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  1. Science & Research (Biologics)

Immunogenicity of Protein-based Therapeutics

Principal Investigator: Zuben E. Sauna, PhD
Office / Division / Lab: OTAT / DPPT / HB


General Overview

A major problem with protein-based therapeutics is their immunogenicity, that is, their tendency to trigger an unwanted immune response against themselves. One form of immune response is activation of B cells, which produce antibodies that bind to the proteins and reduce or eliminate their therapeutic effects. Such antibodies can also cause complications that can be life-threatening. Therefore, a critical part of determining the clinical safety and efficacy of protein-based therapeutic products is measuring their tendency to trigger antibody formation.

The immune response to protein-based therapeutics also involves T-cells, which help to activate B cells so they produce antibodies, including those that block protein therapeutics. This happens if the natural protein made by the body is defective in some way. In that case, the T-cells respond to a normal, artificial protein therapeutic as if it were foreign, since it is different from the defective, natural protein. A T-cell response mismatch like this sometimes occurs in the case of the protein FVIII, a protein that is critical to the body's ability to form blood clots to stop bleeding. People who do not have sufficient quantities of FVIII, or whose FVIII is defective in some way, suffer from hemophilia A, a disease in which blood clotting is defective and leads to excessive bleeding. The problem of defective FVIII is genetically based. Although there is no cure for hemophilia A, infusion of the FVIII therapeutic protein has been one of the most successful examples of management of a chronic disease. Unfortunately, the development of anti-drug antibodies against the infused FVIII is a significant impediment to this strategy. The treatment of patients that develop an immune response is more complex, less effective and exceedingly expensive. It now appears that individual variations in the tendency to develop of anti-drug antibodies may also be based on genetic differences. This is reflected in the clinical observation that persons with hemophilia A of Black African descent are twice as likely as patients of European Caucasian descent to produce antibodies against factor VIII proteins given as replacement therapy.

One strategy for preventing mismatches between natural FVIII and replacement FVIII is to design genetically engineered FVIII proteins so they do not trigger immune reactions. But there are so many differences among the immune systems of people that it is not likely that researchers will be able to design a FVIII protein that is safe for all of them. Therefore we propose to take a personalized approach to predicting--and avoiding--immune responses to FVIII proteins. Our long-term goal is to develop a gene-based approach to identifying individuals whose immune system is likely to react to specific versions of genetically engineered therapeutic proteins so these patients can be treated with versions of these proteins that are less likely to cause immune responses.

We are also addressing the problem of differences in the three-dimensional structures of protein-drugs and natural proteins that trigger B-cells to produce antibodies against therapeutic proteins. The current method for predicting whether certain parts of such proteins will trigger antibody formation is challenging and expensive. Therefore, we are using tiny pieces of DNA-like molecules called aptamers to probe the proteins and determine their exact shapes. Aptamers are made of strings of molecules called nucleic acids that fold up into specific shapes that depend on which nucleic acids are present and the order in which they occur in the aptamer. Therefore, by identifying which aptamer binds tightly to a specific part of a molecule, we can predict the shape of that part of the molecule, somewhat like predicting the shape of a lock by knowing the shape of the key that fits into it.

We are now using this technique to determine the shapes of both FVIII and the part of the anthrax toxin called protective antigen. If an aptamer loses its ability to bind to FVIII, for example, that would indicate that part of this blood clotting protein has changed shaped, increasing the likelihood that it will trigger an immune reaction that reduces its therapeutic activity. We are using this approach to determine if therapeutic proteins have shapes that will trigger antibody production. And we are collaborating with the Center for Drug Evaluation and Research to adapt this technology to analyze new protein products developed as copies of existing, approved protein drugs (biosimilars) to ensure they will be safe and effective.


Scientific Overview

1) Predicting interaction of T-cell epitopes with specific MHC Class II antigens.

Factor VIII (FVIII) is an essential component of the coagulation cascade and individuals deficient in coagulation factors exhibit lifelong bleeding disorders. The development of immunogenicity against therapeutic (infused) versions of FVIII is a significant impediment to the successful treatment of hemophiliacs.

About 50% of the cases of hemophilia A are caused by an inversion of the F gene's exons 1-22, which results in the production of a polypeptide representing those exons, but not 23-26. However, there is a nested gene within the F8 promoter that translates exons 23-26. Nevertheless, the 1-22 inversion means that the overlapping peptides generated from this protein do not include the junction between 1-22 and 23-26. While the peptides from the infused drug-protein FVIII that cover this junction would thus be foreign to the patient's immune system, they are not generally immunogenic. Rather, immunogenicity due to the differences between endogenous and infused FVIII is likely due to a variety of facts, especially single nucleotide polymorphisms (SNPs), but also missense mutations and deletions, and nonsense mutations, as well as inversions,

Therefore, the ideal (but not likely) solution to the immunogenicity problem of infused FVIII would be to design FVIII replacements that match each patient's haplotype and HLA type to avoid triggering an immune response. While designing such biologics to match every patient is not practical, it might be possible in cases where there are clear and significant differences between specific populations (e.g., between those of European Caucasian and Black African descent). In such cases it would be desirable to adapt the designs of endogenous FVIII to each group to ensure that one population does not get a disproportionate share of the benefits of a single version of FVIII while the other population bears a disproportionate share of the risks from the same infused FVIII.

Current technology permits the identification of haplotype backgrounds for FVIII as well as the development of at least a limited array of personalized Factor VIII drug-products. Therefore, our short term goal is to determine the 1) quantitative distribution of different haplotypes (SNPs) in individuals of European-Caucasian and Black-African descent; 2) distribution of MHC Class II antigens in these populations; 3) composition of FVIII used as drugs; and 4) disease-causing mutation, deletion or inversion in the F8 gene (FVIII) of individual patients. We will use this data to predict the immunogenicity of individual FVIII products in different populations and/or individual patients.

2) Development of aptamers as a tool for the investigation of protein-drug conformational epitopes.

Aptamers, nucleic acids capable of forming complex conformations, are potential tools for mapping protein conformation, identification, and prediction of immunogenic sites, and for circumventing immunogenicity. Our laboratory is developing single-stranded DNA aptamers to recombinant human Factor VIII.

We designed a naive DNA library to generate aptamers using defined 5’ and 3’ regions for PCR flanking a randomized 60-base region. The naïve DNA library was denatured and the ssDNA segments were allowed to fold into unique 3-dimensional shapes. (The 60 random bases would theoretically result in 460 unique conformers.) We incubated the pool of folded ssDNA with FVIII and through iterative SELEX (systematic evolution of ligands by exponential enrichment) cycles, we were able to select protein-binding aptamers.

Our laboratory selected a sampling of individual aptamers in cycles 3, 5 and 8 and cloned and sequenced them. We are using these clones to characterize the aptamers through analysis of the predicted 3-D structure, binding properties, and the effect on FVIII activity. In addition, we are doing in silico comparisons of these clones to follow the evolution of the aptamers.

3) Use of diverse analytical techniques to evaluate protein characteristics that may correlate with immunogenicity.

In collaboration with Drs. Mansoor Khan and Rakhi Shah (Division of Product Quality, CDER) we will analyze drug excipient interactions using thermal methods (differential scanning calorimetry, microcalorimetry, thermogravimetric analysis), spectroscopic techniques (Fourier transform infra-red, near infra-red, Raman), crystallography (X-ray diffraction), and nuclear magnetic resonance.

4) Characterization of conformation sensitive antibodies.

An alternative method to studying conformational epitopes of therapeutically important proteins is to develop and characterize antibodies that are sensitive to conformational changes. In collaboration with Dr. Chava Kimchi-Sarfaty (CBER) we characterized several antibodies that are sensitive to the conformation of the zinc metalloprotease ADAMTS13, a multi-domain protein that cleaves von Willebrand Factor and is implicated in thrombotic thrombocytopenic purpura. Our results suggest that these antibodies might be useful reagents for distinguishing functional and non-functional ADAMTS13, and for analyzing conformational transitions during the catalytic cycle.


Publications

  1. PLoS Comput Biol 2024 Mar 1;20(3):e1011247
    Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine.
    Valega-Mackenzie W, Rodriguez Messan M, Yogurtcu ON, Nukala U, Sauna ZE, Yang H
  2. MAbs 2024 Jan-Dec;16(1):2324801
    Proceedings of the 14th European immunogenicity platform open symposium on immunogenicity of biopharmaceuticals.
    Tourdot S, Baltrunkonis D, Denies S, Devanarayan V, Grudzinska-Goebel J, Kromminga A, Lotz GP, Malherbe L, Michaut L, Weldingh KN, Pedras-Vasconcelos JA, Salazar-Fontana LI, Spindeldreher S, Sauna Z, Snoeck V, Verthelyi D, Kramer D
  3. Trends Pharmacol Sci 2023 Dec;44(12):1028-42
    Emerging approaches to induce immune tolerance to therapeutic proteins.
    Noel JC, Lagassé D, Golding B, Sauna ZE
  4. Front Immunol 2023 Oct 16;14:1271120
    The MHC associated peptide proteomics assay is a useful tool for the non-clinical assessment of immunogenicity.
    Jankowski W, Kidchob C, Bunce C, Cloake E, Resende R, Sauna ZE
  5. Gene Ther 2023 Aug;30(7-8):575-80
    Endotoxin contamination in commercially available Cas9 proteins potentially induces T-cell mediated responses.
    Simhadri VL, McGill JR, Sauna ZE
  6. Heliyon 2023 Jun;9(6):e16331
    A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII.
    Rawal A, Kidchob C, Ou J, Yogurtcu ON, Yang H, Sauna ZE
  7. Int Immunopharmacol 2023 Jun;119:109915
    Pharmacokinetics of antibodies during pregnancy: impact of pregnancy on the pharmacokinetics of antibodies (Part 2).
    Tegenge MA, Mahmood I, Struble EB, Sauna Z
  8. Front Immunol 2023 May 12;14:1151888
    Understanding preclinical and clinical immunogenicity risks in novel biotherapeutics development.
    Sauna ZE, Jawa V, Balu-Iyer S, Chirmule N
  9. Heliyon 2023 Apr;9(4):e15032
    Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.
    Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr, Gray JJ, Sauna ZE
  10. Int Immunopharmacol 2023 Apr;117:109914
    Pharmacokinetics of antibodies during pregnancy: general pharmacokinetics and pregnancy related physiological changes (Part 1).
    Tegenge MA, Mahmood I, Struble EB, Sauna Z
  11. Clin Pharmacol Ther 2023 Feb;113(2):221-5
    Summary of a public FDA workshop: model informed drug development approaches for immunogenicity assessments.
    Belov AA, Rodriguez Messan M, Yogurtcu ON, Schultz K, Maxfield K, Thompson L, Revell S, Warren-Henderson Y, Tegenge MA, Sauna ZE, Forshee RA
  12. AAPS J 2023 Feb 9;25(1):24
    A retrospective review of Center for Biologics Evaluation and Research advisory committee meetings in the context of the FDA's benefit-risk framework.
    Mutanga JN, Nukala U, Rodriguez Messan M, Yogurtcu ON, McCormick Q, Sauna ZE, Whitaker BI, Forshee RA, Yang H
  13. Sci Rep 2022 Jul 6;12(1):11388
    A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection.
    McGill JR, Lagasse HAD, Hernandez N, Hopkins L, Jankowski W, McCormick Q, Simhadri V, Golding B, Sauna ZE
  14. Blood Adv 2022 Jul 12;6(13):3932-44
    Structural, functional, and immunogenicity implications of F9 gene recoding.
    Katneni U, Alexaki A, Hunt R, Katagiri N, Hettiarachchi G, Kames J, McGill JR, Holcomb DDF, Athey J, Lin B, Parunov LA, Kafri T, Lu Q, Peters RT, Ovanesov MV, Freedberg D, Bar H, Komar AA, Sauna ZE, Kimchi-Sarfaty C
  15. Trends Mol Med 2021 Nov;27(11):1074-83
    Secondary failure: immune responses to approved protein therapeutics.
    Lagasse HAD, McCormick Q, Sauna ZE
  16. PLoS Comput Biol 2021 Sep 24;17(9):e1009318
    Mathematical model of a personalized neoantigen cancer vaccine and the human immune system.
    Rodriguez Messan M, Yogurtcu ON, McGill JR, Nukala U, Sauna ZE, Yang H
  17. Nat Commun 2021 Aug 24;12(1):5090
    Cas9-derived peptides presented by MHC Class II that elicit proliferation of CD4(+) T-cells.
    Simhadri VL, Hopkins L, McGill JR, Duke BR, Mukherjee S, Zhang K, Sauna ZE
  18. Front Immunol 2021 Jun 28;12:692157
    Factor VIII-Fc activates natural killer cells via Fc-mediated interactions with CD16.
    Lagasse HAD, Hopkins LB, Jankowski W, Jacquemin MG, Sauna ZE, Golding B
  19. Front Med 2021 May 7;8:663396
    HLA variants and inhibitor development in hemophilia A: a retrospective case-controlled study using the ATHNdataset.
    McGill JR, Simhadri VL, Sauna ZE
  20. Sci Rep 2020 Oct 29;10(1):18593
    Modified aptamers as reagents to characterize recombinant human erythropoietin products.
    Jankowski W, Lagasse HAD, Chang WC, McGill J, Jankowska KI, Gelinas AD, Janjic N, Sauna ZE
  21. Front Immunol 2020 Oct 29;11:614856
    Editorial: immunogenicity of proteins used as therapeutics.
    Sauna ZE, Richards SM, Maillere B, Jury EC, Rosenberg AS
  22. Cancers 2020 Sep 28;12(10):E2784
    Efficient propagation of circulating tumor cells: a first step for probing tumor metastasis.
    Xiao J, McGill JR, Stanton K, Kassner JD, Choudhury S, Schlegel R, Sauna ZE, Pohlmann PR, Agarwal S
  23. Int J Mol Sci 2020 Aug 6;21(16):E5621
    A foundational study for normal F8-containing mouse models for the miRNA regulation of hemophilia A: identification and analysis of mouse miRNAS that downregulate the murine F8 gene.
    Jankowska KI, Chattopadhyay M, Sauna ZE, Atreya CD
  24. Front Cell Dev Biol 2020 Jul 30;8:669
    Further evidence that microRNAs can play a role in Hemophilia A disease manifestation: F8 gene downregulation by miR-19b-3p and miR-186-5p.
    Jankowska KI, McGill J, Pezeshkpoor B, Oldenburg J, Sauna ZE, Atreya CD
  25. Int J Mol Sci 2020 May 20;21(10):E3598
    Role of microRNAs in hemophilia and thrombosis in humans.
    Jankowska KI, Sauna ZE, Atreya CD
  26. Transfusion 2020 Feb;60(2):401-13
    Clinical manifestation of hemophilia A in the absence of mutations in the F8 gene that encodes FVIII: role of microRNAs.
    Jankowska KI, McGill J, Pezeshkpoor B, Oldenburg J, Atreya CD, Sauna ZE
  27. J Thromb Haemost 2020 Jan;18(1):201-16
    Quantitative HLA-class-II/Factor VIII (FVIII) peptidomic variation in dendritic cells correlates with the immunogenic potential of therapeutic FVIII proteins in hemophilia A.
    Diego VP, Luu BW, Hofmann M, Dinh LV, Almeida M, Powell JS, Rajalingam R, Peralta JM, Kumar S, Curran JE, Sauna ZE, Kellerman R, Park Y, Key NS, Escobar MA, Huynh H, Verhagen AM, Williams-Blangero S, Lehmann PV, Maraskovsky E, Blangero J, Howard TE
  28. Front Immunol 2019 Dec 20;10:2894
    SampPick: selection of a cohort of subjects matching a population HLA distribution.
    McGill JR, Yogurtcu ON, Verthelyi D, Yang H, Sauna ZE
  29. Sci Rep 2019 Oct 29;9(1):15449
    Effects of codon optimization on coagulation factor IX translation and structure: implications for protein and gene therapies.
    Alexaki A, Hettiarachchi GK, Athey JC, Katneni UK, Simhadri V, Hamasaki-Katagiri N, Nanavaty P, Lin B, Takeda K, Freedberg D, Monroe D, McGill JR, Peters R, Kames JM, Holcomb DD, Hunt RC, Sauna ZE, Gelinas A, Janjic N, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C
  30. AAPS J 2019 Sep;21(5):96
    TCPro: an in silico risk assessment tool for biotherapeutic protein immunogenicity.
    Yogurtcu ON, Sauna ZE, McGill JR, Tegenge MA, Yang H
  31. Blood Adv 2019 Sep 10;3(17):2668-78
    Mitigation of T-cell dependent immunogenicity by reengineering factor VIIa analogue.
    Jankowski W, McGill J, Lagasse HAD, Surov S, Bembridge G, Bunce C, Cloake E, Fogg MH, Jankowska KI, Khan A, Marcotrigiano J, Ovanesov MV, Sauna ZE
  32. AAPS J 2019 Jul;21(4):62
    Fc-Fusion drugs have FcgammaR/C1q binding and signaling properties that may affect their immunogenicity.
    Lagasse HAD, Hengel H, Golding B, Sauna ZE
  33. Am J Physiol Gastrointest Liver Physiol 2019 Jun 1;316(6):G720-34
    Translational and transcriptional responses in human primary hepatocytes under hypoxia.
    Hettiarachchi GK, Katneni UK, Hunt RC, Kames JM, Athey JC, Bar H, Sauna ZE, McGill JR, Ibla JC, Kimchi-Sarfaty C
  34. Blood Adv 2019 May 14;3(9):1429-40
    Peptides identified on monocyte-derived dendritic cells: a marker for clinical immunogenicity to FVIII products.
    Jankowski W, Park Y, McGill J, Maraskovsky E, Hofmann M, Diego VP, Luu BW, Howard TE, Kellerman R, Key NS, Sauna ZE
  35. Trends Biotechnol 2018 Oct;36(10):1068-84
    Evaluating and mitigating the immunogenicity of therapeutic proteins.
    Sauna ZE, Lagasse D, Pedras-Vasconcelos J, Golding B, Rosenberg AS
  36. Hum Immunol 2018 Oct;79(Suppl.):103-4
    Analysis of HLAcII peptidomes presented by dendritic cells (DCs) from healthy donors and hemophilia-A (HA) patients with or without factor VIII (FVIII) inhibitors after ex vivo administration of different therapeutic FVIII proteins (tFVIIIs).
    Howard TE, Diego VP, Hofmann M, Almeida M, Luu BW, Dinh LV, Rajalingam R, Escobar M, Curran J, Williams-Blangero S, Powell J, Blangero J, Maraskovsky E, Key NS, Sauna ZE
  37. Mol Ther Methods Clin Dev 2018 Jun 15;10:105-12
    Prevalence of pre-existing antibodies to CRISPR-associated nuclease Cas9 in the USA population.
    Simhadri VL, McGill J, McMahon S, Wang J, Jiang H, Sauna ZE
  38. J Pharm Pharmacol 2018 May;70(5):584-94
    Immunogenicity assessment during the development of protein therapeutics.
    Rosenberg AS, Sauna ZE
  39. Blood Transfus 2017 Oct;15(6):568-76
    Summary report of the First International Conference on inhibitors in haemophilia A.
    Lacroix-Desmazes S, Scott DW, Goudemand J, Van Den Berg M, Makris M, Van Velzen AS, Santagostino E, Lillicrap D, Rosendaal FR, Hilger A, Sauna ZE, Oldenburg J, Mantovani L, Mancuso ME, Kessler C, Hay CR, Knoebl P, Di Minno G, Hoots K, Bok A, Brooker M, Buoso E, Mannucci PM, Peyvandi F
  40. J Med Genet 2017 May;54(5):338-45
    Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B.
    Simhadri VL, Hamasaki-Katagiri N, Lin BC, Hunt R, Jha S, Tseng SC, Wu A, Bentley AA, Zichel R, Lu Q, Zhu L, Freedberg DI, Monroe DM, Sauna ZE, Peters R, Komar AA, Kimchi-Sarfaty C
  41. J Thromb Haemost 2017 Apr;15(4):721-34
    Modulating immunogenicity of Factor IX by fusion to an immunoglobulin Fc domain: a study using hemophilia B mouse model.
    Levin D, Lagasse HA, Burch E, Strome S, Tan S, Jiang H, Sauna ZE, Golding B
  42. F1000Res 2017 Feb 7;6:113
    Recent advances in (therapeutic protein) drug development.
    Lagasse HA, Alexaki A, Simhadri VL, Katagiri NH, Jankowski W, Sauna ZE, Kimchi-Sarfaty C
  43. Sci Transl Med 2017 Jan 11;9(372):aag1286
    Post hoc assessment of the immunogenicity of bioengineered factor VIIa demonstrates the use of preclinical tools.
    Lamberth K, Reedtz-Runge SL, Simon J, Klementyeva K, Pandey GS, Padkjær SB, Pascal V, León IR, Gudme CN, Buus S, Sauna ZE
  44. Biomed Res Int 2015;2015:456348
    Muscular dystrophy: disease mechanisms and therapies.
    Pandey SN, Kesari A, Yokota T, Pandey GS
  45. Per Med 2015;12(4):403-15
    Personalized approaches to the treatment of hemophilia A and B.
    Simhadri VL, Banerjee AS, Simon J, Kimchi-Sarfaty C, Sauna ZE
  46. PLoS One 2015 Jul 15;10(7):e0132433
    Small ncRNA expression-profiling of blood from hemophilia A patients identifies miR-1246 as a potential regulator of Ffctor 8 gene.
    Sarachana T, Dahiya N, Simhadri VL, Pandey GS, Saini S, Guelcher C, Guerrera MF, Kimchi-Sarfaty C, Sauna ZE, Atreya CD
  47. Nucleic Acids Res 2015 Jul 13;43(12):5699-707
    Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.
    Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM
  48. Blood 2015 Jan 8;125(2):223-8
    The intron-22-inverted F8 locus permits intracellular factor VIII synthesis, explaining its low inhibitor risk and suggesting a role for pharmacogenomics.
    Sauna ZE, Lozier JN, Kasper CK, Yanover C, Nichols T, Howard TE
  49. Trends Biotechnol 2015 Jan;33(1):27-34
    Fc fusion as a platform technology: potential for modulating immunogenicity.
    Levin D, Golding B, Strome SE, Sauna ZE
 
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