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Coyle CW, Knight KA, Brown HC, George SN, Denning G, Branella GM, Childers KC, Spiegel PC, Spencer HT, Doering CB. Humanization and functional characterization of enhanced coagulation factor IX variants identified through ancestral sequence reconstruction. J Thromb Haemost 2024; 22:633-644. [PMID: 38016519 PMCID: PMC10922771 DOI: 10.1016/j.jtha.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Laboratory resurrection of ancient coagulation factor (F) IX variants generated through ancestral sequence reconstruction led to the discovery of a FIX variant, designated An96, which possesses enhanced specific activity independent of and additive to that provided by human p.Arg384Lys, referred to as FIX-Padua. OBJECTIVES The goal of the current study was to identify the amino acid substitution(s) responsible for the enhanced activity of An96 and create a humanized An96 FIX transgene for gene therapy application. METHODS Reductionist screening approaches, including domain swapping and scanning residue substitution, were used and guided by one-stage FIX activity assays. In vitro characterization of top candidates included recombinant high-purity preparation, specific activity determination, and enzyme kinetic analysis. Final candidates were packaged into adeno-associated viral (AAV) vectors and delivered to hemophilia B mice. RESULTS Five of 42 total amino acid substitutions in An96 appear sufficient to retain the enhanced activity of An96 in an otherwise human FIX variant. Additional substitution of the Padua variant further increased the specific activity 5-fold. This candidate, designated ET9, demonstrated 51-fold greater specific activity than hFIX. AAV2/8-ET9 treated hemophilia B mice produced plasma FIX activities equivalent to those observed previously for AAV2/8-An96-Padua, which were 10-fold higher than AAV2/8-hFIX-Padua. CONCLUSION Starting from computationally inferred ancient FIX sequences, novel amino acid substitutions conferring activity enhancement were identified and translated into an AAV-FIX gene therapy cassette demonstrating high potency. This ancestral sequence reconstruction discovery and sequence mapping refinement approach represents a promising platform for broader protein drug and gene therapy candidate optimization.
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Affiliation(s)
- Christopher W Coyle
- Molecular and Systems Pharmacology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kristopher A Knight
- Molecular and Systems Pharmacology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | - Gianna M Branella
- Cancer Biology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kenneth C Childers
- Chemistry Department, Western Washington University, Bellingham, Washington, USA
| | - P Clint Spiegel
- Chemistry Department, Western Washington University, Bellingham, Washington, USA
| | - H Trent Spencer
- Cell and Gene Therapy Program, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - Christopher B Doering
- Cell and Gene Therapy Program, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA.
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2
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Identification of coagulation factor IX variants with enhanced activity through ancestral sequence reconstruction. Blood Adv 2021; 5:3333-3343. [PMID: 34477814 DOI: 10.1182/bloodadvances.2021004742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/29/2021] [Indexed: 11/20/2022] Open
Abstract
Orthologous proteins contain sequence disparity guided by natural selection. In certain cases, species-specific protein functionality predicts pharmacological enhancement, such as greater specific activity or stability. However, immunological barriers generally preclude use of nonhuman proteins as therapeutics, and difficulty exists in the identification of individual sequence determinants among the overall sequence disparity. Ancestral sequence reconstruction (ASR) represents a platform for the prediction and resurrection of ancient gene and protein sequences. Recently, we demonstrated that ASR can be used as a platform to facilitate the identification of therapeutic protein variants with enhanced properties. Specifically, we identified coagulation factor VIII (FVIII) variants with improved specific activity, biosynthesis, stability, and resistance to anti-human FVIII antibody-based inhibition. In the current study, we resurrected a panel of ancient mammalian coagulation factor IX (FIX) variants with the goal of identifying improved pharmaceutical candidates. One variant (An96) demonstrated 12-fold greater FIX activity production than human FIX. Addition of the R338L Padua substitution further increased An96 activity, suggesting independent but additive mechanisms. after adeno-associated virus 2 (AAV2)/8-FIX gene therapy, 10-fold greater plasma FIX activity was observed in hemophilia B mice administered AAV2/8-An96-Padua as compared with AAV2/8-human FIX-Padua. Furthermore, phenotypic correction conferred by the ancestral variant was confirmed using a saphenous vein bleeding challenge and thromboelastography. Collectively, these findings validate the ASR drug discovery platform as well as identify an ancient FIX candidate for pharmaceutical development.
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Sousa Bomfim A, Corrêa de Freitas MC, Picanço Castro V, Abreu Soares Neto M, Pádua R, Covas DT, Sousa Russo EM. Generation of hyperfunctional recombinant human factor IX variants expressed in human cell line SK-Hep-1. Biotechnol Lett 2020; 43:143-152. [PMID: 33130980 DOI: 10.1007/s10529-020-03040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To develop recombinant factor IX (FIX) variants with augmented clotting activity. RESULTS We generated three new variants, FIX-YKALW, FIX-ALL and FIX-LLW, expressed in SK-Hep-1 cells and characterized in vitro and in vivo. FIX-YKALW showed the highest antigen expression level among the variants (2.17 µg-mL), followed by FIX-LLW (1.5 µg-mL) and FIX-ALL (0.9 µg-mL). The expression level of FIX variants was two-five fold lower than FIX-wild-type (FIX-WT) (4.37 µg-mL). However, the biological activities of FIX variants were 15-31 times greater than FIX-WT in the chromogenic assay. Moreover, the new variants FIX-YKALW, FIX-LLW and FIX-ALL also presented higher specific activity than FIX-WT (17, 20 and 29-fold higher, respectively). FIX variants demonstrated a better clotting time than FIX-WT. In hemophilia B mice, we observed that FIX-YKALW promoted hemostatic protection. CONCLUSION We have developed three improved FIX proteins with potential for use in protein replacement therapy for hemophilia B.
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Affiliation(s)
- Aline Sousa Bomfim
- Department of Clinical, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil. .,Laboratory of Biotechnology, Center for Cell-Based Therapy and Regional Blood Center, University of São Paulo, São Paulo, Brazil. .,Department of Clinical, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Café Avenue, Block R, Room 7, Ribeirão Preto, SP, ZIP 14040-903, Brazil.
| | | | - Virgínia Picanço Castro
- Laboratory of Biotechnology, Center for Cell-Based Therapy and Regional Blood Center, University of São Paulo, São Paulo, Brazil
| | - Mario Abreu Soares Neto
- Laboratory of Biotechnology, Center for Cell-Based Therapy and Regional Blood Center, University of São Paulo, São Paulo, Brazil
| | - Ricardo Pádua
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Laboratory of Biotechnology, Center for Cell-Based Therapy and Regional Blood Center, University of São Paulo, São Paulo, Brazil.,Department of Medical Clinic, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Elisa Maria Sousa Russo
- Department of Clinical, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Laboratory of Biotechnology, Center for Cell-Based Therapy and Regional Blood Center, University of São Paulo, São Paulo, Brazil
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4
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Barbon E, Ayme G, Mohamadi A, Ottavi J, Kawecki C, Casari C, Verhenne S, Marmier S, van Wittenberghe L, Charles S, Collaud F, Denis CV, Christophe OD, Mingozzi F, Lenting PJ. Single-domain antibodies targeting antithrombin reduce bleeding in hemophilic mice with or without inhibitors. EMBO Mol Med 2020; 12:e11298. [PMID: 32159286 PMCID: PMC7136963 DOI: 10.15252/emmm.201911298] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/08/2023] Open
Abstract
Novel therapies for hemophilia, including non-factor replacement and in vivo gene therapy, are showing promising results in the clinic, including for patients having a history of inhibitor development. Here, we propose a novel therapeutic approach for hemophilia based on llama-derived single-domain antibody fragments (sdAbs) able to restore hemostasis by inhibiting the antithrombin (AT) anticoagulant pathway. We demonstrated that sdAbs engineered in multivalent conformations were able to block efficiently AT activity in vitro, restoring the thrombin generation potential in FVIII-deficient plasma. When delivered as a protein to hemophilia A mice, a selected bi-paratopic sdAb significantly reduced the blood loss in a model of acute bleeding injury. We then packaged this sdAb in a hepatotropic AAV8 vector and tested its safety and efficacy profile in hemophilic mouse models. We show that the long-term expression of the bi-paratopic sdAb in the liver is safe and poorly immunogenic, and results in sustained correction of the bleeding phenotype in hemophilia A and B mice, even in the presence of inhibitory antibodies to the therapeutic clotting factor.
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Affiliation(s)
- Elena Barbon
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Gabriel Ayme
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Amel Mohamadi
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | | | - Charlotte Kawecki
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Caterina Casari
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Sebastien Verhenne
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Solenne Marmier
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Laetitia van Wittenberghe
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Severine Charles
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Fanny Collaud
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Cecile V Denis
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Olivier D Christophe
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Federico Mingozzi
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Peter J Lenting
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
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5
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Samelson-Jones BJ, Finn JD, George LA, Camire RM, Arruda VR. Hyperactivity of factor IX Padua (R338L) depends on factor VIIIa cofactor activity. JCI Insight 2019; 5:128683. [PMID: 31219805 DOI: 10.1172/jci.insight.128683] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Adeno-associated-viral (AAV) vector liver-directed gene therapy (GT) for hemophilia B (HB) is limited by a vector-dose-dependent hepatotoxicity. Recently, this obstacle has been partially circumvented by the use of a hyperactive factor IX (FIX) variant, R338L (Padua), which has an eightfold increased specific activity compared to FIX-WT. FIX-R338L has emerged as the standard for HB GT. However, the underlying mechanism of its hyperactivity is undefined; as such, safety concerns of unregulated coagulation and the potential for thrombotic complications have not been fully addressed. To this end, we evaluated the enzymatic and clotting activity as well as the activation, inactivation, and cofactor-dependence of FIX-R338L relative to FIX-WT. We observed that the high-specific-activity of FIX-R338L requires factor VIIIa (FVIIIa) cofactor. In a novel system utilizing emicizumab, a FVIII-mimicking bispecific antibody, the hyperactivity of both recombinant FIX-R338L and AAV-mediated-transgene-expressed FIX-R338L from HB GT subjects is ablated without FVIIIa activity. We conclude that the molecular regulation of activation, inactivation, and cofactor-dependence of FIX-R338L is similar to FIX-WT, but that the FVIIIa-dependent hyperactivity of FIX-R338L is the result of a faster rate of factor X activation. This mechanism helps mitigate safety concerns of unregulated coagulation and supports the expanded use of FIX-R338L in HB therapy.
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Affiliation(s)
- Benjamin J Samelson-Jones
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
| | - Jonathan D Finn
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lindsey A George
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
| | - Rodney M Camire
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
| | - Valder R Arruda
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
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6
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Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem J 2016; 473:2395-411. [DOI: 10.1042/bcj20160336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 01/27/2023]
Abstract
Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity-enhanced Factor IXa variants has demonstrated a delicately balanced bidirectional network. Essential molecular interactions across multiple regions of the Factor IXa molecule co-operate in the maturation of the active site. This maturation is specifically facilitated by long-range communication through the Ile212–Ile213 motif unique to Factor IXa and a flexibility of the 170-loop that is further dependent on the conformation in the Cys168–Cys182 disulfide bond. Ultimately, the network consists of compensatory brakes (Val16 and Ile213) and accelerators (Tyr99 and Phe174) that together allow for a subtle fine-tuning of enzymatic activity.
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