework to predict the activity and expression of more than 300 in vitro alanine mutations, once more observing a close agreement between the in silico and the in vitro results. Discussion: Together, the results derived from this study demonstrate how graph-based classifiers can leverage the diagnostic and treatment of a rare disease.
Collapse
Affiliation(s)
| | - Tatiane Nogueira
- Institute of Computing, Federal University of Bahia, Salvador, Brazil
| | - Ricardo A. Rios
- Institute of Computing, Federal University of Bahia, Salvador, Brazil
| | - Tiago J. S. Lopes
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| |
Collapse
|
2
|
Lopes TJS, Rios R, Nogueira T, Mello RF. Protein residue network analysis reveals fundamental properties of the human coagulation factor VIII. Sci Rep 2021; 11:12625. [PMID: 34135429 PMCID: PMC8209229 DOI: 10.1038/s41598-021-92201-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Hemophilia A is an X-linked inherited blood coagulation disorder caused by the production and circulation of defective coagulation factor VIII protein. People living with this condition receive either prophylaxis or on-demand treatment, and approximately 30% of patients develop inhibitor antibodies, a serious complication that limits treatment options. Although previous studies performed targeted mutations to identify important residues of FVIII, a detailed understanding of the role of each amino acid and their neighboring residues is still lacking. Here, we addressed this issue by creating a residue interaction network (RIN) where the nodes are the FVIII residues, and two nodes are connected if their corresponding residues are in close proximity in the FVIII protein structure. We studied the characteristics of all residues in this network and found important properties related to disease severity, interaction to other proteins and structural stability. Importantly, we found that the RIN-derived properties were in close agreement with in vitro and clinical reports, corroborating the observation that the patterns derived from this detailed map of the FVIII protein architecture accurately capture the biological properties of FVIII.
Collapse
Affiliation(s)
- Tiago J S Lopes
- Department of Reproductive Biology, Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Ricardo Rios
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Tatiane Nogueira
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Rodrigo F Mello
- Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil.,Itaú Unibanco, Av. Eng. Armando de Arruda Pereira, 707, Jabaquara, São Paulo, 04309-010, Brazil
| |
Collapse
|
3
|
Lopes TJS, Rios R, Nogueira T, Mello RF. Prediction of hemophilia A severity using a small-input machine-learning framework. NPJ Syst Biol Appl 2021; 7:22. [PMID: 34035274 PMCID: PMC8149871 DOI: 10.1038/s41540-021-00183-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/27/2022] Open
Abstract
Hemophilia A is a relatively rare hereditary coagulation disorder caused by a defective F8 gene resulting in a dysfunctional Factor VIII protein (FVIII). This condition impairs the coagulation cascade, and if left untreated, it causes permanent joint damage and poses a risk of fatal intracranial hemorrhage in case of traumatic events. To develop prophylactic therapies with longer half-lives and that do not trigger the development of inhibitory antibodies, it is essential to have a deep understanding of the structure of the FVIII protein. In this study, we explored alternative ways of representing the FVIII protein structure and designed a machine-learning framework to improve the understanding of the relationship between the protein structure and the disease severity. We verified a close agreement between in silico, in vitro and clinical data. Finally, we predicted the severity of all possible mutations in the FVIII structure – including those not yet reported in the medical literature. We identified several hotspots in the FVIII structure where mutations are likely to induce detrimental effects to its activity. The combination of protein structure analysis and machine learning is a powerful approach to predict and understand the effects of mutations on the disease outcome.
Collapse
Affiliation(s)
- Tiago J S Lopes
- Department of Reproductive Biology, National Center for Child Health and Development Research Institute, Tokyo, Japan.
| | - Ricardo Rios
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, Brazil
| | - Tatiane Nogueira
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, Brazil
| | - Rodrigo F Mello
- Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, Brazil.,Itaú Unibanco, Av. Eng. Armando de Arruda Pereira, São Paulo, Brazil
| |
Collapse
|
4
|
Madsen JJ, Ohkubo YZ, Peters GH, Faber JH, Tajkhorshid E, Olsen OH. Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail. Biochemistry 2015; 54:6123-31. [PMID: 26346528 DOI: 10.1021/acs.biochem.5b00417] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A recently developed membrane-mimetic model was applied to study membrane interaction and binding of the two anchoring C2-like discoidin domains of human coagulation factor VIIIa (FVIIIa), the C1 and C2 domains. Both individual domains, FVIII C1 and FVIII C2, were observed to bind the phospholipid membrane by partial or full insertion of their extruding loops (the spikes). However, the two domains adopted different molecular orientations in their membrane-bound states; FVIII C2 roughly was positioned normal to the membrane plane, while FVIII C1 displayed a multitude of tilted orientations. The results indicate that FVIII C1 may be important in modulating the orientation of the FVIIIa molecule to optimize the interaction with FIXa, which is anchored to the membrane via its γ-carboxyglutamic acid-rich (Gla) domain. Additionally, a structural change was observed in FVIII C1 in the coiled main chain leading the first spike. A tight interaction with one lipid per domain, similar to what has been suggested for the homologous FVa C2, is characterized. Finally, we rationalize known FVIII antibody epitopes and the scarcity of documented hemophilic missense mutations related to improper membrane binding of FVIIIa, based on the prevalent nonspecificity of ionic interactions in the simulated membrane-bound states of FVIII C1 and FVIII C2.
Collapse
Affiliation(s)
- Jesper J Madsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark.,Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | | | - Günther H Peters
- Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | - Johan H Faber
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
| |
Collapse
|
5
|
Molecular orientation of factor VIIIa on the phospholipid membrane surface determined by fluorescence resonance energy transfer. Biochem J 2013; 452:293-301. [PMID: 23521092 DOI: 10.1042/bj20130025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
F (Factor) VIIIa binds to phospholipid membranes during formation of the FXase complex. Free thiols from cysteine residues of isolated FVIIIa A1 and A2 subunits and the A3 domain of the A3C1C2 subunit were labelled with PyMPO maleimide {1-(2-maleimidylethyl)-4-[5-(4-methoxyphenyl)-oxazol-2-yl]pyridinium methanesulfonate} or fluorescein (fluorescence donors). Double mutations of the A3 domain (C2000S/T1872C and C2000S/D1828C) were also produced to utilize Cys(1828) and Cys(1872) residues for labelling. Labelled subunits were reacted with complementary non-labelled subunits to reconstitute FVIIIa. Octadecylrhodamine incorporated into phospholipid vesicles was used as an acceptor for distance measurements between FVIII residues and membrane surface by fluorescence resonance energy transfer. The results of the present study indicate that a FVIII axis on a plane that intersects the approximate centre of each domain is orientated with a tilt angle of ~30-50° on the membrane surface. This orientation predicted the existence of contacts mediated by residues 1713-1725 in the A3 domain in addition to a large area of contacts within the C domains. FVIII variants where Arg(1719) or Arg(1721) were mutated to aspartate showed a >40-fold reduction in membrane affinity. These results identify possible orientations for FVIIIa bound to the membrane surface and support a new interaction between the A3 domain and the membrane probably mediated in part by Arg(1719) and Arg(1721).
Collapse
|
6
|
Alonso B, Beraud C, Meguellati S, Chen SW, Pellequer JL, Armengaud J, Godon C. Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. Cell Cycle 2013; 12:463-72. [PMID: 23324351 PMCID: PMC3587447 DOI: 10.4161/cc.23367] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
GTPases are molecular switches that regulate a wide-range of cellular processes. The GPN-loop GTPase (GPN) is a sub-family of P-loop NTPase that evolved from a single gene copy in archaea to triplicate paralog genes in eukaryotes, each having a non-redundant essential function in cell. In Saccharomyces cerevisiae, yGPN1 and yGPN2 are involved in sister chromatid cohesion mechanism, whereas nothing is known regarding yGPN3 function. Previous high-throughput experiments suggested that GPN paralogs interaction may occur. In this work, GPN|GPN contact was analyzed in details using TAP-Tag approach, yeast two-hybrid assay, in silico energy computation and site-directed mutagenesis of a conserved Glu residue located at the center of the interaction interface. It is demonstrated that this residue is essential for cell viability. A chromatid cohesion assay revealed that, like yGPN1 and yGPN2, yGPN3 also plays a role in sister chromatid cohesion. These results suggest that all three GPN proteins act at the molecular level in sister chromatid cohesion mechanism as a GPN|GPN complex reminiscent of the homodimeric structure of PAB0955, an archaeal member of GPN-loop GTPase.
Collapse
Affiliation(s)
- Béatrice Alonso
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire/LBSP, Bagnols-sur-Cèze, France
| | | | | | | | | | | | | |
Collapse
|
7
|
Plantier JL, Saboulard D, Pellequer JL, Négrier C, Delcourt M. Functional mapping of the A2 domain from human factor VIII. Thromb Haemost 2012; 107:315-27. [PMID: 22234396 DOI: 10.1160/th11-07-0492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/24/2011] [Indexed: 11/05/2022]
Abstract
Coagulation factor VIII (FVIII) is a multidomain glycoprotein in which the FVIII A2 domain is a key structural element. We aimed at identifying residues within FVIII A2 domain that are crucial for the maintenance of the cofactor function. A high number (n=206) of mutants were generated by substituting original residues with alanine. The mutants were expressed in COS-1 cells and their antigen levels and procoagulant activities were measured. The residues were classified in three categories: those with a non-detrimental alteration of their activities (activity >50 % of control FVIII; n=98), those with a moderate alteration (15 %<activity<50%; n=45) and those that were severely affected (activity<15%; n=63). The mutants sensitive to mutation were retrieved in the HAMSTeRS database with a higher percentage than those that were not affected (58.8% vs. 9.2%). The results revealed the existence of clusters of residues that are sensitive (Arg418-Phe436, Thr459-Ile475, Ser535-Gly549, Asn618-Ala635) or not (Leu398-Arg418, Pro485-Asp500, Gly506-Gly520, Pro596-Asp605) to mutations. The stretches of residues sensitive to mutations were buried within the molecule suggesting that these amino acids participate in the maintenance of the A2 domain structure. In contrast, residues resistant to mutations formed external loops without well- defined structures suggesting that these loops were not crucial for the process of factor X activation. This study provided a detailed map of the FVIII A2 domain between residues 371 and 649, identifying residues crucial for maintaining FVIII function and residues that can be mutated without jeopardising the coagulant activity.
Collapse
Affiliation(s)
- Jean-Luc Plantier
- Laboratoire d’Hémobiologie EA4174-IFR62 Faculté de Médecine RTH Laennec, Université de Lyon, Lyon, France.
| | | | | | | | | |
Collapse
|